In search of a viable reaction pathway in the chelation of a metallo-protein

NASA Astrophysics Data System (ADS)

Rose, Frisco; Hodak, Miroslav; Bernholc, Jerry

2010-03-01

Misfolded metallo-proteins are potential causal agents in the onset of neuro-degenerative diseases, such as Alzheimer's and Parkinson's Diseases (PD). Experimental results involving metal chelation have shown significant promise in symptom reduction and misfolding reversal. We explore, through atomistic simulations, potential reaction pathways for the chelation of Cu^2+ from the metal binding site in our representation of a partially misfolded α-synuclein, the protein implicated in PD. Our ab initio simulations use Density Functional Theory (DFT) and nudged elastic band to obtain the minimized energy coordinates of this reaction. Our simulations include ab initio water at the interaction site and in its first solvation shells, while the remainder is fully solvated with orbital-free DFT water representation [1]. Our ongoing studies of viable chelation agents include nicotine, caffeine and other potential reagents, we will review the best case agents in this presentation. [4pt] [1] Hodak M, Lu W, Bernholc J. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J. Chem. Phys. 2008 Jan;128(1):014101-9.

Tight-binding analysis of Si and GaAs ultrathin bodies with subatomic wave-function resolution

NASA Astrophysics Data System (ADS)

Tan, Yaohua P.; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy B.; Klimeck, Gerhard

2015-08-01

Empirical tight-binding (ETB) methods are widely used in atomistic device simulations. Traditional ways of generating the ETB parameters rely on direct fitting to bulk experiments or theoretical electronic bands. However, ETB calculations based on existing parameters lead to unphysical results in ultrasmall structures like the As-terminated GaAs ultrathin bodies (UTBs). In this work, it is shown that more transferable ETB parameters with a short interaction range can be obtained by a process of mapping ab initio bands and wave functions to ETB models. This process enables the calibration of not only the ETB energy bands but also the ETB wave functions with corresponding ab initio calculations. Based on the mapping process, ETB models of Si and GaAs are parameterized with respect to hybrid functional calculations. Highly localized ETB basis functions are obtained. Both the ETB energy bands and wave functions with subatomic resolution of UTBs show good agreement with the corresponding hybrid functional calculations. The ETB methods can then be used to explain realistically extended devices in nonequilibrium that cannot be tackled with ab initio methods.

Time-domain ab initio modeling of photoinduced dynamics at nanoscale interfaces.

PubMed

Wang, Linjun; Long, Run; Prezhdo, Oleg V

2015-04-01

Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics.

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

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

Du, Jincheng; Rimsza, Jessica

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Insight of DFT and ab initio atomistic thermodynamics on the surface stability and morphology of In2O3

NASA Astrophysics Data System (ADS)

Zhang, Minhua; Wang, Wenyi; Chen, Yifei

2018-03-01

In2O3 catalysts show remarkable activity and selectivity in methanol synthesis from CO2 hydrogenation. In order to get insight into the surface stability of this catalyst, density functional theory and ab initio atomistic thermodynamics method were used to investigate the surface free energies of various facets as a function of oxygen chemical potential, as well as the influences of temperature, pressure and gas compositions. The results show that the (111) facet presents lowest surface free energy under oxygen-rich condition, while the indium-terminated (100) facet is the most stable one under oxygen-lean condition. Moreover, we applied Wulff construction to determine the equilibrium shape of In2O3 with different oxygen chemical potentials. The equilibrium shape under oxygen-lean condition is cubic, which only expose (100) facet, while, the equilibrium shape under oxygen-rich condition is octahedron, which only expose (111) facet. Meanwhile, the results agree well with what is observed experimentally. It is further predicted that Wulff shape of In2O3 exists in a truncated octahedron morphology in which the (100) surface becomes predominant plane under CO2 hydrogenation reaction conditions.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Thermoelastic effects across the post-perovskite transition in (Al,Fe)-bearing bridgmanite

NASA Astrophysics Data System (ADS)

Valencia-Cardona, J. J.; Shukla, G.; Sarkar, K.; Wentzcovitch, R. M. M.

2017-12-01

The post-perovskite (PPv) transition in (Al,Fe)-bearing bridgmanite has been intensively investigated by experiments and ab initio calculations. However, there are still important aspects of this transformation to be clarified from the atomistic point of view, especially because of the extreme conditions of pressure and temperature in which it takes place, P=125 GPa and T = 2500 K. Here we systematically address this question in (Al,Fe3+)-, (Fe2+)- and (Fe3+)-bearing bridgmanite using ab initio calculations. We particularly address the effect of velocity changes across this transformation in these systems. Our results are important to further understand and constrain the composition of the D" region, believed to be a thermal and/or compositional boundary layer between the solid mantle and molten outer core.

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

Switching times of nanoscale FePt: Finite size effects on the linear reversal mechanism

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

Ellis, M. O. A.; Chantrell, R. W.

2015-04-20

The linear reversal mechanism in FePt grains ranging from 2.316 nm to 5.404 nm has been simulated using atomistic spin dynamics, parametrized from ab-initio calculations. The Curie temperature and the critical temperature (T{sup *}), at which the linear reversal mechanism occurs, are observed to decrease with system size whilst the temperature window T{sup *}

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Ab Initio Predictions of Hexagonal Zr(B,C,N) Polymorphs for Coherent Interface Design

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

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.

2017-10-27

Density functional theory calculations are used to explore hexagonal (HX) NiAs-like polymorphs of Zr(B,C,N) and compare with corresponding Zr(B,C,N) Hagg-like face-centered cubic rocksalt (B1) phases. While all predicted compounds are mechanically stable according to the Born-Huang criteria, only HX Zr(C,N) are found dynamically stable from ab initio molecular dynamics simulations and lattice dynamics calculations. HX ZrN emerges as a candidate structure with ground state energy, elastic constants, and extrinsic mechanical parameters comparable with those of B1 ZrN. Ab initio band structure and semi-classical Boltzmann transport calculations predict a metallic character and a monotonic increase in electrical conductivity with the numbermore » of valence electrons. Electronic structure calculations indicate that the HX phases gain their stability and mechanical attributes by Zr d- non-metal p hybridization and by broadening of Zr d bands. Furthermore, it is shown that the HX ZrN phase provides a low-energy coherent interface model for connecting B1 ZrN domains, with significant energetic advantage over an atomistic interface model derived from high resolution transmission electron microscopy images. The ab initio characterizations provided herein should aid the experimental identification of non-Hagg-like hard phases. Furthermore, the results can also enrich the variety of crystalline phases potentially available for designing coherent interfaces in superhard nanostructured materials and in materials with multilayer characteristics.« less

A fitting empirical potential for NiTi alloy and its application

NASA Astrophysics Data System (ADS)

Ren, Guowu; Tang, Tiegang; Sehitoglu, Huseyin

Due to its superelastic behavior, NiTi shape memory alloy receives considerable attentions over a wide range of industrial and commercial applications. Limited to its complex structural transformation and multiple variants, semiempirical potentials for performing large-scale molecular dynamics simulations to investigate the atomistic mechanical process, are very few. In this work, we construct a new interatomic potential for the NiTi alloy by fitting to experimental or ab initio data. The fitting potential correctly predicts the lattice parameter, structural stability, equation of state for cubic B2(austenite) and monoclinic B19'(martensite) phases. In particular the elastic properties(three elastic constants for B2 and thirteen ones for B19') are in satisfactory agreement with the experiments or ab initio calculations. Furthermore, we apply this potential to conduct the molecular dynamics simulations of the mechanical behavior for NiTi alloy and the results capture its reversible transformation.

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model.

PubMed

Sisto, Aaron; Stross, Clem; van der Kamp, Marc W; O'Connor, Michael; McIntosh-Smith, Simon; Johnson, Graham T; Hohenstein, Edward G; Manby, Fred R; Glowacki, David R; Martinez, Todd J

2017-06-14

We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail - enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-chlorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, we tune the values of both δ and ε through fitting to the thermally broadened experimental absorption spectrum, giving a linear absorption spectrum that agrees reasonably well with experiment. In part two of this article, we construct a time-resolved picture of the coupled vibrational and excitation energy transfer (EET) dynamics in the sub-picosecond regime following photo-excitation. Assuming Franck-Condon excitation of a narrow eigenstate band centred at 800 nm, we use surface hopping to follow a single nonadiabatic dynamics trajectory within the full eigenstate manifold. Consistent with experimental data, this trajectory gives timescales for B800→B850 population transfer (τ B800→B850 ) between 650-1050 fs, and B800 population decay (τ 800→ ) between 10-50 fs. The dynamical picture that emerges is one of rapidly fluctuating LH2 eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the atomic vibrations of the constituent chromophores. The eigenstate fluctuations arise from disorder that is driven by vibrational dynamics with multiple characteristic timescales. The scalability of our ab initio excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.

Unified theory of quantized electrons, phonons, and photons out of equilibrium: A simplified ab initio approach based on the generalized Baym-Kadanoff ansatz

NASA Astrophysics Data System (ADS)

de Melo, Pedro Miguel M. C.; Marini, Andrea

2016-04-01

We present a full ab initio description of the coupled out-of-equilibrium dynamics of photons, phonons, and electrons. In the present approach, the quantized nature of the electromagnetic field as well as of the nuclear oscillations is fully taken into account. The result is a set of integrodifferential equations, written on the Keldysh contour, for the Green's functions of electrons, phonons, and photons where the different kinds of interactions are merged together. We then concentrate on the electronic dynamics in order to reduce the problem to a computationally feasible approach. By using the generalized Baym-Kadanoff ansatz and the completed collision approximation, we introduce a series of efficient but controllable approximations. In this way, we reduce all equations to a set of decoupled equations for the density matrix that describe all kinds of static and dynamical correlations. The final result is a coherent, general, and inclusive scheme to calculate several physical quantities: carrier dynamics, transient photoabsorption, and light emission, all of which include, at the same time, electron-electron, electron-phonon, and electron-photon interactions. We further discuss how all these observables can be easily calculated within the present scheme using a fully atomistic ab initio approach.

Atomistically determined phase-field modeling of dislocation dissociation, stacking fault formation, dislocation slip, and reactions in fcc systems

NASA Astrophysics Data System (ADS)

Rezaei Mianroodi, Jaber; Svendsen, Bob

2015-04-01

The purpose of the current work is the development of a phase field model for dislocation dissociation, slip and stacking fault formation in single crystals amenable to determination via atomistic or ab initio methods in the spirit of computational material design. The current approach is based in particular on periodic microelasticity (Wang and Jin, 2001; Bulatov and Cai, 2006; Wang and Li, 2010) to model the strongly non-local elastic interaction of dislocation lines via their (residual) strain fields. These strain fields depend in turn on phase fields which are used to parameterize the energy stored in dislocation lines and stacking faults. This energy storage is modeled here with the help of the "interface" energy concept and model of Cahn and Hilliard (1958) (see also Allen and Cahn, 1979; Wang and Li, 2010). In particular, the "homogeneous" part of this energy is related to the "rigid" (i.e., purely translational) part of the displacement of atoms across the slip plane, while the "gradient" part accounts for energy storage in those regions near the slip plane where atomic displacements deviate from being rigid, e.g., in the dislocation core. Via the attendant global energy scaling, the interface energy model facilitates an atomistic determination of the entire phase field energy as an optimal approximation of the (exact) atomistic energy; no adjustable parameters remain. For simplicity, an interatomic potential and molecular statics are employed for this purpose here; alternatively, ab initio (i.e., DFT-based) methods can be used. To illustrate the current approach, it is applied to determine the phase field free energy for fcc aluminum and copper. The identified models are then applied to modeling of dislocation dissociation, stacking fault formation, glide and dislocation reactions in these materials. As well, the tensile loading of a dislocation loop is considered. In the process, the current thermodynamic picture is compared with the classical mechanical one as based on the Peach-Köhler force.

First-principles study of point defects at a semicoherent interface

DOE PAGES

Metsanurk, E.; Tamm, A.; Caro, A.; ...

2014-12-19

Most of the atomistic modeling of semicoherent metal-metal interfaces has so far been based on the use of semiempirical interatomic potentials. Here, we show that key conclusions drawn from previous studies are in contradiction with more precise ab-initio calculations. In particular we find that single point defects do not delocalize, but remain compact near the interfacial plane in Cu-Nb multilayers. Lastly, we give a simple qualitative explanation for this difference on the basis of the well known limited transferability of empirical potentials.

Atomistic characterization of SAM coatings as gate insulators in Si-based FET devices

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

Gala, F.; Zollo, G.

2014-06-19

Many nano-material systems are currently under consideration as possible candidates for gate dielectric insulators in both metal-oxide-semiconductor (MOSFET) and organic (OFET) field-effect transistors. In this contribution, the possibility of employing self-assembled monolayers (SAMs) of hydroxylated octadecyltrichlorosilane (OTS) chains on a (111) Si substrate as gate dielectrics is discussed; in particular ab initio theoretical simulations have been employed to study the structural properties, work function modifications, and the insulating properties of OTS thin film coatings on Si substrates.

Atomistic characterization of SAM coatings as gate insulators in Si-based FET devices

NASA Astrophysics Data System (ADS)

Gala, F.; Zollo, G.

2014-06-01

Many nano-material systems are currently under consideration as possible candidates for gate dielectric insulators in both metal-oxide-semiconductor (MOSFET) and organic (OFET) field-effect transistors. In this contribution, the possibility of employing self-assembled monolayers (SAMs) of hydroxylated octadecyltrichlorosilane (OTS) chains on a (111) Si substrate as gate dielectrics is discussed; in particular ab initio theoretical simulations have been employed to study the structural properties, work function modifications, and the insulating properties of OTS thin film coatings on Si substrates.

An Ab Initio Description of the Excitonic Properties of LH2 and Their Temperature Dependence.

PubMed

Cupellini, Lorenzo; Jurinovich, Sandro; Campetella, Marco; Caprasecca, Stefano; Guido, Ciro A; Kelly, Sharon M; Gardiner, Alastair T; Cogdell, Richard; Mennucci, Benedetta

2016-11-10

The spectroscopic properties of light-harvesting (LH) antennae in photosyntehtic organisms represent a fingerprint that is unique for each specific pigment-protein complex. Because of that, spectroscopic observations are generally combined with structural data from X-ray crystallography to obtain an indirect representation of the excitonic properties of the system. Here, an alternative strategy is presented which goes beyond this empirical approach and introduces an ab initio computational description of both structural and electronic properties and their dependence on the temperature. The strategy is applied to the peripheral light-harvesting antenna complex (LH2) present in purple bacteria. By comparing this model with the one based on the crystal structure, a detailed, molecular level explanation of the absorption and circular dichroism (CD) spectra and their temperature dependence is achieved. The agreement obtained with the experiments at both low and room temperature lays the groundwork for an atomistic understanding of the excitation dynamics in the LH2 system.

Transferable atomistic model to describe the energetics of zirconia

NASA Astrophysics Data System (ADS)

Wilson, Mark; Schönberger, Uwe; Finnis, Michael W.

1996-10-01

We have investigated the energies of a number of phases of ZrO2 using models of an increasing degree of sophistication: the simple ionic model, the polarizable ion model, the compressible ion model, and finally a model including quadrupole polarizability of the oxygen ions. The three structures which are observed with increasing temperatures are monoclinic, tetragonal, and cubic (fluorite). Besides these we have studied some hypothetical structures which certain potentials erroneously predict or which occur in other oxides with this stoichiometry, e.g., the α-PbO2 structure and rutile. We have also performed ab initio density functional calculations with the full-potential linear combination of muffin-tin orbitals method to investigate the cubic-tetragonal distortion. A detailed comparison is made between the results using classical potentials, the experimental data, and our own and other ab initio results. The factors which stabilize the various structure are analyzed. We find the only genuinely transferable model is the one including compressible ions and anion polarizability to the quadrupole level.

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

DOE PAGES

Sisto, Aaron; Stross, Clem; van der Kamp, Marc W.; ...

2017-03-28

We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail – enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-chlorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibratingmore » our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, we tune the values of both δ and ε through fitting to the thermally broadened experimental absorption spectrum, giving a linear absorption spectrum that agrees reasonably well with experiment. In part two of this article, we construct a time-resolved picture of the coupled vibrational and excitation energy transfer (EET) dynamics in the sub-picosecond regime following photo-excitation. Assuming Franck–Condon excitation of a narrow eigenstate band centred at 800 nm, we use surface hopping to follow a single nonadiabatic dynamics trajectory within the full eigenstate manifold. Consistent with experimental data, this trajectory gives timescales for B800→B850 population transfer (τ B800→B850) between 650–1050 fs, and B800 population decay (τ 800→) between 10–50 fs. The dynamical picture that emerges is one of rapidly fluctuating LH2 eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the atomic vibrations of the constituent chromophores. The eigenstate fluctuations arise from disorder that is driven by vibrational dynamics with multiple characteristic timescales. The scalability of our ab initio excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.« less

First-Principles Approach to Model Electrochemical Reactions: Understanding the Fundamental Mechanisms behind Mg Corrosion

NASA Astrophysics Data System (ADS)

Surendralal, Sudarsan; Todorova, Mira; Finnis, Michael W.; Neugebauer, Jörg

2018-06-01

Combining concepts of semiconductor physics and corrosion science, we develop a novel approach that allows us to perform ab initio calculations under controlled potentiostat conditions for electrochemical systems. The proposed approach can be straightforwardly applied in standard density functional theory codes. To demonstrate the performance and the opportunities opened by this approach, we study the chemical reactions that take place during initial corrosion at the water-Mg interface under anodic polarization. Based on this insight, we derive an atomistic model that explains the origin of the anodic hydrogen evolution.

Insights on activation enthalpy for non-Schmid slip in body-centered cubic metals

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

Hale, Lucas M.; Lim, Hojun; Zimmerman, Jonathan A.

2014-12-18

We use insights gained from atomistic simulation to develop an activation enthalpy model for dislocation slip in body-centered cubic iron. Furthermore, using a classical potential that predicts dislocation core stabilities consistent with ab initio predictions, we quantify the non-Schmid stress-dependent effects of slip. The kink-pair activation enthalpy is evaluated and a model is identified as a function of the general stress state. Thus, our model enlarges the applicability of the classic Kocks activation enthalpy model to materials with non-Schmid behavior.

Polarizable atomistic calculation of site energy disorder in amorphous Alq3.

PubMed

Nagata, Yuki

2010-02-01

A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8-hydroxyquinolinato)aluminum (Alq(3)) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight-binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq(3) and the effect of the polarization on the site energy disorder is discussed.

