Ab initio study of structural, elastic, and vibrational properties of transition-metal disilicides NbSi2 and TaSi2 in hexagonal C40 structure

NASA Astrophysics Data System (ADS)

Ertürk, Esra; Gürel, Tanju

2018-05-01

We present an ab initio study of structural, elastic and vibrational properties of transition-metal disilicides NbSi2 and TaSi2. The calculations have been carried out within the density-functional theory and linear-response formalism using norm-conserving pseudopotentials and a plane-wave basis. The calculated lattice parameters, bulk moduli, and elastic constants agree well with previous theoretical and experimental results. The calculated phonon frequencies at the Brillouin zone center are in good agreement with the reported Raman spectra and provide reference values for the future infrared and neutron phonon measurements. Phonon dispersion relations, mode Grüneisen parameters, and total and partial phonon density of states are also discussed. Mode Grüneisen parameters of NbSi2 and TaSi2 at Brillouin zone center show similar trends and all values are found to be positive. From phonon dispersion relations and phonon density of states, we have found a gap around 200 cm-1 for TaSi2, where the frequencies below this gap mainly belong to Ta vibrations and frequencies above the gap is mainly related with Si vibrations. In the case of NbSi2, there is no such gap and both Nb and Si atoms contribute to the phonon density of states in an energy range of 150-270 cm-1.

Ab initio study of the electron-phonon coupling at the Cr(001) surface

NASA Astrophysics Data System (ADS)

Peters, L.; Rudenko, A. N.; Katsnelson, M. I.

2018-04-01

It is experimentally well established that the Cr(001) surface exhibits a sharp resonance around the Fermi level. However, there is no consensus about its physical origin. It is proposed to be either due to a single particle dz2 surface state renormalized by electron-phonon coupling or the orbital Kondo effect involving the degenerate dx z/ dy z states. In this paper we examine the electron-phonon coupling of the Cr(001) surface by means of ab-initio calculations in the form of density functional perturbation theory. More precisely, the electron-phonon mass-enhancement factor of the surface layer is investigated for the 3d states. For the majority and minority spin dz2 surface states we find values of 0.19 and 0.16. We show that these calculated electron-phonon mass-enhancement factors are not in agreement with the experimental data even if we use realistic values for the temperature range and surface Debye frequency for the fit of the experimental data. More precisely, then experimentally an electron-phonon mass-enhancement factor of 0.70 ±0.10 is obtained, which is not in agreement with our calculated values of 0.19 and 0.16. Our findings suggest that the experimentally observed resonance at the Cr(001) surface is not due to electron-phonon effects but due to electron-electron correlation effects.

Development of a machine learning potential for graphene

NASA Astrophysics Data System (ADS)

Rowe, Patrick; Csányi, Gábor; Alfè, Dario; Michaelides, Angelos

2018-02-01

We present an accurate interatomic potential for graphene, constructed using the Gaussian approximation potential (GAP) machine learning methodology. This GAP model obtains a faithful representation of a density functional theory (DFT) potential energy surface, facilitating highly accurate (approaching the accuracy of ab initio methods) molecular dynamics simulations. This is achieved at a computational cost which is orders of magnitude lower than that of comparable calculations which directly invoke electronic structure methods. We evaluate the accuracy of our machine learning model alongside that of a number of popular empirical and bond-order potentials, using both experimental and ab initio data as references. We find that whilst significant discrepancies exist between the empirical interatomic potentials and the reference data—and amongst the empirical potentials themselves—the machine learning model introduced here provides exemplary performance in all of the tested areas. The calculated properties include: graphene phonon dispersion curves at 0 K (which we predict with sub-meV accuracy), phonon spectra at finite temperature, in-plane thermal expansion up to 2500 K as compared to NPT ab initio molecular dynamics simulations and a comparison of the thermally induced dispersion of graphene Raman bands to experimental observations. We have made our potential freely available online at [http://www.libatoms.org].

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

Simulation of Phonon Spectra in Three-Component Two-Dimensional Crystals of Refractory-Metal Dichalcogenides

NASA Astrophysics Data System (ADS)

Alexeev, A. Yu.; Krivosheeva, A. V.; Shaposhnikov, V. L.; Borisenko, V. E.

2017-09-01

A model for ab initio calculation of the phonon properties of three-component solid solutions of refractory-metal dichalcogenides was developed based on the assumption that displacements of the same type of chalcogen atoms and decoupled displacements of the metal atoms were identical. The calculated phonon frequencies at the Γ-point for monomolecular layers of MoS2-xSex and MoS2-xTex agreed with existing experimental Raman spectra.

Ab initio velocity-field curves in monoclinic β-Ga2O3

NASA Astrophysics Data System (ADS)

Ghosh, Krishnendu; Singisetti, Uttam

2017-07-01

We investigate the high-field transport in monoclinic β-Ga2O3 using a combination of ab initio calculations and full band Monte Carlo (FBMC) simulation. Scattering rate calculation and the final state selection in the FBMC simulation use complete wave-vector (both electron and phonon) and crystal direction dependent electron phonon interaction (EPI) elements. We propose and implement a semi-coarse version of the Wannier-Fourier interpolation method [Giustino et al., Phys. Rev. B 76, 165108 (2007)] for short-range non-polar optical phonon (EPI) elements in order to ease the computational requirement in FBMC simulation. During the interpolation of the EPI, the inverse Fourier sum over the real-space electronic grids is done on a coarse mesh while the unitary rotations are done on a fine mesh. This paper reports the high field transport in monoclinic β-Ga2O3 with deep insight into the contribution of electron-phonon interactions and velocity-field characteristics for electric fields ranging up to 450 kV/cm in different crystal directions. A peak velocity of 2 × 107 cm/s is estimated at an electric field of 200 kV/cm.

Phonon thermal transport in 2H, 4H and 6H silicon carbide from first principles

DOE PAGES

Protik, Nakib Haider; Katre, Ankita; Lindsay, Lucas R.; ...

2017-06-07

Here, silicon carbide (SiC) is a wide band gap semiconductor with a variety of industrial applications. Among its many useful properties is its high thermal conductivity, which makes it advantageous for thermal management applications. In this paper we present ab initio calculations of the in-plane and cross-plane thermal conductivities, κ in and κ out, of three common hexagonal polytypes of SiC: 2H, 4H and 6H. The phonon Boltzmann transport equation is solved iteratively using as input interatomic force constants determined from density functional theory. Both κ in and κ out decrease with increasing n in nH SiC because of additionalmore » low-lying optic phonon branches. These optic branches are characterized by low phonon group velocities, and they increase the phase space for phonon-phonon scattering of acoustic modes. Also, for all n, κ in is found to be larger than κ out in the temperature range considered. At electron concentrations present in experimental samples, scattering of phonons by electrons is shown to be negligible except well below room temperature where it can lead to a significant reduction of the lattice thermal conductivity. This work highlights the power of ab initio approaches in giving quantitative, predictive descriptions of thermal transport in materials. It helps explain the qualitative disagreement that exists among different sets of measured thermal conductivity data and provides information of the relative quality of samples from which measured data was obtained.« less

Phonon thermal transport in 2H, 4H and 6H silicon carbide from first principles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Protik, Nakib Haider; Katre, Ankita; Lindsay, Lucas R.

Here, silicon carbide (SiC) is a wide band gap semiconductor with a variety of industrial applications. Among its many useful properties is its high thermal conductivity, which makes it advantageous for thermal management applications. In this paper we present ab initio calculations of the in-plane and cross-plane thermal conductivities, κ in and κ out, of three common hexagonal polytypes of SiC: 2H, 4H and 6H. The phonon Boltzmann transport equation is solved iteratively using as input interatomic force constants determined from density functional theory. Both κ in and κ out decrease with increasing n in nH SiC because of additionalmore » low-lying optic phonon branches. These optic branches are characterized by low phonon group velocities, and they increase the phase space for phonon-phonon scattering of acoustic modes. Also, for all n, κ in is found to be larger than κ out in the temperature range considered. At electron concentrations present in experimental samples, scattering of phonons by electrons is shown to be negligible except well below room temperature where it can lead to a significant reduction of the lattice thermal conductivity. This work highlights the power of ab initio approaches in giving quantitative, predictive descriptions of thermal transport in materials. It helps explain the qualitative disagreement that exists among different sets of measured thermal conductivity data and provides information of the relative quality of samples from which measured data was obtained.« less

Thermally Driven Electronic Topological Transition in FeTi

NASA Astrophysics Data System (ADS)

Yang, F. C.; Muñoz, J. A.; Hellman, O.; Mauger, L.; Lucas, M. S.; Tracy, S. J.; Stone, M. B.; Abernathy, D. L.; Xiao, Yuming; Fultz, B.

2016-08-01

Ab initio molecular dynamics, supported by inelastic neutron scattering and nuclear resonant inelastic x-ray scattering, showed an anomalous thermal softening of the M5- phonon mode in B 2 -ordered FeTi that could not be explained by phonon-phonon interactions or electron-phonon interactions calculated at low temperatures. A computational investigation showed that the Fermi surface undergoes a novel thermally driven electronic topological transition, in which new features of the Fermi surface arise at elevated temperatures. The thermally induced electronic topological transition causes an increased electronic screening for the atom displacements in the M5- phonon mode and an adiabatic electron-phonon interaction with an unusual temperature dependence.

The role of electron-phonon interactions on the coherence lifetime of monolayer transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Stevens, C. E.; Dey, P.; Paul, J.; Wang, Z.; Zhang, H.; Romero, A. H.; Shan, J.; Hilton, D. J.; Karaiskaj, D.

2017-10-01

We investigate the excitonic dephasing of transition metal dichalcogenides, namely MoS2, MoSe2 and WSe2 atomic monolayer thick and bulk crystals, in order to understand the factors that determine the optical coherence in these materials. Coherent nonlinear optical spectroscopy, temperature dependent absorption combined with theoretical calculations of the phonon spectra, reveal the important role electron-phonon interactions plat in dephasing process. The temperature dependence of the electronic band gap and the excitonic linewidth combined with 'ab initio' calculations of the phonon energies and the phonon density of state reveal strong interaction with the E‧ and E″ phonon modes.

Lattice dynamics of Cs2NaYbF6 and Cs2NaYF6 elpasolites: Ab initio calculation

NASA Astrophysics Data System (ADS)

Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.

2015-06-01

The ab initio calculations of the crystal structure and the phonon spectrum of Cs2NaYbF6 and Cs2NaYF6 crystals with the elpasolite structure have been performed. The frequencies and types of fundamental vibrations have been determined. The calculations have been performed in the framework of the density functional theory using the molecular orbital method with hybrid functionals in the CRYSTAL09 program developed for the simulation of periodic structures. The outer 5 s and 5 p shells of the rare-earth ion have been described in Gaussian-type basis sets. The influence of inner shells, including 4 f electron shells, on the outer shells has been described using the pseudopotential. It has been shown that this approach allows the description of the phonon spectrum with the inclusion of the splitting of the longitudinal and transverse optical modes.

Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures.

PubMed

France-Lanord, Arthur; Soukiassian, Patrick; Glattli, Christian; Wimmer, Erich

2016-03-14

In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures.

Transmission eigenchannels for coherent phonon transport

NASA Astrophysics Data System (ADS)

Klöckner, J. C.; Cuevas, J. C.; Pauly, F.

2018-04-01

We present a procedure to determine transmission eigenchannels for coherent phonon transport in nanoscale devices using the framework of nonequilibrium Green's functions. We illustrate our procedure by analyzing a one-dimensional chain, where all steps can be carried out analytically. More importantly, we show how the procedure can be combined with ab initio calculations to provide a better understanding of phonon heat transport in realistic atomic-scale junctions. In particular, we study the phonon eigenchannels in a gold metallic atomic-size contact and different single-molecule junctions based on molecules such as an alkane chain, a brominated benzene-diamine, where destructive phonon interference effects take place, and a C60 junction.

Thermally Driven Electronic Topological Transition in FeTi

DOE PAGES

Yang, F. C.; Muñoz, J. A.; Hellman, O.; ...

2016-08-08

In this paper, ab initio molecular dynamics, supported by inelastic neutron scattering and nuclear resonant inelastic x-ray scattering, showed an anomalous thermal softening of the M 5 - phonon mode in B2-ordered FeTi that could not be explained by phonon-phonon interactions or electron-phonon interactions calculated at low temperatures. A computational investigation showed that the Fermi surface undergoes a novel thermally driven electronic topological transition, in which new features of the Fermi surface arise at elevated temperatures. Finally, the thermally induced electronic topological transition causes an increased electronic screening for the atom displacements in the M 5 - phonon mode andmore » an adiabatic electron-phonon interaction with an unusual temperature dependence.« less

Predicting lattice thermal conductivity with help from ab initio methods

NASA Astrophysics Data System (ADS)

Broido, David

2015-03-01

The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.

Band structure and phonon properties of lithium fluoride at high pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panchal, J. M., E-mail: amitjignesh@yahoo.co.in; Department of Physics, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat; Joshi, Mitesh

2016-05-23

High pressure structural and electronic properties of Lithium Fluoride (LiF) have been studied by employing an ab-initio pseudopotential method and a linear response scheme within the density functional theory (DFT) in conjunction with quasi harmonic Debye model. The band structure and electronic density of states conforms that the LiF is stable and is having insulator behavior at ambient as well as at high pressure up to 1 Mbar. Conclusions based on Band structure, phonon dispersion and phonon density of states are outlined.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Hua; College of Physics and Optoelectronics, Taiyuan University of Technology, Taiyuan 030024; Kioussis, Nicholas, E-mail: nick.kioussis@csun.edu

Using ab initio based calculations, we have calculated the intrinsic lattice thermal conductivity of chiral tellurium. We show that the interplay between the strong covalent intrachain and weak van der Waals interchain interactions gives rise to the phonon band gap between the lower and higher optical phonon branches. The underlying mechanism of the large anisotropy of the thermal conductivity is the anisotropy of the phonon group velocities and of the anharmonic interatomic force constants (IFCs), where large interchain anharmonic IFCs are associated with the lone electron pairs. We predict that tellurium has a large three-phonon scattering phase space that resultsmore » in low thermal conductivity. The thermal conductivity anisotropy decreases under applied hydrostatic pressure.« less

Control of Electronic Structures and Phonon Dynamics in Quantum Dot Superlattices by Manipulation of Interior Nanospace.

PubMed

Chang, I-Ya; Kim, DaeGwi; Hyeon-Deuk, Kim

2016-07-20

Quantum dot (QD) superlattices, periodically ordered array structures of QDs, are expected to provide novel photo-optical functions due to their resonant couplings between adjacent QDs. Here, we computationally demonstrated that electronic structures and phonon dynamics of a QD superlattice can be effectively and selectively controlled by manipulating its interior nanospace, where quantum resonance between neighboring QDs appears, rather than by changing component QD size, shape, compositions, etc. A simple H-passivated Si QD was examined to constitute one-, two-, and three-dimensional QD superlattices, and thermally fluctuating band energies and phonon modes were simulated by finite-temperature ab initio molecular dynamics (MD) simulations. The QD superlattice exhibited a decrease in the band gap energy enhanced by thermal modulations and also exhibited selective extraction of charge carriers out of the component QD, indicating its advantage as a promising platform for implementation in solar cells. Our dynamical phonon analyses based on the ab initio MD simulations revealed that THz-frequency phonon modes were created by an inter-QD crystalline lattice formed in the QD superlattice, which can contribute to low energy thermoelectric conversion and will be useful for direct observation of the dimension-dependent superlattice. Further, we found that crystalline and ligand-originated phonon modes inside each component QD can be independently controlled by asymmetry of the superlattice and by restriction of the interior nanospace, respectively. Taking into account the thermal effects at the finite temperature, we proposed guiding principles for designing efficient and space-saving QD superlattices to develop functional photovoltaic and thermoelectric devices.

Ab initio calculation of resonant Raman intensities of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Reichardt, Sven; Molina-Sanchez, Alejandro; Wirtz, Ludger

Raman spectroscopy is used to characterize optical and vibrational properties of materials. Its computational simulation is important for the interpretation of experimental results. Two approaches are the bond polarizability model and density functional perturbation theory. However, both are known to not capture resonance effects. These resonances and quantum interference effects are important to correctly reproduce the intensities as a function of laser energy as, e.g., reported for the case of multi-layer MoTe21.We present two fully ab initio approaches that overcome this limitation. In the first, we calculate finite difference derivatives of the dielectric susceptibility with the phonon displacements2. In the second we calculate electron-light and electron-phonon matrix elements from density functional theory and use them to evaluate expressions for the Raman intensity derived from time-dependent perturbation theory. These expressions are implemented in a computer code that performs the calculations as a post-processing step. We compare both methods and study the case of triple-layer MoTe2. Luxembourg National Research Fund (FNR).

Doppler broadening of neutron-induced resonances using ab initio phonon spectrum

NASA Astrophysics Data System (ADS)

Noguere, G.; Maldonado, P.; De Saint Jean, C.

2018-05-01

Neutron resonances observed in neutron cross section data can only be compared with their theoretical analogues after a correct broadening of the resonance widths. This broadening is usually carried out by two different theoretical models, namely the Free Gas Model and the Crystal Lattice Model, which, however, are only applicable under certain assumptions. Here, we use neutron transmission experiments on UO2 samples at T=23.7 K and T=293.7 K, to investigate the limitations of these models when an ab initio phonon spectrum is introduced in the calculations. Comparisons of the experimental and theoretical transmissions highlight the underestimation of the energy transferred at low temperature and its impact on the accurate determination of the radiation widths Γ_{γ_{λ}} of the 238U resonances λ. The observed deficiency of the model represents an experimental evidence that the Debye-Waller factor is not correctly calculated at low temperature near the Neel temperature ( TN=30.8 K).

Nonequilibrium dynamics of the phonon gas in ultrafast-excited antimony

NASA Astrophysics Data System (ADS)

Krylow, Sergej; Zijlstra, Eeuwe S.; Kabeer, Fairoja Cheenicode; Zier, Tobias; Bauerhenne, Bernd; Garcia, Martin E.

2017-12-01

The ultrafast relaxation dynamics of a nonequilibrium phonon gas towards thermal equilibrium involves many-body collisions that cannot be properly described by perturbative approaches. Here, we develop a nonperturbative method to elucidate the microscopic mechanisms underlying the decay of laser-excited coherent phonons in the presence of electron-hole pairs, which so far are not fully understood. Our theory relies on ab initio molecular dynamics simulations on laser-excited potential-energy surfaces. Those simulations are compared with runs in which the laser-excited coherent phonon is artificially deoccupied. We apply this method to antimony and show that the decay of the A1 g phonon mode at low laser fluences can be accounted mainly to three-body down-conversion processes of an A1 g phonon into acoustic phonons. For higher excitation strengths, however, we see a crossover to a four-phonon process, in which two A1 g phonons decay into two optical phonons.

Calculated temperature dependence of elastic constants and phonon dispersion of hcp and bcc beryllium

NASA Astrophysics Data System (ADS)

Hahn, Steven; Arapan, Sergiu; Harmon, Bruce; Eriksson, Olle

2011-03-01

Conventional first principle methods for calculating lattice dynamics are unable to calculate high temperature thermophysical properties of materials containing modes that are entropically stabilized. In this presentation we use a relatively new approach called self-consistent ab initio lattice dynamics (SCAILD) to study the hcp to bcc transition (1530 K) in beryllium. The SCAILD method goes beyond the harmonic approximation to include phonon-phonon interactions and produces a temperature-dependent phonon dispersion. In the high temperature bcc structure, phonon-phonon interactions dynamically stabilize the N-point phonon. Fits to the calculated phonon dispersion were used to determine the temperature dependence of the elastic constants in the hcp and bcc phases. Work at the Ames Laboratory was supported by the Department of Energy-Basic Energy Sciences under Contract No. DE-AC02-07CH11358.

Ab initio calculation of electron–phonon coupling in monoclinic β-Ga{sub 2}O{sub 3} crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Krishnendu, E-mail: kghosh3@buffalo.edu; Singisetti, Uttam, E-mail: uttamsin@buffalo.edu

2016-08-15

The interaction between electrons and vibrational modes in monoclinic β-Ga{sub 2}O{sub 3} is theoretically investigated using ab-initio calculations. The large primitive cell of β-Ga{sub 2}O{sub 3} gives rise to 30 phonon modes all of which are taken into account in transport calculation. The electron-phonon interaction is calculated under density functional perturbation theory and then interpolated using Wannier–Fourier interpolation. The long-range interaction elements between electrons and polar optical phonon (POP) modes are calculated separately using the Born effective charge tensor. The direction dependence of the long-range POP coupling in a monoclinic crystal is explored and is included in the transport calculations.more » Scattering rate calculations are done using the Fermi golden rule followed by solving the Boltzmann transport equation using the Rode's method to estimate low field mobility. A room temperature mobility of 115 cm{sup 2}/V s is observed. Comparison with recent experimentally reported mobility is done for a wide range of temperatures (30 K–650 K). It is also found that the POP interaction dominates the electron mobility under low electric field conditions. The relative contribution of the different POP modes is analyzed and the mode 21 meV POP is found to have the highest impact on low field electron mobility at room temperature.« less

Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen

2016-03-01

On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.

Low-energy phonon dispersion in LaFe4Sb12

NASA Astrophysics Data System (ADS)

Leithe-Jasper, Andreas; Boehm, Martin; Mutka, Hannu; Koza, Michael M.

We studied the vibrational dynamics of a single crystal of LaFe4Sb12 by three-axis inelastic neutron spectroscopy. The dispersion of phonons with wave vectors q along [ xx 0 ] and [ xxx ] directions in the energy range of eigenmodes with high amplitudes of lanthanum vibrations, i.e., at ℏω < 12 meV is identified. Symmetry-avoided anticrossing dispersion of phonons is established in both monitored directions and distinct eigenstates at high-symmetry points and at the Brillouin-zone center are discriminated. The experimentally derived phonon dispersion and intensities are compared with and backed up by ab initio lattice dynamics calculations. results of the computer model match well with the experimental data.

Ab initio study of cross-interface electron-phonon couplings in FeSe thin films on SrTiO 3 and BaTiO 3

DOE PAGES

Wang, Y.; Linscheid, A.; Berlijn, T.; ...

2016-04-22

We study the electron-phonon coupling strength near the interface of monolayer and bilayer FeSe thin films on SrTiO 3 , BaTiO 3 , and oxygen-vacant SrTiO 3 substrates, using ab initio methods. The calculated total electron-phonon coupling strength λ = 0.2 – 0.3 cannot account for the high T c ~ 70 K observed in these systems through the conventional phonon-mediated pairing mechanism. In all of these systems, however, we find that the coupling constant of a polar oxygen branch peaks at q = 0 with negligible coupling elsewhere, while the energy of this mode coincides with the offset energymore » of the replica bands measured recently by angle-resolved photoemission spectroscopy experiments. However, the integrated coupling strength for this mode from our current calculations is still too small to produce the observed high T c , even through the more efficient pairing mechanism provided by the forward scattering. Also, we arrive at the same qualitative conclusion when considering a checkerboard antiferromagnetic configuration in the Fe layer. In light of the experimental observations of the replica band feature and the relatively high T c of FeSe monolayers on polar substrates, our results point towards a cooperative role for the electron-phonon interaction, where the cross-interface interaction acts in conjunction with a purely electronic interaction. Finally, we discuss a few scenarios where the coupling strength obtained here may be enhanced.« less

Phonon properties and slow organic-to-inorganic sub-lattice thermalization in hybrid perovskites

NASA Astrophysics Data System (ADS)

Chan, Maria; Chang, Angela; Xia, Yi; Sadasivam, Sridhar; Guo, Peijun; Kinaci, Alper; Lin, Hao-Wu; Darancet, Pierre; Schaller, Richard

Organic-inorganic hybrid perovskite halide compounds have been investigated extensively for photovoltaics (PVs) and related applications. The thermal transport properties of hybrid perovskites, including phonon-carrier and phonon-phonon interactions, are of significance for their PV and solar thermoelectric applications. The interlocking organic and inorganic sublattices can be thought of as an extreme form of nanostructuring. A result of this nanostructuring is the large gap in phonon frequencies between the organic and inorganic sublattices, which is expected to create bottlenecks in phonon equilibration. In this work, we use a combination of ultrafast spectroscopy including photoluminescence and transient absorption, as well as first principles density functional theory (DFT), ab initio molecular dynamics calculations, phonon lifetimes derived from DFT force constants, and non-equilibrium phonon dynamics accounting for phonon lifetimes, to determine the phonon and charge interaction processes. We find evidence that thermalization of carriers occur at an atypically slow 50-100 ps time scale owing to the complex interplay between electronic and phonon excitations.

Anharmonic, dimensionality and size effects in phonon transport

NASA Astrophysics Data System (ADS)

Thomas, Iorwerth O.; Srivastava, G. P.

2017-12-01

We have developed and employed a numerically efficient semi- ab initio theory, based on density-functional and relaxation-time schemes, to examine anharmonic, dimensionality and size effects in phonon transport in three- and two-dimensional solids of different crystal symmetries. Our method uses third- and fourth-order terms in crystal Hamiltonian expressed in terms of a temperature-dependent Grüneisen’s constant. All input to numerical calculations are generated from phonon calculations based on the density-functional perturbation theory. It is found that four-phonon processes make important and measurable contribution to lattice thermal resistivity above the Debye temperature. From our numerical results for bulk Si, bulk Ge, bulk MoS2 and monolayer MoS2 we find that the sample length dependence of phonon conductivity is significantly stronger in low-dimensional solids.

Lattice dynamics in Sn nanoislands and cluster-assembled films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Houben, Kelly; Couet, Sebastien; Trekels, Maarten

2017-04-01

To unravel the effects of phonon confinement, the influence of size and morphology on the atomic vibrations is investigated in Sn nanoislands and cluster-assembled films. Nuclear resonant inelastic x-ray scattering is used to probe the phonon densities of states of the Sn nanostructures which show significant broadening of the features compared to bulk phonon behavior. Supported by ab initio calculations, the broadening is attributed to phonon scattering and can be described within the damped harmonic oscillator model. Contrary to the expectations based on previous research, the appearance of high-energy modes above the cutoff energy is not observed. From the thermodynamicmore » properties extracted from the phonon densities of states, it was found that grain boundary Sn atoms are bound by weaker forces than bulk Sn atoms.« less

Temperature-dependent excitonic effects in the optical properties of single-layer MoS2

NASA Astrophysics Data System (ADS)

Molina-Sánchez, Alejandro; Palummo, Maurizia; Marini, Andrea; Wirtz, Ludger

2016-04-01

Temperature influences the performance of two-dimensional (2D) materials in optoelectronic devices. Indeed, the optical characterization of these materials is usually realized at room temperature. Nevertheless, most ab initio studies are still performed without including any temperature effect. As a consequence, important features are thus overlooked, such as the relative height of the excitonic peaks and their broadening, directly related to the temperature and to the nonradiative exciton relaxation time. We present ab initio calculations of the optical response of single-layer MoS2, a prototype 2D material, as a function of temperature using density functional theory and many-body perturbation theory. We compute the electron-phonon interaction using the full spinorial wave functions, i.e., fully taking into account the effects of spin-orbit interaction. We find that bound excitons (A and B peaks) and resonant excitons (C peak) exhibit different behavior with temperature, displaying different nonradiative linewidths. We conclude that the inhomogeneous broadening of the absorption spectra is mainly due to electron-phonon scattering mechanisms. Our calculations explain the shortcomings of previous (zero-temperature) theoretical spectra and match well with the experimental spectra acquired at room temperature. Moreover, we disentangle the contributions of acoustic and optical phonon modes to the quasiparticles and exciton linewidths. Our model also allows us to identify which phonon modes couple to each exciton state, which is useful for the interpretation of resonant Raman-scattering experiments.

Ab initio study of the effect of vacancies on the thermal conductivity of boron arsenide

NASA Astrophysics Data System (ADS)

Protik, Nakib Haider; Carrete, Jesús; Katcho, Nebil A.; Mingo, Natalio; Broido, David

2016-07-01

Using a first principles theoretical approach, we show that vacancies give anomalously strong suppression of the lattice thermal conductivity κ of cubic Boron arsenide (BAs), which has recently been predicted to have an exceptionally high κ . This effect is tied to the unusually large phonon lifetimes in BAs and results in a stronger reduction in the BAs κ than occurs in diamond. The large changes in bonding around vacancies cannot be accurately captured using standard perturbative methods and are instead treated here using an ab initio Green function approach. As and B vacancies are found to have similar effects on κ . In contrast, we show that commonly used mass disorder models for vacancies fail for large mass ratio compounds such as BAs, incorrectly predicting much stronger (weaker) phonon scattering when the vacancy is on the heavy (light) atom site. The quantitative treatment given here contributes to fundamental understanding of the effect of point defects on thermal transport in solids and provides guidance to synthesis efforts to grow high quality BAs.

Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

NASA Astrophysics Data System (ADS)

Rosenow, Phil; Tonner, Ralf

2016-05-01

The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosenow, Phil; Tonner, Ralf, E-mail: tonner@chemie.uni-marburg.de

2016-05-28

The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. Themore » on-set of H{sub 2} desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).« less

Lattice dynamic properties of Rh2XAl (X=Fe and Y) alloys

NASA Astrophysics Data System (ADS)

Al, Selgin; Arikan, Nihat; Demir, Süleyman; Iyigör, Ahmet

2018-02-01

The electronic band structure, elastic and vibrational spectra of Rh2FeAl and Rh2YAl alloys were computed in detail by employing an ab-initio pseudopotential method and a linear-response technique based on the density-functional theory (DFT) scheme within a generalized gradient approximation (GGA). Computed lattice constants, bulk modulus and elastic constants were compared. Rh2YAl exhibited higher ability to resist volume change than Rh2FeAl. The elastic constants, shear modulus, Young modulus, Poisson's ratio, B/G ratio electronic band structure, total and partial density of states, and total magnetic moment of alloys were also presented. Rh2FeAl showed spin up and spin down states whereas Rh2YAl showed none due to being non-magnetic. The calculated total densities of states for both materials suggest that both alloys are metallic in nature. Full phonon spectra of Rh2FeAl and Rh2YA1 alloys in the L21 phase were collected using the ab-initio linear response method. The obtained phonon frequencies were in the positive region indicating that both alloys are dynamically stable.

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

PubMed

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

Analytic derivative couplings and first-principles exciton/phonon coupling constants for an ab initio Frenkel-Davydov exciton model: Theory, implementation, and application to compute triplet exciton mobility parameters for crystalline tetracene.

PubMed

Morrison, Adrian F; Herbert, John M

2017-06-14

Recently, we introduced an ab initio version of the Frenkel-Davydov exciton model for computing excited-state properties of molecular crystals and aggregates. Within this model, supersystem excited states are approximated as linear combinations of excitations localized on molecular sites, and the electronic Hamiltonian is constructed and diagonalized in a direct-product basis of non-orthogonal configuration state functions computed for isolated fragments. Here, we derive and implement analytic derivative couplings for this model, including nuclear derivatives of the natural transition orbital and symmetric orthogonalization transformations that are part of the approximation. Nuclear derivatives of the exciton Hamiltonian's matrix elements, required in order to compute the nonadiabatic couplings, are equivalent to the "Holstein" and "Peierls" exciton/phonon couplings that are widely discussed in the context of model Hamiltonians for energy and charge transport in organic photovoltaics. As an example, we compute the couplings that modulate triplet exciton transport in crystalline tetracene, which is relevant in the context of carrier diffusion following singlet exciton fission.

AB INITIO STUDY OF PHONON DISPERSION AND ELASTIC PROPERTIES OF L12 INTERMETALLICS Ti3Al AND Y3Al

NASA Astrophysics Data System (ADS)

Arikan, N.; Ersen, M.; Ocak, H. Y.; Iyigör, A.; Candan, A.; UǦUR, Ş.; UǦUR, G.; Khenata, R.; Varshney, D.

2013-12-01

In this paper, the structural, elastic and phonon properties of Ti3Al and Y3Al in L12(Cu3Al) phase are studied by performing first-principles calculations within the generalized gradient approximation. The calculated lattice constants, static bulk moduli, first-order pressure derivative of bulk moduli and elastic constants for both compounds are reported. The phonon dispersion curves along several high-symmetry lines at the Brillouin zone, together with the corresponding phonon density of states, are determined using the first-principles linear-response approach of the density functional perturbation theory. Temperature variations of specific heat in the range of 0-500 K are obtained using the quasi-harmonic model.

Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates

NASA Astrophysics Data System (ADS)

Carbogno, Christian; Scheffler, Matthias

In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.

Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi

NASA Technical Reports Server (NTRS)

Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.

2016-01-01

For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.

Electrons, phonons and superconductivity in rocksalt and tungsten-carbide phases of CrC.

PubMed

Tütüncü, H M; Baǧcı, S; Srivastava, G P; Akbulut, A

2012-11-14

We present results of ab initio theoretical investigations of the electronic structure, phonon dispersion relations, electron-phonon interaction and superconductivity in the rocksalt and tungsten-carbide phases of CrC. It is found that, compared to the stable tungsten-carbide phase, the metastable rocksalt phase is characterized by a much larger electronic density of states at the Fermi level. The phonon spectra of the rocksalt phase exhibit anomalies in the dispersion curves of both the transverse and longitudinal acoustic branches along the main symmetry directions. A combination of these characteristic electronic and phonon properties leads to an order of magnitude larger value of the electron-phonon coupling constant (λ = 2.66) for the rocksalt phase compared to that for the tungsten-carbide phase (λ = 0.24). Our calculations suggest that superconducting transition temperature values of 0.01 K and 25-35 K may be expected for the tungsten-carbide and rocksalt phases, respectively.

Pressure dependence of transverse acoustic phonon energy in ferropericlase across the spin transition.

PubMed

Fukui, Hiroshi; Baron, Alfred Q R; Ishikawa, Daisuke; Uchiyama, Hiroshi; Ohishi, Yasuo; Tsuchiya, Taku; Kobayashi, Hisao; Matsuzaki, Takuya; Yoshino, Takashi; Katsura, Tomoo

2017-06-21

We investigated transverse acoustic (TA) phonons in iron-bearing magnesium oxide (ferropericlase) up to 56 GPa using inelastic x-ray scattering (IXS). The results show that the energy of the TA phonon far from the Brillouin zone center suddenly increases with increasing pressure above the spin transition pressure of ferropericlase. Ab initio calculations revealed that the TA phonon energy far from the Brillouin zone center is higher in the low-spin state than in the high spin state; that the TA phonon energy depend weakly on pressure; and that the energy gap between the TA and the lowest-energy-optic phonons is much narrower in the low-spin state than in the high-spin state. This allows us to conclude that the anomalous behavior of the TA mode in the present experiments is the result of gap narrowing due to the spin transition and explains contradictory results in previous experimental studies.