Atomistic insight into the adsorption site selectivity of stepped Au(111) surfaces

NASA Astrophysics Data System (ADS)

Gaspari, Roberto; Pignedoli, Carlo A.; Fasel, Roman; Treier, Matthias; Passerone, Daniele

2010-07-01

Using classical and ab initio simulations, we study the interplay between the Au(111) surface reconstruction and monoatomic steps on a vicinal face. The experimentally observed discommensuration line patterns on a specific vicinal are reproduced and explained, and a complete description of the structure is given. An unusual atomic arrangement is shown to be responsible for the lower reactivity of hcp segments of step edges compared to the one of fcc segments. Our results provide an unprecedented understanding of the electronic and geometric properties of the complex Au(111) surface.

Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation.

PubMed

Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

2016-12-14

NH 3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH 3 from atmospheric N 2 and oceanic H 2 O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH 3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH 3 . Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N 2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.

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.

Ab initio modeling of steady-state and time-dependent charge transport in hole-only α-NPD devices

NASA Astrophysics Data System (ADS)

Liu, Feilong; Massé, Andrea; Friederich, Pascal; Symalla, Franz; Nitsche, Robert; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.

2016-12-01

We present an ab initio modeling study of steady-state and time-dependent charge transport in hole-only devices of the amorphous molecular semiconductor α-NPD [N ,N'-Di(1 -naphthyl)-N ,N'-diphenyl-(1 ,1'-biphenyl)-4 ,4'-diamine] . The study is based on the microscopic information obtained from atomistic simulations of the morphology and density functional theory calculations of the molecular hole energies, reorganization energies, and transfer integrals. Using stochastic approaches, the microscopic information obtained in simulation boxes at a length scale of ˜10 nm is expanded and employed in one-dimensional (1D) and three-dimensional (3D) master-equation modeling of the charge transport at the device scale of ˜100 nm. Without any fit parameter, predicted current density-voltage and impedance spectroscopy data obtained with the 3D modeling are in very good agreement with measured data on devices with different α-NPD layer thicknesses in a wide range of temperatures, bias voltages, and frequencies. Similarly good results are obtained with the computationally much more efficient 1D modeling after optimizing a hopping prefactor.

Friction of water on graphene and hexagonal boron nitride from ab initio methods: very different slippage despite very similar interface structures.

PubMed

Tocci, Gabriele; Joly, Laurent; Michaelides, Angelos

2014-12-10

Friction is one of the main sources of dissipation at liquid water/solid interfaces. Despite recent progress, a detailed understanding of water/solid friction in connection with the structure and energetics of the solid surface is lacking. Here, we show for the first time that ab initio molecular dynamics can be used to unravel the connection between the structure of nanoscale water and friction for liquid water in contact with graphene and with hexagonal boron nitride. We find that although the interface presents a very similar structure between the two sheets, the friction coefficient on boron nitride is ≈ 3 times larger than that on graphene. This comes about because of the greater corrugation of the energy landscape on boron nitride arising from specific electronic structure effects. We discuss how a subtle dependence of the friction on the atomistic details of a surface, which is not related to its wetting properties, may have a significant impact on the transport of water at the nanoscale, with implications for the development of membranes for desalination and for osmotic power harvesting.

Ab initio molecular dynamics of atomic-scale surface reactions: insights into metal organic chemical vapor deposition of AlN on graphene.

PubMed

Sangiovanni, D G; Gueorguiev, G K; Kakanakova-Georgieva, A

2018-06-19

Metal organic chemical vapor deposition (MOCVD) of group III nitrides on graphene heterostructures offers new opportunities for the development of flexible optoelectronic devices and for the stabilization of conceptually-new two-dimensional materials. However, the MOCVD of group III nitrides is regulated by an intricate interplay of gas-phase and surface reactions that are beyond the resolution of experimental techniques. We use density-functional ab initio molecular dynamics (AIMD) with van der Waals corrections to identify atomistic pathways and associated electronic mechanisms driving precursor/surface reactions during metal organic vapor phase epitaxy at elevated temperatures of aluminum nitride on graphene, considered here as model case study. The results presented provide plausible interpretations of atomistic and electronic processes responsible for delivery of Al, C adatoms, and C-Al, CHx, AlNH2 admolecules on pristine graphene via precursor/surface reactions. In addition, the simulations reveal C adatom permeation across defect-free graphene, as well as exchange of C monomers with graphene carbon atoms, for which we obtain rates of ∼0.3 THz at typical experimental temperatures (1500 K), and extract activation energies Eexca = 0.28 ± 0.13 eV and attempt frequencies Aexc = 2.1 (×1.7±1) THz via Arrhenius linear regression. The results demonstrate that AIMD simulations enable understanding complex precursor/surface reaction mechanisms, and thus propose AIMD to become an indispensable routine prediction-tool toward more effective exploitation of chemical precursors and better control of MOCVD processes during synthesis of functional materials.

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Hierarchical lattice models of hydrogen-bond networks in water

NASA Astrophysics Data System (ADS)

Dandekar, Rahul; Hassanali, Ali A.

2018-06-01

We develop a graph-based model of the hydrogen-bond network in water, with a view toward quantitatively modeling the molecular-level correlational structure of the network. The networks formed are studied by the constructing the model on two infinite-dimensional lattices. Our models are built bottom up, based on microscopic information coming from atomistic simulations, and we show that the predictions of the model are consistent with known results from ab initio simulations of liquid water. We show that simple entropic models can predict the correlations and clustering of local-coordination defects around tetrahedral waters observed in the atomistic simulations. We also find that orientational correlations between bonds are longer ranged than density correlations, determine the directional correlations within closed loops, and show that the patterns of water wires within these structures are also consistent with previous atomistic simulations. Our models show the existence of density and compressibility anomalies, as seen in the real liquid, and the phase diagram of these models is consistent with the singularity-free scenario previously proposed by Sastry and coworkers [Phys. Rev. E 53, 6144 (1996), 10.1103/PhysRevE.53.6144].

Viabilty of atomistic potentials for thermodynamic properties of carbon dioxide at low temperatures.

PubMed

Kuznetsova, Tatyana; Kvamme, Bjørn

2001-11-30

Investigation into volumetric and energetic properties of several atomistic models mimicking carbon dioxide geometry and quadrupole momentum covered the liquid-vapor coexistence curve. Thermodynamic integration over a polynomial and an exponential-polynomial path was used to calculate free energy. Computational results showed that model using GROMOS Lennard-Jones parameters was unsuitable for bulk CO(2) simulations. On the other hand, model with potential fitted to reproduce only correct density-pressure relationship in the supercritical region proved to yield correct enthalpy of vaporization and free energy of liquid CO(2) in the low-temperature region. Except for molar volume at the upper part of the vapor-liquid equilibrium line, the bulk properties of exp-6-1 parametrization of ab initio CO(2) potential were in a close agreement with the experimental results. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1772-1781, 2001

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

Theoretical evidence for unexpected O-rich phases at corners of MgO surfaces

NASA Astrophysics Data System (ADS)

Bhattacharya, Saswata; Berger, Daniel; Reuter, Karsten; Ghiringhelli, Luca M.; Levchenko, Sergey V.

2017-12-01

Realistic oxide materials are often semiconductors, in particular at elevated temperatures, and their surfaces contain undercoordinated atoms at structural defects such as steps and corners. Using hybrid density-functional theory and ab initio atomistic thermodynamics, we investigate the interplay of bond-making, bond-breaking, and charge-carrier trapping at the corner defects at the (100) surface of a p -doped MgO in thermodynamic equilibrium with an O2 atmosphere. We show that by manipulating the coordination of surface atoms, one can drastically change and even reverse the order of stability of reduced versus oxidized surface sites.

Atomic structure of the GaAs(001)-c(4x4) surface: first-principles evidence for diversity of heterodimer motifs.

PubMed

Penev, E; Kratzer, P; Scheffler, M

2004-10-01

The GaAs(001)-c(4x4) surface was studied using ab initio atomistic thermodynamics based on density-functional theory calculations. We demonstrate that in a range of stoichiometries, between those of the conventional three As-dimer and the new three Ga-As-dimer models, there exists a diversity of atomic structures featuring Ga-As heterodimers. These results fully explain the experimental scanning tunneling microscopy images and are likely to be relevant also to the c(4x4)-reconstructed (001) surfaces of other III-V semiconductors.

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.

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

Atomistic Texture of Amorphous Manganese Oxides for Electrochemical Water Splitting Revealed by Ab Initio Calculations Combined with X-ray Spectroscopy.

PubMed

Mattioli, Giuseppe; Zaharieva, Ivelina; Dau, Holger; Guidoni, Leonardo

2015-08-19

Amorphous transition-metal (hydr)oxides are considered as the most promising catalysts that promote the oxidation of water to molecular oxygen, protons, and "energized" electrons, and, in turn, as fundamental parts of "artificial leaves" that can be exploited for large scale generation of chemical fuels (e.g., hydrogen) directly from sunlight. We present here a joint theoretical-experimental investigation of electrodeposited amorphous manganese oxides with different catalytic activities toward water oxidation (MnCats). Combining the information content of X-ray absorption fine structure (XAFS) measurements with the predictive power of ab initio calculations based on density functional theory, we have been able to identify the essential structural and electronic properties of MnCats. We have elucidated (i) the localization and structural connection of Mn(II), Mn(III), and Mn(IV) ions in such amorphous oxides and (ii) the distribution of protons at the MnCat/water interface. Our calculations result in realistic 3D models of the MnCat atomistic texture, formed by the interconnection of small planar Mn-oxo sheets cross-linked through different kinds of defective Mn atoms, isolated or arranged in closed cubane-like units. Essential for the catalytic activity is the presence of undercoordinated Mn(III)O5 units located at the boundary of the amorphous network, where they are ready to act as hole traps that trigger the oxidation of neighboring water molecules when the catalyst is exposed to an external positive potential. The present validation of a sound 3D model of MnCat improves the accuracy of XAFS fits and opens the way for the development of mechanistic schemes of its functioning beyond a speculative level.

Adsorption and dissociation of H2O on the (001) surface of uranium mononitride: energetics and mechanism from first-principles investigation.

PubMed

Bo, Tao; Lan, Jian-Hui; Zhang, Yu-Juan; Zhao, Yao-Lin; He, Chao-Hui; Chai, Zhi-Fang; Shi, Wei-Qun

2016-05-21

The interfacial interaction of uranium mononitride (UN) with water from the environment unavoidably leads to corrosion of nuclear fuels, which affects a lot of processes in the nuclear fuel cycle. In this work, the microscopic adsorption behaviors of water on the UN(001) surface as well as water dissociation and accompanying H2 formation mechanisms have been investigated on the basis of DFT+U calculations and ab initio atomistic thermodynamics. For adsorption of one H2O monomer, the predicted adsorption energies are -0.88, -2.07, and -2.07 eV for the most stable molecular, partially dissociative, and completely dissociative adsorption, respectively. According to our calculations, a water molecule dissociates into OH and H species via three pathways with small energy barriers of 0.78, 0.72, and 0.85 eV, respectively. With the aid of the neighboring H atom, H2 formation through the reaction of H* + OH* can easily occur via two pathways with energy barriers of 0.61 and 0.36 eV, respectively. The molecular adsorption of water shows a slight coverage dependence on the surface while this dependence becomes obvious for partially dissociative adsorption as the water coverage increases from 1/4 to 1 ML. In addition, based on the "ab initio atomistic thermodynamic" simulations, increasing H2O partial pressure will enhance the stability of the adsorbed system and water coverage, while increasing temperature will decrease the H2O coverage. We found that the UN(001) surface reacts easily with H2O at room temperature, leading to dissolution and corrosion of the UN fuel materials.

Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

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

Liu, Shi-Yu, E-mail: buaasyliu@gmail.com; Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong; Liu, Shiyang

Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustainedmore » complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.« less

An ab initio molecular dynamics study of thermal decomposition of 3,6-di(azido)-1,2,4,5-tetrazine.

PubMed

Wu, Qiong; Zhu, Weihua; Xiao, Heming

2014-10-21

Ab initio molecular dynamics simulations were performed to study the thermal decomposition of isolated and crystal 3,6-di(azido)-1,2,4,5-tetrazine (DiAT). During unimolecular decomposition, the three different initiation mechanisms were observed to be N-N2 cleavage, ring opening, and isomerization, respectively. The preferential initial decomposition step is the homolysis of the N-N2 bond in the azido group. The release mechanisms of nitrogen gas are found to be very different in the early and later decomposition stages of crystal DiAT. In the early decomposition, DiAT decomposes very fast and drastically without forming any stable long-chains or heterocyclic clusters, and most of the nitrogen gases are released through rapid rupture of nitrogen-nitrogen and carbon-nitrogen bonds. But in the later decomposition stage, the release of nitrogen gas is inhibited due to low mobility, long distance from each other, and strong carbon-nitrogen bonds. To overcome the obstacles, the nitrogen gases are released through slow formation and disintegration of polycyclic networks. Our simulations suggest a new decomposition mechanism for the organic polyazido initial explosive at the atomistic level.

The shear instability energy: a new parameter for materials design?

NASA Astrophysics Data System (ADS)

Kanani, M.; Hartmaier, A.; Janisch, R.

2017-10-01

Reliable and predictive relationships between fundamental microstructural material properties and observable macroscopic mechanical behaviour are needed for the successful design of new materials. In this study we establish a link between physical properties that are defined on the atomic level and the deformation mechanisms of slip planes and interfaces that govern the mechanical behaviour of a metallic material. To accomplish this, the shear instability energy Γ is introduced, which can be determined via quantum mechanical ab initio calculations or other atomistic methods. The concept is based on a multilayer generalised stacking fault energy calculation and can be applied to distinguish the different shear deformation mechanisms occurring at TiAl interfaces during finite-temperature molecular dynamics simulations. We use the new parameter Γ to construct a deformation mechanism map for different interfaces occurring in this intermetallic. Furthermore, Γ can be used to convert the results of ab initio density functional theory calculations into those obtained with an embedded atom method type potential for TiAl. We propose to include this new physical parameter into material databases to apply it for the design of materials and microstructures, which so far mainly relies on single-crystal values for the unstable and stable stacking fault energy.

Role of hydrogen in volatile behaviour of defects in SiO2-based electronic devices

NASA Astrophysics Data System (ADS)

Wimmer, Yannick; El-Sayed, Al-Moatasem; Gös, Wolfgang; Grasser, Tibor; Shluger, Alexander L.

2016-06-01

Charge capture and emission by point defects in gate oxides of metal-oxide-semiconductor field-effect transistors (MOSFETs) strongly affect reliability and performance of electronic devices. Recent advances in experimental techniques used for probing defect properties have led to new insights into their characteristics. In particular, these experimental data show a repeated dis- and reappearance (the so-called volatility) of the defect-related signals. We use multiscale modelling to explain the charge capture and emission as well as defect volatility in amorphous SiO2 gate dielectrics. We first briefly discuss the recent experimental results and use a multiphonon charge capture model to describe the charge-trapping behaviour of defects in silicon-based MOSFETs. We then link this model to ab initio calculations that investigate the three most promising defect candidates. Statistical distributions of defect characteristics obtained from ab initio calculations in amorphous SiO2 are compared with the experimentally measured statistical properties of charge traps. This allows us to suggest an atomistic mechanism to explain the experimentally observed volatile behaviour of defects. We conclude that the hydroxyl-E' centre is a promising candidate to explain all the observed features, including defect volatility.

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

Xiong, L. H.; Wang, X. D.; Yu, Q.

Temperature-dependent atomistic structure evolution of liquid gallium (Ga) has been investigated by using in situ high energy X-ray diffraction experiment and ab initio molecular dynamics simulation. Both experimental and theoretical results reveal the existence of a liquid structural change around 1000 K in liquid Ga. Below and above this temperature the liquid exhibits differences in activation energy for selfdiffusion, temperature-dependent heat capacity, coordination numbers, density, viscosity, electric resistivity and thermoelectric power, which are reflected from structural changes of the bond-orientational order parameter Q6, fraction of covalent dimers, averaged string length and local atomic packing. This finding will trigger more studiesmore » on the liquid-to-liquid crossover in metallic melts.« less

An atomistic fingerprint algorithm for learning ab initio molecular force fields

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

The atomistic mechanism for Sb segregation and As displacement of Sb in InSb(001) surfaces

NASA Astrophysics Data System (ADS)

Anderson, Evan M.; Millunchick, Joanna M.

2018-01-01

Interfacial broadening occurs in mixed-anion alloy heterostructures such as InAs/InAsSb due to both Sb-segregation and As-for-Sb exchange. In order to determine the atomistic mechanisms for these processes, we conduct ab initio calculations coupled with a cluster expansion formalism to determine the surface reconstructions of the pure and As-exposed InSb(001) surfaces. This approach provides a predicted phase diagram for pure InSb that is in better agreement with experiments. Namely, the α2(2 × 4) and α3c(4 × 4) structures are ultimately stable at 0K, but the α(4 × 3) and α2c(2 × 6) are within 1 meV/Å2. Exposure of the InSb(001) surface to As results in the As atoms infiltrating into the crystal and displacing subsurface Sb, thus providing the atomistic mechanisms for experimental observations of the As-for-Sb exchange reaction and Sb segregation. Experiments show that the widely reported A-(1 × 3) reconstruction is actually comprised of multiple reconstructions, which is consistent with the prediction of several nearly stable possible reconstructions.

Controllable atomistic graphene oxide model and its application in hydrogen sulfide removal.

PubMed

Huang, Liangliang; Seredych, Mykola; Bandosz, Teresa J; van Duin, Adri C T; Lu, Xiaohua; Gubbins, Keith E

2013-11-21

The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H2S and H2O∕H2S mixtures on GO materials and compare the results with experiment. We find that H2S molecules dissociate on the carbonyl functional groups, and H2O, CO2, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H2O∕H2S mixtures, H2O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H2S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

Atomistic absorption spectra and non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

NASA Astrophysics Data System (ADS)

Glowacki, David

Recently, we outlined an efficient multi-tiered parallel excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground/excited state energies and gradients of large supramolecular complexes in atomistic detail. In this paper, we apply our ab initioexciton framework to the 27 coupled bacteriocholorophyll-a chromophores which make up the LH2 complex, using it to compute linear absorption spectra and short-time, on-the-fly nonadiabatic surface-hopping (SH) dynamics of electronically excited LH2. Our ab initio exciton model includes two key parameters whose values are determined by fitting to experiment: d, which is added to the diagonal elements, corrects for the error in TDDFT vertical excitation energies on a single chromophore; and e, which occurs on the off-diagonal matrix elements, describes the average dielectric screening of the inter-chromophore transition-dipole coupling. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, best-fit values of both d and e were obtained by fitting to the thermally broadened experimental absorption spectrum within the Frank-Condon approximation, providing a linear absorption spectrum that agrees reasonably well with the experimental observations. We follow the nonadiabatic dynamics using surface hopping to construct time-resolved visualizations of the EET dynamics in the sub-picosecond regime following photoexcitation. This provides some qualitative insight into the excitonic energy transfer (EET) that results from atomically resolved vibrational fluctuations of the chromophores. The dynamical picture that emerges is one of rapidly fluctuating eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the underlying chromophore vibrational dynamics. The eigenstate fluctuations arise from disorder in both the diagonal chromophore site energies and the off-diagonal inter-chromophore couplings. The scalability of our excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.

Atomistic insights into the nanosecond long amorphization and crystallization cycle of nanoscale G e2S b2T e5 : An ab initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Branicio, Paulo S.; Bai, Kewu; Ramanarayan, H.; Wu, David T.; Sullivan, Michael B.; Srolovitz, David J.

2018-04-01

The complete process of amorphization and crystallization of the phase-change material G e2S b2T e5 is investigated using nanosecond ab initio molecular dynamics simulations. Varying the quench rate during the amorphization phase of the cycle results in the generation of a variety of structures from entirely crystallized (-0.45 K/ps) to entirely amorphized (-16 K/ps). The 1.5-ns annealing simulations indicate that the crystallization process depends strongly on both the annealing temperature and the initial amorphous structure. The presence of crystal precursors (square rings) in the amorphous matrix enhances nucleation/crystallization kinetics. The simulation data are used to construct a combined continuous-cooling-transformation (CCT) and temperature-time-transformation (TTT) diagram. The nose of the CCT-TTT diagram corresponds to the minimum time for the onset of homogenous crystallization and is located at 600 K and 70 ps. That corresponds to a critical cooling rate for amorphization of -4.5 K/ps. The results, in excellent agreement with experimental observations, suggest that a strategy that utilizes multiple quench rates and annealing temperatures may be used to effectively optimize the reversible switching speed and enable fast and energy-efficient phase-change memories.

N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

NASA Astrophysics Data System (ADS)

Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

2015-03-01

We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

Exploring oxidative ageing behaviour of hydrocarbons using ab initio molecular dynamics analysis

NASA Astrophysics Data System (ADS)

Pan, Tongyan; Cheng, Cheng

2016-06-01

With a proper approximate solution to the Schrödinger Equation of a multi-electron system, the method of ab initio molecular dynamics (AIMD) performs first-principles molecular dynamics analysis without pre-defining interatomic potentials as are mandatory in traditional molecular dynamics analyses. The objective of this study is to determine the oxidative-ageing pathway of petroleum asphalt as a typical hydrocarbon system, using the AIMD method. This objective was accomplished in three steps, including (1) identifying a group of representative asphalt molecules to model, (2) determining an atomistic modelling method that can effectively simulate the production of critical functional groups in oxidative ageing of hydrocarbons and (3) evaluating the oxidative-ageing pathway of a hydrocarbon system. The determination of oxidative-ageing pathway of hydrocarbons was done by tracking the generations of critical functional groups in the course of oxidative ageing. The chemical elements of carbon, nitrogen and sulphur all experience oxidative reactions, producing polarised functional groups such as ketones, aldehydes or carboxylic acids, pyrrolic groups and sulphoxides. The electrostatic forces of the polarised groups generated in oxidation are responsible for the behaviour of aged hydrocarbons. The developed AIMD model can be used for modelling the ageing of generic hydrocarbon polymers and developing antioxidants without running expensive experiments.

Computational modeling of carbohydrate recognition in protein complex

NASA Astrophysics Data System (ADS)

Ishida, Toyokazu

2017-11-01

To understand the mechanistic principle of carbohydrate recognition in proteins, we propose a systematic computational modeling strategy to identify complex carbohydrate chain onto the reduced 2D free energy surface (2D-FES), determined by MD sampling combined with QM/MM energy corrections. In this article, we first report a detailed atomistic simulation study of the norovirus capsid proteins with carbohydrate antigens based on ab initio QM/MM combined with MD-FEP simulations. The present result clearly shows that the binding geometries of complex carbohydrate antigen are determined not by one single, rigid carbohydrate structure, but rather by the sum of averaged conformations mapped onto the minimum free energy region of QM/MM 2D-FES.

Atomistic Conversion Reaction Mechanism of WO 3 in Secondary Ion Batteries of Li, Na, and Ca

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

He, Yang; Gu, Meng; Xiao, Haiyan

2016-04-13

Reversible insertion and extraction of ionic species into a host lattice governs the basic operating principle for both rechargeable battery (such as lithium batteries) and electrochromic devices (such as ANA Boeing 787-8 Dreamliner electrochromic window). Intercalation and/or conversion are two fundamental chemical processes for some materials in response to the ion insertion. The interplay between these two chemical processes has never been established. It is speculated that the conversion reaction is initiated by ion intercalation. However, experimental evidence of intercalation and subsequent conversion remains unexplored. Here, using in situ HRTEM and spectroscopy, we captured the atomistic conversion reaction processes duringmore » lithium, sodium and calcium ion insertion into tungsten trioxide (WO3) single crystal model electrodes. An intercalation step right prior to conversion is explicitly revealed at atomic scale for the first time for these three ion species. Combining nanoscale diffraction and ab initio molecular dynamics simulations, it is found that, beyond intercalation, the inserted ion-oxygen bonding formation destabilized the transition-metal framework which gradually shrunk, distorted and finally collapsed to a pseudo-amorphous structure. This study provides a full atomistic picture on the transition from intercalation to conversion, which is of essential for material applications in both secondary ion batteries and electrochromic devices.« less

Mesoscale models for stacking faults, deformation twins and martensitic transformations: Linking atomistics to continuum

NASA Astrophysics Data System (ADS)

Kibey, Sandeep A.

We present a hierarchical approach that spans multiple length scales to describe defect formation---in particular, formation of stacking faults (SFs) and deformation twins---in fcc crystals. We link the energy pathways (calculated here via ab initio density functional theory, DFT) associated with formation of stacking faults and twins to corresponding heterogeneous defect nucleation models (described through mesoscale dislocation mechanics). Through the generalized Peieirls-Nabarro model, we first correlate the width of intrinsic SFs in fcc alloy systems to their nucleation pathways called generalized stacking fault energies (GSFE). We then establish a qualitative dependence of twinning tendency in fee metals and alloys---specifically, in pure Cu and dilute Cu-xAl (x= 5.0 and 8.3 at.%)---on their twin-energy pathways called the generalized planar fault energies (GPFE). We also link the twinning behavior of Cu-Al alloys to their electronic structure by determining the effect of solute Al on the valence charge density redistribution at the SF through ab initio DFT. Further, while several efforts have been undertaken to incorporate twinning for predicting stress-strain response of fcc materials, a fundamental law for critical twinning stress has not yet emerged. We resolve this long-standing issue by linking quantitatively the twin-energy pathways (GPFE) obtained via ab initio DFT to heterogeneous, dislocation-based twin nucleation models. We establish an analytical expression that quantitatively predicts the critical twinning stress in fcc metals in agreement with experiments without requiring any empiricism at any length scale. Our theory connects twinning stress to twin-energy pathways and predicts a monotonic relation between stress and unstable twin stacking fault energy revealing the physics of twinning. We further demonstrate that the theory holds for fcc alloys as well. Our theory inherently accounts for directional nature of twinning which available qualitative models do not necessarily account for. Finally, we extend the present work to martensitic transformations and determine the energy pathway for B2→B19 transformation in NiTi. Based on our ab initio DFT calculations, we propose a combined distortion-shuffle pathway for B2→B19 transformation in NiTi. Our results indicate that in NiTi, a barrier of 0.48 mRyd/atom (relative to B2 phase) must be overcome to transform the parent B2 into orthorhombic B19 phase.

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

Ab initio studies on the adsorption and implantation of Al and Fe to nitride materials

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

Riedl, H., E-mail: helmut.riedl@tuwien.ac.at; Zálešák, J.; Department of Physical Metallurgy and Materials Testing, Montanuniversität Leoben, A-8700 Leoben

2015-09-28

The formation of transfer material products on coated cutting and forming tools is a major failure mechanism leading to various sorts of wear. To describe the atomistic processes behind the formation of transfer materials, we use ab initio to study the adsorption energy as well as the implantation barrier of Al and Fe atoms for (001)-oriented surfaces of TiN, Ti{sub 0.50}Al{sub 0.50}N, Ti{sub 0.90}Si{sub 0.10}N, CrN, and Cr{sub 0.90}Si{sub 0.10}N. The interactions between additional atoms and nitride-surfaces are described for pure adhesion, considering no additional stresses, and for the implantation barrier. The latter, we simplified to the stress required tomore » implant Al and Fe into sub-surface regions of the nitride material. The adsorption energies exhibit pronounced extrema at high-symmetry positions and are generally highest at nitrogen sites. Here, the binary nitrides are comparable to their ternary counterparts and the average adhesive energy is higher (more negative) on CrN than TiN based systems. Contrary, the implantation barrier for Al and Fe atoms is higher for the ternary systems Ti{sub 0.50}Al{sub 0.50}N, Ti{sub 0.90}Si{sub 0.10}N, and Cr{sub 0.90}Si{sub 0.10}N than for their binary counterparts TiN and CrN. Based on our results, we can conclude that TiN based systems outperform CrN based systems with respect to pure adhesion, while the Si-containing ternaries exhibit higher implantation barriers for Al and Fe atoms. The data obtained are important to understand the atomistic interaction of metal atoms with nitride-based materials, which is valid not just for machining operations but also for any combination such as interfaces between coatings and substrates or multilayer and phase arrangements themselves.« less

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...

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1986-01-01

During this reporting period three investigations were carried out. The first area of research concerned the analysis of the structure-energy relationship in small clusters. This study is very closely related to the improvement of the potential energy functions which are suitable and simple enough to be used in atomistic simulation studies. Parameters obtained from ab initio calculations for dimers and trimers of Al were used to estimate energetics and global minimum energy structures of clusters continuing up to 15 Al atoms. The second research topic addressed modeling of the collision process for atoms impinging on surfaces. In this simulation study qualitative aspects of the O atom collision with a graphite surface were analyzed. Four different O/graphite systems were considered and the aftermath of the impact was analyzed. The final area of investigation was related to the simulation of thin amorphous Si films on crystalline Si substrates. Parameters obtained in an earlier study were used to model an exposed amorphous Si surface and an a-Si/c-Si interface. Structural details for various film thicknesses were investigated at an atomistic level.

Object kinetic Monte Carlo model for neutron and ion irradiation in tungsten: Impact of transmutation and carbon impurities

NASA Astrophysics Data System (ADS)

Castin, N.; Bonny, G.; Bakaev, A.; Ortiz, C. J.; Sand, A. E.; Terentyev, D.

2018-03-01

We upgrade our object kinetic Monte Carlo (OKMC) model, aimed at describing the microstructural evolution in tungsten (W) under neutron and ion irradiation. Two main improvements are proposed based on recently published atomistic data: (a) interstitial carbon impurities, and their interaction with radiation-induced defects (point defect clusters and loops), are more accurately parameterized thanks to ab initio findings; (b) W transmutation to rhenium (Re) upon neutron irradiation, impacting the diffusivity of radiation defects, is included, also relying on recent atomistic data. These essential amendments highly improve the portability of our OKMC model, providing a description for the formation of SIA-type loops under different irradiation conditions. The model is applied to simulate neutron and ion irradiation in pure W samples, in a wide range of fluxes and temperatures. We demonstrate that it performs a realistic prediction of the population of TEM-visible voids and loops, as compared to experimental evidence. The impact of the transmutation of W to Re, and of carbon trapping, is assessed.

Improved atomistic simulation of diffusion and sorption in metal oxides

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

2001-01-01

Gas diffusion and sorption on the surface of metal oxides are investigated using atomistic simulations, that make use of two different force fields for the description of the intramolecular and intermolecular interactions. MD and MC computations are presented and estimates of the mean residence time, Henry's constant, and the heat of adsorption are provided for various common gases (CO, CO2, O2, CH4, Xe), and semiconducting substrates that hold promise for gas sensor applications (SnO2, BaTiO3). Comparison is made between the performance of a simple, first generation force field (Universal) and a more detailed, second generation field (COMPASS) under the same conditions and the same assumptions regarding the generation of the working configurations. It is found that the two force fields yield qualitatively similar results in all cases examined here. However, direct comparison with experimental data reveals that the accuracy of the COMPASS-based computations is not only higher than that of the first generation force field but exceeds even that of published specialized methods, based on ab initio computations.

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

Multiscale Modeling of Grain Boundaries in ZrB2: Structure, Energetics, and Thermal Resistance

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W., Jr.

2012-01-01

A combination of ab initio, atomistic and finite element methods (FEM) were used to investigate the structures, energetics and lattice thermal conductance of grain boundaries for the ultra high temperature ceramic ZrB2. Atomic models of idealized boundaries were relaxed using density functional theory. Information about bonding across the interfaces was determined from the electron localization function. The Kapitza conductance of larger scale versions of the boundary models were computed using non-equilibrium molecular dynamics. The interfacial thermal parameters together with single crystal thermal conductivities were used as parameters in microstructural computations. FEM meshes were constructed on top of microstructural images. From these computations, the effective thermal conductivity of the polycrystalline structure was determined.

First principles investigation of heterogeneous catalysis on metal oxide surfaces

NASA Astrophysics Data System (ADS)

Ghoussoub, Mireille

Metal oxides possess unique electronic and structural properties that render them highly favourable for applications in heterogeneous catalysis. In this study, computational atomistic modelling based on Density Functional Theory was used to investigate the reduction of carbon dioxide over hydroxylated indium oxide nanoparticles, as well at the activation of methane over oxygen-covered bimetallic surfaces. The first study employed metadynamics-biased ab initio molecular dynamics to obtain the free energy surface of the various reaction steps at finite temperature. In the second study, the nudged elastic band method was used to probe the C-H activation mechanisms for different surface configurations. In both cases, activation energies, reaction energies, transition state structures, and charge analysis results are used to explain the underlying mechanistic pathways.

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.

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

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

Code of Federal Regulations, 2011 CFR

2011-07-01

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

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. ...

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

PubMed

Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

2016-08-25

The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 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...

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 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...

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.

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.

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.

Surface Passivation in Empirical Tight Binding

NASA Astrophysics Data System (ADS)

He, Yu; Tan, Yaohua; Jiang, Zhengping; Povolotskyi, Michael; Klimeck, Gerhard; Kubis, Tillmann

2016-03-01

Empirical Tight Binding (TB) methods are widely used in atomistic device simulations. Existing TB methods to passivate dangling bonds fall into two categories: 1) Method that explicitly includes passivation atoms is limited to passivation with atoms and small molecules only. 2) Method that implicitly incorporates passivation does not distinguish passivation atom types. This work introduces an implicit passivation method that is applicable to any passivation scenario with appropriate parameters. This method is applied to a Si quantum well and a Si ultra-thin body transistor oxidized with SiO2 in several oxidation configurations. Comparison with ab-initio results and experiments verifies the presented method. Oxidation configurations that severely hamper the transistor performance are identified. It is also shown that the commonly used implicit H atom passivation overestimates the transistor performance.

Atomicrex—a general purpose tool for the construction of atomic interaction models

NASA Astrophysics Data System (ADS)

Stukowski, Alexander; Fransson, Erik; Mock, Markus; Erhart, Paul

2017-07-01

We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms.

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.

Atomistic study of the electronic contact resistivity between the half-Heusler alloys (HfCoSb, HfZrCoSb, HfZrNiSn) and the metal Ag

NASA Astrophysics Data System (ADS)

He, Yuping; Léonard, François; Spataru, Catalin D.

2018-06-01

Half-Heusler (HH) alloys have shown promising thermoelectric properties in the medium- and high-temperature range. To harness these material properties for thermoelectric applications, it is important to realize electrical contacts with low electrical contact resistivity. However, little is known about the detailed structural and electronic properties of such contacts and the expected values of contact resistivity. Here, we employ atomistic ab initio calculations to study electrical contacts in a subclass of HH alloys consisting of the compounds HfCoSb, HfZrCoSb, and HfZrNiSn. By using Ag as a prototypical metal, we show that the termination of the HH material critically determines the presence or absence of strong deformations at the interface. Our study includes contacts to doped materials, and the results indicate that the p -type materials generally form ohmic contacts while the n -type materials have a small Schottky barrier. We calculate the temperature dependence of the contact resistivity in the low- to medium-temperature range and provide quantitative values that set lower limits for these systems.

Accessible, almost ab initio multi-scale modeling of entangled polymers via slip-links

NASA Astrophysics Data System (ADS)

Andreev, Marat

It is widely accepted that dynamics of entangled polymers can be described by the tube model. Here we advocate for an alternative approach to entanglement modeling known as slip-links. Recently, slip-links were shown to possess important advantages over tube models, namely they have strong connections to atomistic, multichain levels of description, agree with non-equilibrium thermodynamics, are applicable to any chain architecture and can be used in linear or non-linear rheology. We present a hierarchy of slip-link models that are connected to each other through successive coarse graining. Models in the hierarchy are consistent in their overlapping domains of applicability in order to allow a straightforward mapping of parameters. In particular, the most--detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. On the other hand, the least--detailed member of the hierarchy is numerically accessible, and allows for non-equilibrium flow predictions of complex chain architectures. Using GPU implementation these predictions can be obtained in minutes of computational time on a single desktop equipped with a mainstream gaming GPU. The GPU code is available online for free download.

Polarizabilities and van der Waals C{sub 6} coefficients of fullerenes from an atomistic electrodynamics model: Anomalous scaling with number of carbon atoms

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

Saidi, Wissam A., E-mail: alsaidi@pitt.edu; Norman, Patrick

2016-07-14

The van der Waals C{sub 6} coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C{sub 6} ∝ N{sup 2.2} as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N{sup 2.75} as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes bymore » fitting against accurate ab initio calculations. This model shows that C{sub 6} ∝ N{sup 2.8}, which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole–dipole term scales almost linearly with the number of carbon atoms.« less

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.

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

NASA Astrophysics Data System (ADS)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high-temperature superconducting materials in order to parameterize the apparently large nonlinear electron-phonon coupling. Thirdly, ab initio simulations are used to investigate the role of pressure-driven structural re-organization in the crystalline-to-amorphous (or, metallic-to-insulating) transition of a common binary phase-change material composed of Ge and Sb. Practical applications of each topic will be discussed. Keywords. Charge-equilibration methods, molecular dynamics, electronic structure calculations, ab initio simulations, high-temperature superconductors, phase-change materials.