Nuclear quantum effect with pure anharmonicity and the anomalous thermal expansion of silicon.

PubMed

Kim, D S; Hellman, O; Herriman, J; Smith, H L; Lin, J Y Y; Shulumba, N; Niedziela, J L; Li, C W; Abernathy, D L; Fultz, B

2018-02-27

Despite the widespread use of silicon in modern technology, its peculiar thermal expansion is not well understood. Adapting harmonic phonons to the specific volume at temperature, the quasiharmonic approximation, has become accepted for simulating the thermal expansion, but has given ambiguous interpretations for microscopic mechanisms. To test atomistic mechanisms, we performed inelastic neutron scattering experiments from 100 K to 1,500 K on a single crystal of silicon to measure the changes in phonon frequencies. Our state-of-the-art ab initio calculations, which fully account for phonon anharmonicity and nuclear quantum effects, reproduced the measured shifts of individual phonons with temperature, whereas quasiharmonic shifts were mostly of the wrong sign. Surprisingly, the accepted quasiharmonic model was found to predict the thermal expansion owing to a large cancellation of contributions from individual phonons.

Elementary excitations and crossover phenomenon in liquids.

PubMed

Iwashita, T; Nicholson, D M; Egami, T

2013-05-17

The elementary excitations of vibration in solids are phonons. But in liquids phonons are extremely short lived and marginalized. In this Letter through classical and ab initio molecular dynamics simulations of the liquid state of various metallic systems we show that different excitations, the local configurational excitations in the atomic connectivity network, are the elementary excitations in high temperature metallic liquids. We also demonstrate that the competition between the configurational excitations and phonons determines the so-called crossover phenomenon in liquids. These discoveries open the way to the explanation of various complex phenomena in liquids, such as fragility and the rapid increase in viscosity toward the glass transition, in terms of these excitations.

Electron-phonon scattering rates in complex polar crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prange, M. P.; Campbell, L. W.; Kerisit, S.

2017-09-01

The thermalization of fast electrons by phonons is studied in CsI, NaI, SrI2, and YAP. This numerical study uses an improvement to a recently developed ab initio method based on a density functional perturbation theoretical description of the phonon modes that provides a way to go beyond widely used phonon models based on binary crystals. Improvements to this method are described, and scattering rates are presented and discussed. The results here treat polar and nonpolar scattering on equal footing and allow an assessment of the relative importance of the two types of scattering. The relative activity of the numerous phononmore » modes in materials with complicated structures is discussed, and a simple criterion for finding the modes that scatter strongly is presented.« less

Adequacy of damped dynamics to represent the electron-phonon interaction in solids

DOE PAGES

Caro, A.; Correa, A. A.; Tamm, A.; ...

2015-10-16

Time-dependent density functional theory and Ehrenfest dynamics are used to calculate the electronic excitations produced by a moving Ni ion in a Ni crystal in the case of energetic MeV range (electronic stopping power regime), as well as thermal energy meV range (electron-phonon interaction regime). Results at high energy compare well to experimental databases of stopping power, and at low energy the electron-phonon interaction strength determined in this way is very similar to the linear response calculation and experimental measurements. This approach to electron-phonon interaction as an electronic stopping process provides the basis for a unified framework to perform classicalmore » molecular dynamics of ion-solid interaction with ab initio type nonadiabatic terms in a wide range of energies.« less

Ab Initio Analysis of Auger-Assisted Electron Transfer.

PubMed

Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

2015-01-15

Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

Ab initio study of the electron energy loss function in a graphene-sapphire-graphene composite system

NASA Astrophysics Data System (ADS)

Despoja, Vito; Djordjević, Tijana; Karbunar, Lazar; Radović, Ivan; Mišković, Zoran L.

2017-08-01

The propagator of a dynamically screened Coulomb interaction W in a sandwichlike structure consisting of two graphene layers separated by a slab of Al2O3 (or vacuum) is derived from single-layer graphene response functions and by using a local dielectric function for the bulk Al2O3 . The response function of graphene is obtained using two approaches within the random phase approximation (RPA): an ab initio method that includes all electronic bands in graphene and a computationally less demanding method based on the massless Dirac fermion (MDF) approximation for the low-energy excitations of electrons in the π bands. The propagator W is used to derive an expression for the effective dielectric function of our sandwich structure, which is relevant for the reflection electron energy loss spectroscopy of its surface. Focusing on the range of frequencies from THz to mid-infrared, special attention is paid to finding an accurate optical limit in the ab initio method, where the response function is expressed in terms of a frequency-dependent conductivity of graphene. It was shown that the optical limit suffices for describing hybridization between the Dirac plasmons in graphene layers and the Fuchs-Kliewer phonons in both surfaces of the Al2O3 slab, and that the spectra obtained from both the ab initio method and the MDF approximation in the optical limit agree perfectly well for wave numbers up to about 0.1 nm-1. Going beyond the optical limit, the agreement between the full ab initio method and the MDF approximation was found to extend to wave numbers up to about 0.3 nm-1 for doped graphene layers with the Fermi energy of 0.2 eV.

Magnetic moments induce strong phonon renormalization in FeSi.

PubMed

Krannich, S; Sidis, Y; Lamago, D; Heid, R; Mignot, J-M; Löhneysen, H v; Ivanov, A; Steffens, P; Keller, T; Wang, L; Goering, E; Weber, F

2015-11-27

The interactions of electronic, spin and lattice degrees of freedom in solids result in complex phase diagrams, new emergent phenomena and technical applications. While electron-phonon coupling is well understood, and interactions between spin and electronic excitations are intensely investigated, only little is known about the dynamic interactions between spin and lattice excitations. Noncentrosymmetric FeSi is known to undergo with increasing temperature a crossover from insulating to metallic behaviour with concomitant magnetic fluctuations, and exhibits strongly temperature-dependent phonon energies. Here we show by detailed inelastic neutron-scattering measurements and ab initio calculations that the phonon renormalization in FeSi is linked to its unconventional magnetic properties. Electronic states mediating conventional electron-phonon coupling are only activated in the presence of strong magnetic fluctuations. Furthermore, phonons entailing strongly varying Fe-Fe distances are damped via dynamic coupling to the temperature-induced magnetic moments, highlighting FeSi as a material with direct spin-phonon coupling and multiple interaction paths.

Hybrid density-functional calculations of phonons in LaCoO3

NASA Astrophysics Data System (ADS)

Gryaznov, Denis; Evarestov, Robert A.; Maier, Joachim

2010-12-01

Phonon frequencies at Γ point in nonmagnetic rhombohedral phase of LaCoO3 were calculated using density-functional theory with hybrid exchange correlation functional PBE0. The calculations involved a comparison of results for two types of basis functions commonly used in ab initio calculations, namely, the plane-wave approach and linear combination of atomic orbitals, as implemented in VASP and CRYSTAL computer codes, respectively. A good qualitative, but also within an error margin of less than 30%, a quantitative agreement was observed not only between the two formalisms but also between theoretical and experimental phonon frequency predictions. Moreover, the correlation between the phonon symmetries in cubic and rhombohedral phases is discussed in detail on the basis of group-theoretical analysis. It is concluded that the hybrid PBE0 functional is able to predict correctly the phonon properties in LaCoO3 .

Experimental metrology to obtain thermal phonon transmission coefficients at solid interfaces

NASA Astrophysics Data System (ADS)

Hua, Chengyun; Chen, Xiangwen; Ravichandran, Navaneetha K.; Minnich, Austin J.

2017-05-01

Interfaces play an essential role in phonon-mediated heat conduction in solids, impacting applications ranging from thermoelectric waste heat recovery to heat dissipation in electronics. From the microscopic perspective, interfacial phonon transport is described by transmission coefficients that link vibrational modes in the materials composing the interface. However, direct experimental determination of these coefficients is challenging because most experiments provide a mode-averaged interface conductance that obscures the microscopic detail. Here, we report a metrology to extract thermal phonon transmission coefficients at solid interfaces using ab initio phonon transport modeling and a thermal characterization technique, time-domain thermoreflectance. In combination with transmission electron microscopy characterization of the interface, our approach allows us to link the atomic structure of an interface to the spectral content of the heat crossing it. Our work provides a useful perspective on the microscopic processes governing interfacial heat conduction.

Experimental metrology to obtain thermal phonon transmission coefficients at solid interfaces

DOE PAGES

Hua, Chengyun; Chen, Xiangwen; Ravichandran, Navaneetha K.; ...

2017-05-17

Interfaces play an essential role in phonon-mediated heat conduction in solids, impacting applications ranging from thermoelectric waste heat recovery to heat dissipation in electronics. From the microscopic perspective, interfacial phonon transport is described by transmission coefficients that link vibrational modes in the materials composing the interface. But, direct experimental determination of these coefficients is challenging because most experiments provide a mode-averaged interface conductance that obscures the microscopic detail. Here, we report a metrology to extract thermal phonon transmission coefficients at solid interfaces using ab initio phonon transport modeling and a thermal characterization technique, time-domain thermoreflectance. In combination with transmission electronmore » microscopy characterization of the interface, our approach allows us to link the atomic structure of an interface to the spectral content of the heat crossing it. This work provides a useful perspective on the microscopic processes governing interfacial heat conduction.« less

Metric for strong intrinsic fourth-order phonon anharmonicity

NASA Astrophysics Data System (ADS)

Yue, Sheng-Ying; Zhang, Xiaoliang; Qin, Guangzhao; Phillpot, Simon R.; Hu, Ming

2017-05-01

Under the framework of Taylor series expansion for potential energy, we propose a simple and robust metric, dubbed "regular residual analysis," to measure the fourth-order phonon anharmonicity in crystals. The method is verified by studying the intrinsic strong higher-order anharmonic effects in UO2 and CeO2. Comparison of the thermal conductivity results, which calculated by the anharmonic lattice dynamics method coupled with the Boltzmann transport equation and the spectral energy density method coupled with ab initio molecular dynamics simulation further validates our analysis. Analysis of the bulk Si and Ge systems confirms that the fourth-order phonon anharmonicity is enhanced and cannot be neglected at high enough temperatures, which agrees with a previous study where the four-phonon scattering was explicitly determined. This metric will facilitate evaluating and interpreting the lattice thermal conductivity of crystals with strong fourth-order phonon anharmonicity.

Interlayer interactions in graphites.

PubMed

Chen, Xiaobin; Tian, Fuyang; Persson, Clas; Duan, Wenhui; Chen, Nan-xian

2013-11-06

Based on ab initio calculations of both the ABC- and AB-stacked graphites, interlayer potentials (i.e., graphene-graphene interaction) are obtained as a function of the interlayer spacing using a modified Möbius inversion method, and are used to calculate basic physical properties of graphite. Excellent consistency is observed between the calculated and experimental phonon dispersions of AB-stacked graphite, showing the validity of the interlayer potentials. More importantly, layer-related properties for nonideal structures (e.g., the exfoliation energy, cleave energy, stacking fault energy, surface energy, etc.) can be easily predicted from the interlayer potentials, which promise to be extremely efficient and helpful in studying van der Waals structures.

Ab initio optimization of phonon drag effect for lower-temperature thermoelectric energy conversion.

PubMed

Zhou, Jiawei; Liao, Bolin; Qiu, Bo; Huberman, Samuel; Esfarjani, Keivan; Dresselhaus, Mildred S; Chen, Gang

2015-12-01

Although the thermoelectric figure of merit zT above 300 K has seen significant improvement recently, the progress at lower temperatures has been slow, mainly limited by the relatively low Seebeck coefficient and high thermal conductivity. Here we report, for the first time to our knowledge, success in first-principles computation of the phonon drag effect--a coupling phenomenon between electrons and nonequilibrium phonons--in heavily doped region and its optimization to enhance the Seebeck coefficient while reducing the phonon thermal conductivity by nanostructuring. Our simulation quantitatively identifies the major phonons contributing to the phonon drag, which are spectrally distinct from those carrying heat, and further reveals that although the phonon drag is reduced in heavily doped samples, a significant contribution to Seebeck coefficient still exists. An ideal phonon filter is proposed to enhance zT of silicon at room temperature by a factor of 20 to ∼ 0.25, and the enhancement can reach 70 times at 100 K. This work opens up a new venue toward better thermoelectrics by harnessing nonequilibrium phonons.

Phonon conductivity metrics for compact, linked-cage, layered, and filled-cage crystals, using ab initio, molecular dynamics and Boltzmann transport treatments

NASA Astrophysics Data System (ADS)

Huang, Baoling

Atomic-level thermal transport in compact, layered, linked-cage, and filled-cage crystals is investigated using a multiscale approach, combines the ab initio calculation, molecular dynamics (MD), Boltzman transport equations (BTE), and the kinetic theory. These materials are of great interests in energy storage, transport, and conversion. The structural metrics of phonon conductivity of these crystals are then explored. An atomic structure-based model is developed for the understanding the relationship between the atomic structure and phonon transport in compact crystals at high temperatures. The elemental electronegativity, element mass, and the arrangement of bonds are found to be the dominant factors to determine the phonon conductivity. As an example of linked-cage crystals, the phonon conductivity of MOF-5 is investigated over a wide temperature range using MD simulations and the Green-Kubo method. The temperature dependence of the thermal conductivity of MOF-5 is found to be weak at high temperatures, which results from the suppression of the long-range acoustic phonon transport by the special linked-cage structure. The mean free path of the majority of phonons in MOF-5 is limited by the cage size. The phonon and electron transport in layered Bi2Te3 structure are investigated using the first-principle calculations, MD, and BTE. Strong anisotropy has been found for both phonon and electron transport due to the special layered structure. The long-range acoustic phonons dominate the phonon transport with a strong temperature and direction dependence. Temperature dependence of the energy gap and appropriate modelling of relaxation times are found to be important for the prediction of the electrical transport in the intrinsic regime. The scattering by the acoustic, optical, and polar-optical phonons are found to dominate the electron transport. For filled skutterudite structure, strong coupling between the filler and the host is found, which contradicts the traditional "rattler" concept. The interatomic bonds of the host are significantly affected by the filler. It is shown that without changing the interatomic potentials for the host, the filler itself can not result in a lower phonon conductivity for the filled structure. It is also found that the behavior of partially-filled skutterudites can be better understood by treating the partially-filled structure as a solid solution of the empty structure and fully-filled structure. The combination of theoretical-analysis methods used in this work, provides for comparative insight into the role of atomic structure on the phonon transport in a variety of crystals used in energy storage, transport, and conversion.

High-throughput density-functional perturbation theory phonons for inorganic materials

NASA Astrophysics Data System (ADS)

Petretto, Guido; Dwaraknath, Shyam; P. C. Miranda, Henrique; Winston, Donald; Giantomassi, Matteo; van Setten, Michiel J.; Gonze, Xavier; Persson, Kristin A.; Hautier, Geoffroy; Rignanese, Gian-Marco

2018-05-01

The knowledge of the vibrational properties of a material is of key importance to understand physical phenomena such as thermal conductivity, superconductivity, and ferroelectricity among others. However, detailed experimental phonon spectra are available only for a limited number of materials, which hinders the large-scale analysis of vibrational properties and their derived quantities. In this work, we perform ab initio calculations of the full phonon dispersion and vibrational density of states for 1521 semiconductor compounds in the harmonic approximation based on density functional perturbation theory. The data is collected along with derived dielectric and thermodynamic properties. We present the procedure used to obtain the results, the details of the provided database and a validation based on the comparison with experimental data.

Estimates of crystalline LiF thermal conductivity at high temperature and pressure by a Green-Kubo method

DOE PAGES

Jones, R. E.; Ward, D. K.

2016-07-18

Here, given the unique optical properties of LiF, it is often used as an observation window in high-temperature and -pressure experiments; hence, estimates of its transmission properties are necessary to interpret observations. Since direct measurements of the thermal conductivity of LiF at the appropriate conditions are difficult, we resort to molecular simulation methods. Using an empirical potential validated against ab initio phonon density of states, we estimate the thermal conductivity of LiF at high temperatures (1000–4000 K) and pressures (100–400 GPa) with the Green-Kubo method. We also compare these estimates to those derived directly from ab initio data. To ascertainmore » the correct phase of LiF at these extreme conditions, we calculate the (relative) phase stability of the B1 and B2 structures using a quasiharmonic ab initio model of the free energy. We also estimate the thermal conductivity of LiF in an uniaxial loading state that emulates initial stages of compression in high-stress ramp loading experiments and show the degree of anisotropy induced in the conductivity due to deformation.« less

Ab-initio study of superconducting state in intercalated MoSe2 and WSe2 bilayers

NASA Astrophysics Data System (ADS)

Szcześniak, R.; Durajski, A. P.; Jarosik, M. W.

2018-05-01

A two-dimensional systems have attracted significant interest due to their outstanding physical, chemical and optoelectronic properties. This paper focuses on the detailed investigations of the electronic, phononic and superconducting properties of transition-metal dichalcogenide bilayers MSe 2 (M = Mo, W) intercalated by calcium atoms. The first-principles calculations show that (MoSe2)2Ca and (WSe2)2Ca systems exhibit metallic behavior and weak phonon-mediated superconductivity with low critical temperature of 0.51 and 0.30 K, respectively. These results confirm other theoretical predictions and suggest that the investigated materials cannot be a good candidates for a nanoscale superconductors.

Observation of soft phonon mode in TbFe 3 ( BO 3 ) 4 by inelastic neutron scattering

DOE PAGES

Pavlovskiy, M. S.; Shaykhutdinov, Krill A.; Wu, L. S.; ...

2018-02-28

In this study, the phonon dispersion in terbium iron borate TbFe 3(BO 3) 4 has been measured by inelastic neutron scattering in a temperature range 180S=192.5 K and studied by ab initio calculations. Significant, but not complete, softening of the transverse acoustic (TA) branch has been observed at the corner of the Brillouin zone (Λ point) at temperatures T≳T S, in full agreement with theoretical calculations. Finally, the TA soft mode undergoes considerable broadening at the Λ point near the transition temperature that can be attributed to the anharmonic interference between transverse acoustic and optical modes.

Observation of soft phonon mode in TbFe 3 ( BO 3 ) 4 by inelastic neutron scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pavlovskiy, M. S.; Shaykhutdinov, Krill A.; Wu, L. S.

In this study, the phonon dispersion in terbium iron borate TbFe 3(BO 3) 4 has been measured by inelastic neutron scattering in a temperature range 180S=192.5 K and studied by ab initio calculations. Significant, but not complete, softening of the transverse acoustic (TA) branch has been observed at the corner of the Brillouin zone (Λ point) at temperatures T≳T S, in full agreement with theoretical calculations. Finally, the TA soft mode undergoes considerable broadening at the Λ point near the transition temperature that can be attributed to the anharmonic interference between transverse acoustic and optical modes.

Dominant phonon wave vectors and strain-induced splitting of the 2D Raman mode of graphene

NASA Astrophysics Data System (ADS)

Narula, Rohit; Bonini, Nicola; Marzari, Nicola; Reich, Stephanie

2012-03-01

The dominant phonon wave vectors q* probed by the 2D Raman mode of pristine and uniaxially strained graphene are determined via a combination of ab initio calculations and a full two-dimensional integration of the transition matrix. We show that q* are highly anisotropic and rotate about K with the polarizer and analyzer condition relative to the lattice. The corresponding phonon-mediated electronic transitions show a finite component along K-Γ that sensitively determines q*. We invalidate the notion of “inner” and “outer” processes. The characteristic splitting of the 2D mode of graphene under uniaxial tensile strain and given polarizer and analyzer setting is correctly predicted only if the strain-induced distortion and red-shift of the in-plane transverse optical (iTO) phonon dispersion as well as the changes in the electronic band structure are taken into account.

Electron-phonon interaction in the binary superconductor lutetium carbide LuC2 via first-principles calculations

NASA Astrophysics Data System (ADS)

Dilmi, S.; Saib, S.; Bouarissa, N.

2018-06-01

Structural, electronic, electron-phonon coupling and superconducting properties of the intermetallic compound LuC2 are investigated by means of ab initio pseudopotential plane wave method within the generalized gradient approximation. The calculated equilibrium lattice parameters yielded a very good accord with experiment. There is no imaginary phonon frequency in the whole Brillouin zone supporting thus the dynamical stability in the material of interest. The average electron-phonon coupling parameter is found to be 0.59 indicating thus a weak-coupling BCS superconductor. Using a reasonable value of μ* = 0.12 for the effective Coulomb repulsion parameter, the superconducting critical temperature Tc is found to be 3.324 which is in excellent agreement with the experimental value of 3.33 K. The effect of the spin-orbit coupling on the superconducting properties of the material of interest has been examined and found to be weak.

Phonon-Mediated Tunneling into Graphene

NASA Astrophysics Data System (ADS)

Wehling, T. O.; Grigorenko, I.; Lichtenstein, A. I.; Balatsky, A. V.

2008-11-01

Recent scanning tunneling spectroscopy experiments on graphene reported an unexpected gap of about ±60meV around the Fermi level [V. W. Brar , Appl. Phys. Lett.APPLAB0003-6951 91, 122102 (2007); 10.1063/1.2771084Y. Zhang , Nature Phys.NPAHAX1745-2481 4, 627 (2008)10.1038/nphys1022]. Here we give a theoretical investigation explaining the experimentally observed spectra and confirming the phonon-mediated tunneling as the reason for the gap: We study the real space properties of the wave functions involved in the tunneling process by means of ab initio theory and present a model for the electron-phonon interaction, which couples the graphene’s Dirac electrons with quasifree-electron states at the Brillouin zone center. The self-energy associated with this electron-phonon interaction is calculated, and its effects on tunneling into graphene are discussed. Good agreement of the tunneling density of states within our model and the experimental dI/dU spectra is found.

Phonon mediated tunneling into graphene

NASA Astrophysics Data System (ADS)

Wehling, Tim; Grigorenko, Ilya; Lichtenstein, Alexander; Balatsky, Alexander

2009-03-01

Recent scanning tunneling spectroscopy experiments [V. W. Brar et al., Appl. Phys. Lett. 91, 122102 (2007); Y. Zhang et al., Nature Phys. 4, 627 (2008)] on graphene reported an unexpected gap of about ±60,eV around the Fermi level. Here, we give a theoretical investigation explaining the experimentally observed spectra and confirming the phonon mediated tunneling as the reason for the gap: We study the real space properties of the wave functions involved in the tunneling process by means of ab-initio theory and present a model for the electron-phonon interaction, which couples the graphene's Dirac electrons with quasi free electron states at the Brillouin zone center. The self-energy associated with this electron-phonon interaction is calculated and its effects on tunneling into graphene are discussed. In particular, good agreement of the tunneling density of states within our model and the experimental dI/dU spectra is found.

Phonon-mediated high-T c superconductivity in hole-doped diamond-like crystalline hydrocarbon

DOE PAGES

Lian, Chao-Sheng; Wang, Jian-Tao; Duan, Wenhui; ...

2017-05-03

We here predict by ab initio calculations phonon-mediated high-T c superconductivity in hole-doped diamond-like cubic crystalline hydrocarbon K 4-CH (space group I2 1/3). This material possesses three key properties: (i) an all-sp 3 covalent carbon framework that produces high-frequency phonon modes, (ii) a steep-rising electronic density of states near the top of the valence band, and (iii) a Fermi level that lies in the σ-band, allowing for a strong coupling with the C-C bond-stretching modes. The simultaneous presence of these properties generates remarkably high superconducting transition temperatures above 80 K at an experimentally accessible hole doping level of only amore » few percent. These results identify a new extraordinary electron-phonon superconductor and pave the way for further exploration of this novel superconducting covalent metal.« less

Self-consistent phonon calculations of lattice dynamical properties in cubic SrTiO3 with first-principles anharmonic force constants

NASA Astrophysics Data System (ADS)

Tadano, Terumasa; Tsuneyuki, Shinji

2015-08-01

We present an ab initio framework to calculate anharmonic phonon frequency and phonon lifetime that is applicable to severely anharmonic systems. We employ self-consistent phonon (SCPH) theory with microscopic anharmonic force constants, which are extracted from density functional calculations using the least absolute shrinkage and selection operator technique. We apply the method to the high-temperature phase of SrTiO3 and obtain well-defined phonon quasiparticles that are free from imaginary frequencies. Here we show that the anharmonic phonon frequency of the antiferrodistortive mode depends significantly on the system size near the critical temperature of the cubic-to-tetragonal phase transition. By applying perturbation theory to the SCPH result, phonon lifetimes are calculated for cubic SrTiO3, which are then employed to predict lattice thermal conductivity using the Boltzmann transport equation within the relaxation-time approximation. The presented methodology is efficient and accurate, paving the way toward a reliable description of thermodynamic, dynamic, and transport properties of systems with severe anharmonicity, including thermoelectric, ferroelectric, and superconducting materials.

Origin of Superconductivity and Latent Charge Density Wave in NbS2

NASA Astrophysics Data System (ADS)

Heil, Christoph; Poncé, Samuel; Lambert, Henry; Schlipf, Martin; Margine, Elena R.; Giustino, Feliciano

2017-08-01

We elucidate the origin of the phonon-mediated superconductivity in 2 H -NbS2 using the ab initio anisotropic Migdal-Eliashberg theory including Coulomb interactions. We demonstrate that superconductivity is associated with Fermi surface hot spots exhibiting an unusually strong electron-phonon interaction. The electron-lattice coupling is dominated by low-energy anharmonic phonons, which place the system on the verge of a charge density wave instability. We also provide definitive evidence for two-gap superconductivity in 2 H -NbS2 , and show that the low- and high-energy peaks observed in tunneling spectra correspond to the Γ - and K -centered Fermi surface pockets, respectively. The present findings call for further efforts to determine whether our proposed mechanism underpins superconductivity in the whole family of metallic transition metal dichalcogenides.

Yttrium aluminium garnet under pressure: Structural, elastic, and vibrational properties from ab initio studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Monteseguro, V.; Rodríguez-Hernández, P.; Muñoz, A., E-mail: amunoz@ull.es

The structural, elastic, and vibrational properties of yttrium aluminum garnet Y{sub 3}Al{sub 5}O{sub 12} are studied under high pressure by ab initio calculations in the framework of the density functional theory. The calculated ground state properties are in good agreement with the available experimental data. Pressure dependences of bond length and bulk moduli of the constituent polyhedra are reported. The evolution of the elastic constants and the major elastic properties, Young and shear modulus, Poisson's ratios, and Zener anisotropy ratio, are described. The mechanical stability is analyzed, on the light of “Born generalized stability criteria,” showing that the garnet ismore » mechanically unstable above 116 GPa. Symmetries, frequencies, and pressure coefficients of the Raman-active modes are discussed on the basis of the calculated total and partial phonon density of states, which reflect the dynamical contribution of each atom. The relations between the phonon modes of Y{sub 3}Al{sub 5}O{sub 12} and the internal and external molecular modes of the different polyhedra are discussed. Infrared-active modes, as well as the silent modes, and their pressure dependence are also investigated. No dynamical instabilities were found below 116 GPa.« less

Electronic Structure, Mechanical and Dynamical Stability of Hexagonal Subcarbides M2C (M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt): Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Suetin, D. V.; Shein, I. R.

2018-02-01

Ab initio calculations were used to study the properties of a series of hexagonal (Fe2N-like) subcarbides M2C, where M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt, and to calculate their equilibrium structural parameters, electronic properties, phase stability, elastic constants, compression modulus, shear modulus, Young's modulus, compressibility, Pugh's indicator, Poisson ratio, elastic anisotropy indices, and also hardness, Debye temperature, sound velocity, and low-temperature heat capacity. It is found based on these results that all the subcarbides are mechanically stable; however, their formation energies E form are positive with respect to a mixture of d-metal and graphite. In addition, the calculation of the phonon spectra of these subcarbides shows the existence of negative modes, which indicates their dynamical instability. Thus, a successful synthesis of these subcarbides at normal conditions is highly improbable.

THE AB INITIO CALCULATION OF THE DYNAMICAL AND THE THERMODYNAMIC PROPERTIES OF THE ZINC-BLENDE GaX (X=N, P, As AND Sb)

NASA Astrophysics Data System (ADS)

Bouhadda, Y.; Bentabet, A.; Fenineche, N. E.; Boudouma, Y.

2012-12-01

By this work, we aim to study the dynamical and the thermodynamic properties of the zinc-blende GaX (X = N, P, As and Sb) using the Ab initio simulation method. Indeed, we studied the lattice dynamics, the constant-volume specific heat (Cv), the internal energy (U), the entropy (S) and the free energy (F). The observed differences between the properties of GaX elements were discussed. Our results and the available literature data (theoretical and experimental) seems to be in good agreement. Moreover, Cv, U, F and S were calculated by using the harmonic approximation in the calculation of the dynamic lattice vibration. The good agreement between our results of both the phonon frequency, the constant-volume specific heat and the experimental data allows us to conclude that our results of S, U and F of GaX were well predicted.

New Equation of State Models for Hydrodynamic Applications

NASA Astrophysics Data System (ADS)

Young, David A.; Barbee, Troy W., III; Rogers, Forrest J.

1997-07-01

Accurate models of the equation of state of matter at high pressures and temperatures are increasingly required for hydrodynamic simulations. We have developed two new approaches to accurate EOS modeling: 1) ab initio phonons from electron band structure theory for condensed matter and 2) the ACTEX dense plasma model for ultrahigh pressure shocks. We have studied the diamond and high pressure phases of carbon with the ab initio model and find good agreement between theory and experiment for shock Hugoniots, isotherms, and isobars. The theory also predicts a comprehensive phase diagram for carbon. For ultrahigh pressure shock states, we have studied the comparison of ACTEX theory with experiments for deuterium, beryllium, polystyrene, water, aluminum, and silicon dioxide. The agreement is good, showing that complex multispecies plasmas are treated adequately by the theory. These models will be useful in improving the numerical EOS tables used by hydrodynamic codes.

DFT-based ab initio MD simulation of the ionic conduction in doped ZrO₂ systems under epitaxial strain.

PubMed

Oka, M; Kamisaka, H; Fukumura, T; Hasegawa, T

2015-11-21

The oxygen ionic conduction in ZrO2 systems under tensile epitaxial strain was investigated by performing ab initio molecular dynamics (MD) calculations based on density functional theory (DFT) to elucidate the essential factors in the colossal ionic conductivity observed in the yttria stabilized ZrO2 (YSZ)/SrTiO3 heterostructure. Three factors were evaluated: lattice strain, oxygen vacancies, and dopants. Phonon calculations based on density functional perturbation theory (DFPT) were used to obtain the most stable structure for nondoped ZrO2 under 7% tensile strain along the a- and b-axes. This structure has the space group Pbcn, which is entirely different from that of cubic ZrO2, suggesting that previous ab initio MD calculations assuming cubic ZrO2 may have overestimated the ionic conductivity due to relaxation from the initial structure to the stable structure (Pbcn). Our MD calculations revealed that the ionic conductivity is enhanced only when tensile strain and oxygen vacancies are incorporated, although the presently obtained diffusion constant is far below the range for the colossal ionic conduction experimentally observed. The enhanced ionic conductivity is due to the combined effects of oxygen sublattice formation induced by strain and deformation of this sublattice by oxygen vacancies.

Solid-state electron spin lifetime limited by phononic vacuum modes.

PubMed

Astner, T; Gugler, J; Angerer, A; Wald, S; Putz, S; Mauser, N J; Trupke, M; Sumiya, H; Onoda, S; Isoya, J; Schmiedmayer, J; Mohn, P; Majer, J

2018-04-01

Longitudinal relaxation is the process by which an excited spin ensemble decays into its thermal equilibrium with the environment. In solid-state spin systems, relaxation into the phonon bath usually dominates over the coupling to the electromagnetic vacuum 1-9 . In the quantum limit, the spin lifetime is determined by phononic vacuum fluctuations 10 . However, this limit was not observed in previous studies due to thermal phonon contributions 11-13 or phonon-bottleneck processes 10, 14,15 . Here we use a dispersive detection scheme 16,17 based on cavity quantum electrodynamics 18-21 to observe this quantum limit of spin relaxation of the negatively charged nitrogen vacancy (NV - ) centre 22 in diamond. Diamond possesses high thermal conductivity even at low temperatures 23 , which eliminates phonon-bottleneck processes. We observe exceptionally long longitudinal relaxation times T 1 of up to 8 h. To understand the fundamental mechanism of spin-phonon coupling in this system we develop a theoretical model and calculate the relaxation time ab initio. The calculations confirm that the low phononic density of states at the NV - transition frequency enables the spin polarization to survive over macroscopic timescales.

Ab initio computation of the transition temperature of the charge density wave transition in TiS e2

NASA Astrophysics Data System (ADS)

Duong, Dinh Loc; Burghard, Marko; Schön, J. Christian

2015-12-01

We present a density functional perturbation theory approach to estimate the transition temperature of the charge density wave transition of TiS e2 . The softening of the phonon mode at the L point where in TiS e2 a giant Kohn anomaly occurs, and the energy difference between the normal and distorted phase are analyzed. Both features are studied as functions of the electronic temperature, which corresponds to the Fermi-Dirac distribution smearing value in the calculation. The transition temperature is found to be 500 and 600 K by phonon and energy analysis, respectively, in reasonable agreement with the experimental value of 200 K.

Ab initio phonon thermal transport in monolayer InSe, GaSe, GaS, and alloys

NASA Astrophysics Data System (ADS)

Pandey, Tribhuwan; Parker, David S.; Lindsay, Lucas

2017-11-01

We compare vibrational properties and phonon thermal conductivities (κ) of monolayer InSe, GaSe, and GaS systems using density functional theory and Peierls-Boltzmann transport methods. In going from InSe to GaSe to GaS, system mass decreases giving both increasing acoustic phonon velocities and decreasing scattering of these heat-carrying modes with optic phonons, ultimately giving {κ }{InSe}< {κ }{GaSe}< {κ }{GaS}. This behavior is demonstrated by correlating the scattering phase space limited by fundamental conservation conditions with mode scattering rates and phonon dispersions for each material. We also show that, unlike flat monolayer systems such as graphene, in InSe, GaSe and GaS thermal transport is governed by in-plane vibrations. Alloying of InSe, GaSe, and GaS systems provides an effective method for modulating their κ through intrinsic vibrational modifications and phonon scattering from mass disorder giving reductions ˜2-3.5 times. This disorder also suppresses phonon mean free paths in the alloy systems compared to those in their crystalline counterparts. This work provides fundamental insights of lattice thermal transport from basic vibrational properties for an interesting set of two-dimensional materials.