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.

PubMed

Daily, Michael D; Baer, Marcel D; Mundy, Christopher J

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.

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.

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.

Exploring N-Rich Phases in Li(x)N(y) Clusters for Hydrogen Storage at Nanoscale.

PubMed

Bhattacharya, Amrita; Bhattacharya, Saswata

2015-09-17

We have performed cascade genetic algorithm and ab initio atomistic thermodynamics under the framework of first-principles-based hybrid density functional theory to study the (meta-)stability of a wide range of Li(x)N(y) clusters. We found that hybrid xc-functional is essential to address this problem as a local/semilocal functional simply fails even to predict a qualitative prediction. Most importantly, we find that though in bulk lithium nitride, the Li-rich phase, that is, Li3N, is the stable stoichiometry; in small Li(x)N(y) clusters, N-rich phases are more stable at thermodynamic equilibrium. We further show that these N-rich clusters are promising hydrogen storage material because of their easy adsorption and desorption ability at respectively low (≤300 K) and moderately high temperature (≥600 K).

Towards a mulitphase equation of state of Carbon from first principles

NASA Astrophysics Data System (ADS)

Correa, Alfredo; Benedict, Lorin; Schwegler, Eric

2007-03-01

Ab initio molecular dynamics and electronic structure calculation had become one of the most useful tools to investigate properties of materials. Unfortunately these atomistic detailed results are rarely reused in calculations at a higher level of description, such as fluid dynamics and finite elements calculations. In this talk we present a concrete example showing the way that first principles results can be expressed in a way that is useful for hydrodynamics calculations, in particular we show how to build a analytic equation of state for Carbon that involves solid (diamond and BC8) and liquid phases. Applications of this newly obtained equation of state will be presented. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48.

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.

Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).

PubMed

Hafner, Jürgen

2008-02-13

The development of modern materials science has led to a growing need to understand the phenomena determining the properties of materials on an atomistic level. As the behavior of atoms and electrons is governed by the laws of quantum mechanics, accurate and efficient techniques for solving the basic quantum-mechanical equations for very complex many-atom, many-electron systems are required. The development of density-functional theory (DFT) represents a decisive step forwards in our efforts to develop tools for ab initio atomistic simulations of complex materials, preparing the way towards computational materials design. The development of these ab initio simulation methods, whose aim is to model processes in materials by solving the coupled Newtonian equations of motion of the atoms and the Schrödinger equation for the electrons from first principles without any other input than the atomic numbers of the constituents, is part of fundamental research. Hence, for a long time the development and application of DFT methods has been a domain of academic research. Only during the past decade, based on the development of increasingly sophisticated codes and better computer performance, has the impact of DFT-based simulation methods has spread from academia to industry. New opportunities are opening for innovative materials research across physics, chemistry, surface science and nanotechnology extending even to earth sciences and molecular biology. In 1998 we organized, at the Vienna University of Technology, a first workshop entitled 'Electronic Structure Calculations for Industry and Basic Sciences' (short title 'Theory meets Industry') to celebrate the start of the European Science Foundation (ESF) research program 'Electronic Structure Calculations for Elucidating the Complex Atomistic Behavior of Solids and Surfaces', known as the Ψ(k)-network. At this workshop, researchers from academia presented recent results in the development of ab initio simulation methods and their application to key areas of condensed matter physics. Researchers from industry mainly focused on challenges arising from applied industrial research; contributions describing successful applications of DFT techniques to industrial problems were more scarce. Progress during the last decade has been very fast. The ESF research program has been renewed under the much bolder title 'Towards Computational Materials Design' and is now approaching the end of this second funding period. Due to the development of accurate, efficient and stable software packages for ab initio simulations, DFT-based techniques are now routinely used in many industrial laboratories worldwide. It was therefore considered timely to organize a second 'Theory meets Industry' workshop. The meeting took place between 12-14 June 2007 at the Erwin-Schrödinger-Institute (ESI) for Mathematical Physics in Vienna (Austria). It was sponsored by the Universität Wien through the VASP (Vienna Ab-initio Simulation Program) project, the Center for Computational Materials Science Vienna, the Erwin-Schrödinger-Institute and the ESF Program 'Towards Computational Materials Design'. The program of the workshop was decided by an international advisory board consisting of Ryoji Asahi (Toyota Central Research and Development Laboratory), Risto Nieminen (Helsinki University of Technology), Herve Toulhoat (Institut Français du Pétrole), Erich Wimmer (Materials Design Inc.), Chris Wolverton (Ford Motor Co. and Northwestern University) and Jürgen Hafner (Universität Wien). The 35 invited talks presented at the meeting were divided equally between researchers from academia and from industry. The contributions from academia concentrated on a wide range of new developments in DFT and post-DFT simulations (with contributions from the developers of leading software packages for ab initio simulations), as well as on applications in front-line materials research. In contrast to the first workshop nine years ago, all industrial speakers presented results of extensive ab initio studies in key areas of modern technology, concentrating on catalysis and chemical processing, information technologies, automotive engineering and energy. The proceedings assemble full papers summarizing 23 of the invited talks, abstracts of the remaining invited talks and abstracts of all the poster contributions. It is complemented by a conference summary written by Erich Wimmer. Erich is certainly excellently qualified for this task, because for many years he has played the role of mediator between academia and industry. I shall not anticipate his summary here, but I think that it is fair to say that tremendous progress has been made since the first workshop. Ab initio DFT simulations are now a well established tool for industrial research and, due to the availability of cheap high-performance server clusters, their use is no longer the reserve of large corporate laboratories equipped with supercomputers, but are also accessible to medium-sized enterprises. The basic methodology is still developed by the leading academic research groups. These groups urgently need support from funding agencies and/or industry not only for the basic code development, but also to bring their research codes up to industrial standards of programming, stability, user-friendliness and documentation. The fundamental challenge to theory, however, remains the same: more accurate total energies, application to larger and even more complex systems, and access to new materials properties. Responding to these challenges will require substantial effort at various levels. Achieving greatly improved accuracy of calculated total energies demands an improved description of electronic exchange and correlation. Possible routes (hybrid functionals for solids, dynamical mean field theory (DMFT), many-body perturbation theory (GW), quantum Monte-Carlo) have been presented at this meeting. Access to larger systems could be realized either by codes achieving O (N)-scaling or by adopting a strategy of multi-scale simulations. At least two different O (N)-codes have been discussed at the workshop. But even if these approaches allow ab initio calculations to be performed for ten times as many atoms as before, in terms of linear dimensions, the accessible systems size increases only by a factor of two. Therefore, multi-scale simulations strategies remain a very important issue. Access to new materials properties requires adding new routines to the basic codes. Again, this meeting has highlighted important new developments: evolutionary crystal structure predictions, transport properties of semiconductors and insulators, and calculations of free-energy reaction barriers to name only a few. The task of providing a full 'tool-box' of routines for fast and efficient calculation of many different materials properties evidently exceeds the capacity of a single group of developers. Here, collaboration is necessary between the developers of the basic DFT codes and the expert users of these codes pushing the application of the methodology to new frontiers. Again, it will be important to bring the newly developed routines into a stable, well documented form and to make them accessible to a wide range of users, both in academia and industry. Supporting these efforts is also a challenge to industry. The academic research needs industry's support in many ways. Industry has to make governmental and funding agencies aware of the vital role of our research for future technological development-and a very persuasive way to do that is to invest directly into leading academic groups. As the workshop organizer and editor of the proceedings, I would like to thank all contributors (especially those who accepted the burden of writing a full paper), the members of the Advisory Board for helping to organize such a good program, and the Institute of Physics for their help in the preparation of the proceedings.

FOREWORD: Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12 14 June 2007)

NASA Astrophysics Data System (ADS)

Hafner, Jürgen

2008-02-01

The development of modern materials science has led to a growing need to understand the phenomena determining the properties of materials on an atomistic level. As the behavior of atoms and electrons is governed by the laws of quantum mechanics, accurate and efficient techniques for solving the basic quantum-mechanical equations for very complex many-atom, many-electron systems are required. The development of density-functional theory (DFT) represents a decisive step forwards in our efforts to develop tools for ab initio atomistic simulations of complex materials, preparing the way towards computational materials design. The development of these ab initio simulation methods, whose aim is to model processes in materials by solving the coupled Newtonian equations of motion of the atoms and the Schrödinger equation for the electrons from first principles without any other input than the atomic numbers of the constituents, is part of fundamental research. Hence, for a long time the development and application of DFT methods has been a domain of academic research. Only during the past decade, based on the development of increasingly sophisticated codes and better computer performance, has the impact of DFT-based simulation methods has spread from academia to industry. New opportunities are opening for innovative materials research across physics, chemistry, surface science and nanotechnology extending even to earth sciences and molecular biology. In 1998 we organized, at the Vienna University of Technology, a first workshop entitled 'Electronic Structure Calculations for Industry and Basic Sciences' (short title 'Theory meets Industry') to celebrate the start of the European Science Foundation (ESF) research program 'Electronic Structure Calculations for Elucidating the Complex Atomistic Behavior of Solids and Surfaces', known as the Ψk-network. At this workshop, researchers from academia presented recent results in the development of ab initio simulation methods and their application to key areas of condensed matter physics. Researchers from industry mainly focused on challenges arising from applied industrial research; contributions describing successful applications of DFT techniques to industrial problems were more scarce. Progress during the last decade has been very fast. The ESF research program has been renewed under the much bolder title 'Towards Computational Materials Design' and is now approaching the end of this second funding period. Due to the development of accurate, efficient and stable software packages for ab initio simulations, DFT-based techniques are now routinely used in many industrial laboratories worldwide. It was therefore considered timely to organize a second 'Theory meets Industry' workshop. The meeting took place between 12-14 June 2007 at the Erwin-Schrödinger-Institute (ESI) for Mathematical Physics in Vienna (Austria). It was sponsored by the Universität Wien through the VASP (Vienna Ab-initio Simulation Program) project, the Center for Computational Materials Science Vienna, the Erwin-Schrödinger-Institute and the ESF Program 'Towards Computational Materials Design'. The program of the workshop was decided by an international advisory board consisting of Ryoji Asahi (Toyota Central Research and Development Laboratory), Risto Nieminen (Helsinki University of Technology), Herve Toulhoat (Institut Français du Pétrole), Erich Wimmer (Materials Design Inc.), Chris Wolverton (Ford Motor Co. and Northwestern University) and Jürgen Hafner (Universität Wien). The 35 invited talks presented at the meeting were divided equally between researchers from academia and from industry. The contributions from academia concentrated on a wide range of new developments in DFT and post-DFT simulations (with contributions from the developers of leading software packages for ab initio simulations), as well as on applications in front-line materials research. In contrast to the first workshop nine years ago, all industrial speakers presented results of extensive ab initio studies in key areas of modern technology, concentrating on catalysis and chemical processing, information technologies, automotive engineering and energy. The proceedings assemble full papers summarizing 23 of the invited talks, abstracts of the remaining invited talks and abstracts of all the poster contributions. It is complemented by a conference summary written by Erich Wimmer. Erich is certainly excellently qualified for this task, because for many years he has played the role of mediator between academia and industry. I shall not anticipate his summary here, but I think that it is fair to say that tremendous progress has been made since the first workshop. Ab initio DFT simulations are now a well established tool for industrial research and, due to the availability of cheap high-performance server clusters, their use is no longer the reserve of large corporate laboratories equipped with supercomputers, but are also accessible to medium-sized enterprises. The basic methodology is still developed by the leading academic research groups. These groups urgently need support from funding agencies and/or industry not only for the basic code development, but also to bring their research codes up to industrial standards of programming, stability, user-friendliness and documentation. The fundamental challenge to theory, however, remains the same: more accurate total energies, application to larger and even more complex systems, and access to new materials properties. Responding to these challenges will require substantial effort at various levels. Achieving greatly improved accuracy of calculated total energies demands an improved description of electronic exchange and correlation. Possible routes (hybrid functionals for solids, dynamical mean field theory (DMFT), many-body perturbation theory (GW), quantum Monte-Carlo) have been presented at this meeting. Access to larger systems could be realized either by codes achieving O (N)-scaling or by adopting a strategy of multi-scale simulations. At least two different O (N)-codes have been discussed at the workshop. But even if these approaches allow ab initio calculations to be performed for ten times as many atoms as before, in terms of linear dimensions, the accessible systems size increases only by a factor of two. Therefore, multi-scale simulations strategies remain a very important issue. Access to new materials properties requires adding new routines to the basic codes. Again, this meeting has highlighted important new developments: evolutionary crystal structure predictions, transport properties of semiconductors and insulators, and calculations of free-energy reaction barriers to name only a few. The task of providing a full 'tool-box' of routines for fast and efficient calculation of many different materials properties evidently exceeds the capacity of a single group of developers. Here, collaboration is necessary between the developers of the basic DFT codes and the expert users of these codes pushing the application of the methodology to new frontiers. Again, it will be important to bring the newly developed routines into a stable, well documented form and to make them accessible to a wide range of users, both in academia and industry. Supporting these efforts is also a challenge to industry. The academic research needs industry's support in many ways. Industry has to make governmental and funding agencies aware of the vital role of our research for future technological development—and a very persuasive way to do that is to invest directly into leading academic groups. As the workshop organizer and editor of the proceedings, I would like to thank all contributors (especially those who accepted the burden of writing a full paper), the members of the Advisory Board for helping to organize such a good program, and the Institute of Physics for their help in the preparation of the proceedings.

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

Ab initio molecular dynamics study on the initial chemical events in nitramines: thermal decomposition of CL-20.

PubMed

Isayev, Olexandr; Gorb, Leonid; Qasim, Mo; Leszczynski, Jerzy

2008-09-04

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.g., RDX, HMX), CL-20 has only one distinct initial reaction channelhomolysis of the N-NO2 bond. We did not observe any HONO elimination reaction during unimolecular decomposition, whereas the ring-breaking reaction was followed by NO 2 fission. Therefore, in spite of limited sampling, that provides a mostly qualitative picture, we proposed here a scheme of unimolecular decomposition of CL-20. The averaged product population over all trajectories was estimated at four HCN, two to four NO2, two to four NO, one CO, and one OH molecule per one CL-20 molecule. Our simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20, allowing elucidation of key features of such processes as composition of primary reaction products, reaction timing, and Arrhenius behavior of the system. The primary reactions leading to NO2, NO, N 2O, and N2 occur at very early stages. We also estimated potential activation barriers for the formation of NO2, which essentially determines overall decomposition kinetics and effective rate constants for NO2 and N2. The calculated solid-phase decomposition pathways correlate with available condensed-phase experimental data.

Mapping energetics of atom probe evaporation events through first principles calculations.

PubMed

Peralta, Joaquín; Broderick, Scott R; Rajan, Krishna

2013-09-01

The purpose of this work is to use atomistic modeling to determine accurate inputs into the atom probe tomography (APT) reconstruction process. One of these inputs is evaporation field; however, a challenge occurs because single ions and dimers have different evaporation fields. We have calculated the evaporation field of Al and Sc ions and Al-Al and Al-Sc dimers from an L1₂-Al₃Sc surface using ab initio calculations and with a high electric field applied to the surface. The evaporation field is defined as the electric field at which the energy barrier size is calculated as zero, corresponding to the minimum field that atoms from the surface can break their bonds and evaporate from the surface. The evaporation field of the surface atoms are ranked from least to greatest as: Al-Al dimer, Al ion, Sc ion, and Al-Sc dimer. The first principles results were compared with experimental data in the form of an ion evaporation map, which maps multi-ion evaporations. From the ion evaporation map of L1₂-Al₃Sc, we extract relative evaporation fields and identify that an Al-Al dimer has a lower evaporation field than an Al-Sc dimer. Additionally, comparatively an Al-Al surface dimer is more likely to evaporate as a dimer, while an Al-Sc surface dimer is more likely to evaporate as single ions. These conclusions from the experiment agree with the ab initio calculations, validating the use of this approach for modeling APT energetics. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

On the use of atomistic simulations to aid bulk metallic glasses structural elucidation with solid-state NMR.

PubMed

Ferreira, Ary R; Rino, José P

2017-08-24

Solid-state nuclear magnetic resonance (ssNMR) experimental 27 Al metallic shifts reported in the literature for bulk metallic glasses (BMGs) were revisited in the light of state-of-the-art atomistic simulations. In a consistent way, the Gauge-Including Projector Augmented-Wave (GIPAW) method was applied in conjunction with classical molecular dynamics (CMD). A series of Zr-Cu-Al alloys with low Al concentrations were selected as case study systems, for which realistic CMD derived structural models were used for a short- and medium-range order mining. That initial procedure allowed the detection of trends describing changes on the microstructure of the material upon Al alloying, which in turn were used to guide GIPAW calculations with a set of abstract systems in the context of ssNMR. With essential precision and accuracy, the ab initio simulations also yielded valuable trends from the electronic structure point of view, which enabled an overview of the bonding nature of Al-centered clusters as well as its influence on the experimental ssNMR outcomes. The approach described in this work might promote the use of ssNMR spectroscopy in research on glassy metals. Moreover, the results presented demonstrate the possibility to expand the applications of this technique, with deeper insight into nuclear interactions and less speculative assignments.

Stability and mobility of Cu-vacancy clusters in Fe-Cu alloys: A computational study based on the use of artificial neural networks for energy barrier calculations

NASA Astrophysics Data System (ADS)

Pascuet, M. I.; Castin, N.; Becquart, C. S.; Malerba, L.

2011-05-01

An atomistic kinetic Monte Carlo (AKMC) method has been applied to study the stability and mobility of copper-vacancy clusters in Fe. This information, which cannot be obtained directly from experimental measurements, is needed to parameterise models describing the nanostructure evolution under irradiation of Fe alloys (e.g. model alloys for reactor pressure vessel steels). The physical reliability of the AKMC method has been improved by employing artificial intelligence techniques for the regression of the activation energies required by the model as input. These energies are calculated allowing for the effects of local chemistry and relaxation, using an interatomic potential fitted to reproduce them as accurately as possible and the nudged-elastic-band method. The model validation was based on comparison with available ab initio calculations for verification of the used cohesive model, as well as with other models and theories.

Thermodynamic stability and structure of cuprous chloride surfaces: a DFT investigation.