Phonovoltaic. I. Harvesting hot optical phonons in a nanoscale p -n junction

NASA Astrophysics Data System (ADS)

Melnick, Corey; Kaviany, Massoud

2016-03-01

The phonovoltaic (pV) cell is similar to the photovoltaic. It harvests nonequilibrium (hot) optical phonons (Ep ,O) more energetic than the band gap (Δ Ee ,g) to generate power in a p-n junction. We examine the theoretical electron-phonon and phonon-phonon scattering rates, the Boltzmann transport of electrons, and the diode equation and hydrodynamic simulations to describe the operation of a pV cell and develop an analytic model predicting its efficiency. Our findings indicate that a pV material with Ep ,O≃Δ Ee ,g≫kBT , where kBT is the thermal energy, and a strong interband electron-phonon coupling surpasses the thermoelectric limit, provided the optical phonon population is excited in a nanoscale cell, enabling the ensuing local nonequilibrium. Finding and tuning a material with these properties is challenging. In Paper II [C. Melnick and M. Kaviany, Phys. Rev. B 93, 125203 (2016), 10.1103/PhysRevB.93.125203], we tune the band gap of graphite within density functional theory through hydrogenation and the application of isotropic strains. The band gap is tuned to resonate with its energetic optical phonon modes and calculate the ab initio electron-phonon and phonon-phonon scattering rates. While hydrogenation degrades the strong electron-phonon coupling in graphene such that the figure of merit vanishes, we outline the methodology for a continued material search.

Atomistic modeling of phonon transport in turbostratic graphitic structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Rui; Chen, Yifeng; Kim, Ki Wook, E-mail: kwk@ncsu.edu

2016-05-28

Thermal transport in turbostratic graphitic systems is investigated by using an atomistic analytical model based on the 4th-nearest-neighbor force constant approximation and a registry-dependent interlayer potential. The developed model is shown to produce an excellent agreement with the experimental data and ab initio results in the calculation of bulk properties. Subsequent analysis of phonon transport in combination with the Green's function method illustrates the significant dependence of key characteristics on the misorientation angle, clearly indicating the importance of this degree of freedom in multi-stacked structures. Selecting three angles with the smallest commensurate unit cells, the thermal resistance is evaluated atmore » the twisted interface between two AB stacked graphite. The resulting values in the range of 35 × 10{sup −10} K m{sup 2}/W to 116 × 10{sup −10} K m{sup 2}/W are as large as those between two dissimilar material systems such as a metal and graphene. The strong rotational effect on the cross-plane thermal transport may offer an effective means of phonon engineering for applications such as thermoelectric materials.« less

Superconductivity and hybrid soft modes in Ti Se 2

DOE PAGES

Maschek, M.; Rosenkranz, S.; Hott, R.; ...

2016-12-12

The interplay between superconductivity and charge-density-wave (CDW) order plays a central role in the layered transition-metal dichalcogenides. 1 T-TiSe 2 forms a prime example, featuring superconducting domes on intercalation as well as under applied pressure. Here, we present high energy-resolution inelastic x-ray scattering measurements of the CDW soft phonon mode in intercalated Cu xTiSe 2 and pressurized 1 T-TiSe 2 along with detailed ab-initio calculations for the lattice dynamical properties and phonon-mediated superconductivity. We find that the intercalation-induced superconductivity can be explained by a solely phonon-mediated pairing mechanism, while this is not possible for the superconducting phase under pressure. Wemore » argue that a hybridization of phonon and exciton modes in the pairing mechanism is necessary to explain the full observed temperature-pressure-intercalation phase diagram. Finally, these results indicate that 1 T-TiSe 2 under pressure is close to the elusive state of the excitonic insulator.« less

Charge Transport Properties of Durene Crystals from First-Principles.

PubMed

Motta, Carlo; Sanvito, Stefano

2014-10-14

We establish a rigorous computational scheme for constructing an effective Hamiltonian to be used for the determination of the charge carrier mobility of pure organic crystals at finite temperature, which accounts for van der Waals interactions, and it includes vibrational contributions from the entire phonon spectrum of the crystal. Such an approach is based on the ab initio framework provided by density functional theory and the construction of a tight-binding effective model via Wannier transformation. The final Hamiltonian includes coupling of the electrons to the crystals phonons, which are also calculated from density functional theory. We apply this methodology to the case of durene, a small π-conjugated molecule, which forms a high-mobility herringbone-stacked crystal. We show that accounting correctly for dispersive forces is fundamental for obtaining a high-quality phonon spectrum, in agreement with experiments. Then, the mobility as a function of temperature is calculated along different crystallographic directions and the phonons most responsible for the scattering are identified.

Probing the interatomic potential of solids with strong-field nonlinear phononics

NASA Astrophysics Data System (ADS)

von Hoegen, A.; Mankowsky, R.; Fechner, M.; Först, M.; Cavalleri, A.

2018-03-01

Nonlinear optical techniques at visible frequencies have long been applied to condensed matter spectroscopy. However, because many important excitations of solids are found at low energies, much can be gained from the extension of nonlinear optics to mid-infrared and terahertz frequencies. For example, the nonlinear excitation of lattice vibrations has enabled the dynamic control of material functions. So far it has only been possible to exploit second-order phonon nonlinearities at terahertz field strengths near one million volts per centimetre. Here we achieve an order-of-magnitude increase in field strength and explore higher-order phonon nonlinearities. We excite up to five harmonics of the A1 (transverse optical) phonon mode in the ferroelectric material lithium niobate. By using ultrashort mid-infrared laser pulses to drive the atoms far from their equilibrium positions, and measuring the large-amplitude atomic trajectories, we can sample the interatomic potential of lithium niobate, providing a benchmark for ab initio calculations for the material. Tomography of the energy surface by high-order nonlinear phononics could benefit many aspects of materials research, including the study of classical and quantum phase transitions.

The Pressure Dependence of Structural, Electronic, Mechanical, Vibrational, and Thermodynamic Properties of Palladium-Based Heusler Alloys

NASA Astrophysics Data System (ADS)

Çoban, Cansu

2017-08-01

The pressure dependent behaviour of the structural, electronic, mechanical, vibrational, and thermodynamic properties of Pd2TiX (X=Ga, In) Heusler alloys was investigated by ab initio calculations. The lattice constant, the bulk modulus and its first pressure derivative, the electronic band structure and the density of states (DOS), mechanical properties such as elastic constants, anisotropy factor, Young's modulus, etc., the phonon dispersion curves and phonon DOS, entropy, heat capacity, and free energy were obtained under pressure. It was determined that the calculated lattice parameters are in good agreement with the literature, the elastic constants obey the stability criterion, and the phonon dispersion curves have no negative frequency which shows that the compounds are stable. The band structures at 0, 50, and 70 GPa showed valence instability at the L point which explains the superconductivity in Pd2TiX (X=Ga, In).

Phonon Softening due to Melting of the Ferromagnetic Order in Elemental Iron

NASA Astrophysics Data System (ADS)

Han, Qiang; Birol, Turan; Haule, Kristjan

2018-05-01

We study the fundamental question of the lattice dynamics of a metallic ferromagnet in the regime where the static long-range magnetic order is replaced by the fluctuating local moments embedded in a metallic host. We use the ab initio density functional theory + embedded dynamical mean-field theory functional approach to address the dynamic stability of iron polymorphs and the phonon softening with an increased temperature. We show that the nonharmonic and inhomogeneous phonon softening measured in iron is a result of the melting of the long-range ferromagnetic order and is unrelated to the first-order structural transition from the bcc to the fcc phase, as is usually assumed. We predict that the bcc structure is dynamically stable at all temperatures at normal pressure and is thermodynamically unstable only between the bcc-α and the bcc-δ phases of iron.

Ab-initio quantum transport simulation of self-heating in single-layer 2-D materials

NASA Astrophysics Data System (ADS)

Stieger, Christian; Szabo, Aron; Bunjaku, Teutë; Luisier, Mathieu

2017-07-01

Through advanced quantum mechanical simulations combining electron transport and phonon transport from first-principles, self-heating effects are investigated in n-type transistors with single-layer MoS2, WS2, and black phosphorus as channel materials. The selected 2-D crystals all exhibit different phonon-limited mobility values, as well as electron and phonon properties, which have a direct influence on the increase in their lattice temperature and on the power dissipated inside their channel as a function of the applied gate voltage and electrical current magnitude. This computational study reveals (i) that self-heating plays a much more important role in 2-D materials than in Si nanowires, (ii) that it could severely limit the performance of 2-D devices at high current densities, and (iii) that black phosphorus appears less sensitive to this phenomenon than transition metal dichalcogenides.

Structural, electronic, mechanical, and dynamical properties of graphene oxides: A first principles study

NASA Astrophysics Data System (ADS)

Dabhi, Shweta D.; Gupta, Sanjay D.; Jha, Prafulla K.

2014-05-01

We report the results of a theoretical study on the structural, electronic, mechanical, and vibrational properties of some graphene oxide models (GDO, a-GMO, z-GMO, ep-GMO and mix-GMO) at ambient pressure. The calculations are based on the ab-initio plane-wave pseudo potential density functional theory, within the generalized gradient approximations for the exchange and correlation functional. The calculated values of lattice parameters, bulk modulus, and its first order pressure derivative are in good agreement with other reports. A linear response approach to the density functional theory is used to derive the phonon frequencies. We discuss the contribution of the phonons in the dynamical stability of graphene oxides and detailed analysis of zone centre phonon modes in all the above mentioned models. Our study demonstrates a wide range of energy gap available in the considered models of graphene oxide and hence the possibility of their use in nanodevices.

The happy marriage between electron-phonon superconductivity and Mott physics in Cs3C60: A first-principle phase diagram

NASA Astrophysics Data System (ADS)

Capone, Massimo; Nomura, Yusuke; Sakai, Shiro; Giovannetti, Gianluca; Arita, Ryotaro

The phase diagram of doped fullerides like Cs3C60 as a function of the spacing between fullerene molecules is characterized by a first-order transition between a Mott insulator and an s-wave superconductor with a dome-shaped behavior of the critical temperature. By means of an ab-initio modeling of the bandstructure, the electron-phonon interaction and the interaction parameter and a Dynamical Mean-Field Theory solution, we reproduce the phase diagram and demonstrate that phonon superconductivity benefits from strong correlations confirming earlier model predictions. The role of correlations is manifest also in infrared measurements carried out by L. Baldassarre. The superconducting phase shares many similarities with ''exotic'' superconductors with electronic pairing, suggesting that the anomalies in the ''normal'' state, rather than the pairing glue, can be the real common element unifying a wide family of strongly correlated superconductors including cuprates and iron superconductors

Phonon-coupled ultrafast interlayer charge oscillation at van der Waals heterostructure interfaces

NASA Astrophysics Data System (ADS)

Zheng, Qijing; Xie, Yu; Lan, Zhenggang; Prezhdo, Oleg V.; Saidi, Wissam A.; Zhao, Jin

2018-05-01

Van der Waals (vdW) heterostructures of transition-metal dichalcogenide (TMD) semiconductors are central not only for fundamental science, but also for electro- and optical-device technologies where the interfacial charge transfer is a key factor. Ultrafast interfacial charge dynamics has been intensively studied, however, the atomic scale insights into the effects of the electron-phonon (e-p) coupling are still lacking. In this paper, using time dependent ab initio nonadiabatic molecular dynamics, we study the ultrafast interfacial charge transfer dynamics of two different TMD heterostructures MoS2/WS2 and MoSe2/WSe2 , which have similar band structures but different phonon frequencies. We found that MoSe2/WSe2 has softer phonon modes compared to MoS2/WS2 , and thus phonon-coupled charge oscillation can be excited with sufficient phonon excitations at room temperature. In contrast, for MoS2/WS2 , phonon-coupled interlayer charge oscillations are not easily excitable. Our study provides an atomic level understanding on how the phonon excitation and e-p coupling affect the interlayer charge transfer dynamics, which is valuable for both the fundamental understanding of ultrafast dynamics at vdW hetero-interfaces and the design of novel quasi-two-dimensional devices for optoelectronic and photovoltaic applications.

Superconductivity in Doped sp3 Semiconductors: The Case of the Clathrates

NASA Astrophysics Data System (ADS)

Connétable, D.; Timoshevskii, V.; Masenelli, B.; Beille, J.; Marcus, J.; Barbara, B.; Saitta, A. M.; Rignanese, G.-M.; Mélinon, P.; Yamanaka, S.; Blase, X.

2003-12-01

We present a joint experimental and theoretical study of the superconductivity in doped silicon clathrates. The critical temperature in Ba8@Si-46 is shown to strongly decrease with applied pressure. These results are corroborated by ab initio calculations using MacMillan's formulation of the BCS theory with the electron-phonon coupling constant λ calculated from perturbative density functional theory. Further, the study of I8@Si-46 and of gedanken pure silicon diamond and clathrate phases doped within a rigid-band approach show that the superconductivity is an intrinsic property of the sp3 silicon network. As a consequence, carbon clathrates are predicted to yield large critical temperatures with an effective electron-phonon interaction much larger than in C60.

Towards predictive many-body calculations of phonon-limited carrier mobilities in semiconductors

NASA Astrophysics Data System (ADS)

Poncé, Samuel; Margine, Elena R.; Giustino, Feliciano

2018-03-01

We probe the accuracy limit of ab initio calculations of carrier mobilities in semiconductors, within the framework of the Boltzmann transport equation. By focusing on the paradigmatic case of silicon, we show that fully predictive calculations of electron and hole mobilities require many-body quasiparticle corrections to band structures and electron-phonon matrix elements, the inclusion of spin-orbit coupling, and an extremely fine sampling of inelastic scattering processes in momentum space. By considering all these factors we obtain excellent agreement with experiment, and we identify the band effective masses as the most critical parameters to achieve predictive accuracy. Our findings set a blueprint for future calculations of carrier mobilities, and pave the way to engineering transport properties in semiconductors by design.

First-principles theory of anharmonicity and the inverse isotope effect in superconducting palladium-hydride compounds.

PubMed

Errea, Ion; Calandra, Matteo; Mauri, Francesco

2013-10-25

Palladium hydrides display the largest isotope effect anomaly known in the literature. Replacement of hydrogen with the heavier isotopes leads to higher superconducting temperatures, a behavior inconsistent with harmonic theory. Solving the self-consistent harmonic approximation by a stochastic approach, we obtain the anharmonic free energy, the thermal expansion, and the superconducting properties fully ab initio. We find that the phonon spectra are strongly renormalized by anharmonicity far beyond the perturbative regime. Superconductivity is phonon mediated, but the harmonic approximation largely overestimates the superconducting critical temperatures. We explain the inverse isotope effect, obtaining a -0.38 value for the isotope coefficient in good agreement with experiments, hydrogen anharmonicity being mainly responsible for the isotope anomaly.

Raman tensor elements of β-Ga2O3.

PubMed

Kranert, Christian; Sturm, Chris; Schmidt-Grund, Rüdiger; Grundmann, Marius

2016-11-03

The Raman spectrum and particularly the Raman scattering intensities of monoclinic β-Ga 2 O 3 are investigated by experiment and theory. The low symmetry of β-Ga 2 O 3 results in a complex dependence of the Raman intensity for the individual phonon modes on the scattering geometry which is additionally affected by birefringence. We measured the Raman spectra in dependence on the polarization direction for backscattering on three crystallographic planes of β-Ga 2 O 3 and modelled these dependencies using a modified Raman tensor formalism which takes birefringence into account. The spectral position of all 15 Raman active phonon modes and the Raman tensor elements of 13 modes were determined and are compared to results from ab-initio calculations.

Raman tensor elements of β-Ga2O3

PubMed Central

Kranert, Christian; Sturm, Chris; Schmidt-Grund, Rüdiger; Grundmann, Marius

2016-01-01

The Raman spectrum and particularly the Raman scattering intensities of monoclinic β-Ga2O3 are investigated by experiment and theory. The low symmetry of β-Ga2O3 results in a complex dependence of the Raman intensity for the individual phonon modes on the scattering geometry which is additionally affected by birefringence. We measured the Raman spectra in dependence on the polarization direction for backscattering on three crystallographic planes of β-Ga2O3 and modelled these dependencies using a modified Raman tensor formalism which takes birefringence into account. The spectral position of all 15 Raman active phonon modes and the Raman tensor elements of 13 modes were determined and are compared to results from ab-initio calculations. PMID:27808113

Bilayer graphene phonovoltaic-FET: In situ phonon recycling

NASA Astrophysics Data System (ADS)

Melnick, Corey; Kaviany, Massoud

2017-11-01

A new heat harvester, the phonovoltaic (pV) cell, was recently proposed. The device converts optical phonons into power before they become heat. Due to the low entropy of a typical hot optical phonon population, the phonovoltaic can operate at high fractions of the Carnot limit and harvest heat more efficiently than conventional heat harvesting technologies such as the thermoelectric generator. Previously, the optical phonon source was presumed to produce optical phonons with a single polarization and momentum. Here, we examine a realistic optical phonon source in a potential pV application and the effects this has on pV operation. Supplementing this work is our investigation of bilayer graphene as a new pV material. Our ab initio calculations show that bilayer graphene has a figure of merit exceeding 0.9, well above previously investigated materials. This allows a room-temperature pV to recycle 65% of a highly nonequilibrium, minimum entropy population of phonons. However, full-band Monte Carlo simulations of the electron and phonon dynamics in a bilayer graphene field-effect transistor (FET) show that the optical phonons emitted by field-accelerated electrons can only be recycled in situ with an efficiency of 50%, and this efficiency falls as the field strength grows. Still, an appropriately designed FET-pV can recycle the phonons produced therein in situ with a much higher efficiency than a thermoelectric generator can harvest heat produced by a FET ex situ.

Ab initio Thermal Transport in Compound Semiconductors

DTIC Science & Technology

2013-04-02

upper bound to the thermal conductivities of cubic aluminum-V, gallium -V, and indium-V compounds as limited by anharmonic phonon scattering. The effects...and GaP [red circles (Ref. 51) and red triangles (Ref. 52)]. B. Gallium -V compounds We previously presented results for κL and P for wurtzite GaN and...data was found. We used this approach to examine κL in aluminum-V, gallium -V, and indium-V compounds as well as the technologically important materials

Report of Research at Technische Universitaet Darmstadt on Ultrahard Materials in the B-C-N-Si System

DTIC Science & Technology

2015-06-01

structure at the micro- and nanoscale. In other words, development of nanocomposites, multilayers, and superlattices via appropriate design and control of...C-B and C-N bonds as C-C and B-N bonds. Later, the same research group , based on first-principles total-energy, and dynamic phonon calculations...Vickers hardness values.7 Another research group employed an ab initio evolutionary algorithm42 to resolve the crystal structure of the observed

Phonon Scattering in Thermoelectrics: Thermal Transport, Strong Anharmonicity, and Emergent Quasiparticles

NASA Astrophysics Data System (ADS)

Delaire, Olivier

Modern neutron and x-ray spectrometers can map phonon dispersions and scattering rates throughout reciprocal space, providing unique insights into microscopic scattering mechanisms, including anharmonicity, electron-phonon coupling, or scattering by defects and nanostructures. In addition, first-principles simulations enable the rationalization of extensive experimental datasets. In particular, ab-initio molecular dynamics simulations can capture striking effects of anharmonicity near lattice instabilities. A number of high-performance thermoelectric materials are found in the vicinity of lattice instabilities, including Pb chalcogenides PbX, SnSe, Cu2Se, among others. The large phonon anharmonicity found in such compounds suppresses the lattice thermal conductivity, enhancing their thermoelectric efficiency. In this presentation, I will present results from our investigations of phonons in these materials using neutron and x-ray scattering combined with first-principles simulations, focusing on anharmonic effects near lattice instabilities. I will show how strong anharmonicity can lead to emergent quasiparticles qualitatively different from harmonic phonons, which we probe in our measurements and simulations of the phonon self-energy. Commonalities between systems will be highlighted, including connections between strong anharmonicity and the electronic structure. Funding from US DOE, Office of Basic Energy Sciences, Materials Science and Engineering Division, Office of Science Early Career program (DE-SC0016166), and as part of the S3TEC EFRC (DE-SC0001299).

Ab initio phonon thermal transport in monolayer InSe, GaSe, GaS, and alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandey, Tribhuwan; Parker, David S.; Lindsay, Lucas

We compare vibrational properties and phonon thermal conductivities (κ) of monolayer InSe, GaSe and GaS systems using density functional theory and Peierls-Boltzmann transport methods. In going from InSe to GaSe to GaS, system mass decreases giving both increasing acoustic phonon velocities and decreasing scattering of these heat-carrying modes with optic phonons, ultimately giving κInSe< κGaSe< κGaS. This behavior is demonstrated by correlating the scattering phase space limited by fundamental conservation conditions with mode scattering rates and phonon dispersions for each material. We also show that, unlike flat monolayer systems such as graphene, thermal transport is governed by in-plane vibrations inmore » InSe, GaSe and GaS, similar to buckled monolayer materials such as silicene. Alloying of InSe, GaSe and GaS systems provides an effective method for modulating their κ through intrinsic vibrational modifications and phonon scattering from mass disorder giving reductions ~2-3.5 times. This disorder also suppresses phonon mean free paths in the alloy systems compared to those in their crystalline counterparts. This work provides fundamental insights of lattice thermal transport from basic vibrational properties for an interesting set of two-dimensional materials.« less

Ab initio theory of spin-orbit coupling for quantum bits in diamond exhibiting dynamic Jahn-Teller effect

NASA Astrophysics Data System (ADS)

Gali, Adam; Thiering, Gergő

Dopants in solids are promising candidates for implementations of quantum bits for quantum computing. In particular, the high-spin negatively charged nitrogen-vacancy defect (NV) in diamond has become a leading contender in solid-state quantum information processing. The initialization and readout of the spin is based on the spin-selective decay of the photo-excited electron to the ground state which is mediated by spin-orbit coupling between excited states states and phonons. Generally, the spin-orbit coupling plays a crucial role in the optical spinpolarization and readout of NV quantum bit (qubit) and alike. Strong electron-phonon coupling in dynamic Jahn-Teller (DJT) systems can substantially influence the effective strength of spin-orbit coupling. Here we show by ab initio supercell density functional theory (DFT) calculations that the intrinsic spin-orbit coupling is strongly damped by DJT effect in the triplet excited state that has a consequence on the rate of non-radiative decay. This theory is applied to the ground state of silicon-vacancy (SiV) and germanium-vacancy (GeV) centers in their negatively charged state that can also act like qubits. We show that the intrinsic spin-orbit coupling in SiV and GeV centers is in the 100 GHz region, in contrast to the NV center of 10 GHz region. Our results provide deep insight in the nature of SiV and GeV qubits in diamond. EU FP7 DIADEMS project (Contract No. 611143).

Zero point motion effect on the electronic properties of diamond, trans-polyacetylene and polyethylene

NASA Astrophysics Data System (ADS)

Cannuccia, E.; Marini, A.

2012-09-01

It has been recently shown, using ab-initio methods, that bulk diamond is characterized by a large band-gap renormalization (˜0.6 eV) induced by the electron-phonon interaction. In this work we show that in polymers, compared to bulk materials, the larger amplitude of the atomic vibrations makes the real excitations of the system be composed by entangled electron-phonon states. We prove that these states carry only a fraction of the electronic charge, thus leading, inevitably, to the failure of the electronic picture. The present results cast doubts on the accuracy of purely electronic calculations. They also lead to a critical revision of the state-of-the-art description of carbon-based nanostructures, opening a wealth of potential implications.

Theoretical investigation of the structural, electronic, dynamical and thermal properties of YSn3 and YPb3

NASA Astrophysics Data System (ADS)

Kılıçarslan, Aynur; Salmankurt, Bahadır; Duman, Sıtkı

2017-02-01

We have performed an ab initio study of the structural, electronic, dynamical and thermal properties of the cubic AuCu3-type YSn3 and YPb3 by using the density functional theory, plane-wave pseudopotential method and a linear response scheme, within the generalized gradient approximation. An analysis of the electronic density of states at the Fermi level is found to be governed by the p states of Sn and Pb atoms with some contributions from the d states of Y atoms. The obtained phonon figures indicate that these material are dynamically stable in the cubic structure. Due to the metallic behavior of the compounds, the calculated zone-center phonon modes are triply degenerate. Also the thermal properties have been examined.

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

Tamm, A.; Samolyuk, G.; Correa, A. A.; ...

2016-07-14

Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

Multiphase Equation of State and Strength Properties of Beryllium from AB INITIO and Quantum Molecular Dynamics Calculations.

NASA Astrophysics Data System (ADS)

Robert, G.; Sollier, A.; Legrand, Ph.

2007-12-01

In the framework of density functional theory, static properties and phonon spectra of beryllium have been calculated under high compression (for pressures up to 4 Mbar) for two solid phases: hexagonal compact (hcp) and body-centered cubic (bcc). The melting curve and some isotherms in the liquid phase have been calculated using quantum molecular dynamics. The coupling of these theoretical data to a quasi-harmonic approach (phonon moments) allows us to suggest a new theoretical phase diagram and to build a multiphase equation of state (EOS) valid in a large range of pressure and temperature. The resulting Hugoniot curves as well as the evolution of the longitudinal sound speed with both pressure and temperature are in good agreement with available experimental data.

Lattice dynamics of the rare-earth element samarium

NASA Astrophysics Data System (ADS)

Bauder, Olga; Piekarz, Przemysław; Barla, Alessandro; Sergueev, Ilya; Rüffer, Rudolf; ŁaŻewski, Jan; Baumbach, Tilo; Parlinski, Krzysztof; Stankov, Svetoslav

2013-12-01

The lattice dynamics of samarium is determined by in situ low-temperature nuclear inelastic scattering on a single crystalline (0001)Sm film, a polycrystalline Sm foil, and by first-principles theory. The ab initio calculated phonon dispersion relations and phonon density of states for the Sm-type structure and the double hexagonal-close-packed (dhcp) lattice, characteristic for light lanthanides, are compared. The dhcp unit cell, which is a factor of 2.24 smaller in height, exhibits more pronounced vibrational anisotropy in comparison to the Sm-type structure. The analysis reveals a minor influence of the spin-orbit coupling in the Sm atom on the lattice dynamics. A broadening of the longitudinal peak, not found in the calculations, suggests the influence of electron correlations on lattice dynamics in metallic samarium.

Ultrafast carrier thermalization and cooling dynamics in few-layer MoS2.

PubMed

Nie, Zhaogang; Long, Run; Sun, Linfeng; Huang, Chung-Che; Zhang, Jun; Xiong, Qihua; Hewak, Daniel W; Shen, Zexiang; Prezhdo, Oleg V; Loh, Zhi-Heng

2014-10-28

Femtosecond optical pump-probe spectroscopy with 10 fs visible pulses is employed to elucidate the ultrafast carrier dynamics of few-layer MoS2. A nonthermal carrier distribution is observed immediately following the photoexcitation of the A and B excitonic transitions by the ultrashort, broadband laser pulse. Carrier thermalization occurs within 20 fs and proceeds via both carrier-carrier and carrier-phonon scattering, as evidenced by the observed dependence of the thermalization time on the carrier density and the sample temperature. The n(-0.37 ± 0.03) scaling of the thermalization time with carrier density suggests that equilibration of the nonthermal carrier distribution occurs via non-Markovian quantum kinetics. Subsequent cooling of the hot Fermi-Dirac carrier distribution occurs on the ∼ 0.6 ps time scale via carrier-phonon scattering. Temperature- and fluence-dependence studies reveal the involvement of hot phonons in the carrier cooling process. Nonadiabatic ab initio molecular dynamics simulations, which predict carrier-carrier and carrier-phonon scattering time scales of 40 fs and 0.5 ps, respectively, lend support to the assignment of the observed carrier dynamics.

Lattice Dynamics Study of Phonon Instability and Thermal Properties of Type-I Clathrate K8Si46 under High Pressure

PubMed Central

Zhang, Wei; Zeng, Zhao Yi; Ge, Ni Na; Li, Zhi Guo

2016-01-01

For a further understanding of the phase transitions mechanism in type-I silicon clathrates K8Si46, ab initio self-consistent electronic calculations combined with linear-response method have been performed to investigate the vibrational properties of alkali metal K atoms encapsulated type-I silicon-clathrate under pressure within the framework of density functional perturbation theory. Our lattice dynamics simulation results showed that the pressure induced phase transition of K8Si46 was believed to be driven by the phonon instability of the calthrate lattice. Analysis of the evolution of the partial phonon density of state with pressure, a legible dynamic picture for both guest K atoms and host lattice, was given. In addition, based on phonon calculations and combined with quasi-harmonic approximation, the specific heat of K8Si46 was derived, which agreed very well with experimental results. Also, other important thermal properties including the thermal expansion coefficients and Grüneisen parameters of K8Si46 under different temperature and pressure were also predicted. PMID:28773736

almaBTE : A solver of the space-time dependent Boltzmann transport equation for phonons in structured materials

NASA Astrophysics Data System (ADS)

Carrete, Jesús; Vermeersch, Bjorn; Katre, Ankita; van Roekeghem, Ambroise; Wang, Tao; Madsen, Georg K. H.; Mingo, Natalio

2017-11-01

almaBTE is a software package that solves the space- and time-dependent Boltzmann transport equation for phonons, using only ab-initio calculated quantities as inputs. The program can predictively tackle phonon transport in bulk crystals and alloys, thin films, superlattices, and multiscale structures with size features in the nm- μm range. Among many other quantities, the program can output thermal conductances and effective thermal conductivities, space-resolved average temperature profiles, and heat-current distributions resolved in frequency and space. Its first-principles character makes almaBTE especially well suited to investigate novel materials and structures. This article gives an overview of the program structure and presents illustrative examples for some of its uses. PROGRAM SUMMARY Program Title:almaBTE Program Files doi:http://dx.doi.org/10.17632/8tfzwgtp73.1 Licensing provisions: Apache License, version 2.0 Programming language: C++ External routines/libraries: BOOST, MPI, Eigen, HDF5, spglib Nature of problem: Calculation of temperature profiles, thermal flux distributions and effective thermal conductivities in structured systems where heat is carried by phonons Solution method: Solution of linearized phonon Boltzmann transport equation, Variance-reduced Monte Carlo

Phonon renormalization and anharmonicity in Al-doped MgB2

NASA Astrophysics Data System (ADS)

Ortiz, Filiberto; Aguayo, Aarón

2005-03-01

We have studied the evolution of the E2g phonon mode dynamics in Mg1-xAlxB2 as a function of doping using the Frozen Phonon Approximation (FPA). The doping was modeled in the ab-initio Virtual Crystal Approximation (VCA). The results were obtained by means of first-principles total-energy calculations using the full potential Linearized Augmented Plane Wave (LAPW) method and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We present results for the evolution of the phonon frequency and anharmonicity of the E2g mode as a function of Al concentration (x). From a comparison of the experimental data with the calculated E2g phonon frequency we show that the VCA-FPA reproduces the observed phonon renormalization in the whole range of Al concentrations. More interestingly, we find that the anharmonicity gradually decreases with Al doping and vanishes for x(Al)>0.5, that behaviour correlates with the evolution of the measured Raman linewidth in Al-doped MgB2. The significance of these results are discussed in the light of the experimentally observed loss of superconductivity in Mg1- xAlxB2.This work was supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant. No. 43830-F.

New equation of state models for hydrodynamic applications

NASA Astrophysics Data System (ADS)

Young, David A.; Barbee, Troy W.; Rogers, Forrest J.

1998-07-01

Two new theoretical methods for computing the equation of state of hot, dense matter are discussed. The ab initio phonon theory gives a first-principles calculation of lattice frequencies, which can be used to compare theory and experiment for isothermal and shock compression of solids. The ACTEX dense plasma theory has been improved to allow it to be compared directly with ultrahigh pressure shock data on low-Z materials. The comparisons with experiment are good, suggesting that these models will be useful in generating global EOS tables for hydrodynamic simulations.

Phonon-Assisted Ultrafast Charge Transfer at van der Waals Heterostructure Interface.

PubMed

Zheng, Qijing; Saidi, Wissam A; Xie, Yu; Lan, Zhenggang; Prezhdo, Oleg V; Petek, Hrvoje; Zhao, Jin

2017-10-11

The van der Waals (vdW) interfaces of two-dimensional (2D) semiconductor are central to new device concepts and emerging technologies in light-electricity transduction where the efficient charge separation is a key factor. Contrary to general expectation, efficient electron-hole separation can occur in vertically stacked transition-metal dichalcogenide heterostructure bilayers through ultrafast charge transfer between the neighboring layers despite their weak vdW bonding. In this report, we show by ab initio nonadiabatic molecular dynamics calculations, that instead of direct tunneling, the ultrafast interlayer hole transfer is strongly promoted by an adiabatic mechanism through phonon excitation occurring on 20 fs, which is in good agreement with the experiment. The atomic level picture of the phonon-assisted ultrafast mechanism revealed in our study is valuable both for the fundamental understanding of ultrafast charge carrier dynamics at vdW heterointerfaces as well as for the design of novel quasi-2D devices for optoelectronic and photovoltaic applications.

Structural, electronic, mechanical, and dynamical properties of graphene oxides: A first principles study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dabhi, Shweta D.; Gupta, Sanjay D.; Jha, Prafulla K., E-mail: prafullaj@yahoo.com

We report the results of a theoretical study on the structural, electronic, mechanical, and vibrational properties of some graphene oxide models (GDO, a-GMO, z-GMO, ep-GMO and mix-GMO) at ambient pressure. The calculations are based on the ab-initio plane-wave pseudo potential density functional theory, within the generalized gradient approximations for the exchange and correlation functional. The calculated values of lattice parameters, bulk modulus, and its first order pressure derivative are in good agreement with other reports. A linear response approach to the density functional theory is used to derive the phonon frequencies. We discuss the contribution of the phonons in themore » dynamical stability of graphene oxides and detailed analysis of zone centre phonon modes in all the above mentioned models. Our study demonstrates a wide range of energy gap available in the considered models of graphene oxide and hence the possibility of their use in nanodevices.« less

Lattice dynamics of A Sb2O6 (A =Cu , Co) with trirutile structure

NASA Astrophysics Data System (ADS)

Maimone, D. T.; Christian, A. B.; Neumeier, J. J.; Granado, E.

2018-03-01

Raman spectroscopy experiments on single crystals of CuSb2O6 and CoSb2O6 quasi-one-dimensional antiferromagnets with trirutile crystal structure were performed, with a focus on the first material. The observed Raman-active phonon modes and previously reported infrared-active modes were identified with the aid of ab initio lattice dynamics calculations. The structural transition between monoclinic β -CuSb2O6 and tetragonal α -CuSb2O6 phases at Ts=400 K is manifested in our spectra by a "repulsion" of two accidentally quasidegenerate symmetric modes below Ts, caused by a phonon mixing effect that is only operative in the monoclinic β -CuSb2O6 phase due to symmetry restrictions. Also, two specific phonons, associated with CuO6 octahedra rotation and with a Jahn-Teller elongation mode, soften and broaden appreciably as T →Ts . A crossover from a displacive to an order-disorder transition at Ts is inferred.

Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon

DOE PAGES

Li, Zhen -Zhen; Wang, Jian -Tao; Xu, Li -Fang; ...