PubMed

Suleiman, Ibrahim A; Radny, Marian W; Gladys, Michael J; Smith, Phillip V; Mackie, John C; Kennedy, Eric M; Dlugogorski, Bogdan Z

2015-03-14

Density functional theory together with ab initio atomistic thermodynamics has been utilized to study the structures and stabilities of the low index CuCl surfaces. It is shown that the Cl-terminated structures are more stable than the Cu-terminated configurations, and that the defective CuCl(110)-Cu structure is more stable than the stoichiometric CuCl(110) surface. The equilibrium shape of a cuprous chloride nanostructure terminated by low-index CuCl surfaces has also been predicted using a Wulff construction. It was found that the (110) facets dominate at low chlorine concentration. As the chlorine concentration is increased, however, the contributions of the (100) and (111) facets to the Wulff construction also increase giving the crystal a semi-prism shape. At high chlorine concentration, and close to the rich limit, the (111) facets were found to be the only contributors to the Wulff construction, resulting in prismatic nanocrystals.

Simulation of ceramic materials relevant for nuclear waste management: Case of La1-xEuxPO4 solid solution

NASA Astrophysics Data System (ADS)

Kowalski, Piotr M.; Ji, Yaqi; Li, Yan; Arinicheva, Yulia; Beridze, George; Neumeier, Stefan; Bukaemskiy, Andrey; Bosbach, Dirk

2017-02-01

Using powerful computational resources and state-of-the-art methods of computational chemistry we contribute to the research on novel nuclear waste forms by providing atomic scale description of processes that govern the structural incorporation and the interactions of radionuclides in host materials. Here we present various results of combined computational and experimental studies on La1-xEuxPO4 monazite-type solid solution. We discuss the performance of DFT + U method with the Hubbard U parameter value derived ab initio, and the derivation of various structural, thermodynamic and radiation-damage related properties. We show a correlation between the cation displacement probabilities and the solubility data, indicating that the binding of cations is the driving factor behind both processes. The combined atomistic modeling and experimental studies result in a superior characterization of the investigated material.

Time-dependent broken-symmetry density functional theory simulation of the optical response of entangled paramagnetic defects: Color centers in lithium fluoride

NASA Astrophysics Data System (ADS)

Janesko, Benjamin G.

2018-02-01

Parameter-free atomistic simulations of entangled solid-state paramagnetic defects may aid in the rational design of devices for quantum information science. This work applies time-dependent density functional theory (TDDFT) embedded-cluster simulations to a prototype entangled-defect system, namely two adjacent singlet-coupled F color centers in lithium fluoride. TDDFT calculations accurately reproduce the experimental visible absorption of both isolated and coupled F centers. The most accurate results are obtained by combining spin symmetry breaking to simulate strong correlation, a large fraction of exact (Hartree-Fock-like) exchange to minimize the defect electrons' self-interaction error, and a standard semilocal approximation for dynamical correlations between the defect electrons and the surrounding ionic lattice. These results motivate application of two-reference correlated ab initio approximations to the M-center, and application of TDDFT in parameter-free simulations of more complex entangled paramagnetic defect architectures.

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...

adwTools Developed: New Bulk Alloy and Surface Analysis Software for the Alloy Design Workbench

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Morse, Jeffrey A.; Noebe, Ronald D.; Abel, Phillip B.

2004-01-01

A suite of atomistic modeling software, called the Alloy Design Workbench, has been developed by the Computational Materials Group at the NASA Glenn Research Center and the Ohio Aerospace Institute (OAI). The main goal of this software is to guide and augment experimental materials research and development efforts by creating powerful, yet intuitive, software that combines a graphical user interface with an operating code suitable for real-time atomistic simulations of multicomponent alloy systems. Targeted for experimentalists, the interface is straightforward and requires minimum knowledge of the underlying theory, allowing researchers to focus on the scientific aspects of the work. The centerpiece of the Alloy Design Workbench suite is the adwTools module, which concentrates on the atomistic analysis of surfaces and bulk alloys containing an arbitrary number of elements. An additional module, adwParams, handles ab initio input for the parameterization used in adwTools. Future modules planned for the suite include adwSeg, which will provide numerical predictions for segregation profiles to alloy surfaces and interfaces, and adwReport, which will serve as a window into the database, providing public access to the parameterization data and a repository where users can submit their own findings from the rest of the suite. The entire suite is designed to run on desktop-scale computers. The adwTools module incorporates a custom OAI/Glenn-developed Fortran code based on the BFS (Bozzolo- Ferrante-Smith) method for alloys, ref. 1). The heart of the suite, this code is used to calculate the energetics of different compositions and configurations of atoms.

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...

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.

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 and Simulation of Amorphous Materials

NASA Astrophysics Data System (ADS)

Pandey, Anup

The general and practical inversion of diffraction data - producing a computer model correctly representing the material explored - is an important unsolved problem for disordered materials. Such modeling should proceed by using our full knowledge base, both from experiment and theory. In this dissertation, we introduce a robust method, Force-Enhanced Atomic Refinement (FEAR), which jointly exploits the power of ab initio atomistic simulation along with the information carried by diffraction data. As a preliminary trial, the method has been implemented using empirical potentials for amorphous silicon (a-Si) and silica ( SiO2). The models obtained are comparable to the ones prepared by the conventional approaches as well as the experiments. Using ab initio interactions, the method is applied to two very different systems: amorphous silicon (a-Si) and two compositions of a solid electrolyte memory material silver-doped GeSe3. It is shown that the method works well for both the materials. Besides that, the technique is easy to implement, is faster and yields results much improved over conventional simulation methods for the materials explored. It offers a means to add a priori information in first principles modeling of materials, and represents a significant step toward the computational design of non-crystalline materials using accurate interatomic interactions and experimental information. Moreover, the method has also been used to create a computer model of a-Si, using highly precise X-ray diffraction data. The model predicts properties that are close to the continuous random network models but with no a priori assumptions. In addition, using the ab initio molecular dynamics simulations (AIMD) we explored the doping and transport in hydrogenated amorphous silicon a-Si:H with the most popular impurities: boron and phosphorous. We investigated doping for these impurities and the role of H in the doping process. We revealed the network motion and H hopping induced by the thermal fluctuations significantly impacts conduction in this material. In the last section of the dissertation, we employed AIMD to model the structure of amorphous zinc oxide (a-ZnO) and trivalent elements (Al, Ga and In) doped a-ZnO. We studied the structure and electronic structure of these models as well as the effect of trivalent dopants in both the structure and electronic structure of a-ZnO.

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.

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.

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.

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

Molecular simulations, based on atomistic force fields are a standard theoretical tool in materials, polymers and biosciences. While various methods, with quantum chemistry incorporated, have been developed for condensed phase simulations during the last decade, there is another line of development with the purpose to bridge the time and length scales based on coarse-graining. This is expected to lead to some very interesting breakthroughs in the near future. In this lecture we will first give some background to common atomistic force fields. After that, we review a few common simple techniques for reducing the number of motional degrees of freedom to speed up the simulations. Finally, we present a powerful method for reducing uninteresting degrees of freedom. This is done by solving the Inverse Problem to obtain the interaction potentials. More precisely, we make use of the radial distribution functions, and by using the method of Inverse Monte Carlo [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)], we can construct effective potentials which are consistent with the original RDFs. This makes it possible to simulate much larger system than would have been possible by using atomistic force fields. We present many examples: How to simulate aqueous electrolyte solutions without any water molecules but still having the hydration structure around the ions - at the speed of a primitive electrolyte model calculation. We demonstrate how a coarse-grained model can be constructed for a double-helix DNA and how it can be used. It is accurate enough to reproduce the experimental results for ion condensation around DNA for several different counterions. We also show how we can construct site-site potentials for large-scale atomistic classical simulations of arbitrary liquids from smaller scale ab initio simulations. This methodology allows us to start from a simulation with the electrons and atomic nuclei, to construct a set of atomistic effective interaction potentials, and to use them in classical simulations. As a next step we can construct a new set of potentials beyond the atomistic description and carry out mesoscopic simulations, for example by using Dissipative Particle Dynamics. In this way we can tie together three different levels of description. The Dissipative Particle Dynamics method appears as a very promising tool to use with our coarse-grained potentials.

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

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

An Atomistic View of the Incipient Growth of Zinc Oxide Nanolayers

DOE PAGES

Chu, Manh Hung; Tian, Liang; Chaker, Ahmad; ...

2016-08-09

The growth of zinc oxide thin films by atomic layer deposition is believed to proceed through an embryonic step in which three-dimensional nanoislands form and then coalesce to trigger a layer-by-layer growth mode. This transient initial state is characterized by a poorly ordered atomic structure, which may be inaccessible by X-ray diffraction techniques. Here in this work, we apply X-ray absorption spectroscopy in situ to address the local structure of Zn after each atomic layer deposition cycle, using a custom-built reactor mounted at a synchrotron beamline, and we shed light on the atomistic mechanisms taking place during the first stagesmore » of the growth. We find that such mechanisms are surprisingly different for zinc oxide growth on amorphous (silica) and crystalline (sapphire) substrate. Ab initio simulations and quantitative data analysis allow the formulation of a comprehensive growth model, based on the different effects of surface atoms and grain boundaries in the nanoscale islands, and the consequent induced local disorder. From a comparison of these spectroscopy results with those from X-ray diffraction reported recently, we observe that the final structure of the zinc oxide nanolayers depends strongly on the mechanisms taking place during the initial stages of growth. Finally, the approach followed here for the case of zinc oxide will be of general interest for characterizing and optimizing the growth and properties of more complex nanostructures.« less

Implications for plastic flow in the deep mantle from modelling dislocations in MgSiO3 minerals.

PubMed

Carrez, Philippe; Ferré, Denise; Cordier, Patrick

2007-03-01

The dynamics of the Earth's interior is largely controlled by mantle convection, which transports radiogenic and primordial heat towards the surface. Slow stirring of the deep mantle is achieved in the solid state through high-temperature creep of rocks, which are dominated by the mineral MgSiO3 perovskite. Transformation of MgSiO3 to a 'post-perovskite' phase may explain the peculiarities of the lowermost mantle, such as the observed seismic anisotropy, but the mechanical properties of these mineralogical phases are largely unknown. Plastic flow of solids involves the motion of a large number of crystal defects, named dislocations. A quantitative description of flow in the Earth's mantle requires information about dislocations in high-pressure minerals and their behaviour under stress. This property is currently out of reach of direct atomistic simulations using either empirical interatomic potentials or ab initio calculations. Here we report an alternative to direct atomistic simulations based on the framework of the Peierls-Nabarro model. Dislocation core models are proposed for MgSiO3 perovskite (at 100 GPa) and post-perovskite (at 120 GPa). We show that in perovskite, plastic deformation is strongly influenced by the orthorhombic distortions of the unit cell. In silicate post-perovskite, large dislocations are relaxed through core dissociation, with implications for the mechanical properties and seismic anisotropy of the lowermost mantle.

Atomistic Simulation of Initiation in Hexanitrostilbene

NASA Astrophysics Data System (ADS)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

An Atomistic View of the Incipient Growth of Zinc Oxide Nanolayers

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

Chu, Manh Hung; Tian, Liang; Chaker, Ahmad

The growth of zinc oxide thin films by atomic layer deposition is believed to proceed through an embryonic step in which three-dimensional nanoislands form and then coalesce to trigger a layer-by-layer growth mode. This transient initial state is characterized by a poorly ordered atomic structure, which may be inaccessible by X-ray diffraction techniques. Here in this work, we apply X-ray absorption spectroscopy in situ to address the local structure of Zn after each atomic layer deposition cycle, using a custom-built reactor mounted at a synchrotron beamline, and we shed light on the atomistic mechanisms taking place during the first stagesmore » of the growth. We find that such mechanisms are surprisingly different for zinc oxide growth on amorphous (silica) and crystalline (sapphire) substrate. Ab initio simulations and quantitative data analysis allow the formulation of a comprehensive growth model, based on the different effects of surface atoms and grain boundaries in the nanoscale islands, and the consequent induced local disorder. From a comparison of these spectroscopy results with those from X-ray diffraction reported recently, we observe that the final structure of the zinc oxide nanolayers depends strongly on the mechanisms taking place during the initial stages of growth. Finally, the approach followed here for the case of zinc oxide will be of general interest for characterizing and optimizing the growth and properties of more complex nanostructures.« 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)

Ab initio calculations of the lattice dynamics of silver halides

NASA Astrophysics Data System (ADS)

Gordienko, A. B.; Kravchenko, N. G.; Sedelnikov, A. N.

2010-12-01

Based on ab initio pseudopotential calculations, the results of investigations of the lattice dynamics of silver halides AgHal (Hal = Cl, Br, I) are presented. Equilibrium lattice parameters, phonon spectra, frequency densities and effective atomic-charge values are obtained for all types of crystals under study.

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] ...

Defect states and charge transport in quantum dot solids

DOE PAGES

Brawand, Nicholas P.; Goldey, Matthew B.; Vörös, Márton; ...

2017-01-16

Defects at the surface of semiconductor quantum dots (QDs) give rise to electronic states within the gap, which are detrimental to charge transport properties of QD devices. We investigated charge transport in silicon quantum dots with deep and shallow defect levels, using ab initio calculations and constrained density functional theory. We found that shallow defects may be more detrimental to charge transport than deep ones, with associated transfer rates differing by up to 5 orders of magnitude for the small dots (1-2 nm) considered here. Hence, our results indicate that the common assumption, that the ability of defects to trapmore » charges is determined by their position in the energy gap of the QD, is too simplistic, and our findings call for a reassessment of the role played by shallow defects in QD devices. Altogether, our results highlight the key importance of taking into account the atomistic structural properties of QD surfaces when investigating transport properties.« less

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules

NASA Astrophysics Data System (ADS)

Smith, Justin S.; Isayev, Olexandr; Roitberg, Adrian E.

2017-12-01

One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials, such as neural networks, comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of more than 20 M off equilibrium conformations for 57,462 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community.

Ab initio calculation of the deprotonation constants of an atomistically defined nanometer-sized, aluminium hydroxide oligomer

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

Wander, Matthew C. F.; Shuford, Kevin L.; Rustad, James R.

Aluminium possesses significant and diverse chemistry. Numerous compounds have been defined, and the elucidation of their chemistry is of significant geochemical interest. In this paper, a brucite-like, eight-aluminium aqueous cluster is modelled with density functional theory to identify its primary site of deprotonation and the associated pK(a) constant using both explicit (a full first solvent shell) and implicit solvent. Two methods for calculating the pK(a) are compared. We found that a bond density approach is better than a direct energy calculation for ions with large charge and high symmetry. The terminal aluminium atoms have equatorial ligated waters that in solventmore » have one long O-H bond. This site is more reactive than any of the other protons on the particle. Insights into the experimental crystal structure and Bader's Atoms in Molecules density analysis are presented as routes to reduce the computational time required for the identification of protonation sites.« less

SchNet - A deep learning architecture for molecules and materials

NASA Astrophysics Data System (ADS)

Schütt, K. T.; Sauceda, H. E.; Kindermans, P.-J.; Tkatchenko, A.; Müller, K.-R.

2018-06-01

Deep learning has led to a paradigm shift in artificial intelligence, including web, text, and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning, in general, and deep learning, in particular, are ideally suitable for representing quantum-mechanical interactions, enabling us to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for molecules and materials, where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study on the quantum-mechanical properties of C20-fullerene that would have been infeasible with regular ab initio molecular dynamics.

Pinning of topological solitons at extrinsic defects in a quasi one-dimensional charge density wave

NASA Astrophysics Data System (ADS)

Razzaq, Samad; Wippermann, Stefan; Tae Hwan Kim Collaboration; Han Woong Yeom Collaboration

Quasi one-dimensional (1D) electronic systems are known to exhibit exotic physical phenomena, such as, e.g., Jahn Teller distortions, charge density wave (CDW) formation and non-Fermi liquid behavior. Solitonic excitations of the charge density wave ordered ground state and associated topological edge states in atomic wires are presently the focus of increasing attention. We carried out a combined ab initio and scanning tunneling microscopy (STM) study of solitonic and non-solitonic phase defects in the In/Si(111) atomic wire array. While free solitons move too fast to be imaged directly in STM, they can become trapped at extrinsic de- fects within the wire. We discuss the detailed atomistic structure of the responsible extrinsic defects and trapped solitons. Our study highlights the key role of coupled theory-experimental investigations in order to understand also the elusive fast moving solitons. S. W. gratefully acknowledges financial support from the German Research Foundation (DFG), Grant No. FOR1700.

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

Frontiers of Theoretical Research on Shape Memory Alloys: A General Overview

NASA Astrophysics Data System (ADS)

Chowdhury, Piyas

2018-03-01

In this concise review, general aspects of modeling shape memory alloys (SMAs) are recounted. Different approaches are discussed under four general categories, namely, (a) macro-phenomenological, (b) micromechanical, (c) molecular dynamics, and (d) first principles models. Macro-phenomenological theories, stemming from empirical formulations depicting continuum elastic, plastic, and phase transformation, are primarily of engineering interest, whereby the performance of SMA-made components is investigated. Micromechanical endeavors are generally geared towards understanding microstructural phenomena within continuum mechanics such as the accommodation of straining due to phase change as well as role of precipitates. By contrast, molecular dynamics, being a more recently emerging computational technique, concerns attributes of discrete lattice structures, and thus captures SMA deformation mechanism by means of empirically reconstructing interatomic bonding forces. Finally, ab initio theories utilize quantum mechanical framework to peek into atomistic foundation of deformation, and can pave the way for studying the role of solid-sate effects. With specific examples, this paper provides concise descriptions of each category along with their relative merits and emphases.

High resistance to sulfur poisoning of Ni with copper skin under electric field

NASA Astrophysics Data System (ADS)

Xu, Xiaopei; Zhang, Yanxing; Yang, Zongxian

2017-02-01

The effects of sulfur poisoning on the (1 0 0), (1 1 0) and (1 1 1) surfaces of pure Ni and Cu/Ni alloy are studied in consideration of the effect of electric field. The effects of Cu dopants on the S poisoning characteristics are analyzed by the means of the density functional theory results in combination with thermodynamics data using the ab initio atomistic thermodynamic method. When the Cu concentration increases to 50% on the surface layer of the Cu/Ni alloy, the (1 1 0) surface becomes the most vulnerable to the sulfur poisoning. Ni with a copper skin can mostly decrease the sulfur poisoning effect. Especially under the electric field of 1.0 V/Å, the sulfur adsorption and phase transition temperature can be further reduced. We therefore propose that Ni surfaces with copper skin can be very effective to improve the resistance to sulfur poisoning of the Ni anode under high electric field.

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 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.

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.

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.

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.

Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.

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

Prezhdo, Oleg V.

2012-03-22

Funded by the DOE grant (i) we continued to study and analyze the atomistic detail of the electron transfer (ET) across the chromophore-TiO2 interface in Gratzel cell systems for solar hydrogen production. (ii) We extensively investigated the nature of photoexcited states and excited state dynamics in semiconductor quantum dots (QD) designed for photovoltaic applications. (iii) We continued a newly initiated research direction focusing on excited state properties and electron-phonon interactions in nanoscale carbon materials. Over the past year, the results of the DOE funded research were summarized in 3 review articles. 12 original manuscripts were written. The research results weremore » reported in 28 invited talks at conferences and university seminars. 20 invitations were accepted for talks in the near future. 2 symposia at national and international meetings have being organized this year on topics closely related to the DOE funded project, and 2 more symposia have been planned for the near future. We summarized the insights into photoinduced dynamics of semiconductor QDs, obtained from our time-domain ab initio studies. QDs exhibit both molecular and bulk properties. Unlike either bulk or molecular materials, QD properties can be modified continuously by changing QD shape and size. However, the chemical and physical properties of molecular and bulk materials often contradict each other, which can lead to differing viewpoints about the behavior of QDs. For example, the molecular view suggests strong electron-hole and charge-phonon interactions, as well as slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. In contrast, the bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. By synthesizing the bulk and molecular viewpoints, we clarified the controversies and provided a unified atomistic picture of the nature and dynamics of photoexcited states in semiconductor QDs. We also summarized our recent findings about the photoinduced electron dynamics at the chromophore-semiconductor interfaces from a time-domain ab initio perspective. The interface provides the foundation for a new, promising type of solar cell and presents a fundamentally important case study for several fields, including photo-, electro- and analytical chemistries, molecular electronics, and photography. Further, the interface offers a classic example of an interaction between an organic molecular species and an inorganic bulk material. Scientists employ different concepts and terminologies to describe molecular and solid states of matter, and these differences make it difficult to describe the interface with a single model. At the basic atomistic level of description, however, this challenge can be largely overcome. Recent advances in non-adiabatic molecular dynamics and time-domain density functional theory have created a unique opportunity for simulating the ultrafast, photoinduced processes on a computer very similar to the way that they occur in nature. These state-of-the-art theoretical tools offered a comprehensive picture of a variety of electron transfer processes that occur at the interface, including electron injection from the chromophore to the semiconductor, electron relaxation and delocalization inside the semiconductor, back-transfer of the electron to the chromophore and to the electrolyte, and regeneration of the neutral chromophore by the electrolyte. The ab initio time-domain modeling is particularly valuable for understanding these dynamic features of the ultrafast electron transfer processes, which cannot be represented by a simple rate description. We demonstrated using symmetry adapted cluster theory with configuration interaction (SAC-CI) that charging of small PbSe nanocrystals (NCs) greatly modifies their electronic states and optical excitations. Conduction and valence band transitions that are not available in neutral NCs dominate low energy electronic excitations and show weak optical activity. At higher energies these transitions mix with both single excitons (SEs) and multiple excitons (MEs) associated with transitions across the band-gap. As a result, both SEs and MEs are significantly blue-shifted, and ME generation is drastically hampered. The overall contribution of MEs to the electronic excitations of the charged NCs is small even at very high energies. The calculations supported the recent view that the observed strong dependence of the ME yields on the experimental conditions is likely due to the effects of NC charging. The electron-hole excitonic nature of high energy states was investigated in neutral and charged Si clusters, motivated by the ME generation (MEG) process that is highly debated in photovoltaic literature.« less

{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.

Role of atomistic structure in the stochastic nature of conductivity in substoichiometric tantalum pentoxide

DOE PAGES

Bondi, Robert James; Fox, Brian Philip; Marinella, Matthew J.

2016-03-22

In this study, first-principles calculations of electrical conductivity (σ o) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta 2O 5, where each structure contains a neutral O monovacancy (V O 0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each V O 0 location. Bader charge decomposition using a commonality analysis approach based on the σ o distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic chargemore » on the Ta subnetwork have a profound influence on σ o. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σ o in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized V O 0 interaction with the a-Ta 2O 5 network; conversely, delocalization of V O 0 corresponds to metallic character and high σ o. The random network of a-Ta 2O 5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σ o; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.« less

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

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.

Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

PubMed

Yang, Lina; Minnich, Austin J

2017-03-14

Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.

Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation

PubMed Central

Yang, Lina; Minnich, Austin J.

2017-01-01

Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials. PMID:28290484

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.

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.

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.

Atomistic determination of flexoelectric properties of crystalline dielectrics

NASA Astrophysics Data System (ADS)

Maranganti, R.; Sharma, P.

2009-08-01

Upon application of a uniform strain, internal sublattice shifts within the unit cell of a noncentrosymmetric dielectric crystal result in the appearance of a net dipole moment: a phenomenon well known as piezoelectricity. A macroscopic strain gradient on the other hand can induce polarization in dielectrics of any crystal structure, even those which possess a centrosymmetric lattice. This phenomenon, called flexoelectricity, has both bulk and surface contributions: the strength of the bulk contribution can be characterized by means of a material property tensor called the bulk flexoelectric tensor. Several recent studies suggest that strain-gradient induced polarization may be responsible for a variety of interesting and anomalous electromechanical phenomena in materials including electromechanical coupling effects in nonuniformly strained nanostructures, “dead layer” effects in nanocapacitor systems, and “giant” piezoelectricity in perovskite nanostructures among others. In this work, adopting a lattice dynamics based microscopic approach we provide estimates of the flexoelectric tensor for certain cubic crystalline ionic salts, perovskite dielectrics, III-V and II-VI semiconductors. We compare our estimates with experimental/theoretical values wherever available and also revisit the validity of an existing empirical scaling relationship for the magnitude of flexoelectric coefficients in terms of material parameters. It is interesting to note that two independent groups report values of flexoelectric properties for perovskite dielectrics that are orders of magnitude apart: Cross and co-workers from Penn State have carried out experimental studies on a variety of materials including barium titanate while Catalan and co-workers from Cambridge used theoretical ab initio techniques as well as experimental techniques to study paraelectric strontium titanate as well as ferroelectric barium titanate and lead titanate. We find that, in the case of perovskite dielectrics, our estimates agree to an order of magnitude with the experimental and theoretical estimates for strontium titanate. For barium titanate however, while our estimates agree to an order of magnitude with existing ab initio calculations, there exists a large discrepancy with experimental estimates. The possible reasons for the observed deviations are discussed.

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.

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 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.

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…

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.

Small-angle neutron scattering study of a monoclonal antibody using free-energy constraints.

PubMed

Clark, Nicholas J; Zhang, Hailiang; Krueger, Susan; Lee, Hyo Jin; Ketchem, Randal R; Kerwin, Bruce; Kanapuram, Sekhar R; Treuheit, Michael J; McAuley, Arnold; Curtis, Joseph E

2013-11-14

Monoclonal antibodies (mAbs) contain hinge-like regions that enable structural flexibility of globular domains that have a direct effect on biological function. A subclass of mAbs, IgG2, have several interchain disulfide bonds in the hinge region that could potentially limit structural flexibility of the globular domains and affect the overall configuration space available to the mAb. We have characterized human IgG2 mAb in solution via small-angle neutron scattering (SANS) and interpreted the scattering data using atomistic models. Molecular Monte Carlo combined with molecular dynamics simulations of a model mAb indicate that a wide range of structural configurations are plausible, spanning radius of gyration values from ∼39 to ∼55 Å. Structural ensembles and representative single structure solutions were derived by comparison of theoretical SANS profiles of mAb models to experimental SANS data. Additionally, molecular mechanical and solvation free-energy calculations were carried out on the ensemble of best-fitting mAb structures. The results of this study indicate that low-resolution techniques like small-angle scattering combined with atomistic molecular simulations with free-energy analysis may be helpful to determine the types of intramolecular interactions that influence function and could lead to deleterious changes to mAb structure. This methodology will be useful to analyze small-angle scattering data of many macromolecular systems.

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.

Density functional theory fragment descriptors to quantify the reactivity of a molecular family: application to amino acids.

PubMed

Senet, P; Aparicio, F

2007-04-14

By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a blind test, the method is applied to the lateral chains of the 20 isolated amino acids. One demonstrates that the local softness of the lateral chain is a quantitative measure of the similarity of the amino acids. It predicts the separation of amino acids in different biochemical groups (aliphatic, basic, acidic, sulfur contained, and aromatic). The present approach may find applications in quantitative structure activity relationship methodology.

Electronic and local atomistic structure of MgSiO3 glass under pressure: a study of X-ray Raman scattering at the silicon and magnesium L-edges

NASA Astrophysics Data System (ADS)

Fukui, Hiroshi; Hiraoka, Nozomu

2018-02-01

We applied X-ray Raman scattering technique to MgSiO3 glass, a precursor to magnesium silicate melts, with respect to magnesium and silicon under high-pressure conditions as well as some polycrystalline phases of MgSiO3 at ambient conditions. We also performed ab initio calculations to interpret the X-ray Raman spectra. Experimentally obtained silicon L-edge spectra indicate that the local environment around silicon started changing at pressure above 10 GPa, where the electronic structure of oxygen is known to change. In contrast, the shape of the magnesium L-edge spectrum changed below 10 GPa. This indicates that the magnesium sites in MgSiO3 glass first distort and that the local structure around magnesium shows a wide variation under pressure. The framework structure consisting of silicon and oxygen changed above 10 GPa, where the coordination number of silicon was more than four. Our results imply that 6-oxygen-coordinated silicon was formed above 20 GPa.

Variational Identification of Markovian Transition States

NASA Astrophysics Data System (ADS)

Martini, Linda; Kells, Adam; Covino, Roberto; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

2017-07-01

We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5 , and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting) transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

Bowl Inversion and Electronic Switching of Buckybowls on Gold.

PubMed

Fujii, Shintaro; Ziatdinov, Maxim; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kiguchi, Manabu

2016-09-21

Bowl-shaped π-conjugated compounds, or buckybowls, are a novel class of sp(2)-hybridized nanocarbon materials. In contrast to tubular carbon nanotubes and ball-shaped fullerenes, the buckybowls feature structural flexibility. Bowl-to-bowl structural inversion is one of the unique properties of the buckybowls in solutions. Bowl inversion on a surface modifies the metal-molecule interactions through bistable switching between bowl-up and bowl-down states on the surface, which makes surface-adsorbed buckybowls a relevant model system for elucidation of the mechano-electronic properties of nanocarbon materials. Here, we report a combination of scanning tunneling microscopy (STM) measurements and ab initio atomistic simulations to identify the adlayer structure of the sumanene buckybowl on Au(111) and reveal its unique bowl inversion behavior. We demonstrate that the bowl inversion can be induced by approaching the STM tip toward the molecule. By tuning the local metal-molecule interaction using the STM tip, the sumanene buckybowl exhibits structural bistability with a switching rate that is two orders of magnitude faster than that of the stochastic inversion process.

Simulation of gas diffusion and sorption in nanoceramic semiconductors

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

1999-05-01

Gas diffusion and sorption in nanoceramic semiconductors are studied using atomistic simulation techniques and numerical results are presented for a variety of sorbate-sorbent systems. SnO2, BaTiO3, CuO, and MgO substrates are built on the computer using lattice constants and atomic parameters that have been either measured or computed by ab initio methods. The Universal force field is employed here for the description of both intramolecular and nonbonded interactions for various gas sorbates, including CH4, CO, CO2, and O2, pure and in binary mixtures. Mean residence times are determined by molecular dynamics computations, whereas the Henry constant and the isosteric heat of adsorption are estimated by a Monte Carlo technique. The effects of surface hydroxylation on the diffusion and sorption characteristics are quantified and discussed in view of their significance in practical gas sensing applications. The importance of fast diffusion on the response time of the sensitive layer and of the sorption efficiency on the overall sensitivity as well as the potential synergy of the two phenomena are discussed.

Understanding and revisiting the most complex perovskite system via atomistic simulations

NASA Astrophysics Data System (ADS)

Yang, Yali; Xu, Bin; Xu, Changsong; Ren, Wei; Bellaiche, Laurent

2018-05-01

A first-principles-based effective Hamiltonian is developed and used, along with direct ab initio techniques, to investigate finite-temperature properties of the system commonly coined the most complex perovskite, that is NaNbO3. Such simulations successfully reproduce the existence of seven different phases in its phase diagram. The decomposition of the total energy of this effective Hamiltonian into different terms, altogether with the values of the parameters associated with these terms, also allow us to shed some light into puzzling features of such a compound. Examples include revealing the microscopic reasons of why R 3 c is its ground state and why it solely adopts in-phase tiltings at high temperatures versus complex nanotwins for intermediate temperatures. The results of the computations also call for a revisiting of the so-called P ,R , and S states, in the sense that an unexpected and previously overlooked inhomogeneous electrical polarization is numerically found in the P state while complex tiltings associated with the simultaneous condensation of several k points are predicted for the controversial R and S phases.

Interplay between interstitial displacement and displacive lattice transformations

NASA Astrophysics Data System (ADS)

Zhang, Xie; Hickel, Tilmann; Rogal, Jutta; Neugebauer, Jörg

2016-09-01

Diffusionless displacive lattice rearrangements, which include martensitic transformations, are in real materials often accompanied by a displacive drag of interstitials. The interplay of both processes leads to a particular atomistic arrangement of the interstitials in the product phase, which is decisive for its performance. An archetype example is the martensitic transformation in Fe-C alloys. One of the puzzles for this system is that the deviation from the cubic symmetry (i.e., the tetragonality) in the martensite resulting from this interplay is lower than what thermodynamics dictates. In our ab initio approach, the relative motion of C in the transforming lattice is studied with the nudged elastic band method. We prove that an atomic shearlike shuffle mechanism of adjacent (11 2 ¯) Fe layers along the ±[111] bcc directions is essential to achieve a redistribution of C atoms during the fcc → bcc transition, which fully explains the abnormal behavior. Furthermore, the good agreement with experiment validates our method to treat a diffusionless redistribution of interstitials and a displacive rearrangement of the host lattice simultaneously.

W and X Photoluminescence Centers in Crystalline Si: Chasing Candidates at Atomic Level Through Multiscale Simulations

NASA Astrophysics Data System (ADS)

Aboy, María; Santos, Iván; López, Pedro; Marqués, Luis A.; Pelaz, Lourdes

2018-04-01

Several atomistic techniques have been combined to identify the structure of defects responsible for X and W photoluminescence lines in crystalline Si. We used kinetic Monte Carlo simulations to reproduce irradiation and annealing conditions used in photoluminescence experiments. We found that W and X radiative centers are related to small Si self-interstitial clusters but coexist with larger Si self-interstitials clusters that can act as nonradiative centers. We used molecular dynamics simulations to explore the many different configurations of small Si self-interstitial clusters, and selected those having symmetry compatible with W and X photoluminescence centers. Using ab initio simulations, we calculated their formation energy, donor levels, and energy of local vibrational modes. On the basis of photoluminescence experiments and our multiscale theoretical calculations, we discuss the possible atomic configurations responsible for W and X photoluminescence centers in Si. Our simulations also reveal that the intensity of photoluminescence lines is the result of competition between radiative centers and nonradiative competitors, which can explain the experimental quenching of W and X lines even in the presence of the photoluminescence centers.

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.

Atomistic modeling of crystal-to-amorphous transition and associated kinetics in the Ni-Nb system by molecular dynamics simulations.

PubMed

Dai, X D; Li, J H; Liu, B X

2005-03-17

With the aid of ab initio calculations, an n-body potential of the Ni-Nb system is constructed under the Finnis-Sinclair formalism and the constructed potential is capable of not only reproducing some static physical properties but also revealing the atomistic mechanism of crystal-to-amorphous transition and associated kinetics. With application of the constructed potential, molecular dynamics simulations using the solid solution models reveal that the physical origin of crystal-to-amorphous transition is the crystalline lattice collapsing while the solute atoms are exceeding the critical solid solubilities, which are determined to be 19 atom % Ni and 13 atom % Nb for the Nb- and Ni-based solid solutions, respectively. It follows that an intrinsic glass-forming ability of the Ni-Nb system is within 19-87 atom % Ni, which matches well with that observed in ion beam mixing/solid-state reaction experiments. Simulations using the Nb/Ni/Nb (Ni/Nb/Ni) sandwich models indicate that the amorphous layer at the interfaces grows in a layer-by-layer mode and that, upon dissolving solute atoms, the Ni lattice approaches and exceeds its critical solid solubility faster than the Nb lattice, revealing an asymmetric behavior in growth kinetics. Moreover, an energy diagram is obtained by computing the energetic sequence of the Ni(x)Nb(100)(-)(x) alloy in fcc, bcc, and amorphous structures, respectively, over the entire composition range, and the diagram could serve as a guide for predicting the metastable alloy formation in the Ni-Nb system.

Role of atomistic structure in the stochastic nature of conductivity in substoichiometric tantalum pentoxide

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

Bondi, Robert J., E-mail: rjbondi@sandia.gov; Fox, Brian P.; Marinella, Matthew J.

2016-03-28

First-principles calculations of electrical conductivity (σ{sub o}) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta{sub 2}O{sub 5}, where each structure contains a neutral O monovacancy (V{sub O}{sup 0}). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each V{sub O}{sup 0} location. Bader charge decomposition using a commonality analysis approach based on the σ{sub o} distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork havemore » a profound influence on σ{sub o}. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σ{sub o} in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized V{sub O}{sup 0} interaction with the a-Ta{sub 2}O{sub 5} network; conversely, delocalization of V{sub O}{sup 0} corresponds to metallic character and high σ{sub o}. The random network of a-Ta{sub 2}O{sub 5} provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σ{sub o}; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.« less

Atomistic Models of General Anesthetics for Use in in Silico Biological Studies

PubMed Central

2015-01-01

While small molecules have been used to induce anesthesia in a clinical setting for well over a century, a detailed understanding of the molecular mechanism remains elusive. In this study, we utilize ab initio calculations to develop a novel set of CHARMM-compatible parameters for the ubiquitous modern anesthetics desflurane, isoflurane, sevoflurane, and propofol for use in molecular dynamics (MD) simulations. The parameters generated were rigorously tested against known experimental physicochemical properties including dipole moment, density, enthalpy of vaporization, and free energy of solvation. In all cases, the anesthetic parameters were able to reproduce experimental measurements, signifying the robustness and accuracy of the atomistic models developed. The models were then used to study the interaction of anesthetics with the membrane. Calculation of the potential of mean force for inserting the molecules into a POPC bilayer revealed a distinct energetic minimum of 4–5 kcal/mol relative to aqueous solution at the level of the glycerol backbone in the membrane. The location of this minimum within the membrane suggests that anesthetics partition to the membrane prior to binding their ion channel targets, giving context to the Meyer–Overton correlation. Moreover, MD simulations of these drugs in the membrane give rise to computed membrane structural parameters, including atomic distribution, deuterium order parameters, dipole potential, and lateral stress profile, that indicate partitioning of anesthetics into the membrane at the concentration range studied here, which does not appear to perturb the structural integrity of the lipid bilayer. These results signify that an indirect, membrane-mediated mechanism of channel modulation is unlikely. PMID:25303275

Nanopatterning of Group V Elements for Tailoring the Electronic Properties of Semiconductors by Monolayer Doping.