2016-11-02

The design and synthesis of three-dimensional denser carbons are one of the hot issues in condensed matter physics because of their fascinating properties. Here we identify by ab initio calculations several tetragonal and monoclinic polymorphs of carbon that adopt the t32, t32*, m32, and m32* structures in P4¯2 1c, P4 32 12, P2 1/c, and C2 symmetry, respectively. These carbon polymorphs have large 32-atom unit cells in all-sp 3 bonding networks comprising five- and six-membered rings that are dynamically stable, as verified by a phonon mode analysis. Electronic band structure calculations show that they are insulators with band gaps inmore » the range of 5.19–5.41 eV, close to the calculated band gap of 5.34 eV for diamond. Remarkably, these carbon phases possess an extremely high atom number density exceeding that of diamond. Lastly, the present results establish different types of carbon phases and offer insights into their outstanding structural and electronic properties.« less

Ab Initio -Based Bond Order Potential to Investigate Low Thermal Conductivity of Stanene Nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cherukara, Mathew J.; Narayanan, Badri; Kinaci, Alper

2016-08-28

We introduce a bond order potential (BOP) for stanene based on an ab initio derived training data set. The potential is optimized to accurately describe the energetics, as well as thermal and mechanical properties of a free-standing sheet, and used to study diverse nanostructures of stanene, including tubes and ribbons. As a representative case study, using the potential, we perform molecular dynamics simulations to study stanene’s structure and temperature-dependent thermal conductivity. We find that the structure of stanene is highly rippled, far in excess of other 2-D materials (e.g., graphene), owing to its low in-plane stiffness (stanene: ~ 25 N/m;more » graphene: ~ 480 N/ m). The extent of stanene’s rippling also shows stronger temperature dependence compared to that in graphene. Furthermore, we find that stanene based nanostructures have significantly lower thermal conductivity compared to graphene based structures owing to their softness (i.e., low phonon group velocities) and high anharmonic response. Our newly developed BOP will facilitate the exploration of stanene based low dimensional heterostructures for thermoelectric and thermal management applications.« less

Ab Initio Calculations of Ultrashort Carrier Dynamics in Two-Dimensional Materials: Valley Depolarization in Single-Layer WSe2

NASA Astrophysics Data System (ADS)

Molina-Sánchez, Alejandro; Sangalli, Davide; Wirtz, Ludger; Marini, Andrea

2017-08-01

In single-layer WSe$_2$, a paradigmatic semiconducting transition metal dichalcogenide, a circularly polarized laser field can selectively excite electronic transitions in one of the inequivalent $K^{\\pm}$ valleys. Such selective valley population corresponds to a pseudospin polarization. This can be used as a degree of freedom in a valleytronic device provided that the time scale for its depolarization is sufficiently large. Yet, the mechanism behind the valley depolarization still remains heavily debated. Recent time-dependent Kerr experiments have provided an accurate way to visualize the valley dynamics by measuring the rotation of a linearly polarized probe pulse applied after a circularly polarized pump pulse. We present here a clear, accurate and parameter-free description of the valley dynamics. By using an atomistic, ab initio, approach we fully disclose the elemental mechanisms that dictate the depolarization effects. Our results are in excellent agreement with recent time-dependent Kerr experiments. We explain the Kerr dynamics and its temperature dependence in terms of electron-phonon mediated processes that induce spin-flip inter-valley transitions.

An ab-initio coupled mode theory for near field radiative thermal transfer.

PubMed

Chalabi, Hamidreza; Hasman, Erez; Brongersma, Mark L

2014-12-01

We investigate the thermal transfer between finite-thickness planar slabs which support surface phonon polariton modes (SPhPs). The thickness-dependent dispersion of SPhPs in such layered materials provides a unique opportunity to manipulate and enhance the near field thermal transfer. The key accomplishment of this paper is the development of an ab-initio coupled mode theory that accurately describes all of its thermal transfer properties. We illustrate how the coupled mode parameters can be obtained in a direct fashion from the dispersion relation of the relevant modes of the system. This is illustrated for the specific case of a semi-infinite SiC substrate placed in close proximity to a thin slab of SiC. This is a system that exhibits rich physics in terms of its thermal transfer properties, despite the seemingly simple geometry. This includes a universal scaling behavior of the thermal conductance with the slab thickness and spacing. The work highlights and further increases the value of coupled mode theories in rapidly calculating and intuitively understanding near-field transfer.

Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection from a PbSe quantum dot into the TiO2 surface.

PubMed

Long, Run; Prezhdo, Oleg V

2011-11-30

Following recent experiments [Science 2010, 328, 1543; PNAS 2011, 108, 965], we report an ab initio nonadiabatic molecular dynamics (NAMD) simulation of the ultrafast photoinduced electron transfer (ET) from a PbSe quantum dot (QD) into the rutile TiO(2) (110) surface. The system forms the basis for QD-sensitized semiconductor solar cells and demonstrates that ultrafast interfacial ET is instrumental for achieving high efficiencies in solar-to-electrical energy conversion. The simulation supports the observation that the ET successfully competes with energy losses due to electron-phonon relaxation. The ET proceeds by the adiabatic mechanism because of strong donor-acceptor coupling. High frequency polar vibrations of both QD and TiO(2) promote the ET, since these modes can rapidly influence the donor-acceptor state energies and coupling. Low frequency vibrations generate a distribution of initial conditions for ET, which shows a broad variety of scenarios at the single-molecule level. Compared to the molecule-TiO(2) interfaces, the QD-TiO(2) system exhibits pronounced differences that arise due to the larger size and higher rigidity of QDs relative to molecules. Both donor and acceptor states are more delocalized in the QD system, and the ET is promoted by optical phonons, which have relatively low frequencies in the QD materials composed of heavy elements. In contrast, in molecular systems, optical phonons are not thermally accessible under ambient conditions. Meanwhile, TiO(2) acceptor states resemble surface impurities due to the local influence of molecular chromophores. At the same time, the photoinduced ET at both QD-TiO(2) and molecule-TiO(2) interfaces is ultrafast and occurs by the adiabatic mechanism, as a result of strong donor-acceptor coupling. The reported state-of-the-art simulation generates a detailed time-domain atomistic description of the interfacial ET process that is fundamental to a wide variety of applications.

Spin-phonon coupling and high-pressure phase transitions of RMnO 3 (R=Ca and Pr): An inelastic neutron scattering and first-principles study

DOE PAGES

Mishra, S. K.; Gupta, M. K.; Mittal, R.; ...

2016-06-22

Here, we report inelastic neutron scattering measurements over 7–1251 K in CaMnO 3 covering various phase transitions, and over 6–150 K in PrMnO 3 covering the magnetic transition. The excitations around 20 meV in CaMnO 3 and at 17 meV in PrMnO 3 at low temperatures are found to be associated with magnetic origin. We observe coherent magnetic neutron scattering in localized regions in reciprocal space and show it to arise from long-range correlated magnetic spin-waves below the magnetic transition temperature (TN) and short-range stochastic spin-spin fluctuations above T N. In spite of the similarity of the structure of themore » two compounds, the neutron inelastic spectrum of PrMnO 3 exhibits broad features at 150 K unlike well-defined peaks in the spectrum of CaMnO 3. This might result from the difference in the nature of interactions in the two compounds (magnetic and Jahn-Teller distortion). Ab initio phonon calculations have been used to interpret the observed phonon spectra. The ab initio calculations at high pressures show that the variations of Mn-O distances are isotropic for CaMnO 3 and highly anisotropic for PrMnO 3. The calculation in PrMnO 3 shows the suppression of Jahn-Teller distortion and simultaneous insulator-to-metal transition. It appears that this transition may not be associated with the occurrence of the tetragonal phase above 20 GPa as reported in the literature, since the tetragonal phase is found to be dynamically unstable, although it is found to be energetically favored over the orthorhombic phase above 20 GPa. CaMnO 3 does not show any phase transition up to 60 GPa.« less

Theoretical ultra-fast spectroscopy in transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Molina-Sanchez, Alejandro; Sangalli, Davide; Marini, Andrea; Wirtz, Ludger

Semiconducting 2D-materials like the transition metal dichalcogenides (TMDs) MoS2, MoSe2, WS2, WSe2 are promising alternatives to graphene for designing novel opto-electronic devices. The strong spin-orbit interaction along with the breaking of inversion symmetry in single-layer TMDs allow using the valley-index as a new quantum number. The practical use of valley physics depends on the lifetimes of valley-polarized excitons which are affected by scattering at phonons, impurities and by carrier-carrier interactions. The carrier dynamics can be monitored using ultra-fast spectroscopies such as pump-probe experiments. The carrier dynamics is simulated using non-equilibrium Green's function theory in an ab-initio framework. We include carrier relaxation through electron-phonon interaction. We obtain the transient absorption spectra of single-layer TMD and compare our simulations with recent pump-probe experiments

Ab-initio study of thermodynamic properties of boron nanowire at atomic scale

NASA Astrophysics Data System (ADS)

Bhuyan, Prabal D.; Gupta, Sanjeev K.; Sonvane, Y.; Gajjar, P. N.

2018-04-01

In the present work, we have optimized ribbon like zigzag structure of boron (B) nanowire (NW) and investigated vibrational and thermodynamic properties using quasi-harmonic approximations (QHA). All positive phonon in the phonon dispersive curve have confirmed dynamical stability of ribbon B-NW. The thermodynamic properties, like Debye temperature, internal energy and specific heat, are calculated as a function of temperature. The variation of specific heat is proportional to T3 Debye law at lower temperature for B-NW, while it becomes constant above room temperature at 1200K; obeys Dulong-Petit's law. The high Debye temperature of 1120K is observed at ambient temperature, which can be attributed to high thermal conductivity. Our study shows that B-NW with high thermal conductivity could be the next generation electron connector for nanoscale electronic devices.

One-shot calculation of temperature-dependent optical spectra and phonon-induced band-gap renormalization

NASA Astrophysics Data System (ADS)

Zacharias, Marios; Giustino, Feliciano

2016-08-01

Recently, Zacharias et al. [Phys. Rev. Lett. 115, 177401 (2015), 10.1103/PhysRevLett.115.177401] developed an ab initio theory of temperature-dependent optical absorption spectra and band gaps in semiconductors and insulators. In that work, the zero-point renormalization and the temperature dependence were obtained by sampling the nuclear wave functions using a stochastic approach. In the present work, we show that the stochastic sampling of Zacharias et al. can be replaced by fully deterministic supercell calculations based on a single optimal configuration of the atomic positions. We demonstrate that a single calculation is able to capture the temperature-dependent band-gap renormalization including quantum nuclear effects in direct-gap and indirect-gap semiconductors, as well as phonon-assisted optical absorption in indirect-gap semiconductors. In order to demonstrate this methodology, we calculate from first principles the temperature-dependent optical absorption spectra and the renormalization of direct and indirect band gaps in silicon, diamond, and gallium arsenide, and we obtain good agreement with experiment and with previous calculations. In this work we also establish the formal connection between the Williams-Lax theory of optical transitions and the related theories of indirect absorption by Hall, Bardeen, and Blatt, and of temperature-dependent band structures by Allen and Heine. The present methodology enables systematic ab initio calculations of optical absorption spectra at finite temperature, including both direct and indirect transitions. This feature will be useful for high-throughput calculations of optical properties at finite temperature and for calculating temperature-dependent optical properties using high-level theories such as G W and Bethe-Salpeter approaches.

Role of hydrodynamic viscosity on phonon transport in suspended graphene

NASA Astrophysics Data System (ADS)

Li, Xun; Lee, Sangyeop

2018-03-01

When phonon transport is in the hydrodynamic regime, the thermal conductivity exhibits peculiar dependences on temperatures (T ) and sample widths (W ). These features were used in the past to experimentally confirm the hydrodynamic phonon transport in three-dimensional bulk materials. Suspended graphene was recently predicted to exhibit strong hydrodynamic features in thermal transport at much higher temperature than the three-dimensional bulk materials, but its experimental confirmation requires quantitative guidance by theory and simulation. Here we quantitatively predict those peculiar dependences using the Monte Carlo solution of the Peierls-Boltzmann equation with an ab initio full three-phonon scattering matrix. Thermal conductivity is found to increase as Tα where α ranges from 1.89 to 2.49 depending on a sample width at low temperatures, much larger than 1.68 of the ballistic case. The thermal conductivity has a width dependence of W1.17 at 100 K, clearly distinguished from the sublinear dependence of the ballistic-diffusive regime. These peculiar features are explained with a phonon viscous damping effect of the hydrodynamic regime. We derive an expression for the phonon hydrodynamic viscosity from the Peierls-Boltzmann equation, and discuss the fact that the phonon viscous damping explains well those peculiar dependences of thermal conductivity at 100 K. The phonon viscous damping still causes significant thermal resistance when a temperature is 300 K and a sample width is around 1 µm, even though the hydrodynamic regime is not dominant over other regimes at this condition.

Calculation of the Raman intensity in graphene and carbon nanotubes

NASA Astrophysics Data System (ADS)

Moutinho, Marcus; Venezuela, Pedro

2014-03-01

Raman spectroscopy is one of the most important experimental techniques for characterization of carbon materials because it can give a lot of information about electronic and phonon structure in a non destructive way. We use a third-order quantum field model to obtain the theoretical Raman intensity for graphene and carbon nanotubes (CNT). The most important Raman peaks in graphitic materials comes from to the iLo and iTo phonon branches near to Γ and K points and, in this work, we focus our attention on some of these peaks, like the G, D and 2D bands, as a function of laser energy. The electronic and phonon dispersion used in our calculations reproduces the graphene ab initio results with GW corrections and the zone folding method is used to obtain the CNT ones. Our results show that the experimental G band Raman excitation profile for CNT can be reproduced if we use the proper electronic and phonon dispersions. We also show that the phonon dispersion may influence the shape of the graphene D band and the dispersive behavior of the 2D band for graphene and CNT. This work was supported by the Brazilian Nanocarbon Institute of Science and Technology (INCT/Nanocarbono), the Brazilian Network on Carbon Nanotube Research and the Brazilian agency CAPES

Phonon induced magnetism in ionic materials

NASA Astrophysics Data System (ADS)

Restrepo, Oscar D.; Antolin, Nikolas; Jin, Hyungyu; Heremans, Joseph P.; Windl, Wolfgang

2014-03-01

Thermoelectric phenomena in magnetic materials create exciting possibilities in future spin caloritronic devices by manipulating spin information using heat. An accurate understanding of the spin-lattice interactions, i.e. the coupling between magnetic excitations (magnons) and lattice vibrations (phonons), holds the key to unraveling their underlying physics. We report ab initio frozen-phonon calculations of CsI that result in non-zero magnetization when the degeneracy between spin-up and spin-down electronic density of states is lifted for certain phonon displacement patterns. For those, the magnetization as a function of atomic displacement shows a sharp resonance due to the electronic states on the displaced Cs atoms, while the electrons on indium form a continuous background magnetization. We relate this resonance to the generation of a two-level system in the spin-polarized Cs partial density of states as a function of displacement, which we propose to be described by a simple resonant-susceptibility model. Current work extends these investigations to semiconductors such as InSb. ODR and WW are supported by the Center for Emergent Materials, an NSF MRSEC at OSU (Grant DMR-0820414).HJ and JPH are supported by AFOSR MURI Cryogenic Peltier Cooling, Contract #FA9550-10-1-0533.

Ab initio modeling of point defects, self-diffusion, and incorporation of impurities in thorium

NASA Astrophysics Data System (ADS)

Daroca, D. Pérez

2017-02-01

Research on Generation-IV nuclear reactors has boosted the investigation of thorium as nuclear fuel. By means of first-principles calculations within the framework of density functional theory, structural properties and phonon dispersion curves of Th are obtained. These results agreed very well with previous ones. The stability and formation energies of vacancies, interstitial and divacancies are studied. It is found that vacancies are the energetically preferred defects. The incorporation energies of He, Xe, and Kr atoms in Th defects are analyzed. Self-diffusion, migration paths and activation energies are also calculated.

Phonon transport properties of two-dimensional group-IV materials from ab initio calculations

NASA Astrophysics Data System (ADS)

Peng, Bo; Zhang, Hao; Shao, Hezhu; Xu, Yuanfeng; Ni, Gang; Zhang, Rongjun; Zhu, Heyuan

2016-12-01

It has been argued that stanene has lowest lattice thermal conductivity among two-dimensional (2D) group-IV materials because of its largest atomic mass, weakest interatomic bonding, and enhanced ZA phonon scattering due to the breaking of an out-of-plane symmetry selection rule. However, we show that, although the lattice thermal conductivity κ for graphene, silicene, and germanene decreases monotonically with decreasing Debye temperature, unexpected higher κ is observed in stanene. By enforcing all the invariance conditions in 2D materials and including Ge 3 d and Sn 4 d electrons as valence electrons for germanene and stanene, respectively, the lattice dynamics in these materials are accurately described. A large acoustic-optical gap and the bunching of the acoustic-phonon branches significantly reduce phonon scattering in stanene, leading to higher thermal conductivity than germanene. The vibrational origin of the acoustic-optical gap can be attributed to the buckled structure. Interestingly, a buckled system has two competing influences on phonon transport: the breaking of the symmetry selection rule leads to reduced thermal conductivity, and the enlarging of the acoustic-optical gap results in enhanced thermal conductivity. The size dependence of thermal conductivity is investigated as well. In nanoribbons, the κ of silicene, germanene, and stanene is much less sensitive to size effect due to their short intrinsic phonon mean-free paths. This work sheds light on the nature of phonon transport in buckled 2D materials.

Finite-temperature lattice dynamics and superionic transition in ceria from first principles

NASA Astrophysics Data System (ADS)

Klarbring, Johan; Skorodumova, Natalia V.; Simak, Sergei I.

2018-03-01

Ab initio molecular dynamics (AIMD) in combination with the temperature dependent effective potential (TDEP) method has been used to go beyond the quasiharmonic approximation and study the lattice dynamics in ceria, CeO2, at finite temperature. The results indicate that the previously proposed connection between the B1 u phonon mode turning imaginary and the transition to the superionic phase in fluorite structured materials is an artifact of the failure of the quasiharmonic approximation in describing the lattice dynamics at elevated temperatures. We instead show that, in the TDEP picture, a phonon mode coupling to the Eu mode prevents the B1 u mode from becoming imaginary. We directly observe the superionic transition at high temperatures in our AIMD simulations and find that it is initiated by the formation of oxygen Frenkel pairs (FP). These FP are found to form in a collective process involving simultaneous motion of two oxygen ions.

Anisotropic Eliashberg theory of MgB 2: Tc, isotope effects, superconducting energy gaps, quasiparticles, and specific heat

NASA Astrophysics Data System (ADS)

Choi, Hyoung Joon; Cohen, Marvin L.; Louie, Steven G.

2003-03-01

The anisotropic Eliashberg formalism, employing results from the ab initio pseudopotential density functional calculations, is applied to study the superconducting properties of MgB 2. It is shown that the relatively high transition temperature of MgB 2 originates from strong electron-phonon coupling of the hole states in the boron σ-bonds although the coupling strength averaged over the Fermi surface is moderate, and the reduction of the isotope effect arises from the large anharmonicity of the relevant phonons. The superconducting energy gap is nodeless but its value varies strongly on different pieces of the Fermi surface. The gap values Δ( k) cluster into two groups at low temperature, a small value of ∼2 meV and a large value of ∼7 meV, resulting in two thresholds in the quasiparticle density of states and an increase in the specific heat at low temperature due to quasiparticle excitations over the small gap. All of these results are in good agreement with corresponding experiments and support the view that MgB 2 is a phonon-mediated multiple-gap superconductor.

Ab-initio study of thermal expansion in pure graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mann, Sarita; Kumar, Ranjan; Jindal, V. K., E-mail: jindal@pu.ac.in

Graphene is a zero band gap semiconductor with exceptionally high thermal conductivity. The electronic properties having been studied, therole of phonon in contributing to thermal expansion, thermal conductivity and other thermodynamic properties, is required to be investigated. This paper focuses more on thermal expansion. Some others results like phonon dispersion, Grüneisenparameters and bulk modulus,which are essential to estimation of thermal expansion, are also presented. The dynamical matrix was calculated using VASP code using both DFT and DFPT and the phonon frequencies were calculated using phonopy code under harmonic approximation. The linear thermal expansion coefficient of graphene is found to bemore » strongly dependent on temperature but remains negative upto 470 K and positive thereafter, with a room temperature value of −1.44×10{sup −6}. The negative expansion coefficient is very interesting and is found to be in conformity with experimental as well as with recent theoretical estimates. There is only qualitative agreement of our results with experimental data and motivates further investigation, primarily on the high negative values of Grüneisen parameters.« less

Electron and ion dynamics study of iron in warm dense matter regime by time-resolved XAS measurements and from first-principles

NASA Astrophysics Data System (ADS)

Ogitsu, T.; Fernandez-Paãella, A.; Correa, A.; Engelhorn, K.; Barbrel, B.; Prendergast, D. G.; Pemmaraju, D.; Beckwith, M.; Kraus, D.; Hamel, S.; Cho, B. I.; Jin, L.; Wong, J.; Heinman, P.; Collins, G. W.; Falcone, R.; Ping, Y.

2016-10-01

We present a study of the electron-phonon coupling of warm dense iron upon femtosecond laser excitation by time-resolved x-ray absorption near edge spectroscopy (XANES). The dynamics of iron in electron-ion non-equilibrium conditions was studied using ab-initio density-functional-theory (DFT) simulations combined with the Two Temperature Model (TTM) where spatial inhomogeneity of electron (and ion) temperature(s) due to short ballistic electron transport length in iron was explicitly taken into consideration. Detailed comparison between our simulation results and experiments indicates that the ion temperature dependence on specific heat and on electron-phonon coupling also plays a relevant role in modeling the relaxation dynamics of electrons and ions. These results are the first experimental evidence of the suppression of the electron-phonon coupling factor of a transition metal at electron temperatures ranging 5000- 10000 K. This work was performed under DOE contract DE-AC52-07NA27344 with support from OFES Early Career program and LLNL LDRD program.

Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

2015-07-15

There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

Overcoming nanoscale friction barriers in transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Cammarata, Antonio; Polcar, Tomas

2017-08-01

We study the atomic contributions to the nanoscale friction in layered M X2 (M =Mo , W; X =S , Se, Te) transition metal dichalcogenides by combining ab initio techniques with group-theoretical analysis. Starting from stable atomic configurations, we propose a computational method, named normal-modes transition approximation (NMTA), to individuate possible sliding paths from only the analysis of the phonon modes of the stable geometry. The method provides a way to decompose the atomic displacements realizing the layer sliding in terms of phonon modes of the stable structure, so as to guide the selection and tuning of specific atomic motions promoting M X2 sheets gliding, and to adjust the corresponding energy barrier. The present results show that main contributions to the nanoscale friction are due to few low frequency phonon modes, corresponding to rigid shifts of M X2 layers. We also provide further evidences that a previously reported Ti-doped MoS2 phase is a promising candidate as new material with enhanced tribologic properties. The NMTA approach can be exploited to tune the energetic and the structural features of specific phonon modes, and, thanks to its general formulation, can also be applied to any solid state system, irrespective of the chemical composition and structural topology.

Understanding lattice thermal conductivity in thermoelectric clathrates: A density functional theory study on binary Si-based type-I clathrates

NASA Astrophysics Data System (ADS)

Euchner, Holger; Pailhès, Stéphane; Giordano, Valentina M.; de Boissieu, Marc

2018-01-01

Despite their crystalline nature, thermoelectric clathrates exhibit a strongly reduced lattice thermal conductivity. While the reason for this unexpected behavior is known to lie in the peculiarities of the complex crystal structure and the interplay of the underlying guest-host framework, their respective roles are still not fully disentangled and understood. Our ab initio study of the most simple type-I clathrate phase, the binary compound Ba8Si46 and its derivatives Ba8 -xSi46 seeks to identify these mechanisms and provides insight into their origin. Indeed, the strongly decreased lattice thermal conductivity in thermoelectric clathrates is a consequence of a reduction of the acoustic phonon bandwidth, a lowering of the acoustic phonon group velocities, and the amplification of three-phonon-scattering processes. While the complexity of the crystal structure is demonstrated not to be the leading factor, the reasons are manifold. A modified Si-Si interaction causes a first decrease of the sound velocity, whereas the presence of flat Ba modes results in an additional lowering. These modes correspond to confined Bloch states that are localized on the Ba atoms and significantly increase the scattering phase space and, together with an increased anharmonicity of the interatomic interactions, strongly affect the phonon lifetimes.

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giret, Y.; Gelle, A.; Arnaud, B.

We introduce a thermodynamical model based on the two-temperature approach in order to fully understand the dynamics of the coherent A{sub 1g} phonon in laser-excited bismuth. Using this model, we simulate the time evolution of (111) Bragg peak intensities measured by Fritz et al.[Science 315, 633 (2007)] in femtosecond x-ray diffraction experiments performed on a bismuth film for different laser fluences. The agreement between theoretical and experimental results is striking not only because we use fluences very close to the experimental ones but also because most of the model parameters are obtained from ab initio calculations performed for different electronmore » temperatures.« less

Ultrafast core-loss spectroscopy in four-dimensional electron microscopy

PubMed Central

van der Veen, Renske M.; Penfold, Thomas J.; Zewail, Ahmed H.

2015-01-01

We demonstrate ultrafast core-electron energy-loss spectroscopy in four-dimensional electron microscopy as an element-specific probe of nanoscale dynamics. We apply it to the study of photoexcited graphite with femtosecond and nanosecond resolutions. The transient core-loss spectra, in combination with ab initio molecular dynamics simulations, reveal the elongation of the carbon-carbon bonds, even though the overall behavior is a contraction of the crystal lattice. A prompt energy-gap shrinkage is observed on the picosecond time scale, which is caused by local bond length elongation and the direct renormalization of band energies due to temperature-dependent electron–phonon interactions. PMID:26798793

Energy-free machine learning force field for aluminum.

PubMed

Kruglov, Ivan; Sergeev, Oleg; Yanilkin, Alexey; Oganov, Artem R

2017-08-17

We used the machine learning technique of Li et al. (PRL 114, 2015) for molecular dynamics simulations. Atomic configurations were described by feature matrix based on internal vectors, and linear regression was used as a learning technique. We implemented this approach in the LAMMPS code. The method was applied to crystalline and liquid aluminum and uranium at different temperatures and densities, and showed the highest accuracy among different published potentials. Phonon density of states, entropy and melting temperature of aluminum were calculated using this machine learning potential. The results are in excellent agreement with experimental data and results of full ab initio calculations.

Optimization of a hybrid exchange-correlation functional for silicon carbides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oda, Takuji; Zhang, Yanwen; Weber, William J

2013-01-01

A hybrid exchange-correlation functional is optimized in order to accurately describe the nature of silicon carbides (SiC) in the framework of ab-initio calculations based on density functional theory (DFT), especially with an aim toward future applications in defect studies. It is shown that the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional with the screening parameter of 0.15 -1 outperforms conventional exchange-correlation functionals and other popular hybrid functionals regarding description of band structures in SiC. High transferability is proven through assessment over various SiC polytypes, silicon and diamond. Excellent performance is also confirmed for other fundamental material properties including elastic constants and phonon frequency.

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Phonon optimized interatomic potential for aluminum

NASA Astrophysics Data System (ADS)

Muraleedharan, Murali Gopal; Rohskopf, Andrew; Yang, Vigor; Henry, Asegun

2017-12-01

We address the problem of generating a phonon optimized interatomic potential (POP) for aluminum. The POP methodology, which has already been shown to work for semiconductors such as silicon and germanium, uses an evolutionary strategy based on a genetic algorithm (GA) to optimize the free parameters in an empirical interatomic potential (EIP). For aluminum, we used the Vashishta functional form. The training data set was generated ab initio, consisting of forces, energy vs. volume, stresses, and harmonic and cubic force constants obtained from density functional theory (DFT) calculations. Existing potentials for aluminum, such as the embedded atom method (EAM) and charge-optimized many-body (COMB3) potential, show larger errors when the EIP forces are compared with those predicted by DFT, and thus they are not particularly well suited for reproducing phonon properties. Using a comprehensive Vashishta functional form, which involves short and long-ranged interactions, as well as three-body terms, we were able to better capture interactions that reproduce phonon properties accurately. Furthermore, the Vashishta potential is flexible enough to be extended to Al2O3 and the interface between Al-Al2O3, which is technologically important for combustion of solid Al nano powders. The POP developed here is tested for accuracy by comparing phonon thermal conductivity accumulation plots, density of states, and dispersion relations with DFT results. It is shown to perform well in molecular dynamics (MD) simulations as well, where the phonon thermal conductivity is calculated via the Green-Kubo relation. The results are within 10% of the values obtained by solving the Boltzmann transport equation (BTE), employing Fermi's Golden Rule to predict the phonon-phonon relaxation times.

Phonons and superconductivity in fcc and dhcp lanthanum

NASA Astrophysics Data System (ADS)

Baǧcı, S.; Tütüncü, H. M.; Duman, S.; Srivastava, G. P.

2010-04-01

We have investigated the structural and electronic properties of lanthanum in the face-centered-cubic (fcc) and double hexagonal-close-packed (dhcp) phases using a generalized gradient approximation of the density functional theory and the ab initio pseudopotential method. It is found that double hexagonal-close-packed is the more stable phase for lanthanum. Differences in the density of states at the Fermi level between these two phases are pointed out and discussed in detail. Using the calculated lattice constant and electronic band structure for both phases, a linear response approach based on the density functional theory has been applied to study phonon modes, polarization characteristics of phonon modes, and electron-phonon interaction. Our phonon results show a softening behavior of the transverse acoustic branch along the Γ-L direction and the Γ-M direction for face-centered-cubic and double hexagonal-close-packed phases, respectively. Thus, the transverse-phonon linewidth shows a maximum at the zone boundary M(L) for the double hexagonal-close-packed phase (face-centered-cubic phase), where the transverse-phonon branch exhibits a dip. The electron-phonon coupling parameter λ is found to be 0.97 (1.06) for the double hexagonal-close-packed phase (face-centered-cubic phase), and the superconducting critical temperature is estimated to be 4.87 (dhcp) and 5.88 K (fcc), in good agreement with experimental values of around 5.0 (dhcp) and 6.0 K (fcc). A few superconducting parameters for the double hexagonal-close-packed phase have been calculated and compared with available theoretical and experimental results. Furthermore, the calculated superconducting parameters for both phases are compared between each other in detail.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment.

PubMed

Liu, Hanchao; Wang, Yimin; Bowman, Joel M

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

NASA Astrophysics Data System (ADS)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

PubMed

Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

2015-12-14

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

Ab Initio Study of Electronic Excitation Effects on SrTiO 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

Interaction of energetic ions or lasers with solids often induces electronic excitations that may modify material properties significantly. In this study, effects of electronic excitations on strontium titanate SrTiO 3 (STO) are investigated based on first-principles calculations. The lattice structure, electronic properties, lattice vibrational frequencies, and dynamical stabilities are studied in detail. The results suggest that electronic excitation induces charge redistribution that is mainly observed in Ti–O bonds. The electronic band gap increases with increasing electronic excitation, as excitation mainly induces depopulation of Ti 3d states. Phonon analysis indicates that there is a large phonon band gap induced by electronicmore » excitation because of the changes in the vibrational properties of Ti and O atoms. In addition, a new peak appears in the phonon density of states with imaginary frequencies, an indication of lattice instability. Further dynamics simulations confirm that STO undergoes transition to an amorphous structure under strong electronic excitations. In conclusion, the optical properties of STO under electronic excitation are consistent with the evolution of atomic and electronic structures, which suggests a possibility to probe the properties of STO in nonequilibrium state using optical measurement.« less

Nature of the octahedral tilting phase transitions in perovskites: A case study of CaMnO3

NASA Astrophysics Data System (ADS)

Klarbring, Johan; Simak, Sergei I.

2018-01-01

The temperature-induced antiferrodistortive (AFD) structural phase transitions in CaMnO3, a typical perovskite oxide, are studied using first-principles density functional theory calculations. These transitions are caused by tilting of the MnO6 octahedra that are related to unstable phonon modes in the high-symmetry cubic perovskite phase. Transitions due to octahedral tilting in perovskites normally are believed to fit into the standard soft-mode picture of displacive phase transitions. We calculate phonon-dispersion relations and potential-energy landscapes as functions of the unstable phonon modes and argue based on the results that the phase transitions are better described as being of order-disorder type. This means that the cubic phase emerges as a dynamical average when the system hops between local minima on the potential-energy surface. We then perform ab initio molecular dynamics simulations and find explicit evidence of the order-disorder dynamics in the system. Our conclusions are expected to be valid for other perovskite oxides, and we finally suggest how to predict the nature (displacive or order-disorder) of the AFD phase transitions in any perovskite system.

Ab Initio Study of Electronic Excitation Effects on SrTiO 3

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-11-14

Interaction of energetic ions or lasers with solids often induces electronic excitations that may modify material properties significantly. In this study, effects of electronic excitations on strontium titanate SrTiO 3 (STO) are investigated based on first-principles calculations. The lattice structure, electronic properties, lattice vibrational frequencies, and dynamical stabilities are studied in detail. The results suggest that electronic excitation induces charge redistribution that is mainly observed in Ti–O bonds. The electronic band gap increases with increasing electronic excitation, as excitation mainly induces depopulation of Ti 3d states. Phonon analysis indicates that there is a large phonon band gap induced by electronicmore » excitation because of the changes in the vibrational properties of Ti and O atoms. In addition, a new peak appears in the phonon density of states with imaginary frequencies, an indication of lattice instability. Further dynamics simulations confirm that STO undergoes transition to an amorphous structure under strong electronic excitations. In conclusion, the optical properties of STO under electronic excitation are consistent with the evolution of atomic and electronic structures, which suggests a possibility to probe the properties of STO in nonequilibrium state using optical measurement.« less

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

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40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

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Code of Federal Regulations, 2012 CFR

2012-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu; Yang, Mo

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heatmore » transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.« less

Dynamics of valley pseudospin in single-layer WSe2. Inter-valley scattering mediated by electron-phonon interaction

NASA Astrophysics Data System (ADS)

Molina-Sanchez, Alejandro; Sangalli, Davide; Wirtz, Ludger; Marini, Andrea

In a time-dependent Kerr experiment a circularly polarized laser field is used to selectively populate the K+/- electronic valleys of single-layer WSe2. This carrier population corresponds to a finite pseudospin polarization that dictates the valleytronic properties of WSe2, but whose decay mechanism still remains largely debated. Time-dependent Kerr experiments provide an accurate way to visualize the pseudospin dynamics by measuring the rotation of a linearly polarized probe pulse applied after a circularly polarized and short pump pulse. We present here a clear, accurate and parameter-free description of the valley pseudospin dynamics in single-layer WSe2. By using an ab-initio approach we solve unambiguously the long standing debate about the dominant mechanism that drives the valley depolarization. Our results are in excellent agreement with recent time-dependent Kerr experiments. The decay dynamics and peculiar temperature dependence is explained in terms of electron phonon mediated processes that induce spin-flip inter-valley transitions.