PubMed

Thissen, Peter; Cho, Kyeongjae; Longo, Roberto C

2017-01-18

Control of the electronic properties of semiconductors is primarily achieved through doping. While scaling down the device dimensions to the molecular regime presents an increasing number of difficulties, doping control at the nanoscale is still regarded as one of the major challenges of the electronic industry. Within this context, new techniques such as monolayer doping (MLD) represent a substantial improvement toward surface doping with atomic and specific doping dose control at the nanoscale. Our previous work has explained in detail the atomistic mechanism behind MLD by means of density-functional theory calculations (Chem. Mater. 2016, 28, 1975). Here, we address the key questions that will ultimately allow one to optimize the scalability of the MLD process. First, we show that dopant coverage control cannot be achieved by simultaneous reaction of several group V elements, but stepwise reactions make it possible. Second, using ab initio molecular dynamics, we investigate the thermal decomposition of the molecular precursors, together with the stability of the corresponding binary and ternary dopant oxides, prior to the dopant diffusion into the semiconductor surface. Finally, the effect of the coverage and type of dopant on the electronic properties of the semiconductor is also analyzed. Furthermore, the atomistic characterization of the MLD process raises unexpected questions regarding possible crystal damage effects by dopant exchange with the semiconductor ions or the final distribution of the doping impurities within the crystal structure. By combining all our results, optimization recipes to create ultrashallow doped junctions at the nanoscale are finally proposed.

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

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.

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.

Ab initio calculations for the elastic properties of magnesium under pressure

NASA Astrophysics Data System (ADS)

Sin'Ko, G. V.; Smirnov, N. A.

2009-09-01

Results of ab initio calculations of the elastic constants for the hcp, bcc, double hcp (dhcp), and fcc magnesium in a wide range of pressures are presented. The calculated elastic constants are compared with available experimental and theoretical data. We discuss the effect of the electron topological transition that occurs when the hcp structure is compressed on results of calculations and consider possibility of observing the hcp→dhcp transition on the magnesium Hugoniot.

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE PAGES

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

2017-04-26

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

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

Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate ismore » about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.« less

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

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

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Experimental and Ab Initio Studies of the HDO Absorption Spectrum in the 13165-13500 1/cm Spectral Region

NASA Technical Reports Server (NTRS)

Schwenke, David; Naumenko, Olga; Bertseva, Elena; Campargue, Alain; Arnold, James O. (Technical Monitor)

2000-01-01

The HDO absorption spectrum has been recorded in the 13165 - 13500 cm(exp-1) spectral region by Intracavity Laser Absorption Spectroscopy. The spectrum (615 lines), dominated by the 2n2 + 3n3 and n1+3n3 bands was assigned and modeled leading to the derivation of 196 accurate energy levels of the (103) and (023) vibrational states. Finally, 150 of these levels have been reproduced by an effective Hamiltonian involving two vibrational dark states interacting with the (023) and ( 103) bright states. The rms deviation achieved by variation of 28 parameters is 0.05-1 cm, compared to an averaged experimental uncertainty of 0.007-1 cm, indicating the limit of validity of the effective Hamiltonian approach for HDO at high vibrational excitation. The predictions of previous ab initio calculations of the HDO spectrum were extensively used in the assignment process. The particular spectral region under consideration has been used to test and discuss the improvements of new ab initio calculations recently performed on the basis of the same potential energy surface but with an improved dipole moment surface. The improvements concern both the energy levels and the line intensities. In particular, the strong hybrid character of the n1+3n3 band is very well accounted for by the the new ab initio calculations.

Magnetic Excitations in Polyoxotungstate-Supported Lanthanoid Single-Molecule Magnets: An Inelastic Neutron Scattering and ab Initio Study.

PubMed

Vonci, Michele; Giansiracusa, Marcus J; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2017-01-03

Inelastic neutron scattering (INS) has been used to investigate the crystal field (CF) magnetic excitations of the analogs of the most representative lanthanoid-polyoxometalate single-molecule magnet family: Na 9 [Ln(W 5 O 18 ) 2 ] (Ln = Nd, Tb, Ho, Er). Ab initio complete active space self-consistent field/restricted active space state interaction calculations, extended also to the Dy analog, show good agreement with the experimentally determined low-lying CF levels, with accuracy better in most cases than that reported for approaches based only on simultaneous fitting to CF models of magnetic or spectroscopic data for isostructural Ln families. In this work we demonstrate the power of a combined spectroscopic and computational approach. Inelastic neutron scattering has provided direct access to CF levels, which together with the magnetometry data, were employed to benchmark the ab initio results. The ab initio determined wave functions corresponding to the CF levels were in turn employed to assign the INS transitions allowed by selection rules and interpret the observed relative intensities of the INS peaks. Ultimately, we have been able to establish the relationship between the wave function composition of the CF split Ln III ground multiplets and the experimentally measured magnetic and spectroscopic properties for the various analogs of the Na 9 [Ln(W 5 O 18 ) 2 ] family.

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well. The robustness of the algorithm with respect to the only free parameter it involves is ascertained. The method is then applied to perform tensile tests on gold nanopillars on strain rates as low as 100/s, bringing out the perils of high strain-rate molecular dynamics calculations. We also calculate temperature and stress dependence of activation free energy for surface nucleation of dislocations in pristine gold nanopillars under realistic loads. While maintaining fully atomistic resolution, we reach the fraction-of-a-second time scale regime. It is found that the activation free energy depends significantly and nonlinearly on the driving force (stress or strain) and temperature, leading to very high activation entropies for surface dislocation nucleation.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Spin-orbit coupled potential energy surfaces and properties using effective relativistic coupling by asymptotic representation.

PubMed

Ndome, Hameth; Eisfeld, Wolfgang

2012-08-14

A new method has been reported recently [H. Ndome, R. Welsch, and W. Eisfeld, J. Chem. Phys. 136, 034103 (2012)] that allows the efficient generation of fully coupled potential energy surfaces (PESs) including derivative and spin-orbit (SO) coupling. The method is based on the diabatic asymptotic representation of the molecular fine structure states and an effective relativistic coupling operator and therefore is called effective relativistic coupling by asymptotic representation (ERCAR). The resulting diabatic spin-orbit coupling matrix is constant and the geometry dependence of the coupling between the eigenstates is accounted for by the diabatization. This approach allows to generate an analytical model for the fully coupled PESs without performing any ab initio SO calculations (except perhaps for the atoms) and thus is very efficient. In the present work, we study the performance of this new method for the example of hydrogen iodide as a well-established test case. Details of the diabatization and the accuracy of the results are investigated in comparison to reference ab initio calculations. The energies of the adiabatic fine structure states are reproduced in excellent agreement with reference ab initio data. It is shown that the accuracy of the ERCAR approach mainly depends on the quality of the underlying ab initio data. This is also the case for dissociation and vibrational level energies, which are influenced by the SO coupling. A method is presented how one-electron operators and the corresponding properties can be evaluated in the framework of the ERCAR approach. This allows the computation of dipole and transition moments of the fine structure states in good agreement with ab initio data. The new method is shown to be very promising for the construction of fully coupled PESs for more complex polyatomic systems to be used in quantum dynamics studies.

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

DOE PAGES

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr; ...

2016-05-10

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier.

PubMed

Xia, Jiaqi; Peng, Zhenling; Qi, Dawei; Mu, Hongbo; Yang, Jianyi

2017-03-15

Protein fold classification is a critical step in protein structure prediction. There are two possible ways to classify protein folds. One is through template-based fold assignment and the other is ab-initio prediction using machine learning algorithms. Combination of both solutions to improve the prediction accuracy was never explored before. We developed two algorithms, HH-fold and SVM-fold for protein fold classification. HH-fold is a template-based fold assignment algorithm using the HHsearch program. SVM-fold is a support vector machine-based ab-initio classification algorithm, in which a comprehensive set of features are extracted from three complementary sequence profiles. These two algorithms are then combined, resulting to the ensemble approach TA-fold. We performed a comprehensive assessment for the proposed methods by comparing with ab-initio methods and template-based threading methods on six benchmark datasets. An accuracy of 0.799 was achieved by TA-fold on the DD dataset that consists of proteins from 27 folds. This represents improvement of 5.4-11.7% over ab-initio methods. After updating this dataset to include more proteins in the same folds, the accuracy increased to 0.971. In addition, TA-fold achieved >0.9 accuracy on a large dataset consisting of 6451 proteins from 184 folds. Experiments on the LE dataset show that TA-fold consistently outperforms other threading methods at the family, superfamily and fold levels. The success of TA-fold is attributed to the combination of template-based fold assignment and ab-initio classification using features from complementary sequence profiles that contain rich evolution information. http://yanglab.nankai.edu.cn/TA-fold/. yangjy@nankai.edu.cn or mhb-506@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

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

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

Curved-line search algorithm for ab initio atomic structure relaxation

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

2017-09-01

Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

Kinetic study on the H + SiH4 abstraction reaction using an ab initio potential energy surface.

PubMed

Cao, Jianwei; Zhang, Zhijun; Zhang, Chunfang; Bian, Wensheng; Guo, Yin

2011-01-14

Variational transition state theory calculations with the correction of multidimensional tunneling are performed on a 12-dimensional ab initio potential energy surface for the H + SiH(4) abstraction reaction. The surface is constructed using a dual-level strategy. For the temperature range 200-1600 K, thermal rate constants are calculated and kinetic isotope effects for various isotopic species of the title reaction are investigated. The results are in very good agreement with available experimental data.

Ab initio theory of the N2V defect in diamond for quantum memory implementation

NASA Astrophysics Data System (ADS)

Udvarhelyi, Péter; Thiering, Gergő; Londero, Elisa; Gali, Adam

2017-10-01

The N2V defect in diamond is characterized by means of ab initio methods relying on density functional theory calculated parameters of a Hubbard model Hamiltonian. It is shown that this approach appropriately describes the energy levels of correlated excited states induced by this defect. By determining its critical magneto-optical parameters, we propose to realize a long-living quantum memory by N2V defect, i.e., H 3 color center in diamond.

Ab initio calculations of potential energy curves of Hg/sub 2/ and TlHg

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

Celestino, K.C.; Ermler, W.C.

1984-08-15

Potential energy curves for electronic states of Hg/sub 2/ and TlHg are presented and analyzed. They are derived using large scale configuration interaction procedures for the valence electrons, with the core electrons represented by ab initio relativistic effective potentials. The effect of spin-orbit coupling are investigated for the low-lying excimer states. It is determined that neither system possesses strongly bound electronic states for which transitions to the repulsive ground states are optically allowed.

Development and Application of New Algorithms for the Simulation of Viscous Compressible Flows with Moving Bodies in Three Dimensions.

DTIC Science & Technology

1996-12-01

ranging from academic to industrial demonstrated the utility of the developed procedure for ab initio surface meshing from discrete data, such as...academic to industrial demonstrate the utility of the pro- hypersonic reentry problems, where ray-tracing based on posed procedure for ab initio surface...data input within industrial simulations. The origi- nal CAD dataset had over 500 surface patches, many All of the surface grids shown were obtained

Ab initio SCF calculations on the potential energy surface of potassium cyanide (KCN)

NASA Astrophysics Data System (ADS)

Wormer, Paul E. S.; Tennyson, Jonathan

1981-08-01

The potential energy surface of KCN has been generated by ab initio SCF calculations in the region of equilibrium bond distances. An analytic representation of the surface is presented. The calculations show that the bonding between K and CN is ionic, and that the structure of KCN is triangular, which confirms recent experimental findings. The computed geometry is &KCN = 62.4°, rCK = 5.492a0, and rCN = 2.186a0.

Determination of the electronic energy levels of colloidal nanocrystals using field-effect transistors and Ab-initio calculations.

PubMed

Bisri, Satria Zulkarnaen; Degoli, Elena; Spallanzani, Nicola; Krishnan, Gopi; Kooi, Bart Jan; Ghica, Corneliu; Yarema, Maksym; Heiss, Wolfgang; Pulci, Olivia; Ossicini, Stefano; Loi, Maria Antonietta

2014-08-27

Colloidal nanocrystals electronic energy levels are determined by strong size-dependent quantum confinement. Understanding the configuration of the energy levels of nanocrystal superlattices is vital in order to use them in heterostructures with other materials. A powerful method is reported to determine the energy levels of PbS nanocrystal assemblies by combining the utilization of electric-double-layer-gated transistors and advanced ab-initio theory. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab-initio study of pressure evolution of structural, mechanical and magnetic properties of cementite (Fe3C) phase

NASA Astrophysics Data System (ADS)

Gorai, S.; Ghosh, P. S.; Bhattacharya, C.; Arya, A.

2018-04-01

The pressure evolution of phase stability, structural and mechanical properties of Fe3C in ferro-magnetic (FM) and high pressure non magnetic (NM) phase is investigated from first principle calculations. The 2nd order FM to NM phase transition of Fe3C is identified around 60 GPa. Pressure (or density) variation of sound velocities from our ab-initio calculated single crystal elastic constants are determined to predict these parameters at Earth's outer core pressure.

The study of molecular spectroscopy by ab initio methods

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1991-01-01

This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

Ab initio Kinetics and Thermal Decomposition Mechanism of Mononitrobiuret and 1,5-Dinitrobiuret

DTIC Science & Technology

2016-03-14

Journal Article 3. DATES COVERED (From - To) Feb 2015-May 2015 4. TITLE AND SUBTITLE Ab initio Kinetics and Thermal Decomposition Mechanism of 5a...tetrazole-free, nitrogen-rich, energetic compounds. For the first time, the thermal decomposition mechanisms of MNB and DNB have been investigated...potential energy surfaces for thermal decomposition of MNB and DNB were characterized at the RCCSD(T)/cc-pV∞Z//M06-2X/aug- cc-pVTZ level of theory

Data files for ab initio calculations of the lattice parameter and elastic stiffness coefficients of bcc Fe with solutes

DOE PAGES

Fellinger, Michael R.; Hector, Jr., Louis G.; Trinkle, Dallas R.

2016-11-29

Here, we present computed datasets on changes in the lattice parameter and elastic stiffness coefficients of BCC Fe due to substitutional Al, B, Cu, Mn, and Si solutes, and octahedral interstitial C and N solutes. The data is calculated using the methodology based on density functional theory (DFT). All the DFT calculations were performed using the Vienna Ab initio Simulations Package (VASP). The data is stored in the NIST dSpace repository.

Ab initio tensile experiment on a model of an intergranular glassy film in β-Si3N4 with prismatic surfaces

NASA Astrophysics Data System (ADS)

Ching, W. Y.; Rulis, Paul; Ouyang, Lizhi; Misra, A.

2009-02-01

We report the results of a large-scale ab initio simulation of an intergranular glassy film (IGF) model in β-Si3N4. It is shown that the stress-strain behavior under uniaxial load in the model with prismatic surfaces and few defective bonds is very different from an earlier IGF model with basal planes. The results are explained by the fundamental electronic structure of the model.

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

Operator evolution for ab initio electric dipole transitions of 4He

DOE PAGES

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; ...

2015-07-24

A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopic internucleon forces. A major element of such an effort is applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for nonscalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity renormalization group method and apply the renormalized matrix elements to the calculationmore » of the 4He total photoabsorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. Furthermore, we find that, although seemingly small, the effects of evolved operators on the photoabsorption cross section are comparable in magnitude to the correction produced by including the chiral three-nucleon force and cannot be neglected.« less

Three-cluster dynamics within an ab initio framework

DOE PAGES

Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

2013-09-26

In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core ( 4He) polarization effects.« less

Ab initio calculations of the concentration dependent band gap reduction in dilute nitrides

NASA Astrophysics Data System (ADS)

Rosenow, Phil; Bannow, Lars C.; Fischer, Eric W.; Stolz, Wolfgang; Volz, Kerstin; Koch, Stephan W.; Tonner, Ralf

2018-02-01

While being of persistent interest for the integration of lattice-matched laser devices with silicon circuits, the electronic structure of dilute nitride III/V-semiconductors has presented a challenge to ab initio computational approaches. The origin of the computational problems is the strong distortion exerted by the N atoms on most host materials. Here, these issues are resolved by combining density functional theory calculations based on the meta-GGA functional presented by Tran and Blaha (TB09) with a supercell approach for the dilute nitride Ga(NAs). Exploring the requirements posed to supercells, it is shown that the distortion field of a single N atom must be allowed to decrease so far that it does not overlap with its periodic images. This also prevents spurious electronic interactions between translational symmetric atoms, allowing us to compute band gaps in very good agreement with experimentally derived reference values. In addition to existing approaches, these results offer a promising ab initio avenue to the electronic structure of dilute nitride semiconductor compounds.

Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands

NASA Astrophysics Data System (ADS)

Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe

2013-06-01

Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.

Effects of Mg II and Ca II ionization on ab-initio solar chromosphere models

NASA Technical Reports Server (NTRS)

Rammacher, W.; Cuntz, M.

1991-01-01

Acoustically heated solar chromosphere models are computed considering radiation damping by (non-LTE) emission from H(-) and by Mg II and Ca II emission lines. The radiative transfer equations for the Mg II k and Ca II K emission lines are solved using the core-saturation method with complete redistribution. The Mg II k and Ca II K cooling rates are compared with the VAL model C. Several substantial improvements over the work of Ulmschneider et al. (1987) are included. It is found that the rapid temperature rises caused by the ionization of Mg II are not formed in the middle chromosphere, but occur at larger atmospheric heights. These models represent the temperature structure of the 'real' solar chromosphere much better. This result is a major precondition for the study of ab-initio models for solar flux tubes based on MHD wave propagation and also for ab-initio models for the solar transition layer.

Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

PubMed

Hoy, Erik P; Mazziotti, David A

2015-08-14

Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

Ab initio simulations of iron-nickel alloys at Earth's core conditions

NASA Astrophysics Data System (ADS)

Côté, Alexander S.; Vočadlo, Lidunka; Brodholt, John P.