Tuning the thermal conductance of molecular junctions with interference effects

NASA Astrophysics Data System (ADS)

Klöckner, J. C.; Cuevas, J. C.; Pauly, F.

2017-12-01

We present an ab initio study of the role of interference effects in the thermal conductance of single-molecule junctions. To be precise, using a first-principles transport method based on density functional theory, we analyze the coherent phonon transport in single-molecule junctions made of several benzene and oligo(phenylene ethynylene) derivatives. We show that the thermal conductance of these junctions can be tuned via the inclusion of substituents, which induces destructive interference effects and results in a decrease of the thermal conductance with respect to the unmodified molecules. In particular, we demonstrate that these interference effects manifest as antiresonances in the phonon transmission, whose energy positions can be tuned by varying the mass of the substituents. Our work provides clear strategies for the heat management in molecular junctions and, more generally, in nanostructured metal-organic hybrid systems, which are important to determine how these systems can function as efficient energy-conversion devices such as thermoelectric generators and refrigerators.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Phonovoltaic. III. Electron-phonon coupling and figure of merit of graphene:BN

NASA Astrophysics Data System (ADS)

Melnick, Corey; Kaviany, Massoud

2016-12-01

The phonovoltaic cell harvests optical phonons like a photovoltaic harvests photons, that is, a nonequilibrium (hot) population of optical phonons (at temperature Tp ,O) more energetic than the band gap produces electron-hole pairs in a p -n junction, which separates these pairs to produce power. A phonovoltaic material requires an optical phonon mode more energetic than its band gap and much more energetic than the thermal energy (Ep ,O>Δ Ee ,g≫kBT ), which relaxes by generating electrons and power (at rate γ˙e -p) rather than acoustic phonons and heat (at rate γ˙p -p). Graphene (h-C) is the most promising material candidate: when its band gap is tuned to its optical phonon energy without greatly reducing the electron-phonon (e -p ) coupling, it reaches a substantial figure of merit [ZpV=Δ Ee ,gγ˙e -p/Ep ,O(γ˙e -p+γ˙p -p) ≈0.8 ] . A simple tight-binding (TB) model presented here predicts that lifting the sublattice symmetry of graphene in order to open a band gap proscribes the e -p interaction at the band edge, such that γ˙e -p→0 as Δ Ee ,g→Ep ,O . However, ab initio (DFT-LDA) simulations of layered h-C/BN and substitutional h-C:BN show that the e -p coupling remains substantial in these asymmetric crystals. Indeed, h-C:BN achieves a high figure of merit (ZpV≈0.6 ). At 300 K and for a Carnot limit of 0.5 (Tp ,O=600 K) , a h-C:BN phonovoltaic can reach an efficiency of ηpV≈0.2 , double the thermoelectric efficiency (Z T ≈1 ) under similar conditions.

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

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40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

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40 CFR 86.007-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate may be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... of conformity, the Administrator may deem such certificate void ab initio. (4) In any case in which...

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

Structural modeling of Ge6.25As32.5Se61.25 using a combination of reverse Monte Carlo and Ab initio molecular dynamics.

PubMed

Opletal, George; Drumm, Daniel W; Wang, Rong P; Russo, Salvy P

2014-07-03

Ternary glass structures are notoriously difficult to model accurately, and yet prevalent in several modern endeavors. Here, a novel combination of Reverse Monte Carlo (RMC) modeling and ab initio molecular dynamics (MD) is presented, rendering these complicated structures computationally tractable. A case study (Ge6.25As32.5Se61.25 glass) illustrates the effects of ab initio MD quench rates and equilibration temperatures, and the combined approach's efficacy over standard RMC or random insertion methods. Submelting point MD quenches achieve the most stable, realistic models, agreeing with both experimental and fully ab initio results. The simple approach of RMC followed by ab initio geometry optimization provides similar quality to the RMC-MD combination, for far fewer resources.

Effect of the quantum zero-point atomic motion on the optical and electronic properties of diamond and trans-polyacetylene.

PubMed

Cannuccia, Elena; Marini, Andrea

2011-12-16

The quantum zero-point motion of the carbon atoms is shown to induce strong effects on the optical and electronic properties of diamond and trans-polyacetylene, a conjugated polymer. By using an ab initio approach, we interpret the subgap states experimentally observed in diamond in terms of entangled electron-phonon states. These states also appear in trans-polyacetylene causing the formation of strong structures in the band structure that even call into question the accuracy of the band theory. This imposes a critical revision of the results obtained for carbon-based nanostructures by assuming the atoms frozen in their equilibrium positions. © 2011 American Physical Society

Terahertz disorder-localized rotational modes and lattice vibrational modes in the orientationally-disordered and ordered phases of camphor.

PubMed

Nickel, Daniel V; Ruggiero, Michael T; Korter, Timothy M; Mittleman, Daniel M

2015-03-14

The temperature-dependent terahertz spectra of the partially-disordered and ordered phases of camphor (C10H16O) are measured using terahertz time-domain spectroscopy. In its partially-disordered phases, a low-intensity, extremely broad resonance is found and is characterized using both a phenomenological approach and an approach based on ab initio solid-state DFT simulations. These two descriptions are consistent and stem from the same molecular origin for the broad resonance: the disorder-localized rotational correlations of the camphor molecules. In its completely ordered phase(s), multiple lattice phonon modes are measured and are found to be consistent with those predicted using solid-state DFT simulations.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previousmore » spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.« less

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

Thiessen, P. A.; Treder, H.-J.

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

Control of thermal conductivity with species mass in transition-metal dichalcogenides

NASA Astrophysics Data System (ADS)

Thomas, Iorwerth O.; Srivastava, G. P.

2018-04-01

In this paper, we examine how the behaviour of the thermal conductivity of bulk and monolayer transition-metal dichalcogenides XY2 in their 2-H form can be controlled with different choices of cation and anion masses. We employ a semi-ab-initio approach, which combines first-principles phonon eigensolutions, the elastic anharmonic Hamiltonian for phonon-phonon interactions, a quasi-harmonic scheme for the temperature-dependent Grüneisen's constant, and a relaxation-time solution of the Boltzmann transport equation. Our results confirm an earlier finding [Gu and Yang, Appl. Phys. Lett. 105, 131903 (2014)] that the thermal conductivity of 2-H MoS2 is lower than that of 2-H WS2 contrary to what would be expected from the relative masses of Mo and W and the relative stiffnesses of both compounds. In addition to confirming this anomaly as a result of the larger acoustic optical gap of WS2 relative to that of MoS2, it is found that where one constituent species is fixed, more profound changes on the thermal conductivity occur for different anion masses than for different cation masses. We explain how these behaviours arise from the dispersion relations of each compound and the anharmonic interactions of phonon modes, and its connection with the relative masses of the constituent species. This finding provides useful insight into which 2-H dichalcogenides might be suitable for which thermal applications.

Towards Accurate Ab Initio Predictions of the Spectrum of Methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Kwak, Dochan (Technical Monitor)

2001-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

Ab-initio study of liquid systems: Concentration dependence of electrical resistivity of binary liquid alloy Rb1-xCsx

NASA Astrophysics Data System (ADS)

Thakur, Anil; Sharma, Nalini; Chandel, Surjeet; Ahluwalia, P. K.

2013-02-01

The electrical resistivity (ρL) of Rb1-XCsX binary alloys has been made calculated using Troullier Martins ab-initio pseudopotentials. The present results of the electrical resistivity (ρL) of Rb1-XCsX binary alloys have been found in good agreement with the experimental results. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys. Hence ab-initio pseudopotentials can be used instead of model pseudopotentials having problem of transferability.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

PubMed

Exner, Kai S; Over, Herbert

2017-05-16

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born-Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Transverse discrete breathers in unstrained graphene

NASA Astrophysics Data System (ADS)

Barani, Elham; Lobzenko, Ivan P.; Korznikova, Elena A.; Soboleva, Elvira G.; Dmitriev, Sergey V.; Zhou, Kun; Marjaneh, Aliakbar Moradi

2017-02-01

Discrete breathers (DB) are spatially localized vibrational modes of large amplitude in defect-free nonlinear lattices. The search for DBs in graphene is of high importance, taking into account that this one atom thick layer of carbon is promising for a number of applications. There exist several reports on successful excitation of DBs in graphene, based on molecular dynamics and ab initio simulations. In a recent work by Hizhnyakov with co-authors the possibility to excite a DB with atoms oscillating normal to the graphene sheet has been reported. In the present study we use a systematic approach for finding initial conditions to excite transverse DBs in graphene. The approach is based on the analysis of the frequency-amplitude dependence for a delocalized, short-wavelength vibrational mode. This mode is a symmetry-dictated exact solution to the dynamic equations of the atomic motion, regardless the mode amplitude and regardless the type of interatomic potentials used in the simulations. It is demonstrated that if the AIREBO potential is used, the mode frequency increases with the amplitude bifurcating from the upper edge of the phonon spectrum for out-of-plane phonons. Then a bell-shaped function is superimposed on this delocalized mode to obtain a spatially localized vibrational mode, i.e., a DB. Placing the center of the bell-shaped function at different positions with respect to the lattice sites, three different DBs are found. Typically, the degree of spatial localization of DBs increases with the DB amplitude, but the transverse DBs in graphene reported here demonstrate the opposite trend. The results are compared to those obtained with the use of the Savin interatomic potential and no transverse DBs are found in this case. The results of this study contribute to a better understanding of the nonlinear dynamics of graphene and they call for the ab initio simulations to verify which of the two potentials used in this study is more precise.

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

Miller, Thomas F., III; Clary, David C.

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule.

HPAM: Hirshfeld Partitioned Atomic Multipoles

PubMed Central

Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

2011-01-01

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank lmax on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from lmax = 0 (atomic charges) to lmax = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank lmax are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ lmax. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (lmax = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. PMID:22140274

On the incorporation of the geometric phase in general single potential energy surface dynamics: A removable approximation to ab initio data.

PubMed

Malbon, Christopher L; Zhu, Xiaolei; Guo, Hua; Yarkony, David R

2016-12-21

For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian H d (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the H d by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding H d determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.

Thermal Conductivity of Metallic Uranium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hin, Celine

This project has developed a modeling and simulation approaches to predict the thermal conductivity of metallic fuels and their alloys. We focus on two methods. The first method has been developed by the team at the University of Wisconsin Madison. They developed a practical and general modeling approach for thermal conductivity of metals and metal alloys that integrates ab-initio and semi-empirical physics-based models to maximize the strengths of both techniques. The second method has been developed by the team at Virginia Tech. This approach consists of a determining the thermal conductivity using only ab-initio methods without any fitting parameters. Bothmore » methods were complementary. The models incorporated both phonon and electron contributions. Good agreement with experimental data over a wide temperature range were found. The models also provided insight into the different physical factors that govern the thermal conductivity under different temperatures. The models were general enough to incorporate more complex effects like additional alloying species, defects, transmutation products and noble gas bubbles to predict the behavior of complex metallic alloys like U-alloy fuel systems under burnup. 3 Introduction Thermal conductivity is an important thermal physical property affecting the performance and efficiency of metallic fuels [1]. Some experimental measurement of thermal conductivity and its correlation with composition and temperature from empirical fitting are available for U, Zr and their alloys with Pu and other minor actinides. However, as reviewed in by Kim, Cho and Sohn [2], due to the difficulty in doing experiments on actinide materials, thermal conductivities of metallic fuels have only been measured at limited alloy compositions and temperatures, some of them even being negative and unphysical. Furthermore, the correlations developed so far are empirical in nature and may not be accurate when used for prediction at conditions far from those used in the original fitting. Moreover, as fuels burn up in the reactor and fission products are built up, thermal conductivity is also significantly changed [3]. Unfortunately, fundamental understanding of the effect of fission products is also currently lacking. In this project, we probe thermal conductivity of metallic fuels with ab initio calculations, a theoretical tool with the potential to yield better accuracy and predictive power than empirical fitting. This work will both complement experimental data by determining thermal conductivity in wider composition and temperature ranges than is available experimentally, and also develop mechanistic understanding to guide better design of metallic fuels in the future. So far, we focused on α-U perfect crystal, the ground-state phase of U metal. We focus on two methods. The first method has been developed by the team at the University of Wisconsin Madison. They developed a practical and general modeling approach for thermal conductivity of metals and metal alloys that integrates ab-initio and semi-empirical physics-based models to maximize the strengths of both techniques. The second method has been developed by the team at Virginia Tech. This approach consists of a determining the thermal conductivity using only ab-initio methods without any fitting parameters. Both methods were complementary and very helpful to understand the physics behind the thermal conductivity in metallic uranium and other materials with similar characteristics. In Section I, the combined model developed at UWM is explained. In Section II, the ab-initio method developed at VT is described along with the uranium pseudo-potential and its validation. Section III is devoted to the work done by Jianguo Yu at INL. Finally, we will present the performance of the project in terms of milestones, publications, and presentations.« less

Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it; Tosoni, Sergio

2013-11-28

The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, andmore » phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.« less

Spectroscopy of Cold LiCa Molecules Formed on Helium Nanodroplets

PubMed Central

2013-01-01

We report on the formation of mixed alkali–alkaline earth molecules (LiCa) on helium nanodroplets and present a comprehensive experimental and theoretical study of the ground and excited states of LiCa. Resonance enhanced multiphoton ionization time-of-flight (REMPI-TOF) spectroscopy and laser induced fluorescence (LIF) spectroscopy were used for the experimental investigation of LiCa from 15000 to 25500 cm–1. The 42Σ+ and 32Π states show a vibrational structure accompanied by distinct phonon wings, which allows us to determine molecular parameters as well as to study the interaction of the molecule with the helium droplet. Higher excited states (42Π, 52Σ+, 52Π, and 62Σ+) are not vibrationally resolved and vibronic transitions start to overlap. The experimental spectrum is well reproduced by high-level ab initio calculations. By using a multireference configuration interaction (MRCI) approach, we calculated the 19 lowest lying potential energy curves (PECs) of the LiCa molecule. On the basis of these calculations, we could identify previously unobserved transitions. Our results demonstrate that the helium droplet isolation approach is a powerful method for the characterization of tailor-made alkali–alkaline earth molecules. In this way, important contributions can be made to the search for optimal pathways toward the creation of ultracold alkali–alkaline earth ground state molecules from the corresponding atomic species. Furthermore, a test for PECs calculated by ab initio methods is provided. PMID:24028555

First-principles investigations on elastic, thermodynamic and lattice thermal conductivity of topological insulator LaAs

NASA Astrophysics Data System (ADS)

Zhou, Yu; Cheng, Yan; Chen, Xiang-Rong; Hu, Cui-E.; Chen, Qi-Feng

2018-07-01

Topological insulators are always a hot topic owing to their various peculiar physical effects, which are useful in spintronics and quantum information processing. Herein, we systematically investigate the elastic, thermodynamic and lattice thermal conductivity of a new typical topological insulator LaAs by combining the first-principles approach and an iterative solution of the Boltzmann transport equation. The obtained elastic constants and other lattice structural parameters of LaAs are well consistent with the experimental and other theoretical results. For the first time, the lattice thermal conductivity (5.46 W/(m•K)) and mean free path (14.4 nm) of LaAs are obtained, which manifests that the LaAs is more likely to be a desirable thermoelectric material. It is noted that the obtained mode-averaged Grüneisen parameters by different ab initio simulation packages are very similar, suggesting that our results are rather responsible. From the phonon scattering rates of LaAs, we speculate that the reduction of acoustic-optical gap and the larger phonon scattering may jointly result in reduction of thermal conductivity for LaAs. Meanwhile, the temperature dependence curves of the lattice thermal conductivity, heat capacity and phonon mean free path are also presented. We expect our work can provide more information for further experimental studies.

High-field Transport in Low Symmetry β-Ga2O3 Crystal

NASA Astrophysics Data System (ADS)

Ghosh, Krishnendu; Singisetti, Uttam

High-field carrier transport plays an important role in many disciplines of electronics. Conventional transport theories work well on high-symmetry materials but lacks insight as the crystal symmetry goes down. Newly emerging materials, many of which possess low symmetry, demand more rigorous treatment of charge transport. We will present a comprehensive study of high-field transport using ab initio electron-phonon interaction (EPI) elements in a full-band Monte Carlo (FBMC) algorithm. We use monoclinic β-Ga2O3 as a benchmark low-symmetry material which is also an emerging wide-bandgap semiconductor. β-Ga2O3 has a C2m space group and a 10 atom primitive cell. In this work the EPIs are calculated under density-functional perturbation theory framework. We will focus on the computational challenges arising from many phonon modes and low crystal symmetry. Significant insights will be presented on the details of energy relaxation by the hot electrons mediated by different phonon modes. We will also show the velocity-field curves of electrons in different crystal directions. The authors acknowledge the support from the National Science Foundation Grant (ECCS 1607833). The authors also acknowledge the computing support provided by the Center for Computational Research at the University at Buffalo.

Ab Initio Calculations of Transport Properties of Vanadium Oxides

NASA Astrophysics Data System (ADS)

Lamsal, Chiranjivi; Ravindra, N. M.

2018-04-01

The temperature-dependent transport properties of vanadium oxides have been studied near the Fermi energy using the Kohn-Sham band structure approach combined with Boltzmann transport equations. V2O5 exhibits significant thermoelectric properties, which can be attributed to its layered structure and stability. Highly anisotropic electrical conduction in V2O5 is clearly manifested in the calculations. Due to specific details of the band structure and anisotropic electron-phonon interactions, maxima and crossovers are also seen in the temperature-dependent Seebeck coefficient of V2O5. During the phase transition of VO2, the Seebeck coefficient changes by 18.9 µV/K, which is close to (within 10% of) the observed discontinuity of 17.3 µV/K.

Single nickel-related defects in molecular-sized nanodiamonds for multicolor bioimaging: an ab initio study.

PubMed

Thiering, Gergő; Londero, Elisa; Gali, Adam

2014-10-21

Fluorescent nanodiamonds constitute an outstanding alternative to semiconductor quantum dots and dye molecules for in vivo biomarker applications, where the fluorescence comes from optically active point defects acting as color centers in the nanodiamonds. For practical purposes, these color centers should be photostable as a function of the laser power or the surface termination of nanodiamonds. Furthermore, they should exhibit a sharp and nearly temperature-independent zero-phonon line. In this study, we show by hybrid density functional theory calculations that nickel doped nanodiamonds exhibit the desired properties, thus opening the avenue to practical applications. In particular, harnessing the strong quantum confinement effect in molecule-sized nanodiamonds is very promising for achieving multicolor imaging by single nickel-related defects.

Single nickel-related defects in molecular-sized nanodiamonds for multicolor bioimaging: an ab initio study

NASA Astrophysics Data System (ADS)

Thiering, Gergő; Londero, Elisa; Gali, Adam

2014-09-01

Fluorescent nanodiamonds constitute an outstanding alternative to semiconductor quantum dots and dye molecules for in vivo biomarker applications, where the fluorescence comes from optically active point defects acting as color centers in the nanodiamonds. For practical purposes, these color centers should be photostable as a function of the laser power or the surface termination of nanodiamonds. Furthermore, they should exhibit a sharp and nearly temperature-independent zero-phonon line. In this study, we show by hybrid density functional theory calculations that nickel doped nanodiamonds exhibit the desired properties, thus opening the avenue to practical applications. In particular, harnessing the strong quantum confinement effect in molecule-sized nanodiamonds is very promising for achieving multicolor imaging by single nickel-related defects.

Analytic Interatomic Forces in the Random Phase Approximation

NASA Astrophysics Data System (ADS)

Ramberger, Benjamin; Schäfer, Tobias; Kresse, Georg

2017-03-01

We discuss that in the random phase approximation (RPA) the first derivative of the energy with respect to the Green's function is the self-energy in the G W approximation. This relationship allows us to derive compact equations for the RPA interatomic forces. We also show that position dependent overlap operators are elegantly incorporated in the present framework. The RPA force equations have been implemented in the projector augmented wave formalism, and we present illustrative applications, including ab initio molecular dynamics simulations, the calculation of phonon dispersion relations for diamond and graphite, as well as structural relaxations for water on boron nitride. The present derivation establishes a concise framework for forces within perturbative approaches and is also applicable to more involved approximations for the correlation energy.

Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2004-01-01

We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

A note on AB INITIO semiconductor band structures

NASA Astrophysics Data System (ADS)

Fiorentini, Vincenzo

1992-09-01

We point out that only the internal features of the DFT ab initio theoretical picture of a crystal should be used in a consistent ab initio calculation of the band structure. As a consequence, we show that ground-state band structure calculations should be performed for the system in equilibrium at zero pressure, i.e. at the computed equilibrium cell volume ω th. Examples of consequences of this attitude are considered.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.

PubMed

Brasil, Christiane Regina Soares; Delbem, Alexandre Claudio Botazzo; da Silva, Fernando Luís Barroso

2013-07-30

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment-based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well-designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β-sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called "Multiobjective evolutionary algorithms with many tables" (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG , I-PAES, and Quark) that use different levels of earlier knowledge. Copyright © 2013 Wiley Periodicals, Inc.

Lattice-mediated magnetic order melting in TbMnO 3

DOE PAGES

Baldini, Edoardo; Kubacka, Teresa; Mallett, Benjamin P. P.; ...

2018-03-15

Recent ultrafast magnetic-sensitive measurements have revealed a delayed melting of the long-range cycloid spin order in TbMnO 3 following photoexcitation across the fundamental Mott-Hubbard gap. The microscopic mechanism behind this slow transfer of energy from the photoexcited carriers to the spin degrees of freedom is still elusive and not understood. Here, we address this problem by combining spectroscopic ellipsometry, ultrafast broadband optical spectroscopy, and ab initio calculations. Upon photoexcitation, we observe the emergence of a complex collective response, which is due to high-energy coherent optical phonons coupled to the out-of-equilibrium charge density. This response precedes the magnetic order melting andmore » is interpreted as the fingerprint of the formation of anti-Jahn-Teller polarons. We propose that the charge localization in a long-lived self-trapped state hinders the emission of magnons and other spin-flip mechanisms, causing the energy transfer from the charge to the spin system to be mediated by the reorganization of the lattice. In conclusion, we provide evidence for the coherent excitation of a phonon mode associated with the ferroelectric phase transition.« less

An efficient and accurate framework for calculating lattice thermal conductivity of solids: AFLOW—AAPL Automatic Anharmonic Phonon Library

NASA Astrophysics Data System (ADS)

Plata, Jose J.; Nath, Pinku; Usanmaz, Demet; Carrete, Jesús; Toher, Cormac; de Jong, Maarten; Asta, Mark; Fornari, Marco; Nardelli, Marco Buongiorno; Curtarolo, Stefano

2017-10-01

One of the most accurate approaches for calculating lattice thermal conductivity, , is solving the Boltzmann transport equation starting from third-order anharmonic force constants. In addition to the underlying approximations of ab-initio parameterization, two main challenges are associated with this path: high computational costs and lack of automation in the frameworks using this methodology, which affect the discovery rate of novel materials with ad-hoc properties. Here, the Automatic Anharmonic Phonon Library (AAPL) is presented. It efficiently computes interatomic force constants by making effective use of crystal symmetry analysis, it solves the Boltzmann transport equation to obtain , and allows a fully integrated operation with minimum user intervention, a rational addition to the current high-throughput accelerated materials development framework AFLOW. An "experiment vs. theory" study of the approach is shown, comparing accuracy and speed with respect to other available packages, and for materials characterized by strong electron localization and correlation. Combining AAPL with the pseudo-hybrid functional ACBN0 is possible to improve accuracy without increasing computational requirements.

Electronic Structure and Thermoelectric Properties of Transition Metal Monosilicides

NASA Astrophysics Data System (ADS)

Pshenay-Severin, D. A.; Ivanov, Yu. V.; Burkov, A. T.; Novikov, S. V.; Zaitsev, V. K.; Reith, H.

2018-06-01

We present theoretical and experimental results on electronic structure and thermoelectric properties of cobalt monosilicide (CoSi) and of Co1- x M x Si diluted alloys (M = Fe and Ni) at temperatures from 2 K to 800 K. CoSi crystallizes into a non-centrosymmetric cubic B20 structure, which suggests the possibility of a topologically non-trivial electronic structure. We show that the electronic structure of CoSi exhibits linear band crossings in close vicinity to Fermi energy, confirming the possibility of non-trivial topology. The proximity of the linear-dispersion bands to Fermi energy implies their important contribution to the electronic transport. Calculation of thermopower of CoSi, using ab initio band structure and the constant relaxation time approximation, is carried out. It reveals that many body corrections to the electronic spectrum are important in order to obtain qualitative agreement of theoretical and experimental temperature dependences of thermopower. Phonon dispersion and lattice thermal conductivity are calculated. The phonons give a major contribution to the thermal conductivity of the compound below room temperature.

Phonon Conduction in Silicon Nanobeam Labyrinths

DOE PAGES

Park, Woosung; Romano, Giuseppe; Ahn, Ethan C.; ...

2017-07-24

Here we study single-crystalline silicon nanobeams having 470 nm width and 80 nm thickness cross section, where we produce tortuous thermal paths (i.e. labyrinths) by introducing slits to control the impact of the unobstructed “line-of-sight” (LOS) between the heat source and heat sink. The labyrinths range from straight nanobeams with a complete LOS along the entire length to nanobeams in which the LOS ranges from partially to entirely blocked by introducing slits, s = 95, 195, 245, 295 and 395 nm. The measured thermal conductivity of the samples decreases monotonically from ~47 W m -1K -1 for straight beam tomore » ~31 W m -1 K -1 for slit width of 395 nm. A model prediction through a combination of the Boltzmann transport equation and ab initio calculations shows an excellent agreement with the experimental data to within ~8%. The model prediction for the most tortuous path (s = 395 nm) is reduced by ~14% compared to a straight beam of equivalent cross section. This study suggests that LOS is an important metric for characterizing and interpreting phonon propagation in nanostructures.« less

Theoretical study of stability and superconductivity of ScHn (n =4 -8 ) at high pressure

NASA Astrophysics Data System (ADS)

Qian, Shifeng; Sheng, Xiaowei; Yan, Xiaozhen; Chen, Yangmei; Song, Bo

2017-09-01

The synthesis of hydrogen sulfides, with the potential of high-temperature superconductivity, was recently proposed at high Tc = 203 K. It motivated us to employ an ab initio approach for the predictions of crystal structures to find the stable scandium hydrides. In addition to the earlier predicted three stoichiometries of ScH, ScH2, and ScH3, we identify three other metallic stoichiometries of ScH4, ScH6, and ScH8, which show superconductivity at significantly higher temperatures. The phases of ScH4 and ScH6, whose stability does not require extremely high pressures (<150 GPa with ZPE), are primarily ionic compounds containing exotic quasimolecular H2 arrangements. The present electron-phonon calculations revealed the superconductive potential of ScH4 and ScH6 with estimated Tc of 98 K and 129 K at 200 GPa and 130 GPa, respectively. The superconductivity of ScHn stems from the large electron-phonon coupling associated with the wagging, bending, and intermediate-frequency modes attributed mainly to the hydrogen atoms.

Lattice-mediated magnetic order melting in TbMnO 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldini, Edoardo; Kubacka, Teresa; Mallett, Benjamin P. P.

Recent ultrafast magnetic-sensitive measurements have revealed a delayed melting of the long-range cycloid spin order in TbMnO 3 following photoexcitation across the fundamental Mott-Hubbard gap. The microscopic mechanism behind this slow transfer of energy from the photoexcited carriers to the spin degrees of freedom is still elusive and not understood. Here, we address this problem by combining spectroscopic ellipsometry, ultrafast broadband optical spectroscopy, and ab initio calculations. Upon photoexcitation, we observe the emergence of a complex collective response, which is due to high-energy coherent optical phonons coupled to the out-of-equilibrium charge density. This response precedes the magnetic order melting andmore » is interpreted as the fingerprint of the formation of anti-Jahn-Teller polarons. We propose that the charge localization in a long-lived self-trapped state hinders the emission of magnons and other spin-flip mechanisms, causing the energy transfer from the charge to the spin system to be mediated by the reorganization of the lattice. In conclusion, we provide evidence for the coherent excitation of a phonon mode associated with the ferroelectric phase transition.« less

Mechanical, electronic, and thermodynamic properties of zirconium carbide from first-principles calculations

NASA Astrophysics Data System (ADS)

Yang, Xiao-Yong; Lu, Yong; Zheng, Fa-Wei; Zhang, Ping

2015-11-01

Mechanical, electronic, and thermodynamic properties of zirconium carbide have been systematically studied using the ab initio calculations. The calculated equilibrium lattice parameter, bulk modulus, and elastic constants are all well consistent with the experimental data. The electronic band structure indicates that the mixture of C 2p and Zr 4d and 4p orbitals around the Fermi level makes a large covalent contribution to the chemical bonds between the C and Zr atoms. The Bader charge analysis suggests that there are about 1.71 electrons transferred from each Zr atom to its nearest C atom. Therefore, the Zr-C bond displays a mixed ionic/covalent character. The calculated phonon dispersions of ZrC are stable, coinciding with the experimental measurement. A drastic expansion in the volume of ZrC is seen with increasing temperature, while the bulk modulus decreases linearly. Based on the calculated phonon dispersion curves and within the quasi-harmonic approximation, the temperature dependence of the heat capacities is obtained, which gives a good description compared with the available experimental data. Project supported by the National Natural Science Foundation of China (Grant No. 51071032).

Coupled forward-backward trajectory approach for nonequilibrium electron-ion dynamics

NASA Astrophysics Data System (ADS)

Sato, Shunsuke A.; Kelly, Aaron; Rubio, Angel

2018-04-01

We introduce a simple ansatz for the wave function of a many-body system based on coupled forward and backward propagating semiclassical trajectories. This method is primarily aimed at, but not limited to, treating nonequilibrium dynamics in electron-phonon systems. The time evolution of the system is obtained from the Euler-Lagrange variational principle, and we show that this ansatz yields Ehrenfest mean-field theory in the limit that the forward and backward trajectories are orthogonal, and in the limit that they coalesce. We investigate accuracy and performance of this method by simulating electronic relaxation in the spin-boson model and the Holstein model. Although this method involves only pairs of semiclassical trajectories, it shows a substantial improvement over mean-field theory, capturing quantum coherence of nuclear dynamics as well as electron-nuclear correlations. This improvement is particularly evident in nonadiabatic systems, where the accuracy of this coupled trajectory method extends well beyond the perturbative electron-phonon coupling regime. This approach thus provides an attractive route forward to the ab initio description of relaxation processes, such as thermalization, in condensed phase systems.

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

Segall, M. D.; Payne, M. C.; Boyes, R. N.

An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

NASA Astrophysics Data System (ADS)

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

2016-07-01

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

PubMed

Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

2016-09-21

Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

PubMed

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

2016-07-07

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

Exotic s-wave superconductivity in alkali-doped fullerides.

PubMed

Nomura, Yusuke; Sakai, Shiro; Capone, Massimo; Arita, Ryotaro

2016-04-20

Alkali-doped fullerides (A3C60 with A = K, Rb, Cs) show a surprising phase diagram, in which a high transition-temperature (Tc) s-wave superconducting state emerges next to a Mott insulating phase as a function of the lattice spacing. This is in contrast with the common belief that Mott physics and phonon-driven s-wave superconductivity are incompatible, raising a fundamental question on the mechanism of the high-Tc superconductivity. This article reviews recent ab initio calculations, which have succeeded in reproducing comprehensively the experimental phase diagram with high accuracy and elucidated an unusual cooperation between the electron-phonon coupling and the electron-electron interactions leading to Mott localization to realize an unconventional s-wave superconductivity in the alkali-doped fullerides. A driving force behind the exotic physics is unusual intramolecular interactions, characterized by the coexistence of a strongly repulsive Coulomb interaction and a small effectively negative exchange interaction. This is realized by a subtle energy balance between the coupling with the Jahn-Teller phonons and Hund's coupling within the C60 molecule. The unusual form of the interaction leads to a formation of pairs of up- and down-spin electrons on the molecules, which enables the s-wave pairing. The emergent superconductivity crucially relies on the presence of the Jahn-Teller phonons, but surprisingly benefits from the strong correlations because the correlations suppress the kinetic energy of the electrons and help the formation of the electron pairs, in agreement with previous model calculations. This confirms that the alkali-doped fullerides are a new type of unconventional superconductors, where the unusual synergy between the phonons and Coulomb interactions drives the high-Tc superconductivity.

Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

NASA Astrophysics Data System (ADS)

Mishra, S. B.; Nanda, B. R. K.

2017-05-01

Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

Ab initio theory and modeling of water.

PubMed

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

2017-10-10

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Ab initio theory and modeling of water

PubMed Central

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

2017-01-01

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations.

PubMed

Alexandrova, Anastassia N; Boldyrev, Alexander I; Li, Xiang; Sarkas, Harry W; Hendricks, Jay H; Arnold, Susan T; Bowen, Kit H

2011-01-28

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.

Modeling non-harmonic behavior of materials from experimental inelastic neutron scattering and thermal expansion measurements

NASA Astrophysics Data System (ADS)

Bansal, Dipanshu; Aref, Amjad; Dargush, Gary; Delaire, Olivier

2016-09-01

Based on thermodynamic principles, we derive expressions quantifying the non-harmonic vibrational behavior of materials, which are rigorous yet easily evaluated from experimentally available data for the thermal expansion coefficient and the phonon density of states. These experimentally-derived quantities are valuable to benchmark first-principles theoretical predictions of harmonic and non-harmonic thermal behaviors using perturbation theory, ab initio molecular-dynamics, or Monte-Carlo simulations. We illustrate this analysis by computing the harmonic, dilational, and anharmonic contributions to the entropy, internal energy, and free energy of elemental aluminum and the ordered compound \\text{FeSi} over a wide range of temperature. Results agree well with previous data in the literature and provide an efficient approach to estimate anharmonic effects in materials.

First-principles investigation of structural, elastic, lattice dynamical and thermodynamic properties of lithium sulfur under pressure

NASA Astrophysics Data System (ADS)

Saib, S.; Bouarissa, N.

2017-10-01

In this study we report on the influence of hydrostatic pressure on structural, elastic, lattice dynamical and thermal properties of Li2S in the anti-fluorite structure using ab initio pseudopotential approach based on the density functional perturbation theory. Our results are found to be in good agreement with those existing in the literature. The present phonon dispersion spectra, dielectric constants and Born effective charges may be seen as the first investigation for the material under load. The pressure dependence of all features of interest has been examined and discussed. Besides, the temperature dependence of the lattice parameter and bulk modulus is predicted. The generalized elastic stability criteria showed that the material of interest is mechanically unstable for pressures beyond 55 GPa.

Ab initio description of the first stages of laser-induced ultra-fast nonthermal melting of InSb

NASA Astrophysics Data System (ADS)

Zijlstra, E. S.; Walkenhorst, J.; Gilfert, C.; Sippel, C.; Töws, W.; Garcia, M. E.

2008-12-01

Using first principles, all-electron calculations and dynamical simulations we study the behavior of solid InSb immediately after intense femtosecond excitation. First, we determine the laser-excited potential energy surfaces with high accuracy for different electronic temperatures (corresponding to different laser fluences). Then, we demonstrate that, although most phonon modes become only slightly softened even for high electron temperatures, the transverse acoustic modes at the boundary of the Brillouin zone undergo dramatic changes and become unstable. This is the origin of nonthermal melting. Based on these results, the dynamics during the first hundreds of femtoseconds after laser excitation can be unambiguously elucidated. Our results are in agreement with recent experiments and support the predictions made by Stampfli and Bennemann for silicon.

Ultralow Thermal Conductivity in Full Heusler Semiconductors.

PubMed

He, Jiangang; Amsler, Maximilian; Xia, Yi; Naghavi, S Shahab; Hegde, Vinay I; Hao, Shiqiang; Goedecker, Stefan; Ozoliņš, Vidvuds; Wolverton, Chris

2016-07-22

Semiconducting half and, to a lesser extent, full Heusler compounds are promising thermoelectric materials due to their compelling electronic properties with large power factors. However, intrinsically high thermal conductivity resulting in a limited thermoelectric efficiency has so far impeded their widespread use in practical applications. Here, we report the computational discovery of a class of hitherto unknown stable semiconducting full Heusler compounds with ten valence electrons (X_{2}YZ, X=Ca, Sr, and Ba; Y=Au and Hg; Z=Sn, Pb, As, Sb, and Bi) through high-throughput ab initio screening. These new compounds exhibit ultralow lattice thermal conductivity κ_{L} close to the theoretical minimum due to strong anharmonic rattling of the heavy noble metals, while preserving high power factors, thus resulting in excellent phonon-glass electron-crystal materials.

Ab initio study of the temperature-dependent structural properties of Al(110)

NASA Astrophysics Data System (ADS)

Scharoch, Pawel

2009-09-01

Temperature-dependent structural properties of Al(110) surface have been studied ab initio employing the concepts of the potential-energy surface (PES) and the free-energy surface (FES), with the latter based on the harmonic approximation for lattice dynamics. Three effects have been identified as contributing to the temperature-dependent multilayer relaxation: the bulk-substrate thermal expansion, the effect of asymmetry of PESs, and the entropy-driven shift of the minima of FESs. Thanks to the proper choice of constraints for PESs and FESs, it was possible to find relative contribution of the three effects to variation with temperature of the first three interlayer distances. A very satisfactory agreement of the calculation results with experimental data has been obtained. Also, a reference of the theoretical data to the experimentally observed anisotropic surface melting has been noticed. A softening phonon mode has been identified which is responsible for both: the entropy-driven spectacular expansion of the second interlayer distance and the loss of the surface stability. The latter can be associated with the anisotropic surface melting. The methodology applied has been found to be complementary to previous theoretical works [N. Marzari, D. Vanderbilt, A. De Vita, and M. C. Payne, Phys. Rev. Lett. 82, 3296 (1999); S. Narasimhan, Phys. Rev. B 64, 125409 (2001)], by offering another point of view and additional insight into the relative contribution of different physical effects to the temperature-dependent structural phenomena in Al(110) surface.

Real-time ab initio simulations of excited-state dynamics in nanostructures

NASA Astrophysics Data System (ADS)

Tomanek, David

2007-03-01

Combining time-dependent ab initio density functional calculations for electrons with molecular dynamics simulations for ions, we investigate the effect of excited-state dynamics in nanostructures. In carbon nanotubes, we find electronic excitations to last for a large fraction of a picosecond. The de-excitation process is dominated by coupling to other electronic degrees of freedom during the first few hundred femtoseconds. Later, the de-excitation process becomes dominated by coupling to ionic motion. The onset point and damping rate in that regime change with initial ion velocities, a manifestation of temperature dependent electron-phonon coupling. Considering the fact that the force field in the electronically excited state differs significantly from the ground state, as reflected in the Franck-Condon effect, atomic bonds can easily be broken or restored during the relatively long lifetime of electronic excitations. This effect can be utilized in a ``photo-surgery" of nanotubes, causing structural self-healing at vacancy sites or selective de-oxidation processes induced by photo-absorption. Also, electronic excitations are a key ingredient for the understanding of sputtering processes in nanostructures, induced by energetic collisions with ions. Yoshiyuki Miyamoto, Angel Rubio, and David Tomanek, Phys. Rev. Lett. 97, 126104 (2006). Yoshiyuki Miyamoto, Savas Berber, Mina Yoon, Angel Rubio, and David Tomanek, Chem. Phys. Lett. 392, 209 (2004). Yoshiyuki Miyamoto, Noboru Jinbo, Hisashi Nakamura, Angel Rubio, and David Tomanek, Phys. Rev. B 70, 233408 (2004). Yoshiyuki Miyamoto, Arkady Krasheninnikov, and David Tomanek (in preparation).

Ab initio computational study on the lattice thermal conductivity of Zintl clathrates [Si19P4] Cl4 and Na4[Al4Si19

NASA Astrophysics Data System (ADS)

Härkönen, Ville J.; Karttunen, Antti J.

2016-08-01

The lattice thermal conductivity of silicon clathrate framework Si23 and two Zintl clathrates, [Si19P4] Cl4 and Na4[Al4Si19] , is investigated by using an iterative solution of the linearized Boltzmann transport equation in conjunction with ab initio lattice dynamical techniques. At 300 K, the lattice thermal conductivities for Si23, [Si19P4] Cl4 , and Na4[Al4Si19] were found to be 43 W/(m K), 25 W/(m K), and 2 W/(m K), respectively. In the case of Na4[Al4Si19] , the order-of-magnitude reduction in the lattice thermal conductivity was found to be mostly due to relaxation times and group velocities differing from Si23 and [Si19P4] Cl4 . The difference in the relaxation times and group velocities arises primarily due to the phonon spectrum at low frequencies, resulting eventually from the differences in the second-order interatomic force constants (IFCs). The obtained third-order IFCs were rather similar for all materials considered here. The present findings are similar to those obtained earlier for some skutterudites. The predicted lattice thermal conductivity of Na4[Al4Si19] is in line with the experimentally measured thermal conductivity of recently synthesized type-I Zintl clathrate Na8[Al8Si38] (polycrystalline samples).

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 86.094-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., the Administrator may deem such certificate void ab initio. (4) In any case in which certification of... fraud or other misconduct as makes the certification invalid ab initio. (6) The manufacturer may request...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

PubMed Central

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

2012-01-01

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

77 FR 21154 - BNSF Railway Company-Abandonment Exemption-in Oklahoma County, OK

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-09

... proceeding and reject BNSF's notice of exemption as void ab initio on the grounds that BNSF had provided... misleading information, the exemption is void ab initio. BNSF has filed a combined environmental and historic... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. AB 6 (Sub-No. 480X)] BNSF...

DSMC study of oxygen shockwaves based on high-fidelity vibrational relaxation and dissociation models

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Kulakhmetov, Marat; Alexeenko, Alina

2017-01-01

This work evaluates high-fidelity vibrational-translational (VT) energy relaxation and dissociation models for pure O2 normal shockwave simulations with the direct simulation Monte Carlo (DSMC) method. The O2-O collisions are described using ab initio state-specific relaxation and dissociation models. The Macheret-Fridman (MF) dissociation model is adapted to the DSMC framework by modifying the standard implementation of the total collision energy (TCE) model. The O2-O2 dissociation is modeled with this TCE+MF approach, which is calibrated with O2-O ab initio data and experimental equilibrium dissociation rates. The O2-O2 vibrational relaxation is modeled via the Larsen-Borgnakke model, calibrated to experimental VT rates. All the present results are compared to experimental data and previous calculations available in the literature. It is found that, in general, the ab initio dissociation model is better than the TCE model at matching the shock experiments. Therefore, when available, efficient ab initio models are preferred over phenomenological models. We also show that the proposed TCE + MF formulation can be used to improve the standard TCE model results when ab initio data are not available or limited.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

21 CFR 701.9 - Exemptions from labeling requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., become void ab initio if the cosmetic comprising such shipment, delivery, or part is adulterated or... a cosmetic under paragraph (a)(2) of this section shall become void ab initio with respect to the...

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

PubMed

Salim, Michael A; Willow, Soohaeng Yoo; Hirata, So

2016-05-28

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D2O ice greater than that of H2O 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.

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

NASA Astrophysics Data System (ADS)

Salim, Michael A.; Willow, Soohaeng Yoo; Hirata, So

2016-05-01

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D2O ice greater than that of H2O 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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salim, Michael A.; Willow, Soohaeng Yoo; Hirata, So, E-mail: sohirata@illinois.edu

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 ismore » 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.« less

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

21 CFR 501.100 - Animal food; exemptions from labeling.

Code of Federal Regulations, 2014 CFR

2014-04-01

... become void ab initio if the food comprising such shipment, delivery, or part is adulterated or... a food under paragraph (d)(2) of this section shall become void ab initio with respect to the person...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

Cubic and orthorhombic structures of aluminum hydride Al H3 predicted by a first-principles study

NASA Astrophysics Data System (ADS)

Ke, Xuezhi; Kuwabara, Akihide; Tanaka, Isao

2005-05-01

The most stable structure of aluminum hydride AlH3 is believed to be a hexagonal symmetry. However, using the density functional theory, we have identified two more stable structures for the AlH3 with the cubic and orthorhombic symmetries. Based on the quasiharmonic approximation, the cubic and orthorhombic AlH3 are almost degenerate when the zero-point energies are included. The geometric and electronic structures, the phonon, and the thermodynamic properties for the hexagonal, cubic, and orthorhombic AlH3 have been studied by means of density functional theory and direct ab initio force constant approach. The calculated electronic structures, phonon density of states, and thermodynamic functions [including S(T) and H(T)-H(0) ] for the three hydrides are similar. The results show that these three hydrides have negative enthalpies of formation, but positive free energies of formation. This conclusion is the same as that made by Wolverton for the hexagonal AlH3 [Phys. Rev. B 69, 144109 (2004)]. The thermodynamic properties indicate that the orthorhombic and cubic AlH3 should be more difficult to dissociate than the hexagonal AlH3 .

Order and disorder and their influences on optical absorption of glasses in the gap region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baník, Ivan, E-mail: ivan.banik@stuba.sk; Kubliha, Marian, E-mail: marian.kubliha@stuba.sk; Lukovičová, Jozefa, E-mail: jozefa.lukovicova@stuba.sk

2016-07-07

The exponential increase of the absorption coefficient near the absorption edge is usually explained by existence of the density-of-states tails. Among the quoted theoretical models which are widely used to explain the manifestations of the Urbach rule in semiconductors, are the Sumi–Toyozava and the Dow–Redfield models and ab initio (from beginning) theory. Our barrier-cluster-heating model assumes the different creating mechanism of exponential tails. The energy by optical transition is provided to electrons except from photons also from vibration of microregion. It deals about the replenishment of absented photons energy, which is smaller as gap width. Absented energy needed for themore » transition by light absorption is accumulated in certain microregions of material in the form of vibrational energy. At absorption sufficiently big package of accumulated energy can be used. Energy of emptied microarea is filled by phonons from surrounding of microarea (as result of temperature status of surrounding), resp. phonons of optical background which are created in given microarea at non radiative recombination of carriers. In this work simplified process at derivating of Urbach rule is listed.« less

The Effects of the Organic-Inorganic Interactions on the Thermal Transport Properties of CH3NH3PbI3.

PubMed

Hata, Tomoyuki; Giorgi, Giacomo; Yamashita, Koichi

2016-04-13

Methylammonium lead iodide perovskite (CH3NH3PbI3), the most investigated hybrid organic-inorganic halide perovskite, is characterized by a quite low thermal conductivity. The rotational motion of methylammonium cations is considered responsible for phonon transport suppression; however, to date, the specific mechanism of the process has not been clarified. In this study, we elucidate the role of rotations in thermal properties based on molecular dynamics simulations. To do it, we developed an empirical potential for CH3NH3PbI3 by fitting to ab initio calculations and evaluated its thermal conductivity by means of nonequilibrium molecular dynamics. Results are compared with model systems that include different embedded cations, and this comparison shows a dominant suppression effect provided by rotational motions. We also checked the temperature dependence of the vibrational density of states and specified the energy range in which anharmonic couplings occur. By means of phonon dispersion analysis, we were able to fully elucidate the suppression mechanism: the rotations are coupled with translational motions of cations, via which inorganic lattice vibrations are coupled and scatter each other.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

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.

Modeling non-harmonic behavior of materials from experimental inelastic neutron scattering and thermal expansion measurements

DOE PAGES

Bansal, Dipanshu; Aref, Amjad; Dargush, Gary; ...

2016-07-20

Based on thermodynamic principles, we derive expressions quantifying the non-harmonic vibrational behavior of materials, which are rigorous yet easily evaluated from experimentally available data for the thermal expansion coefficient and the phonon density of states. These experimentally-derived quantities are valuable to benchmark first-principles theoretical predictions of harmonic and non-harmonic thermal behaviors using perturbation theory, ab initio molecular-dynamics, or Monte-Carlo simulations. In this study, we illustrate this analysis by computing the harmonic, dilational, and anharmonic contributions to the entropy, internal energy, and free energy of elemental aluminum and the ordered compound FeSi over a wide range of temperature. Our results agreemore » well with previous data in the literature and provide an efficient approach to estimate anharmonic effects in materials.« less

Modeling non-harmonic behavior of materials from experimental inelastic neutron scattering and thermal expansion measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bansal, Dipanshu; Aref, Amjad; Dargush, Gary

Based on thermodynamic principles, we derive expressions quantifying the non-harmonic vibrational behavior of materials, which are rigorous yet easily evaluated from experimentally available data for the thermal expansion coefficient and the phonon density of states. These experimentally-derived quantities are valuable to benchmark first-principles theoretical predictions of harmonic and non-harmonic thermal behaviors using perturbation theory, ab initio molecular-dynamics, or Monte-Carlo simulations. In this study, we illustrate this analysis by computing the harmonic, dilational, and anharmonic contributions to the entropy, internal energy, and free energy of elemental aluminum and the ordered compound FeSi over a wide range of temperature. Our results agreemore » well with previous data in the literature and provide an efficient approach to estimate anharmonic effects in materials.« less

FeRh ground state and martensitic transformation

DOE PAGES

Zarkevich, Nikolai A.; Johnson, Duane D.

2018-01-09

Cubic B2 FeRh exhibits a metamagnetic transition [(111) antiferromagnet (AFM) to ferromagnet (FM)] around 353 K and remains structurally stable at higher temperatures. However, the calculated zero-Kelvin phonons of AFM FeRh exhibit imaginary modes at M points in the Brillouin zone, indicating a premartensitic instability, which is a precursor to a martensitic transformation at low temperatures. Combining electronic-structure calculations with ab initio molecular dynamics, conjugate gradient relaxation, and the solid-state nudged-elastic band methods, we predict that AFM B2 FeRh becomes unstable at ambient pressure and transforms without a barrier to an AFM(111) orthorhombic (martensitic) ground state below 90±10K. In conclusion,more » we also consider competing structures, in particular, a tetragonal AFM(100) phase that is not the global ground state, as proposed, but a constrained solution.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zarkevich, Nikolai A.; Johnson, Duane D.

Cubic B2 FeRh exhibits a metamagnetic transition [(111) antiferromagnet (AFM) to ferromagnet (FM)] around 353 K and remains structurally stable at higher temperatures. However, the calculated zero-Kelvin phonons of AFM FeRh exhibit imaginary modes at M points in the Brillouin zone, indicating a premartensitic instability, which is a precursor to a martensitic transformation at low temperatures. Combining electronic-structure calculations with ab initio molecular dynamics, conjugate gradient relaxation, and the solid-state nudged-elastic band methods, we predict that AFM B2 FeRh becomes unstable at ambient pressure and transforms without a barrier to an AFM(111) orthorhombic (martensitic) ground state below 90±10K. In conclusion,more » we also consider competing structures, in particular, a tetragonal AFM(100) phase that is not the global ground state, as proposed, but a constrained solution.« less

Ab Initio: And a New Era of Airline Pilot Training.

ERIC Educational Resources Information Center

Gesell, Laurence E.

1995-01-01

Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)

Concentration dependence of electrical resistivity of binary liquid alloy HgZn: Ab-initio study

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2013-06-01

The electrical resistivity of HgZn liquid alloy has been made calculated using Troullier and Martins ab-initio pseudopotential as a function of concentration. Hard sphere diameters of Hg and Zn are obtained through the inter-ionic pair potential have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys.

Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Analysis of fcc metals fracture behaviour: Fracture behaviour of fcc metals: brittle/ductile behaviour criteria : with ab-initio, embedded atom and pseudopotential parameterization for Au, Ir and Al. analysis for Au, Ir and Al.

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.; Katsnelson, M. I.; Mryasov, Oleg N.; Freeman, A. J.; Trefilov, M. V.

1998-03-01

Theoretical analysis of the fracture behaviour of fcc Au, Ir and Al have been performed within various brittle/ductile criteria (BDC) with ab-initio, embedded atom (EAM), and pseudopotential parameterizations. We systematically examined several important aspects of the fracture behaviour: (i) dislocation structure, (ii) energetics of the cleavage decohesion and (iii) character of the interatomic interactions. Unit dislocation structures were analyzed within a two dimensional generalization of the Peierls-Nabarro model with restoring forces determined from ab-initio total energy calculations and found to be split with well defined highly mobile partials for all considered metals. We find from ab-initio and pseudopotential that in contrast with most of fcc metals, cleavage decohesion curve for Al appreciably differs from UBER relation. Finally, using ab-initio, EAM and pseudopotential parameterizations, we demonstrate that (i) Au (as a typical example of a ductile metal) is well described within existing BDC's, (ii) anomalous cleavage-like crack propagation of Ir is driven predominantly by it's high elastic modulus and (iii) Al is not described within BDC due to it's long-range interatomic interactions (and hence requires adjustments of the brittle/ductile criteria).

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

PubMed Central

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian

2017-01-01

Abstract Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

PubMed Central

Zhang, Yang

2014-01-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

PubMed

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

2017-05-01

Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

NASA Astrophysics Data System (ADS)

Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

PubMed

Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

2014-08-01

In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

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 asmore » 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.« less

Structures, phase stabilities, and electrical potentials of Li-Si battery anode materials

NASA Astrophysics Data System (ADS)

Tipton, William W.; Bealing, Clive R.; Mathew, Kiran; Hennig, Richard G.

2013-05-01

The Li-Si materials system holds promise for use as an anode in Li-ion battery applications. For this system, we determine the charge capacity, voltage profiles, and energy storage density solely by ab initio methods without any experimental input. We determine the energetics of the stable and metastable Li-Si phases likely to form during the charging and discharging of a battery. Ab initio molecular dynamics simulations are used to model the structure of amorphous Li-Si as a function of composition, and a genetic algorithm coupled to density-functional theory searches the Li-Si binary phase diagram for small-cell, metastable crystal structures. Calculations of the phonon densities of states using density-functional perturbation theory for selected structures determine the importance of vibrational, including zero-point, contributions to the free energies. The energetics and local structural motifs of these metastable Li-Si phases closely resemble those of the amorphous phases, making these small unit cell crystal phases good approximants of the amorphous phase for use in further studies. The charge capacity is estimated, and the electrical potential profiles and the energy density of Li-Si anodes are predicted. We find, in good agreement with experimental measurements, that the formation of amorphous Li-Si only slightly increases the anode potential. Additionally, the genetic algorithm identifies a previously unreported member of the Li-Si binary phase diagram with composition Li5Si2 which is stable at 0 K with respect to previously known phases. We discuss its relationship to the partially occupied Li7Si3 phase.

Ab initio modeling of nonequilibrium electron-ion dynamics of iron in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Ogitsu, T.; Fernandez-Pañella, A.; Hamel, S.; Correa, A. A.; Prendergast, D.; Pemmaraju, C. D.; Ping, Y.

2018-06-01

The spatiotemporal electron and ion relaxation dynamics of iron induced by femtosecond laser pulses was studied using a one-dimensional two-temperature model (1D-TTM) where electron and ion temperature-dependent thermophysical parameters such as specific heat (C ), electron-phonon coupling (G ), and thermal conductivity (K ) were calculated with ab initio density-functional-theory (DFT) simulations. Based on the simulated time evolutions of electron and ion temperature distributions [Te(x ,t ) and Ti(x ,t ) ], the time evolution of x-ray absorption near-edge spectroscopy (XANES) was calculated and compared with experimental results reported by Fernandez-Pañella et al., where the slope of XANES spectrum at the onset of absorption (s ) was used due to its excellent sensitivity to the electron temperature. Our results indicate that the ion temperature dependence on G and C , which is largely neglected in the past studies, is very important for studying the nonequilibrium electron-ion relaxation dynamics of iron in warm dense matter (WDM) conditions. It is also shown that the 1 /s behavior becomes very sensitive to the thermal gradient profile, in other words, to the values of K in a TTM simulation, for target thickness of about two to four times the mean free path of conduction electrons. Our approach based on 1D-TTM and XANES simulations can be used to determine the optimal combination of target geometry and laser fluence for a given target material, which will enable us to tightly constrain the thermophysical parameters under electron-ion nonequilibrium WDM conditions.

Controlling Magnetic and Ferroelectric Order Through Geometry: Synthesis, Ab Initio Theory, Characterization of New Multi-Ferric Fluoride Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halasyamani, Shiv; Fennie, Craig

2016-11-03

We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.

7Be(p,gamma)8B S-factor from Ab Initio Wave Functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Navratil, P; Bertulani, C A; Caurier, E

2006-10-12

There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) predicts low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. We present here a brief overview of the first steps taken toward nuclear reaction applications. In particular, we discuss our calculation of the {sup 7}Be(p,{gamma}){sup 8}B S-factor. We also present our first results of the {sup 3}He({alpha},{gamma}){sup 7}Be S-factor and of the S-factor of the mirror reaction {sup 3}H({alpha},{gamma}){sup 7}Li.more » The {sup 7}Be(p,{gamma}){sup 8}B and {sup 3}He({alpha},{gamma}){sup 7}Be reactions correspond to the most important uncertainties in solar model predictions of neutrino fluxes.« less

An ab initio-based Er–He interatomic potential in hcp Er

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Li; ye, Yeting; Fan, K. M.

2014-09-01

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations.more » The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.« less

Ab initio Studies of Magnetism in the Iron Chalcogenides FeTe and FeSe

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Misawa, Takahiro; Miyake, Takashi; Imada, Masatoshi

2015-09-01

The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

PubMed

Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

2018-01-18

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

Resolution of ab initio shapes determined from small-angle scattering.

PubMed

Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I

2016-11-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction.

PubMed

Huang, Ying; Chen, Shi-Yi; Deng, Feilong

2016-01-01

In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.

Resolution of ab initio shapes determined from small-angle scattering

PubMed Central

Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.

2016-01-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

A highly accurate ab initio potential energy surface for methane.

PubMed

Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

2016-09-14

A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 reproduced with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

Ab-initio study of the energetics and thermodynamics of the reaction CH3H + O( 3P) → CF3H … O → CF3 + OH

NASA Astrophysics Data System (ADS)

Kreye, W. C.

1996-07-01

Ab-initio computations at 298.15 K were made of the activation quantities ΔH ‡, ΔS ‡, and ΔG ‡ and of the reaction quantities ΔHr and ΔSr for CF3H + O( 3P) → CF3H … O → .CF3.OH. CF 3H … O is the transition state (TS). GAUSSIAN92 was used and energies computed at a slightly modified Gaussian-2 level. Two potential surfaces for the TS had symmetries 3A' and 3A″. The two rate constants included a semi-classical, quantum-mechanical-tunneling transmission coefficient. The ab-initio ΔH ‡and ΔH r values were in excellent agreement (± 1 kcal/mol) with experiment; but the ΔS ‡, ΔG ‡, and ΔS r values yielded somewhat poorer agreement. Experimental and ab-initio structures were in excellent agreement.

Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.

2015-09-14

We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t tomore » be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.« less

Control of Multiple Exciton Generation and Electron-Phonon Coupling by Interior Nanospace in Hyperstructured Quantum Dot Superlattice.

PubMed

Chang, I-Ya; Kim, DaeGwi; Hyeon-Deuk, Kim

2017-09-20

The possibility of precisely manipulating interior nanospace, which can be adjusted by ligand-attaching down to the subnanometer regime, in a hyperstructured quantum dot (QD) superlattice (QDSL) induces a new kind of collective resonant coupling among QDs and opens up new opportunities for developing advanced optoelectric and photovoltaic devices. Here, we report the first real-time dynamics simulations of the multiple exciton generation (MEG) in one-, two-, and three-dimensional (1D, 2D, and 3D) hyperstructured H-passivated Si QDSLs, accounting for thermally fluctuating band energies and phonon dynamics obtained by finite-temperature ab initio molecular dynamics simulations. We computationally demonstrated that the MEG was significantly accelerated, especially in the 3D QDSL compared to the 1D and 2D QDSLs. The MEG acceleration in the 3D QDSL was almost 1.9 times the isolated QD case. The dimension-dependent MEG acceleration was attributed not only to the static density of states but also to the dynamical electron-phonon couplings depending on the dimensionality of the hyperstructured QDSL, which is effectively controlled by the interior nanospace. Such dimension-dependent modifications originated from the short-range quantum resonance among component QDs and were intrinsic to the hyperstructured QDSL. We propose that photoexcited dynamics including the MEG process can be effectively controlled by only manipulating the interior nanospace of the hyperstructured QDSL without changing component QD size, shape, compositions, ligand, etc.

Investigation of the structural, mechanical, dynamical and thermal properties of CsCaF3 and CsCdF3

NASA Astrophysics Data System (ADS)

Salmankurt, Bahadır; Duman, Sıtkı

2016-04-01

The structural, mechanical, dynamical and thermal properties of CsCaF3 and CsCdF3 are presented by using an ab initio pseudopotential method and a linear response scheme, within the generalized gradient approximation. The obtained structural and mechanical properties are in good agreement with other available theoretical and experimental studies. The calculated elastic constants of these materials obey the cubic stability conditions. It has been found that CsCaF3 is brittle whereas CsCdF3 has ductile manner. The full phonon dispersion curves of these materials are reported for the first time in the literature. We have found that calculated phonon modes are positive along the all symmetry directions, indicating that these materials are dynamically stable at the cubic structure. The obtained zone-center phonon modes for CsCaF3 (IR data) are found to be 83 (98) cm-1, 104 (115) cm-1, 120 cm-1, 180 (192) cm-1, 231 (250.5) cm-1, 361 (374) cm-1, 446 (449) cm-1. Also, we have calculated internal energy, Helmholtz free energy, constant-volume specific heat, entropy and Debye temperature as function of temperature. At the 300 K, specific heats are calculated to be 113.36 J mol-1 K-1 and 115.58 J mol-1 K-1 for CsCaF3 and CsCdF3 ,respectively, which are lower than Doulong-Petit limit (12 472 J mol-1 K-1).

Nonempirical Calculation of Superconducting Transition Temperatures in Light-Element Superconductors.

PubMed

Arita, Ryotaro; Koretsune, Takashi; Sakai, Shiro; Akashi, Ryosuke; Nomura, Yusuke; Sano, Wataru

2017-07-01

Recent progress in the fully nonempirical calculation of the superconducting transition temperature (T c ) is reviewed. Especially, this study focuses on three representative light-element high-T c superconductors, i.e., elemental Li, sulfur hydrides, and alkali-doped fullerides. Here, it is discussed how crucial it is to develop the beyond Migdal-Eliashberg (ME) methods. For Li, a scheme of superconducting density functional theory for the plasmon mechanism is formulated and it is found that T c is dramatically enhanced by considering the frequency dependence of the screened Coulomb interaction. For sulfur hydrides, it is essential to go beyond not only the static approximation for the screened Coulomb interaction, but also the constant density-of-states approximation for electrons, the harmonic approximation for phonons, and the Migdal approximation for the electron-phonon vertex, all of which have been employed in the standard ME calculation. It is also shown that the feedback effect in the self-consistent calculation of the self-energy and the zero point motion considerably affect the calculation of T c . For alkali-doped fullerides, the interplay between electron-phonon coupling and electron correlations becomes more nontrivial. It has been demonstrated that the combination of density functional theory and dynamical mean field theory with the ab initio downfolding scheme for electron-phonon coupled systems works successfully. This study not only reproduces the experimental phase diagram but also obtains a unified view of the high-T c superconductivity and the Mott-Hubbard transition in the fullerides. The results for these high-T c superconductors will provide a firm ground for future materials design of new superconductors. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First-principles theory of iron up to earth-core pressures: Structural, vibrational, and elastic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soederlind, P.; Moriarty, J.A.; Wills, J.M.

1996-06-01

{ital Ab} {ital initio} electronic-structure calculations, based on density-functional theory and a full-potential linear-muffin-tin-orbital method, have been used to predict crystal-structure phase stabilities, elastic constants, and Brillouin-zone-boundary phonons for iron under compression. Total energies for five crystal structures, bcc, fcc, bct, hcp, and dhcp, have been calculated over a wide volume range. In agreement with experiment and previous theoretical calculations, a magnetic bcc ground state is obtained at ambient pressure and a nonmagnetic hcp ground state is found at high pressure, with a predicted bcc {r_arrow} hcp phase transition at about 10 GPa. Also in agreement with very recent diamond-anvil-cellmore » experiments, a metastable dhcp phase is found at high pressure, which remains magnetic and consequently accessible at high temperature up to about 50 GPa. In addition, the bcc structure becomes mechanically unstable at pressures above 2 Mbar (200 GPa) and a metastable, but still magnetic, bct phase ({ital c}/{ital a} {approx_equal} 0.875) develops. For high-pressure nonmagnetic iron, fcc and hcp elastic constants and fcc phonon frequencies have been calculated to above 4 Mbar. These quantities rise smoothly with pressure, but an increasing tendency towards elastic anisotropy as a function of compression is observed, and this has important implications for the solid inner-core of the earth. The fcc elastic-constant and phonon data have also been used in combination with generalized pseudopotential theory to develop many-body interatomic potentials, from which high-temperature thermodynamic properties and melting can be obtained. In this paper, these potentials have been used to calculate full fcc and hcp phonon spectra and corresponding Debye temperatures as a function of compression. {copyright} {ital 1996 The American Physical Society.}« less

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sano, Yukio; Sano, Tomokazu

A quadratic equation for the temperature-independent Grueneisen coefficient {gamma} was derived by a method in which the Walsh-Christian and Mie-Grueneisen equations are combined. Some previously existing ab initio temperature Hugoniots for hexagonal close-packed solid Fe are inaccurate because the constant-volume specific heats on the Hugoniots CVH, which are related uniquely to the solutions of the quadratic equation, have values that are too small. A CVH distribution in the solid phase range was demonstrated to agree approximately with a previous ab initio distribution. In contrast, the corresponding {gamma} distribution was significantly different from the ab initio distribution in the lower pressuremore » region. The causes of these disagreements are clarified.« less

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

Ab initio calculation of one-nucleon halo states

NASA Astrophysics Data System (ADS)

Rodkin, D. M.; Tchuvil'sky, Yu M.

2018-02-01

We develop an approach to microscopic and ab initio description of clustered systems, states with halo nucleon and one-nucleon resonances. For these purposes a basis combining ordinary shell-model components and cluster-channel terms is built up. The transformation of clustered wave functions to the uniform Slater-determinant type is performed using the concept of cluster coefficients. The resulting basis of orthonormalized wave functions is used for calculating the eigenvalues and the eigenvectors of Hamiltonians built in the framework of ab initio approaches. Calculations of resonance and halo states of 5He, 9Be and 9B nuclei demonstrate that the approach is workable and labor-saving.

40 CFR 86.096-7 - Maintenance of records; submittal of information; right of entry.

Code of Federal Regulations, 2010 CFR

2010-07-01

...] (ii) EPA may void ab initio a certificate for a 1994 or 1995 model year light-duty vehicle or light... Administrator upon request. (iii) Any voiding ab initio of a certificate under § 86.091-7(c)(6) and paragraph (h...

40 CFR 80.607 - What are the requirements for obtaining an exemption for diesel fuel or ECA marine fuel used for...

Code of Federal Regulations, 2010 CFR

2010-07-01

... section, will cause the exemption to be void ab initio. (6) If any information required under paragraph (c... void ab initio, and may make the party liable for a violation of this subpart. (f) Effects of exemption...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.

ERIC Educational Resources Information Center

Duke, B. J.; O'Leary, Brian

1988-01-01

Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

Body-centered orthorhombic C 16 : A novel topological node-line semimetal

DOE PAGES

Wang, Jian -Tao; Weng, Hongming; Nie, Simin; ...

2016-05-11

We identify by ab initio calculations a novel topological semimetal carbon phase in all-sp 2 bonding networks with a 16-atom body-centered orthorhombic unit cell, termed bco-C 16. Total-energy calculations show that bco-C 16 is comparable to solid fcc-C 60 in energetic stability, and phonon and molecular dynamics simulations confirm its dynamical stability. This all-sp 2 carbon allotrope can be regarded as a three-dimensional modification of graphite, and its simulated x-ray diffraction (XRD) pattern matches well a previously unexplained diffraction peak in measured XRD spectra of detonation and chimney soot, indicating its presence in the specimen. Electronic band structure calculations revealmore » that bco-C 16 is a topological node-line semimetal with a single nodal ring. Lastly, these findings establish a novel carbon phase with intriguing structural and electronic properties of fundamental significance and practical interest.« less

Temperature effect on the structural stabilities and electronic properties of X22H28 (X=C, Si and Ge) nanocrystals: A first-principles study

NASA Astrophysics Data System (ADS)

Deng, Xiao-Lin; Zhao, Yu-Jun; Wang, Ya-Ting; Liao, Ji-Hai; Yang, Xiao-Bao

2016-12-01

Based on ab initio molecular dynamic simulations, we have theoretically investigated the structural stabilities and electronic properties of X22H28 (X=C, Si, and Ge) nanocrystals, as a function of temperature with consideration of vibrational entropy effects. To compare the relative stabilities of X22H28 isomers, the vibration free energies are obtained according to the calculated phonon spectrum, where the typical modes are shown to be dominant to the structural stabilities. In addition, there is a significant gap reduction as the temperature increases from 0 K to 300 K, where the decrements are 0.2 /0.5 /0.6eV for C/Si/Ge nanocrystals, respectively. The dependence of energy gap on the variance of bond length is also analyzed according to the corresponding atomic attributions to the HOMO and LUMO levels.

Prediction of superconducting iron–bismuth intermetallic compounds at high pressure

PubMed Central

Amsler, Maximilian; Naghavi, S. Shahab

2017-01-01

The synthesis of materials in high-pressure experiments has recently attracted increasing attention, especially since the discovery of record breaking superconducting temperatures in the sulfur–hydrogen and other hydrogen-rich systems. Commonly, the initial precursor in a high pressure experiment contains constituent elements that are known to form compounds at ambient conditions, however the discovery of high-pressure phases in systems immiscible under ambient conditions poses an additional materials design challenge. We performed an extensive multi component ab initio structural search in the immiscible Fe–Bi system at high pressure and report on the surprising discovery of two stable compounds at pressures above ≈36 GPa, FeBi2 and FeBi3. According to our predictions, FeBi2 is a metal at the border of magnetism with a conventional electron–phonon mediated superconducting transition temperature of T c = 1.3 K at 40 GPa. PMID:28507678

FeRh ground state and martensitic transformation

NASA Astrophysics Data System (ADS)

Zarkevich, Nikolai A.; Johnson, Duane D.

2018-01-01

Cubic B 2 FeRh exhibits a metamagnetic transition [(111) antiferromagnet (AFM) to ferromagnet (FM)] around 353 K and remains structurally stable at higher temperatures. However, the calculated zero-Kelvin phonons of AFM FeRh exhibit imaginary modes at M points in the Brillouin zone, indicating a premartensitic instability, which is a precursor to a martensitic transformation at low temperatures. Combining electronic-structure calculations with ab initio molecular dynamics, conjugate gradient relaxation, and the solid-state nudged-elastic band methods, we predict that AFM B 2 FeRh becomes unstable at ambient pressure and transforms without a barrier to an AFM(111) orthorhombic (martensitic) ground state below 90 ±10 K . We also consider competing structures, in particular, a tetragonal AFM(100) phase that is not the global ground state, as proposed [Phys. Rev. B 94, 180407(R) (2016), 10.1103/PhysRevB.94.180407], but a constrained solution.

Prediction of superconducting iron–bismuth intermetallic compounds at high pressure

DOE PAGES

Amsler, Maximilian; Naghavi, S. Shahab; Wolverton, Chris

2016-12-07

The synthesis of materials in high-pressure experiments has recently attracted increasing attention, especially since the discovery of record breaking superconducting temperatures in the sulfur–hydrogen and other hydrogen-rich systems. Commonly, the initial precursor in a high pressure experiment contains constituent elements that are known to form compounds at ambient conditions, however the discovery of high-pressure phases in systems immiscible under ambient conditions poses an additional materials design challenge. We performed an extensive multi component ab initio structural search in the immiscible Fe–Bi system at high pressure and report on the surprising discovery of two stable compounds at pressures above ≈36 GPa,more » FeBi 2 and FeBi 3. According to our predictions, FeBi 2 is a metal at the border of magnetism with a conventional electron–phonon mediated superconducting transition temperature of T c = 1.3 K at 40 GPa.« less

Two-dimensional tricycle arsenene with a direct band gap.

PubMed

Ma, ShuangYing; Zhou, Pan; Sun, L Z; Zhang, K W

2016-03-28

Based on a comprehensive investigation including ab initio phonon and finite-temperature molecular dynamics calculations, we find that two-dimensional tricycle-shaped arsenene (T-As) is robust and even stable under high temperature. T-As is energetically comparable to previously reported chair-shaped arsenene (C-As) and more stable than stirrup-shaped arsenene (S-As). In contrast to C-As and S-As, the monolayer T-As is a direct band gap semiconductor with an energy gap of 1.377 eV. Our results indicate that the electronic structure of T-As can be effectively modulated by stacking, strain, and patterning, which shows great potential of T-As in future nano-electronics. Moreover, by absorbing H or F atoms on the surface of T-As along a specific direction, nanoribbons with desired edge type and even width can be obtained, which is suitable for the fabrication of nano-devices.

Electron transport in NH3/NO2 sensed buckled antimonene

NASA Astrophysics Data System (ADS)

Srivastava, Anurag; Khan, Md. Shahzad; Ahuja, Rajeev

2018-04-01

The structural and electronic properties of buckled antimonene have been analysed using density functional theory based ab-initio approach. Geometrical parameters in terms of bond length and bond angle are found close to the single ruffle mono-layer of rhombohedral antimony. Inter-frontier orbital analyses suggest localization of lone pair electrons at each atomic centre. Phonon dispersion along with high symmetry point of Brillouin zone does not signify any soft mode. With an electronic band gap of 1.8eV, the quasi-2D nano-surface has been further explored for NH3/NO2 molecules sensing and qualities of interaction between NH3/NO2 gas and antimonene scrutinized in terms of electronic charges transfer. A current-voltage characteristic has also been analysed, using Non Equilibrium Green's function (NEGF), for antimonene, in presence of incoming NH3/NO2 molecules.

Metastable structure of Li13Si4

NASA Astrophysics Data System (ADS)

Gruber, Thomas; Bahmann, Silvia; Kortus, Jens

2016-04-01

The Li13Si4 phase is one out of several crystalline lithium silicide phases, which is a potential electrode material for lithium ion batteries and contains a high theoretical specific capacity. By means of ab initio methods like density functional theory (DFT) many properties such as heat capacity or heat of formation can be calculated. These properties are based on the calculation of phonon frequencies, which contain information about the thermodynamical stability. The current unit cell of "Li13Si4" given in the ICSD database is unstable with respect to DFT calculations. We propose a modified unit cell that is stable in the calculations. The evolutionary algorithm EVO found a structure very similar to the ICSD one with both of them containing metastable lithium positions. Molecular dynamic simulations show a phase transition between both structures where these metastable lithium atoms move. This phase transition is achieved by a very fast one-dimensional lithium diffusion and stabilizes this phase.

Ultrafast electron dynamics reveal the high potential of InSe for hot-carrier optoelectronics

NASA Astrophysics Data System (ADS)

Chen, Zhesheng; Giorgetti, Christine; Sjakste, Jelena; Cabouat, Raphael; Véniard, Valérie; Zhang, Zailan; Taleb-Ibrahimi, Amina; Papalazarou, Evangelos; Marsi, Marino; Shukla, Abhay; Peretti, Jacques; Perfetti, Luca

2018-06-01

We monitor the dynamics of hot carriers in InSe by means of two-photon photoelectron spectroscopy (2PPE). The electrons excited by photons of 3.12 eV experience a manifold relaxation. First, they thermalize to electronic states degenerate with the M ¯ valley. Subsequently, the electronic cooling is dictated by Fröhlich coupling with phonons of small momentum transfer. Ab initio calculations predict cooling rates that are in good agreement with the observed dynamics. We argue that electrons accumulating in states degenerate with the M ¯ valley could travel through a multilayer flake of InSe with a lateral size of 1 μ m . The hot carriers pave a viable route to the realization of below-band-gap photodiodes and Gunn oscillators. Our results indicate that these technologies may find a natural implementation in future devices based on layered chalcogenides.

Stability limits and transformation pathways of α-quartz under high pressure

NASA Astrophysics Data System (ADS)

Hu, Q. Y.; Shu, J.-F.; Yang, W. G.; Park, C.; Chen, M. W.; Fujita, T.; Mao, H.-K.; Sheng, H. W.

2017-03-01

Ubiquitous on Earth, α-quartz plays an important role in modern science and technology. However, despite extensive research in the past, the mechanism of the polymorphic transitions of α-quartz at high pressures remains poorly understood. Here, combining in situ single-crystal x-ray diffraction experiment and advanced ab initio modeling, we report two stability limits and competing transition pathways of α-quartz under high pressure. Under near-equilibrium compression conditions at room temperature, α-quartz transits to a new P 2 /c silica phase via a structural intermediate. If the thermally activated transition is kinetically suppressed, the ultimate stability of α-quartz is controlled by its phonon instability and α-quartz collapses into a different crystalline phase. Our studies reveal that pressure-induced solid-state transformation of α-quartz undergoes a succession of structural stability limits, due to thermodynamic and mechanical catastrophes, and exhibits a hierarchy of transition pathways contingent upon kinetic conditions.

Pair potentials for warm dense matter and their application to x-ray Thomson scattering in aluminum and beryllium.

PubMed

Harbour, L; Dharma-Wardana, M W C; Klug, D D; Lewis, L J

2016-11-01

Ultrafast laser experiments yield increasingly reliable data on warm dense matter, but their interpretation requires theoretical models. We employ an efficient density functional neutral-pseudoatom hypernetted-chain (NPA-HNC) model with accuracy comparable to ab initio simulations and which provides first-principles pseudopotentials and pair potentials for warm-dense matter. It avoids the use of (i) ad hoc core-repulsion models and (ii) "Yukawa screening" and (iii) need not assume ion-electron thermal equilibrium. Computations of the x-ray Thomson scattering (XRTS) spectra of aluminum and beryllium are compared with recent experiments and with density-functional-theory molecular-dynamics (DFT-MD) simulations. The NPA-HNC structure factors, compressibilities, phonons, and conductivities agree closely with DFT-MD results, while Yukawa screening gives misleading results. The analysis of the XRTS data for two of the experiments, using two-temperature quasi-equilibrium models, is supported by calculations of their temperature relaxation times.

Ab initio molecular crystal structures, spectra, and phase diagrams.

PubMed

Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

2014-09-16

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher.

Ab initio theories for light nuclei and neutron stars

NASA Astrophysics Data System (ADS)

Gezerlis, Alexandros

2016-09-01

In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).

Ab initio calculation of the shear viscosity of neon in the liquid and hypercritical state over a wide pressure and temperature range

NASA Astrophysics Data System (ADS)

Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

1992-08-01

The shear viscosity is calculated ab initio for the liquid and hypercritical state, i.e. a previously published potential for Ne 2, obtained from ab initio calculations including electron correlation, is used in classical equilibrium molecular dynamics simulations to obtain the shear viscosity from a Green-Kubo integral. The quality of the results is quite uniform over a large pressure range up to 1000 MPa and a wide temperature range from 26 to 600 K. In most cases the calculated shear viscosity deviates by less than 10% from the experimental value, in general the error being only a few percent.

Ab initio determination of mode coupling in HSSH - The torsional splitting in the first excited S-S stretching state

NASA Technical Reports Server (NTRS)

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

NASA Astrophysics Data System (ADS)

Fujimori, Mitsuki; Sogawa, Haruki; Ota, Shintaro; Karpov, Pavel; Shulga, Sergey; Blume, Yaroslav; Kurita, Noriyuki

2018-01-01

Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigated their specific interactions with FtsZ, using ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) calculations. Based on FMO calculations, we specified the most preferable site of curcumin binding to FtsZ and highlighted the key amino acid residues for curcumin binding at an electronic level. The result will be useful for proposing novel inhibitors against FtsZ based on curcumin derivatives.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

AB INITIO Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions

NASA Astrophysics Data System (ADS)

Goldman, Nir; Fried, Laurence E.; Mundy, Christopher J.; Kuo, I.-F. William; Curioni, Alessandro; Reed, Evan J.

2007-12-01

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

One Size Fits All? Learning Conditions and Working Memory Capacity in "Ab Initio" Language Development

ERIC Educational Resources Information Center

Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.

2016-01-01

The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…

Ab initio theory of noble gas atoms in bcc transition metals

DOE PAGES

Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; ...

2018-01-01

Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe).

Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

ERIC Educational Resources Information Center

Halpern, Arthur M.

2011-01-01

A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

Infrared Emission Spectrum of the Hydroxyl Radical: A Novel Experiment in Molecular Spectroscopy.

ERIC Educational Resources Information Center

Henderson, Giles; And Others

1982-01-01

Describes an experiment in which parameters from an "ab-initio" potential are used to calculate vibrational-rotational energy levels and construct a "stick spectrum" for the overtone emission of the hydroxyl radical. Provides background information on ab-initio spectrum, experimental procedures, and analysis of data. (Author/JN)

Vibrational modes in thymine molecule from an ab initio MO calculation

NASA Astrophysics Data System (ADS)

Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ueda, Toyotoshi; Ushizawa, Koichi; Ito, Gen; Kumakura, Akiko; Tsuboi, Masamichi

1997-03-01

Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

NSSEFF COMPUTATIONAL AND THEORETICAL DESIGN OF PHOTO AND MECHANORESPONSIVE MOLECULAR DEVICES

DTIC Science & Technology

2016-11-10

R. McGibbon, F. Liu, V.S. Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014...Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014). New discoveries, inventions, or patent

Ab initio calculations for industrial materials engineering: successes and challenges.

PubMed

Wimmer, Erich; Najafabadi, Reza; Young, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James; Chambers, James J; Niimi, Hiroaki; Shaw, Judy B; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul

2010-09-29

Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO(2) junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.

Diffusion in liquid Germanium using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

1996-03-01

We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

2002-01-01

The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

Ab initio and empirical energy landscapes of (MgF2)n clusters (n = 3, 4).

PubMed

Neelamraju, S; Schön, J C; Doll, K; Jansen, M

2012-01-21

We explore the energy landscape of (MgF(2))(3) on both the empirical and ab initio level using the threshold algorithm. In order to determine the energy landscape and the dynamics of the trimer we investigate not only the stable isomers but also the barriers separating these isomers. Furthermore, we study the probability flows in order to estimate the stability of all the isomers found. We find that there is reasonable qualitative agreement between the ab initio and empirical potential, and important features such as sub-basins and energetic barriers follow similar trends. However, we observe that the energies are systematically different for the less compact clusters, when comparing empirical and ab initio energies. Since the underlying motivation of this work is to identify the possible clusters present in the gas phase during a low-temperature atom beam deposition synthesis of MgF(2), we employ the same procedure to additionally investigate the energy landscape of the tetramer. For this case, however, we use only the empirical potential.

Lattice modes of hexamethylbenzene studied by inelastic neutron scattering

NASA Astrophysics Data System (ADS)

Stride, J. A.; Adams, J. M.; Johnson, M. R.

2005-10-01

The combination of inelastic neutron scattering and detailed ab initio calculations has been used to arrive at accurate assignments of the low energy lattice mode region of hexamethylbenzene (HMB) across the low temperature first order phase transition at 117.5 K. This was also extended well into the mid-infrared spectral region and a good agreement was found between observed and calculated frequencies, which were also confirmed with isotopically substituted d-HMB. At low temperature, the lattice region is dominated by the methyl group torsions around 15 and 20 meV, which soften dramatically on passing into the higher temperature phase. The lowest energy methyl torsion corresponds to a coherent gear wheel motion, observed here for the first time and predicted in previous numerical studies of HMB. The three acoustic phonons lie to lower energy, centered around 6-7 meV, whilst the three optic phonons are very close in energy to the lowest methyl torsions. Other assignments are found to be in accord with literature values and so an unambiguous assignment of all spectral modes has been obtained for the first time. We conclude that due to the behaviour of the lattice modes either side of the phase transition, its nature is predominantly that of a thermally activated dynamic order-disorder transition.

Lattice-mediated magnetic order melting in TbMnO3

NASA Astrophysics Data System (ADS)

Baldini, Edoardo; Kubacka, Teresa; Mallett, Benjamin P. P.; Ma, Chao; Koohpayeh, Seyed M.; Zhu, Yimei; Bernhard, Christian; Johnson, Steven L.; Carbone, Fabrizio

2018-03-01

Recent ultrafast magnetic-sensitive measurements [Johnson et al., Phys. Rev. B 92, 184429 (2015), 10.1103/PhysRevB.92.184429; Bothschafter et al., Phys. Rev. B 96, 184414 (2017), 10.1103/PhysRevB.96.184414] have revealed a delayed melting of the long-range cycloid spin order in TbMnO3 following photoexcitation across the fundamental Mott-Hubbard gap. The microscopic mechanism behind this slow transfer of energy from the photoexcited carriers to the spin degrees of freedom is still elusive and not understood. Here, we address this problem by combining spectroscopic ellipsometry, ultrafast broadband optical spectroscopy, and ab initio calculations. Upon photoexcitation, we observe the emergence of a complex collective response, which is due to high-energy coherent optical phonons coupled to the out-of-equilibrium charge density. This response precedes the magnetic order melting and is interpreted as the fingerprint of the formation of anti-Jahn-Teller polarons. We propose that the charge localization in a long-lived self-trapped state hinders the emission of magnons and other spin-flip mechanisms, causing the energy transfer from the charge to the spin system to be mediated by the reorganization of the lattice. Furthermore, we provide evidence for the coherent excitation of a phonon mode associated with the ferroelectric phase transition.

Ab initio study of phonon dispersion and thermodynamic properties of pure and doped pyrites

NASA Astrophysics Data System (ADS)

Musari, Abolore A.; Joubert, Daniel P.; Olowofela, Joseph A.; Akinwale, Adio T.; Adebayo, Gboyega A.

2017-12-01

Pyrites (FeS2) are solid minerals that are found abundantly in Nigeria and are easy to prepare in laboratories. In this work, FeS2 is studied extensively in its pure state as well as when iron is substitutionally doped with zinc and calcium at concentrations of 0, 0.25, 0.5, 0.75 and 1. Using density functional theory, the eectronic, dynamic and thermodynamic properties were calculated. The results revealed that the lattice parameters and bulk modulus increases with increasing concentration and the obtained values are in agreement with available experimental and theoretical values. Though pyrite, when doped with zinc, obeys Vegard's law, doping with calcium revealed pronounced deviation from this law. The calculated band structures showed that FeS2 has an indirect band gap whose size decreases after introducing zinc while doping with calcium increases the band gap. The phonon dispersion of the end members FeS2 and ZnS2 indicate that the systems are dynamically stable while CaS2 is dynamically unstate. Also, the thermodynamic properties of the pure and doped pyrites were calculated and the ranges of temperature at which the lattice and electronic degrees of freedom contribute to the specific heat capacity are presented.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Ab Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vibrational States and Intramolecular Mode Coupling of N-Methylacetamide

NASA Technical Reports Server (NTRS)

Gregurick, Susan K.; Chaban, Galina M.; Gerber, R. Benny; Kwak, Dochou (Technical Monitor)

2001-01-01

The second-order Moller-Plesset ab initio electronic structure method is used to compute points for the anharmonic mode-coupled potential energy surface of N-methylacetamide (NMA) in the trans(sub ct) configuration, including all degrees of freedom. The vibrational states and the spectroscopy are directly computed from this potential surface using the Correlation Corrected Vibrational Self-Consistent Field (CC-VSCF) method. The results are compared with CC-VSCF calculations using both the standard and improved empirical Amber-like force fields and available low temperature experimental matrix data. Analysis of our calculated spectroscopic results show that: (1) The excellent agreement between the ab initio CC-VSCF calculated frequencies and the experimental data suggest that the computed anharmonic potentials for N-methylacetamide are of a very high quality; (2) For most transitions, the vibrational frequencies obtained from the ab initio CC-VSCF method are superior to those obtained using the empirical CC-VSCF methods, when compared with experimental data. However, the improved empirical force field yields better agreement with the experimental frequencies as compared with a standard AMBER-type force field; (3) The empirical force field in particular overestimates anharmonic couplings for the amide-2 mode, the methyl asymmetric bending modes, the out-of-plane methyl bending modes, and the methyl distortions; (4) Disagreement between the ab initio and empirical anharmonic couplings is greater than the disagreement between the frequencies, and thus the anharmonic part of the empirical potential seems to be less accurate than the harmonic contribution;and (5) Both the empirical and ab initio CC-VSCF calculations predict a negligible anharmonic coupling between the amide-1 and other internal modes. The implication of this is that the intramolecular energy flow between the amide-1 and the other internal modes may be smaller than anticipated. These results may have important implications for the anharmonic force fields of peptides, for which N-methylacetamide is a model.

Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands.

PubMed

Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A

2017-02-14

Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16 O 3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV 3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν 3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm -1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

NASA Technical Reports Server (NTRS)

Allen, B. Danette; Alexandrov, Natalia

2016-01-01

Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that contains the system and other systems evolves with the CAS as well. The effects of the emerging adaptation and co-evolution are difficult to capture with only combined mathematical and computational experimentation. Therefore, an ab initio flight simulation environment must accommodate individual vehicles, groups of self-organizing vehicles, and large-scale infrastructure behavior. Inspired by Massively Multiplayer Online Role Playing Games (MMORPG) and Serious Gaming, the proposed ab initio simulation environment is similar to online gaming environments in which player participants interact with each other, affect their environment, and expect the simulation to persist and change regardless of any individual player's active participation.

Time-Domain Ab Initio Analysis of Excitation Dynamics in a Quantum Dot/Polymer Hybrid: Atomistic Description Rationalizes Experiment.

PubMed

Long, Run; Prezhdo, Oleg V

2015-07-08

Hybrid organic/inorganic polymer/quantum dot (QD) solar cells are an attractive alternative to the traditional cells. The original, simple models postulate that one-dimensional polymers have continuous energy levels, while zero-dimensional QDs exhibit atom-like electronic structure. A realistic, atomistic viewpoint provides an alternative description. Electronic states in polymers are molecule-like: finite in size and discrete in energy. QDs are composed of many atoms and have high, bulk-like densities of states. We employ ab initio time-domain simulation to model the experimentally observed ultrafast photoinduced dynamics in a QD/polymer hybrid and show that an atomistic description is essential for understanding the time-resolved experimental data. Both electron and hole transfers across the interface exhibit subpicosecond time scales. The interfacial processes are fast due to strong electronic donor-acceptor, as evidenced by the densities of the photoexcited states which are delocalized between the donor and the acceptor. The nonadiabatic charge-phonon coupling is also strong, especially in the polymer, resulting in rapid energy losses. The electron transfer from the polymer is notably faster than the hole transfer from the QD, due to a significantly higher density of acceptor states. The stronger molecule-like electronic and charge-phonon coupling in the polymer rationalizes why the electron-hole recombination inside the polymer is several orders of magnitude faster than in the QD. As a result, experiments exhibit multiple transfer times for the long-lived hole inside the QD, ranging from subpicoseconds to nanoseconds. In contrast, transfer of the short-lived electron inside the polymer does not occur beyond the first picosecond. The energy lost by the hole on its transit into the polymer is accommodated by polymer's high-frequency vibrations. The energy lost by the electron injected into the QD is accommodated primarily by much lower-frequency collective and QD modes. The electron dynamics is exponential, whereas evolution of the injected hole through the low density manifold of states of the polymer is highly nonexponential. The time scale of the electron-hole recombination at the interface is intermediate between those in pristine polymer and QD and is closer to that in the polymer. The detailed atomistic insights into the photoinduced charge and energy dynamics at the polymer/QD interface provide valuable guidelines for optimization of solar light harvesting and photovoltaic efficiency in modern nanoscale materials.

Ab initio and shell model studies of structural, thermoelastic and vibrational properties of SnO2 under pressure

NASA Astrophysics Data System (ADS)

Casali, R. A.; Lasave, J.; Caravaca, M. A.; Koval, S.; Ponce, C. A.; Migoni, R. L.

2013-04-01

The pressure dependences of the structural, thermoelastic and vibrational properties of SnO2 in its rutile phase are studied, as well as the pressure-induced transition to a CaCl2-type phase. These studies have been performed by means of ab initio (AI) density functional theory calculations using the localized basis code SIESTA. The results are employed to develop a shell model (SM) for application in future studies of nanostructured SnO2. A good agreement of the SM results for the pressure dependences of the above properties with the ones obtained from present and previous AI calculations as well as from experiments is achieved. The transition is characterized by a rotation of the Sn-centered oxygen octahedra around the tetragonal axis through the Sn. This rotation breaks the tetragonal symmetry of the lattice and an orthorhombic distortion appears above the critical pressure Pc. A zone-center phonon of B1g symmetry in the rutile phase involves such rotation and softens on approaching Pc. It becomes an Ag mode which stabilizes with increasing pressure in the CaCl2 phase. This behavior, together with the softening of the shear modulus (C11-C12)/2 related to the orthorhombic distortion, allows a precise determination of a value for Pc. An additional determination is provided by the splitting of the basal plane lattice parameters. Both the AI and the experimentally observed softening of the B1g mode are incomplete, indicating a small discontinuity at the transition. However, all results show continuous changes in volume and lattice parameters, indicating a second-order transition. All these results indicate that there should be sufficient confidence for the future employment of the shell model.

Vacuum Ultraviolet Laser Probe of Chemical Dynamics of Aerospace Relevance

DTIC Science & Technology

2012-09-12

carbide cation”, J. Phys. Chem. A (invited), 113, 4242 (2009). 5. Kai-Chung Lau , Yih-Chung Chang, Chow-Sheng Lam , and C. Y. Ng, “High-level ab...Chem. A (invited), 113, 14321 (2009). 6. Kai-Chung Lau , Yih-Chung Chang, Chow-Sheng Lam , and C. Y. Ng, “High-level ab initio predictions of the...VI. Selected scientific findings 1. Kai-Chung Lau , Yih-Chung Chang, Xiaoyu Shi, and C. Y. Ng, “High-level ab initio predictions of the ionization

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Einstein coefficients and oscillator strengths for low lying state of CO molecules

NASA Astrophysics Data System (ADS)

Swer, S.; Syiemiong, A.; Ram, M.; Jha, A. K.; Saxena, A.

2018-04-01

Einstein Coefficients and Oscillator Strengths for different state of CO molecule have been calculated using LEROY'S LEVEL program and MOLCAS ab initio code. Using the wave function derived from Morse potential and transition dipole moment obtained from ab initio calculation, The potential energy functions were computed for these states using the spectroscopic constants. The Morse potential of these states and electronic transition dipole moment of the transition calculated in a recent ab initio study have been used in LEVEL program to produce transition dipole matrix element for a large number of bands. Einstein Coefficients have also been used to compute the radiative lifetimes of several vibrational levels and the calculated values are compared with other theoretical results and experimental values.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.

PubMed

Zeng, Lu; Kortschak, R Daniel; Raison, Joy M; Bertozzi, Terry; Adelson, David L

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

PubMed

Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

PubMed Central

Zeng, Lu; Kortschak, R. Daniel; Raison, Joy M.

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. PMID:29538441

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Strategic L2 Lexical Innovation: Case Study of a University-Level Ab Initio Learner of German.

ERIC Educational Resources Information Center

Ridley, Jennifer; Singleton, David

1995-01-01

This article presents a case study of one English-speaking ab initio learner of German. It found that in target language production tasks performed over a two-year period, the subject exhibited a particular tendency toward lexical innovation as a strategy to cope with the lack of target language lexical knowledge. (38 references) (MDM)

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Binbin; Liu, Lihong; Cui, Ganglong

2015-11-21

In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as themore » final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.« less

Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

NASA Astrophysics Data System (ADS)

Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

Common lines modeling for reference free Ab-initio reconstruction in cryo-EM.

PubMed

Greenberg, Ido; Shkolnisky, Yoel

2017-11-01

We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab initio models with resolutions of 20Å or better, even from class averages consisting of as few as three raw images per class. Copyright © 2017 Elsevier Inc. All rights reserved.

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

PubMed

Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

2016-10-26

For CO and N 2 on Mg 2+ sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.

Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2016-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2015-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

PubMed

Hagiwara, Yohsuke; Tateno, Masaru

2010-10-20

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

Ab initio NMR parameters of BrCH3 and ICH3 with relativistic and vibrational corrections

NASA Astrophysics Data System (ADS)

Uhlíková, Tereza; Urban, Štěpán

2018-05-01

This study is focused on two effects identified when NMR parameters are calculated based on first principles. These effects are 1. vibrational correction of properties when using ab initio optimized equilibrium geometry; 2. relativistic effects and limits of using the Flygare equation. These effects have been investigated and determined for nuclear spin-rotation constants and nuclear magnetic shieldings for the CH3Br and CH3I molecules. The most significant result is the difference between chemical shieldings determined based on the ab initio relativistic four-component Dirac-Coulomb Hamiltonian and chemical shieldings calculated using experimental values and the Flygare equation. This difference is approximately 320 ppm and 1290 ppm for 79Br and 127I in the CH3X molecule, respectively.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

PubMed

Li, Yumin; Francisco, Joseph S

2005-08-31

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.

PubMed

Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

2015-04-21

Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yimin, E-mail: yimin.wang@emory.edu; Bowman, Joel M., E-mail: jmbowma@emory.edu; Kamarchik, Eugene, E-mail: eugene.kamarchik@gmail.com

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na{sup +}H{sub 2}O, F{sup −}H{sub 2}O, and Cl{sup −}H{sub 2}O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H{sub 2}O potentials are permutationally invariant fits to roughly 20 000more » coupled cluster CCSD(T) energies (awCVTZ basis for Na{sup +} and aVTZ basis for Cl{sup −} and F{sup −}), over a large range of distances and H{sub 2}O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.« less

Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

PubMed

Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

2016-12-15

MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

PubMed

Simkovic, Felix; Thomas, Jens M H; Keegan, Ronan M; Winn, Martyn D; Mayans, Olga; Rigden, Daniel J

2016-07-01

For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds

PubMed Central

Simkovic, Felix; Thomas, Jens M. H.; Keegan, Ronan M.; Winn, Martyn D.; Mayans, Olga; Rigden, Daniel J.

2016-01-01

For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (‘decoys’), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing. PMID:27437113

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

NASA Astrophysics Data System (ADS)

Raff, L. M.; Malshe, M.; Hagan, M.; Doughan, D. I.; Rockley, M. G.; Komanduri, R.

2005-02-01

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.

Decohesion models informed by first-principles calculations: The ab initio tensile test

NASA Astrophysics Data System (ADS)

Enrique, Raúl A.; Van der Ven, Anton

2017-10-01

Extreme deformation and homogeneous fracture can be readily studied via ab initio methods by subjecting crystals to numerical "tensile tests", where the energy of locally stable crystal configurations corresponding to elongated and fractured states are evaluated by means of density functional method calculations. The information obtained can then be used to construct traction curves of cohesive zone models in order to address fracture at the macroscopic scale. In this work, we perform an in depth analysis of traction curves and how ab initio calculations must be interpreted to rigorously parameterize an atomic scale cohesive zone model, using crystalline Ag as an example. Our analysis of traction curves reveal the existence of two qualitatively distinct decohesion criteria: (i) an energy criterion whereby the released elastic energy equals the energy cost of creating two new surfaces and (ii) an instability criterion that occurs at a higher and size independent stress than that of the energy criterion. We find that increasing the size of the simulation cell renders parts of the traction curve inaccessible to ab initio calculations involving the uniform decohesion of the crystal. We also find that the separation distance below which a crack heals is not a material parameter as has been proposed in the past. Finally, we show that a large energy barrier separates the uniformly stressed crystal from the decohered crystal, resolving a paradox predicted by a scaling law based on the energy criterion that implies that large crystals will decohere under vanishingly small stresses. This work clarifies confusion in the literature as to how a cohesive zone model is to be parameterized with ab initio "tensile tests" in the presence of internal relaxations.

Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2014-04-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.

Towards ab initio Calculations with the Dynamical Vertex Approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

2018-04-01

While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

Crossover of cation partitioning in olivines: a combination of ab initio and Monte Carlo study

NASA Astrophysics Data System (ADS)

Chatterjee, Swastika; Bhattacharyya, Sirshendu; Sengupta, Surajit; Saha-Dasgupta, Tanusri

2011-04-01

We report studies based on a combination of ab initio electronic structure and Monte Carlo (MC) technique on the problem of cation partitioning among inequivalent octahedral sites, M1 and M2 in mixed olivines containing Mg2+ and Fe2+ ions. Our MC scheme uses interactions derived out of ab initio, density functional calculations carried out on measured crystal structure data. Our results show that there is no reversal of the preference of Fe for M1 over M2 as a function of temperature. Our findings do not agree with the experimental findings of Redfern et al. (Phys Chem Miner 27:630-637, 2000), but are in agreement with those of Heinemann et al. (Eur J Mineral 18:673-689, 2006) and Morozov et al. (Eur J Mineral 17:495-500, 2005).

Determination of NMR chemical shifts for cholesterol crystals from first-principles

NASA Astrophysics Data System (ADS)

Kucukbenli, Emine; de Gironcoli, Stefano

2011-03-01

Solid State Nuclear Magnetic Resonance (NMR) is a powerful tool in crystallography when combined with theoretical predictions. So far, empirical calculations of spectra have been employed for an unambiguous identification. However, many complex systems are outside the scope of these methods. Our implementation of ultrasoft and projector augmented wave pseudopotentials within ab initio gauge including projector augmented plane wave (GIPAW) method in Quantum Espresso simulation package allows affordable calculations of NMR spectra for systems of thousands of electrons. We report here the first ab initio determination of NMR spectra for several crystal structures of cholesterol. Cholesterol crystals, the main component of human gallstones, are of interest to medical research as their structural properties can shed light on the pathologies of gallbladder. With our application we show that ab initio calculations can be employed to aid NMR crystallography.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

2018-05-01

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

Ab initio structures and polarizabilities of sodium clusters

NASA Astrophysics Data System (ADS)

Kronik, Leeor; Vasiliev, Igor; Jain, Manish; Chelikowsky, James R.

2001-09-01

We present quantitative ab initio calculations for Na cluster structures and polarizabilities, for all cluster sizes up to 20 atoms. Our calculations are performed by combining an ab initio core-corrected pseudopotential and a gradient-corrected density functional within a real space approach. We find the cluster bonding to be very floppy and catalog a host of low-energy quasi-degenerate isomers for all second-decade clusters. The existence of these isomers results in a band of polarizability values for each cluster size even at zero temperature. This eliminates any finer structure in the polarizability curve. We further show that the experimental polarizability values are consistently underestimated by calculations at zero temperature. By computing the effects of structure expansion and distortion due to a finite temperature we arrive at a quantitative agreement between theory and experiment.

Ab initio molecular orbital studies of the positive muon and muonium in 4-arylmethyleneamino-TEMPO derivatives

NASA Astrophysics Data System (ADS)

Briere, T. M.; Jeong, J.; Das, T. P.; Ohira, S.; Nagamine, K.

2000-08-01

The muon and muonium bonding sites of the 4-arylmethyleneamino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical crystals with aryl groups consisting of biphenyl and 4-pyridyl were studied via ab initio Hartree-Fock theory. The hyperfine fields, including both intramolecular and intermolecular interactions, were calculated at the sites of interest and compared to zero field μSR results.

Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…

Atomistic and Ab Initio Calculations or Ternary II-IV-V2 Semiconductors

DTIC Science & Technology

1999-12-07

consisting of two- and three-body terms is developed reproducing crystal lattice constants, elastic and dielectric constants very well. The calculated...the lattice . This difference may well be due to defect-induced lattice distortion which plays a key role in stabilizing the hole states in the... lattice . 15. SUBJECT TERMS Chalcopyrites, Defects, Atomistic and AB Initio Calculations 16. SECURITY CLASSIFICATION OF: a. REPORT u b. ABSTRACT U

An ab initio mechanism for efficient population of triplet states in cytotoxic sulfur substituted DNA bases: the case of 6-thioguanine.

PubMed

Martínez-Fernández, Lara; González, Leticia; Corral, Inés

2012-02-18

The deactivation mechanism of the cytotoxic 6-thioguanine, the 6-sulfur-substituted analogue of the canonical DNA base, is unveiled by ab initio calculations. Oxygen-by-sulfur substitution leads to efficient population of triplet states-the first step for generating singlet oxygen-which is responsible for its cytotoxicity. This journal is © The Royal Society of Chemistry 2012

Ab initio optical potentials and nucleon scattering on medium mass nuclei

NASA Astrophysics Data System (ADS)

Idini, A.; Barbieri, C.; Navrátil, P.

2018-03-01

We show first results for the elastic scattering of neutrons off oxygen and calcium isotopes obtained from ab initio optical potentials. The potential is derived using self-consistent Green’s function theory (SCGF) with the saturating chiral interaction NNLOsat. Calculations are compared to available scattering data and show that it is possible to reproduce low energy scattering observables in medium mass nuclei from first principles.

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions,

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions.

State of the art for ab initio vs empirical potentials for HeH+ (2e-), BeH+ (4e-), BeH (5e-), Li2 (6e-) and BH (6e-)

NASA Astrophysics Data System (ADS)

Dattani, Nike

For large internuclear distances, the potential energy between two atoms is known analytically, based on constants that are calculated from atomic ab initio rather than molecular ab initio. This analytic form can be built into models for molecular potentials that are fitted to spectroscopic data. Such empirical potentials constitute the most accurate molecular potentials known. For HeH+, and BeH+, the long-range form of the potential is based only on the polarizabilities for He and H respectively, for which we have included up to 4th order QED corrections. For BeH, the best ab initio potential matches all but one observed vibrational spacing to < 1 cm- accuracy, and for Li2 the discrepancy in the spacings is < 0.08 cm-1 for all vibrational levels. But experimental methods such as photoassociation require the absolute energies, not spacings, and these are still several in several cm-1 disagreement. So empirical potentials are still the only reliable way to predict energies for few-electron systems. We also give predictions for various unobserved ''halo nucleonic molecules'' containing the ''halo'' isotopes: 6,8He, 11Li, 11,14Be and 8 , 17 , 19B.

Ab Initio Crystal Field for Lanthanides.

PubMed

Ungur, Liviu; Chibotaru, Liviu F

2017-03-13

An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc) 2 ] - (Pc=phthalocyanine) and Dy 4 K 2 ([Dy 4 K 2 O(OtBu) 12 ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H 3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

PubMed

Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

2018-06-07

The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

A Complete and Accurate Ab Initio Repeat Finding Algorithm.

PubMed

Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

2016-03-01

It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy.

Sulfamerazine: Understanding the Influence of Slip Planes in the Polymorphic Phase Transformation through X-Ray Crystallographic Studies and ab Initio Lattice Dynamics.

PubMed

Pallipurath, Anuradha R; Skelton, Jonathan M; Warren, Mark R; Kamali, Naghmeh; McArdle, Patrick; Erxleben, Andrea

2015-10-05

Understanding the polymorphism exhibited by organic active-pharmaceutical ingredients (APIs), in particular the relationships between crystal structure and the thermodynamics of polymorph stability, is vital for the production of more stable drugs and better therapeutics, and for the economics of the pharmaceutical industry in general. In this article, we report a detailed study of the structure-property relationships among the polymorphs of the model API, Sulfamerazine. Detailed experimental characterization using synchrotron radiation is complemented by computational modeling of the lattice dynamics and mechanical properties, in order to study the origin of differences in millability and to investigate the thermodynamics of the phase equilibria. Good agreement is observed between the simulated phonon spectra and mid-infrared and Raman spectra. The presence of slip planes, which are found to give rise to low-frequency lattice vibrations, explains the higher millability of Form I compared to Form II. Energy/volume curves for the three polymorphs, together with the temperature dependence of the thermodynamic free energy computed from the phonon frequencies, explains why Form II converts to Form I at high temperature, whereas Form III is a rare polymorph that is difficult to isolate. The combined experimental and theoretical approach employed here should be generally applicable to the study of other systems that exhibit polymorphism.

Strain mapping in single-layer two-dimensional crystals via Raman activity

NASA Astrophysics Data System (ADS)

Yagmurcukardes, M.; Bacaksiz, C.; Unsal, E.; Akbali, B.; Senger, R. T.; Sahin, H.

2018-03-01

By performing density functional theory-based ab initio calculations, Raman-active phonon modes of single-layer two-dimensional (2D) materials and the effect of in-plane biaxial strain on the peak frequencies and corresponding activities of the Raman-active modes are calculated. Our findings confirm the Raman spectrum of the unstrained 2D crystals and provide expected variations in the Raman-active modes of the crystals under in-plane biaxial strain. The results are summarized as follows: (i) frequencies of the phonon modes soften (harden) under applied tensile (compressive) strains; (ii) the response of the Raman activities to applied strain for the in-plane and out-of-plane vibrational modes have opposite trends, thus, the built-in strains in the materials can be monitored by tracking the relative activities of those modes; (iii) in particular, the A peak in single-layer Si and Ge disappears under a critical tensile strain; (iv) especially in mono- and diatomic single layers, the shift of the peak frequencies is a stronger indication of the strain rather than the change in Raman activities; (v) Raman-active modes of single-layer ReX2 (X =S , Se) are almost irresponsive to the applied strain. Strain-induced modifications in the Raman spectrum of 2D materials in terms of the peak positions and the relative Raman activities of the modes could be a convenient tool for characterization.

Ab initio calculations of ideal strength and lattice instability in W-Ta and W-Re alloys

NASA Astrophysics Data System (ADS)

Yang, Chaoming; Qi, Liang

2018-01-01

An important theoretical criterion to evaluate the ductility of metals with a body-centered cubic (bcc) lattice is the mechanical failure mode of their perfect crystals under tension along <;100 >; directions. When the tensile stress reaches the ideal tensile strength, the pure W crystal fails by a cleavage fracture along the {100 } plane so that it is intrinsically brittle. To discover the strategy to improve its ductility, we performed density functional theory and density functional perturbation theory calculations to study the ideal tensile strength and the lattice instability under <100 > tension for both W-Ta and W-Re alloys. Anisotropic linear elastic fracture mechanics (LEFM) theory and Rice's criterion were also applied to analyze the mechanical instability at the crack tip under <100 > tension based on the competition between cleavage propagation and dislocation emission. The results show that the intrinsic ductility can be achieved in both W-Ta and W-Re, however, by different mechanisms. Even though W-Ta alloys with low Ta concentrations are still intrinsically brittle, the intrinsic ductility of W-Ta alloys with high Ta concentrations is promoted by elastic shear instability before the cleavage failure. The intrinsic ductility of W-Re alloys is produced by unstable transverse phonon waves before the cleavage failure, and the corresponding phonon mode is related to the generation of 1/2 <111 > {2 ¯11 } dislocation in bcc crystals. The ideal tensile calculations, phonon analyses, and anisotropic LEFM examinations are mutually consistent in the evaluation of intrinsic ductility. These results bring us physical insights on the ductility-brittle mechanisms of W alloys under extreme stress conditions.

Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

NASA Astrophysics Data System (ADS)

Zaharieva, Roussislava; Hanagud, Sathya

2009-06-01

Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

Interplay between plasmon and single-particle excitations in a metal nanocluster

DOE PAGES

Ma, Jie; Wang, Zhi; Wang, Lin-Wang

2015-12-17

Plasmon-generated hot carriers are used in photovoltaic or photochemical applications. However, the interplays between the plasmon and single-particle excitations in nanosystems have not been theoretically addressed using ab initio methods. Here we show such interplays in a Ag 55 nanocluster using real-time time-dependent density functional theory simulations. We find that the disappearance of the zero-frequency peak in the Fourier transform of the band-to-band transition coefficient is a hallmark of the plasmon. We show the importance of the d-states for hot-carrier generations. If the single-particle d-to-s excitations are resonant to the plasmon frequency, the majority of the plasmon energy will bemore » converted into hot carriers, and the overall hot-carrier generation is enhanced by the plasmon; if such resonance does not exist, we observe an intriguing Rabi oscillation between the plasmon and hot carriers. Phonons play a minor role in plasmonic dynamics in such small systems. Ultimately, this study provides guidance on improving plasmonic applications.« less

Charge and energy transports via poly-phenylacetylene based dendrimers

NASA Astrophysics Data System (ADS)

Shin, Yongwoo; Li, Minghai; Lin, Xi

2010-03-01

Poly-Phenylacetylene (PPA) is widely used in photoconductivity, photoluminescence, and light harvesting applications. In this work, we investigate the charge and exciton transport energetics and mechanisms in the PPA-based dendrimers using our recently developed adapted Su-Schrieffer-Heeger (SSH) model Hamiltonians and ab initio Hartree-Fock (HF) calculations. We found both doping and photo-excitation lead to the formation of optical phonon dressed pi electron states, namely the self-localized polarons, in the energy gap. Independent from their origins, these polarons can be self-trapped at multiple lattice locations along the PPA chain, and migrate from one to the next with an activation barrier of ˜0.006 eV, slightly higher than the corresponding barrier found in trans-polyacetylene. The PPA-based dendrimers can be constructed via the meta-positions of phenyl rings. In this case, we found the dendrimer junctions form attractive potential wells for both polarons and excitons, and the width and height of these junction potential wells can be controlled by the geometry of the dendrimers.

Towards room-temperature superconductivity in low-dimensional C60 nanoarrays: An ab initio study

NASA Astrophysics Data System (ADS)

Erbahar, Dogan; Liu, Dan; Berber, Savas; Tománek, David

2018-04-01

We propose to raise the critical temperature Tc for superconductivity in doped C60 molecular crystals by increasing the electronic density of states at the Fermi level N (EF) and thus the electron-phonon coupling constant in low-dimensional C60 nanoarrays. We consider both electron and hole dopings and present numerical results for N (EF) , which increases with the decreasing bandwidth of the partly filled hu- and t1 u-derived frontier bands with the decreasing coordination number of C60. Whereas a significant increase in N (EF) occurs in two-dimensional (2D) arrays of doped C60 intercalated in-between graphene layers, we propose that the highest-Tc values approaching room temperature may occur in bundles of nanotubes filled by one-dimensional (1D) arrays of externally doped C60 or La @C60 or in diluted three-dimensional (3D) crystals where quasi-1D arrangements of C60 form percolation paths.

Learning from data to design functional materials without inversion symmetry

PubMed Central

Balachandran, Prasanna V.; Young, Joshua; Lookman, Turab; Rondinelli, James M.

2017-01-01

Accelerating the search for functional materials is a challenging problem. Here we develop an informatics-guided ab initio approach to accelerate the design and discovery of noncentrosymmetric materials. The workflow integrates group theory, informatics and density-functional theory to uncover design guidelines for predicting noncentrosymmetric compounds, which we apply to layered Ruddlesden-Popper oxides. Group theory identifies how configurations of oxygen octahedral rotation patterns, ordered cation arrangements and their interplay break inversion symmetry, while informatics tools learn from available data to select candidate compositions that fulfil the group-theoretical postulates. Our key outcome is the identification of 242 compositions after screening ∼3,200 that show potential for noncentrosymmetric structures, a 25-fold increase in the projected number of known noncentrosymmetric Ruddlesden-Popper oxides. We validate our predictions for 19 compounds using phonon calculations, among which 17 have noncentrosymmetric ground states including two potential multiferroics. Our approach enables rational design of materials with targeted crystal symmetries and functionalities. PMID:28211456

JDFTx: Software for joint density-functional theory

DOE PAGES

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.; ...

2017-11-14

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

Resonant-Raman Intensities of N-layer Transition Metal Dichalcogenides from First Principles

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Froehlicher, Guillaume; Lorchat, Ettienne; Fernique, François; Molina-Sánchez, Alejandro; Berciaud, Stéphane; Wirtz, Ludger

Transition metal dichalcogenides (TMDs) have interesting optical and electronic properties that make them good candidates for nano-engineering applications. Raman spectroscopy provides information about the vibrational modes and optical spectrum at the same time: when the laser energy is close to an electronic transition, the intensity is increased due to resonance. We investigate these effects combining different ab initio methods: we obtain ground-state and vibrational properties from density functional theory and the optical absorption spectrum using GW corrections and the Bethe-Salpeter equation to account for the excitonic effects which are known to play an important role in TMDs. Using a quasi-static finite differences approach, we calculate the dielectric susceptibility for different light polarizations and different phonon modes in order to determine the Raman tensor of TMDs, in particular of multi-layer and bulk MoTe2. We explain recent experimental results for the splitting of high-frequency modes and deviations from the non-resonant Raman model. We also give a brief outlook on possible improvements of the methodology.

Properties at the interface of graphene and Ti2C MXene

NASA Astrophysics Data System (ADS)

Paul, Pallavi; Chakraborty, Poulami; Das, Tilak; Nafday, Dhani; Saha-Dasgupta, Tanusri

2017-07-01

Employing ab initio calculations, we characterize the interfaces formed between graphene, a much discussed two-dimensional material, and MXene, another two-dimensional material of recent interest. Our study considering the specific case of Ti2C , a member of the MXene family, shows the formation of chemical bonds between Ti atoms and C atoms of graphene. This results in reconstruction of the electronic structure at the interface, making the interface metallic, though graphene is a zero-gap semiconductor and Ti2C is an antiferromagnetic insulator in their respective native form. The optical and phonon properties of the interfaces are found to be strongly dependent on the stacking arrangement, driven by the nature of chemical-bond formation. Consideration of O-passivated Ti2C is found to weaken the interaction between graphene and Ti2C substantially, making it a physisorption process rather than chemisorption in the unpassivated situation. Our first-principles study is expected to motivate future experimental investigation.

JDFTx: Software for joint density-functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

Three-dimensional carbon allotropes comprising phenyl rings and acetylenic chains in sp+ sp 2 hybrid networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jian -Tao; Chen, Changfeng; Li, Han -Dong

Here, we here identify by ab initio calculations a new type of three-dimensional (3D) carbon allotropes that consist of phenyl rings connected by linear acetylenic chains in sp+ sp 2 bonding networks. These structures are constructed by inserting acetylenic or diacetylenic bonds into an all sp 2-hybridized rhombohedral polybenzene lattice, and the resulting 3D phenylacetylene and phenyldiacetylene nets comprise a 12-atom and 18-atom rhombohedral primitive unit cells R - 3m symmetry, which are characterized as the 3D chiral crystalline modification of 2D graphyne and graphdiyne, respectively. Simulated phonon spectra reveal that these structures are dynamically stable. Electronic band calculations indicatemore » that phenylacetylene is metallic, while phenyldiacetylene is a semiconductor with an indirect band gap of 0.58 eV. The present results establish a new type of carbon phases and offer insights into their outstanding structural and electronic properties.« less

Selective ultrafast probing of transient hot chemisorbed and precursor states of CO on Ru(0001).

PubMed

Beye, M; Anniyev, T; Coffee, R; Dell'Angela, M; Föhlisch, A; Gladh, J; Katayama, T; Kaya, S; Krupin, O; Møgelhøj, A; Nilsson, A; Nordlund, D; Nørskov, J K; Öberg, H; Ogasawara, H; Pettersson, L G M; Schlotter, W F; Sellberg, J A; Sorgenfrei, F; Turner, J J; Wolf, M; Wurth, W; Oström, H

2013-05-03

We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302 (2013)] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical laser fluence. Ab initio molecular dynamics simulations of CO adsorbed on Ru(0001) were performed at 1500 and 3000 K providing insight into the desorption process.

Beyond a phenomenological description of magnetostriction

DOE PAGES

Reid, A. H.; Shen, X.; Maldonado, P.; ...

2018-01-26

Magnetostriction, the strain induced by a change in magnetization, is a universal effect in magnetic materials. Owing to the difficulty in unraveling its microscopic origin, it has been largely treated phenomenologically. Here in this paper, we show how the source of magnetostriction—the underlying magnetoelastic stress—can be separated in the time domain, opening the door for an atomistic understanding. X-ray and electron diffraction are used to separate the sub-picosecond spin and lattice responses of FePt nanoparticles. Following excitation with a 50-fs laser pulse, time-resolved X-ray diffraction demonstrates that magnetic order is lost within the nanoparticles with a time constant of 146more » fs. Ultrafast electron diffraction reveals that this demagnetization is followed by an anisotropic, three-dimensional lattice motion. Analysis of the size, speed, and symmetry of the lattice motion, together with ab initio calculations accounting for the stresses due to electrons and phonons, allow us to reveal the magnetoelastic stress generated by demagnetization.« less

Ab initio study of the structural, vibrational and thermal properties of Ge2Sb2Te5

NASA Astrophysics Data System (ADS)

Odhiambo, Henry; Othieno, Herick

2015-05-01

The structural, vibrational and thermal properties of hexagonal as well as cubic Ge2Sb2Te5 (GST) have been calculated from first principles. The relative stability of the possible stacking sequences of hexagonal GST has been confirmed to depend on the choice for the exchange-correlation (XC) energy functional. It is apparent that without the inclusion of the Te 4d orbitals in the valence states, the lattice parameters can be underestimated by as much as 3.9% compared to experiment and all-electron calculations. From phonon dispersion curves, it has been confirmed that the hexagonal phase is, indeed, stable whereas the cubic phase is metastable. In particular, calculations based on the quasi-harmonic approximation (QHA) reveal an extra heat capacity beyond the Dulong-Petit limit at high temperatures for both hexagonal and cubic GST. Moreover, cubic GST exhibits a residual entropy at 0 K, in agreement with experimental studies which attribute this phenomenon to substitutional disorder on the Sb/Ge/v sublattice.

Three-dimensional carbon allotropes comprising phenyl rings and acetylenic chains in sp+ sp 2 hybrid networks

DOE PAGES

Wang, Jian -Tao; Chen, Changfeng; Li, Han -Dong; ...

2016-04-18

Here, we here identify by ab initio calculations a new type of three-dimensional (3D) carbon allotropes that consist of phenyl rings connected by linear acetylenic chains in sp+ sp 2 bonding networks. These structures are constructed by inserting acetylenic or diacetylenic bonds into an all sp 2-hybridized rhombohedral polybenzene lattice, and the resulting 3D phenylacetylene and phenyldiacetylene nets comprise a 12-atom and 18-atom rhombohedral primitive unit cells R - 3m symmetry, which are characterized as the 3D chiral crystalline modification of 2D graphyne and graphdiyne, respectively. Simulated phonon spectra reveal that these structures are dynamically stable. Electronic band calculations indicatemore » that phenylacetylene is metallic, while phenyldiacetylene is a semiconductor with an indirect band gap of 0.58 eV. The present results establish a new type of carbon phases and offer insights into their outstanding structural and electronic properties.« less

Interplay between plasmon and single-particle excitations in a metal nanocluster

PubMed Central

Ma, Jie; Wang, Zhi; Wang, Lin-Wang

2015-01-01

Plasmon-generated hot carriers are used in photovoltaic or photochemical applications. However, the interplays between the plasmon and single-particle excitations in nanosystems have not been theoretically addressed using ab initio methods. Here we show such interplays in a Ag55 nanocluster using real-time time-dependent density functional theory simulations. We find that the disappearance of the zero-frequency peak in the Fourier transform of the band-to-band transition coefficient is a hallmark of the plasmon. We show the importance of the d-states for hot-carrier generations. If the single-particle d-to-s excitations are resonant to the plasmon frequency, the majority of the plasmon energy will be converted into hot carriers, and the overall hot-carrier generation is enhanced by the plasmon; if such resonance does not exist, we observe an intriguing Rabi oscillation between the plasmon and hot carriers. Phonons play a minor role in plasmonic dynamics in such small systems. This study provides guidance on improving plasmonic applications. PMID:26673449

Transverse excitations in liquid metals

NASA Astrophysics Data System (ADS)

Hosokawa, S.; Munejiri, S.; Inui, M.; Kajihara, Y.; Pilgrim, W.-C.; Baron, A. Q. R.; Shimojo, F.; Hoshino, K.

2013-02-01

The transverse acoustic excitation modes were detected by inelastic x-ray scattering in liquid Ga, Cu and Fe in the Q range around 10 nm-1 using a third-generation synchrotron radiation facility, SPring-8, although these liquid metals are mostly described by a simple hard-sphere liquid. Ab initio molecular dynamics simulations clearly support this finding for liquid Ga. From the detailed analyses for the S(Q,ω) spectra with good statistic qualities, the lifetime of less than 1 ps and the propagating length of less than 1 nm can be estimated for the transverse acoustic phonon modes, which correspond to the lifetime and size of cages formed instantaneously in these liquid metals. The microscopic Poisson's ratio estimated from the dynamic velocities of sound is 0.42 for liquid Ga and about -0.2 for liquid transition metals, indicating a rubber-like soft and extremely hard elastic properties of the cage clusters, respectively. The origin of these microscopic elastic properties is discussed in detail.

Computational prediction of body-centered cubic carbon in an all- s p 3 six-member ring configuration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Zhen -Zhen; Lian, Chao -Sheng; Xu, Jing

2015-06-11

Recent shock compression experiments produced clear evidence of a new carbon phase, but a full structural identification has remained elusive. Here we establish by ab initio calculations a body-centered cubic carbon phase in Ia3¯d(O 10 h) symmetry, which contains twelve atoms in its primitive cell, thus termed BC12, and comprises all-sp 3 six-membered rings. This structural configuration places BC12 carbon in the same bonding type as cubic diamond, and its stability is verified by phonon mode analysis. Simulated x-ray diffraction patterns provide an excellent match to the previously unexplained distinct diffraction peak found in shock compression experiments. Electronic band andmore » density of states calculations reveal that BC12 is a semiconductor with a direct band gap of ~2.97eV. Lastly, these results provide a solid foundation for further exploration of this new carbon allotrope.« less

Structure models: From shell model to ab initio methods. A brief introduction to microscopic theories for exotic nuclei

NASA Astrophysics Data System (ADS)

Bacca, Sonia

2016-04-01

A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

Ab initio density functional theory investigation of structural and electronic properties of double-walled silicon carbide nanotubes

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

2009-12-01

By using ab initio density functional theory, the structural and electronic properties of (n,n)@(11,11) double-walled silicon carbide nanotubes (SiCNTs) are investigated. Our calculations reveal the existence of an energetically favorable double-walled nanotube whose interwall distance is about 4.3 Å. Interwall spacing and curvature difference are found to be essential for the electronic states around the Fermi level.

Vibrational spectra for uric acid and its D- and 15N-substituted analogues. Assignments for its normal modes from ab initio 3-21G force field.

NASA Astrophysics Data System (ADS)

Majoube, M.; Vergoten, G.

1993-03-01

FTR, Raman, FTIR spectra are obtained for polycrystalline uric acid and seven of its D-and 15N-substituted analogues. Assignments are given from a normal coordinate analysis carried out using a 3-21G ab initio force field. These are discussed by considering observed and calculated frequencies and D- and 15N-isotopic shifts.

Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil

2015-05-15

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factormore » shows the presence of liquid state in the considered alloys.« less

Kubo–Greenwood approach to conductivity in dense plasmas with average atom models

DOE PAGES

Starrett, C. E.

2016-04-13

In this study, a new formulation of the Kubo–Greenwood conductivity for average atom models is given. The new formulation improves upon previous treatments by explicitly including the ionic-structure factor. Calculations based on this new expression lead to much improved agreement with ab initio results for DC conductivity of warm dense hydrogen and beryllium, and for thermal conductivity of hydrogen. We also give and test a slightly modified Ziman–Evans formula for the resistivity that includes a non-free electron density of states, thus removing an ambiguity in the original Ziman–Evans formula. Again, results based on this expression are in good agreement withmore » ab initio simulations for warm dense beryllium and hydrogen. However, for both these expressions, calculations of the electrical conductivity of warm dense aluminum lead to poor agreement at low temperatures compared to ab initio simulations.« less

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method [Non-Adiabatic Ab Initio Molecular Dynamics with Floating Occupation Molecular Orbitals CASCI Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hollas, Daniel; Sistik, Lukas; Hohenstein, Edward G.

Here, we show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest thatmore » the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.« less

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

NASA Astrophysics Data System (ADS)

Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

2015-02-01

The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

NASA Astrophysics Data System (ADS)

Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

2017-09-01

Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Nalini, E-mail: nalini-2808@yahoo.co.in; Ahluwalia, P. K.; Thakur, Anil

2016-05-23

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70,.} Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30}, and Hg{sub 90}Pb{sub 10}) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the localmore » arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.« less

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

PubMed

Brela, Mateusz Z; Boczar, Marek; Malec, Leszek M; Wójcik, Marek J; Nakajima, Takahito

2018-05-15

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers. Copyright © 2018 Elsevier B.V. All rights reserved.

Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

NASA Astrophysics Data System (ADS)

Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

2018-05-01

Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

DOE PAGES

Dytrych, T.; Maris, P.; Launey, K. D.; ...

2016-06-22

We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU3-selected subspaces. We demonstrate LSU3shell’s strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states withmore » a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

2015-03-01

Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

Ab initio results for intermediate-mass, open-shell nuclei

NASA Astrophysics Data System (ADS)

Baker, Robert B.; Dytrych, Tomas; Launey, Kristina D.; Draayer, Jerry P.

2017-01-01

A theoretical understanding of nuclei in the intermediate-mass region is vital to astrophysical models, especially for nucleosynthesis. Here, we employ the ab initio symmetry-adapted no-core shell model (SA-NCSM) in an effort to push first-principle calculations across the sd-shell region. The ab initio SA-NCSM's advantages come from its ability to control the growth of model spaces by including only physically relevant subspaces, which allows us to explore ultra-large model spaces beyond the reach of other methods. We report on calculations for 19Ne and 20Ne up through 13 harmonic oscillator shells using realistic interactions and discuss the underlying structure as well as implications for various astrophysical reactions. This work was supported by the U.S. NSF (OCI-0904874 and ACI -1516338) and the U.S. DOE (DE-SC0005248), and also benefitted from the Blue Waters sustained-petascale computing project and high performance computing resources provided by LSU.

Ab initio theoretical calculations of the electronic excitation energies of small water clusters.

PubMed

Tachikawa, Hiroto; Yabushita, Akihiro; Kawasaki, Masahiro

2011-12-14

A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

General Rule of Negative Effective Ueff System & Materials Design of High-Tc Superconductors by ab initio Calculations

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, Hiroshi; Nakanishi, Akitaka; Uede, Hiroki; Takawashi, Yuki; Fukushima, Tetsuya; Sato, Kazunori

2014-03-01

Based upon ab initio electronic structure calculation, I will discuss the general rule of negative effective U system by (1) exchange-correlation-induced negative effective U caused by the stability of the exchange-correlation energy in Hund's rule with high-spin ground states of d5 configuration, and (2) charge-excitation-induced negative effective U caused by the stability of chemical bond in the closed-shell of s2, p6, and d10 configurations. I will show the calculated results of negative effective U systems such as hole-doped CuAlO2 and CuFeS2. Based on the total energy calculations of antiferromagnetic and ferromagnetic states, I will discuss the magnetic phase diagram and superconductivity upon hole doping. I also discuss the computational materials design method of high-Tc superconductors by ab initio calculation to go beyond LDA and multi-scale simulations.

A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

NASA Technical Reports Server (NTRS)

Bentley, Joseph A.; Bowman, Joel M.; Gazdy, Bela; Lee, Timothy J.; Dateo, Christopher E.

1992-01-01

An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

Linear free-energy relationships between a single gas-phase ab initio equilibrium bond length and experimental pKa values in aqueous solution.

PubMed

Alkorta, Ibon; Popelier, Paul L A

2015-02-02

Remarkably simple yet effective linear free energy relationships were discovered between a single ab initio computed bond length in the gas phase and experimental pKa values in aqueous solution. The formation of these relationships is driven by chemical features such as functional groups, meta/para substitution and tautomerism. The high structural content of the ab initio bond length makes a given data set essentially divide itself into high correlation subsets (HCSs). Surprisingly, all molecules in a given high correlation subset share the same conformation in the gas phase. Here we show that accurate pKa values can be predicted from such HCSs. This is achieved within an accuracy of 0.2 pKa units for 5 drug molecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic and Ab Initio Determination of the Ring-Twisting Potential Energy Function for 1,3-Cyclohexadiene

NASA Astrophysics Data System (ADS)

Autrey, Daniel; Choo, Jaebum; Laane, Jaan

2000-10-01

The ring-twisting vibration of 1,3-cyclohexadiene has been studied using Raman and infrared spectroscopy of the molecule in the vapor phase. The Raman spectrum shows five ring-twisting transitions in the 150 - 200 cm-1 region. The far-infrared spectrum shows only two transitions for this vibration, which is infrared forbidden in the C_2v (planar) approximation. Three ring-twisting combination bands were also observed off a fundamental vibration at 926.1 cm-1. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function. Ab initio calculations were performed using Moller-Plesset perturbation theory (MP2) using different basis sets. The barrier to planarity of 1150 cm-1 was determined from the spectroscopic data. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range.

Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

NASA Astrophysics Data System (ADS)

Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

2018-04-01

The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

NASA Astrophysics Data System (ADS)

de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

2000-09-01

The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

Nuclear shielding constants by density functional theory with gauge including atomic orbitals

NASA Astrophysics Data System (ADS)

Helgaker, Trygve; Wilson, Philip J.; Amos, Roger D.; Handy, Nicholas C.

2000-08-01

Recently, we introduced a new density-functional theory (DFT) approach for the calculation of NMR shielding constants. First, a hybrid DFT calculation (using 5% exact exchange) is performed on the molecule to determine Kohn-Sham orbitals and their energies; second, the constants are determined as in nonhybrid DFT theory, that is, the paramagnetic contribution to the constants is calculated from a noniterative, uncoupled sum-over-states expression. The initial results suggested that this semiempirical DFT approach gives shielding constants in good agreement with the best ab initio and experimental data; in this paper, we further validate this procedure, using London orbitals in the theory, having implemented DFT into the ab initio code DALTON. Calculations on a number of small and medium-sized molecules confirm that our approach produces shieldings in excellent agreement with experiment and the best ab initio results available, demonstrating its potential for the study of shielding constants of large systems.

Ab-initio calculations on melting of thorium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukherjee, D., E-mail: debojyoti@barc.gov.in; Sahoo, B. D.; Joshi, K. D.

2016-05-23

Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a{sub 0}){sup 3} and (1.02a{sub 0}){sup 3} and (1.04a{sub 0}){sup 3} increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a{sub 0} = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures asmore » melting point. The melting point of 2100 K is close to the experimental value of 2023 K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.« less

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dytrych, T.; Maris, Pieter; Launey, K. D.

2016-06-09

We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations ofmore » states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

NASA Astrophysics Data System (ADS)

Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi

2007-04-01

The intermolecular potentials for the NO(XΠ2)-Kr and NO(AΣ+2)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1A'2 state [NO(XΠ2)-Kr ] and the multireference singles and doubles configuration interaction method for the excited 2A'2 state [NO(AΣ+2)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system. pectroscopy, yields a mean absolute deviation of about 5cm-1 over the 22 levels. The dissociation energy with respect to the lowest vibrational energy is calculated within 30cm-1 of the experimental value of 12953±8cm-1. The reported agreement of the theoretical spectrum and dissociation energy with experiment is contingent upon the inclusion of the effects of core-generated electron correlation, spin-orbit coupling, and scalar relativity. The Dunham analysis [Phys. Rev. 41, 721 (1932)] of the spectrum is found to be very accurate. New values are given for the spectroscopic constants.

Ab initio study of the ground and excited electronic states of the methyl radical

PubMed Central

Zanchet, A.; Bañares, L.; Senent, M. L.; García-Vela, A.

2016-01-01

The ground and some excited electronic states of the methyl radical have been characterized by means of highly correlated ab intio techniques. The specific excited states investigated are those involved in the dissociation of the radical, namely the 3s and 3pz Rydberg states, and the A1 and B1 valence states crossing them, respectively. The C-H dissociative coordinate and the HCH bending angle were considered in order to generate the first two-dimensional ab initio representation of the potential surfaces of the above electronic states of CH3, along with the nonadiabatic couplings between them. Spectroscopic constants and frequencies calculated for the ground and bound excited states agree well with most of the available experimental data. Implications of the shape of the excited potential surfaces and couplings for the dissociation pathways of CH3 are discussed in the light of recent experimental results for dissociation from low-lying vibrational states of CH3. Based on the ab initio data some predictions are made regarding methyl photodissociation from higher initial vibrational states. PMID:27892569

The role of electron-phonon interactions on the coherence lifetime of monolayer transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Stevens, C. E.; Dey, P.; Paul, J.; Wang, Z.; Zhang, H.; Romero, A. H.; Shan, J.; Hilton, D. J.; Karaiskaj, D.

2017-06-01

We investigate the excitonic dephasing of transition metal dichalcogenides, namely MoS2, MoSe2 and WSe2 atomic monolayer thick and bulk crystals, in order to understand the factors that determine the optical coherence in these materials. Coherent nonlinear optical spectroscopy, temperature dependent absorption combined with theoretical calculations of the phonon spectra, reveal the important role electron-phonon interactions plat in dephasing process. The temperature dependence of the electronic band gap and the excitonic linewidth combined with ‘ab initio’ calculations of the phonon energies and the phonon density of state reveal strong interaction with the E’ and E” phonon modes.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111).

PubMed

Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J

2014-08-07

Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the range 0.2-0.3 eV due to ehp excitation, which should be possible to observe. The average non-adiabatic energy losses for non-penetrative scattering exceed the adiabatic losses to phonons by 0.9-1.0 eV. This suggests that for scattering of hyperthermal H-atoms from coinage metals the dominant energy dissipation channel should be to ehp excitation. These predictions can be tested by experiments that combine techniques for generating H-atom beams that are well resolved in translational energy and for detecting the scattered atoms with high energy-resolution.

Investigations of Reactive Processes at Temperatures Relevant to the Hypersonic Flight Regime

DTIC Science & Technology

2014-10-31

molecule is constructed based on high- level ab-initio calculations and interpolated using the reproducible kernel Hilbert space (RKHS) method and...a potential energy surface (PES) for the ground state of the NO2 molecule is constructed based on high- level ab initio calculations and interpolated...between O(3P) and NO(2Π) at higher temperatures relevant to the hypersonic flight regime of reentering space- crafts. At a more fundamental level , we

GAUSSIAN 76: An ab initio Molecular Orbital Program

DOE R&D Accomplishments Database

Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

1978-01-01

Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.