2012-09-01

We report ab initio density functional theory calculations on iron-nickel (FeNi) alloys at conditions representative of the Earth's inner core. We test different concentrations of Ni, up to ∼39 wt% using ab initio lattice dynamics, and investigate the thermodynamic and vibrational stability of the three candidate crystal structures (bcc, hcp and fcc). First of all, at inner core pressures, we find that pure Fe transforms from the hcp to the fcc phase at around 6000 K. Secondly, in agreement with low pressure experiments on Fe-Ni alloys, we find the fcc structure is stabilised by the incorporation of Ni under core pressures and temperatures. Our results show that the fcc structure may, therefore, be stable under core conditions depending on the temperature in the inner core and the Ni content. Lastly, we find that within the quasi-harmonic approximation, there is no stability field for FeNi alloys in the bcc structure under core conditions.

Towards an ab-initio treatment of nonlocal electronic correlations with dynamical vertex approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten

Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.

Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.

PubMed

Aalbergsjø, Siv G; Pauwels, Ewald; Van Yperen-De Deyne, Andy; Van Speybroeck, Veronique; Sagstuen, Einar

2014-08-28

As the chemical structures of radiation damaged molecules may differ greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline α-l-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move. Diversity in the radical production is gained by using different points on the potential energy surface of the intact crystal as starting points for the ionizations and letting the initial velocities of the nuclei after ionization be generated randomly. 160 ab initio MD runs produced 12 unique radical structures for investigation. Out of these, 7 of the potential products have never previously been discussed, and 3 products are found to match with radicals previously observed by electron magnetic resonance experiments.

Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

2011-01-01

Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

Phenolic Polymer Solvation in Water and Ethylene Glycol, II: Ab Initio Computations.

PubMed

Bauschlicher, Charles W; Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Lawson, John W

2017-04-06

Ab initio techniques are used to study the interaction of ethylene glycol and water with a phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as those of water, but the potential energy surface is further complicated by CH 2 -phenolic interactions, different conformers of ethylene glycol, and two OH groups on each molecule. Thus, the ethylene glycol-phenolic potential is more complicated than the water-phenolic potential. The results of the ab initio calculations are compared to those obtained using a force field. These calibration studies show that the water system is easier to describe than the ethylene glycol system. The calibration studies confirm the reliability of force fields used in our companion molecular dynamics study of a phenolic polymer in water and ethylene solutions.

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations

NASA Astrophysics Data System (ADS)

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-01

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and/or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S1) as well as the second excited singlet (S2) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S1 state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S2 state. Ab initio calculations using the density functional theory at B3LYP/6-31G** level corroborate well with the experimental observations.

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations.

PubMed

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-28

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and∕or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S(1)) as well as the second excited singlet (S(2)) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S(1) state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S(2) state. Ab initio calculations using the density functional theory at B3LYP∕6-31G∗∗ level corroborate well with the experimental observations.

Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kumar, Sanjay

2007-12-01

State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.

Nonconventional screening of the Coulomb interaction in FexOy clusters: An ab initio study

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Rossen, S.; Friedrich, C.; Blügel, S.; Katsnelson, M. I.

2017-04-01

From microscopic point-dipole model calculations of the screening of the Coulomb interaction in nonpolar systems by polarizable atoms, it is known that screening strongly depends on dimensionality. For example, in one-dimensional systems, the short-range interaction is screened, while the long-range interaction is antiscreened. This antiscreening is also observed in some zero-dimensional structures, i.e., molecular systems. By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the FLAPW method, we study screening of the Coulomb interaction in FexOy clusters. For completeness, these results are compared with their bulk counterpart magnetite. It appears that the on-site Coulomb interaction is very well screened both in the clusters and bulk. On the other hand, for the intersite Coulomb interaction, the important observation is made that it is almost constant throughout the clusters, while for the bulk it is almost completely screened. More precisely and interestingly, in the clusters antiscreening is observed by means of ab initio calculations.

A permutationally invariant full-dimensional ab initio potential energy surface for the abstraction and exchange channels of the H + CH{sub 4} system

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

Li, Jun, E-mail: jli15@cqu.edu.cn, E-mail: zhangdh@dicp.ac.cn; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131; Chen, Jun

2015-05-28

We report a permutationally invariant global potential energy surface (PES) for the H + CH{sub 4} system based on ∼63 000 data points calculated at a high ab initio level (UCCSD(T)-F12a/AVTZ) using the recently proposed permutation invariant polynomial-neural network method. The small fitting error (5.1 meV) indicates a faithful representation of the ab initio points over a large configuration space. The rate coefficients calculated on the PES using tunneling corrected transition-state theory and quasi-classical trajectory are found to agree well with the available experimental and previous quantum dynamical results. The calculated total reaction probabilities (J{sub tot} = 0) including themore » abstraction and exchange channels using the new potential by a reduced dimensional quantum dynamic method are essentially the same as those on the Xu-Chen-Zhang PES [Chin. J. Chem. Phys. 27, 373 (2014)].« less

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

2016-05-01

We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

Ab initio study of the structural properties of acetonitrile-water mixtures

NASA Astrophysics Data System (ADS)

Chen, Jinfan; Sit, Patrick H.-L.

2015-08-01

Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

Using Ab-Initio Calculations to Appraise Stm-Based - and Kink-Formation Energies

NASA Astrophysics Data System (ADS)

Feibelman, Peter J.

2001-03-01

Ab-initio total energies can and should be used to test the typically model-dependent results of interpreting STM morphologies. The benefits of such tests are illustrated here by ab-initio energies of step- and kink-formation on Pb and Pt(111) which show that the STM-based values of the kink energies must be revised. On Pt(111), the computed kink-energies for (100)- and (111)-microfacet steps are about 0.25 and 0.18 eV. These results imply a specific ratio of formation energies for the two step types, namely 1.14, in excellent agreement with experiment. If kink-formation actually cost the same energy on the two step types, an inference drawn from scanning probe observations of step wandering,(M. Giesen et al., Surf. Sci. 366, 229(1996).) this ratio ought to be 1. In the case of Pb(111), though computed energies to form (100)- and (111)-microfacet steps agree with measurement, the ab-initio kink-formation energies for the two step types, 41 and 60 meV, are 40-50% below experimental values drawn from STM images.(K. Arenhold et al., Surf. Sci. 424, 271(1999).) The discrepancy results from interpreting the images with a step-stiffness vs. kink-energy relation appropriate to (100) but not (111) surfaces. Good agreement is found when proper account of the trigonal symmetry of Pb(111) is taken in reinterpreting the step-stiffness data.

Summary of Research/Publications

NASA Technical Reports Server (NTRS)

1997-01-01

Summary of research/publications include:(1) Comment on broadening of water microwave lines by collisions with helium atoms; (2) Calculations of ion-molecule deuterium fractionation reactions involving HD; (3) Ab initio predictions on the rotational spectra of carbon-chain carbene molecules; (4) Theoretical IR spectra of ionized naphthalene; (5) Improved collisional excitation rates for interstellar water; (6) Calculations on the competition between association and reaction for C3H+ + H2; (7) Theoretical infrared spectra of some model polycyclic aromatic hydrocarbons: effect of ionization; (8) Calculations concerning interstellar isomeric abundance ratios for C3H and C3H2; (9) New calculations on the ion-molecule processes C2H2+ + H2 C2H3+ + H and C2H2+ + H2 C2H4+; (10) Anisotropic rigid rotor potential energy function for H2O-H2; (11) A correlated ab initio study of linear carbon-chain radicals CnH (n=2-7); (12) Ab initio characterization of MgCCH, MgCCH+, and MgC2 and pathways to their formation in the interstellar medium; (13) Why HOC+ is detectable in interstellar clouds: The rate of the reaction between HOC+ and H2; (14) A correlated ab initio study of the X 2A 1 and A 2E states of MgCH3; (15) On the stability of interstellar carbon clusters: The rate of the reaction between C3 and O; and (16) The rate of the reaction between CN and C2H2 at interstellar temperatures.

Interaction of single-walled carbon nanotubes and saxitoxin: Ab initio simulations and biological responses in hippocampal cell line HT-22.

PubMed

Ramos, Patrícia; Schmitz, Marcos; Filgueira, Daza; Votto, Ana Paula; Durruthy, Michael; Gelesky, Marcos; Ruas, Caroline; Yunes, João; Tonel, Mariana; Fagan, Solange; Monserrat, José

2017-07-01

Saxitoxins (STXs) are potent neurotoxins that also induce cytotoxicity through the generation of reactive oxygen species. Carbon nanotubes (CNTs) are nanomaterials that can promote a Trojan horse effect, facilitating the entry of toxic molecules to cells when adsorbed to nanomaterials. The interaction of pristine single-walled (SW)CNTs and carboxylated (SWCNT-COOH) nanotubes with STX was evaluated by ab initio simulation and bioassays using the cell line HT-22. Cells (5 × 10 4  cells/mL) were exposed to SWCNT and SWCNT-COOH (5 μg mL -1 ), STX (200 μg L -1 ), SWCNT+STX, and SWCNT-COOH+STX for 30 min or 24 h. Results of ab initio simulation showed that the interaction between SWCNT and SWCNT-COOH with STX occurs in a physisorption. The interaction of SWCNT+STX induced a decrease in cell viability. Cell proliferation was not affected in any treatment after 30 min or 24 h of exposure (p > 0.05). Treatment with SWCNT-COOH induced high reactive oxygen species levels, an effect attenuated in SWCNT-COOH+STX treatment. In terms of cellular oxygen consumption, both CNTs when coexposed with STX antagonize the toxin effect. Based on these results, it can be concluded that the results obtained in vitro corroborate the semiempirical evidence found using density functional theory ab initio simulation. Environ Toxicol Chem 2017;36:1728-1737. © 2016 SETAC. © 2016 SETAC.

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

NASA Astrophysics Data System (ADS)

Pietrucci, Fabio; Andreoni, Wanda

2011-08-01

Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

Pseudopotential for ab initio calculations of uranium compounds

NASA Astrophysics Data System (ADS)

Smirnov, G. S.; Pisarev, V. V.; Stegailov, V. V.

2018-01-01

The density functional theory (DFT) is a research tool of the highest importance for electronic structure calculations. It is often the only affordable method for ab initio calculations of complex materials. The pseudopotential approach allows reducing the total number of electrons in the model that speeds up calculations. However, there is a lack of pseudopotentials for heavy elements suitable for condensed matter DFT models. In this work, we present a pseudopotential for uranium developed in the Goedecker-Teter-Hutter form. Its accuracy is illustrated using several molecular and solid-state calculations.

Ab-initio study of several static and dynamic properties of liquid palladium and platinum

NASA Astrophysics Data System (ADS)

González, L. E.; González, D. J.; Molla, Mohammad Riazuddin; Ahmed, A. Z. Ziauddin; Bhuiyan, G. M.

2017-08-01

We report a study on several static and dynamic properties of liquid Pd and Pt metals at thermodynamic conditions near their respective triple points. The calculations have been carried out by an ab initio molecular dynamics simulation technique. Results are reported for several static structural magnitudes which are compared with the available X-ray diffraction. As for the dynamic properties, results have been obtained for both single and collective dynamical magnitudes as well as for some transport coeffcients which are compared with the corresponding experimental data.

Comment on 'Parametrization of Stillinger-Weber potential based on a valence force field model: application to single-layer MoS2 and black phosphorus'.

PubMed

Midtvedt, Daniel; Croy, Alexander

2016-06-10

We compare the simplified valence-force model for single-layer black phosphorus with the original model and recent ab initio results. Using an analytic approach and numerical calculations we find that the simplified model yields Young's moduli that are smaller compared to the original model and are almost a factor of two smaller than ab initio results. Moreover, the Poisson ratios are an order of magnitude smaller than values found in the literature.

Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen

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

Holst, Bastian; French, Martin; Redmer, Ronald

2011-06-15

Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

High order discretization techniques for real-space ab initio simulations

NASA Astrophysics Data System (ADS)

Anderson, Christopher R.

2018-03-01

In this paper, we present discretization techniques to address numerical problems that arise when constructing ab initio approximations that use real-space computational grids. We present techniques to accommodate the singular nature of idealized nuclear and idealized electronic potentials, and we demonstrate the utility of using high order accurate grid based approximations to Poisson's equation in unbounded domains. To demonstrate the accuracy of these techniques, we present results for a Full Configuration Interaction computation of the dissociation of H2 using a computed, configuration dependent, orbital basis set.

Ab initio study of the alkaline hydrolysis of a thio-β-lactam structure

NASA Astrophysics Data System (ADS)

Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

2000-08-01

The alkaline hydrolysis of a thio-β-lactam in the gas phase was examined in the light of RHF and DFT ab initio calculations. The solvent effect was considered via IPCM computations. The tetrahedral intermediate for the thio-β-lactam studied is unstable, so the compound evolves directly to the corresponding thio-azethidin-2-one open ring with cleavage of the C-S bond. The end-products obtained bear a carbamate group, which suggests that the thio-β-lactam might be an effective inhibitor for β-lactamases.

Ab initio R-matrix calculations of e+-molecule scattering

NASA Technical Reports Server (NTRS)

Danby, Grahame; Tennyson, Jonathan

1990-01-01

The adaptation of the molecular R-matrix method, originally developed for electron-molecule collision studies, to positron scattering is discussed. Ab initio R-matrix calculations are presented for collisions of low energy positrons with a number of diatomic systems including H2, HF and N2. Differential elastic cross sections for positron-H2 show a minimum at about 45 deg for collision energies between 0.3 and 0.5 Ryd. The calculations predict a bound state of positronHF. Calculations on inelastic processes in N2 and O2 are also discussed.

Electronic states of Zn2 - Ab initio calculations of a prototype for Hg2

NASA Technical Reports Server (NTRS)

Hay, P. J.; Dunning, T. H., Jr.; Raffenetti, R. C.

1976-01-01

The electronic states of Zn2 are investigated by ab initio polarization configuration-interaction calculations. Molecular states dissociating to Zn(1S) + Zn(1S, 3P, 1P) and Zn(3P) + Zn(3P) are treated. Important effects from states arising from Zn(+)(25) + Zn(-)(2P) are found in the potential-energy curves and electronic-transition moments. A model calculation for Hg2 based on the Zn2 curves and including spin-orbit coupling leads to a new interpretation of the emission bands in Hg vapor.

Vibrational energy levels for CH4 from an ab initio potential

NASA Technical Reports Server (NTRS)

Schwenke, D. W.; Partridge, H.

2001-01-01

Many areas of astronomy and astrophysics require an accurate high temperature spectrum of methane (CH4). The goal of the present research is to determine an accurate ab initio potential energy surface (PES) for CH4. As a first step towards this goal, we have determined a PES including up to octic terms. We compare our results with experiment and to a PES based on a quartic expansion. Our octic PES gives good agreement with experiment for all levels, while the quartic PES only for the lower levels.

Ab initio molecular dynamics simulations of the initial stages of solid-electrolyte interphase formation on lithium ion battery graphitic anodes.

PubMed

Leung, Kevin; Budzien, Joanne L

2010-07-07

The decomposition of ethylene carbonate (EC) during the initial growth of solid-electrolyte interphase (SEI) films at the solvent-graphitic anode interface is critical to lithium ion battery operations. Ab initio molecular dynamics simulations of explicit liquid EC/graphite interfaces are conducted to study these electrochemical reactions. We show that carbon edge terminations are crucial at this stage, and that achievable experimental conditions can lead to surprisingly fast EC breakdown mechanisms, yielding decomposition products seen in experiments but not previously predicted.

Hybrid classical/quantum simulation for infrared spectroscopy of water

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

Quantum Drude oscillator model of atoms and molecules: Many-body polarization and dispersion interactions for atomistic simulation

NASA Astrophysics Data System (ADS)

Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.

2013-04-01

Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.

75 FR 41277 - Central of Georgia Railroad Company-Discontinuance of Service Exemption-Newton County, GA; Great...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-15

... misleading information, the exemptions are void ab initio. Board decisions and notices are available on our... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. AB 290 (Sub-No. 319X); Docket No. AB 1060X] Central of Georgia Railroad Company--Discontinuance of Service Exemption--Newton...

Triple-twin domains in Mg doped GaN wurtzite nanowires: structural and electronic properties of this zinc-blende-like stacking

NASA Astrophysics Data System (ADS)

Arbiol, Jordi; Estradé, Sònia; Prades, Joan D.; Cirera, Albert; Furtmayr, Florian; Stark, Christoph; Laufer, Andreas; Stutzmann, Martin; Eickhoff, Martin; Gass, Mhairi H.; Bleloch, Andrew L.; Peiró, Francesca; Morante, Joan R.

2009-04-01

We report on the effect of Mg doping on the properties of GaN nanowires grown by plasma assisted molecular beam epitaxy. The most significant feature is the presence of triple-twin domains, the density of which increases with increasing Mg concentration. The resulting high concentration of misplaced atoms gives rise to local changes in the crystal structure equivalent to the insertion of three non-relaxed zinc-blende (ZB) atomic cells, which result in quantum wells along the wurtzite (WZ) nanowire growth axis. High resolution electron energy loss spectra were obtained exactly on the twinned (zinc-blende) and wurtzite planes. These atomically resolved measurements, which allow us to identify modifications in the local density of states, revealed changes in the band to band electronic transition energy from 3.4 eV for wurtzite to 3.2 eV in the twinned lattice regions. These results are in good agreement with specific ab initio atomistic simulations and demonstrate that the redshift observed in previous photoluminescence analyses is directly related to the presence of these zinc-blende domains, opening up new possibilities for band-structure engineering.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

2014-03-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

Impact of surface energy on the shock properties of granular explosives.

PubMed

Bidault, X; Pineau, N

2018-01-21

This paper presents the first part of a two-fold molecular dynamics study of the impact of the granularity on the shock properties of high explosives. Recent experimental studies show that the granularity can have a substantial impact on the properties of detonation products {i.e., variations in the size distributions of detonation nanodiamonds [V. Pichot et al., Sci. Rep. 3, 2159 (2013)]}. These variations can have two origins: the surface energy, which is a priori enhanced from micro- to nano-scale, and the porosity induced by the granular structure. In this first report, we study the impact of the surface-energy contribution on the inert shock compression of TATB, TNT, α-RDX, and β-HMX nano-grains (triaminotrinitrobenzene, trinitrotoluene, hexogen and octogen, respectively). We compute the radius-dependent surface energy and combine it with an ab initio-based equation of state in order to obtain the resulting shock properties through the Rankine-Hugoniot relations. We find that the enhancement of the surface energy results in a moderate overheating under shock compression. This contribution is minor with respect to porosity, when compared to a simple macroscopic model. This result motivates further atomistic studies on the impact of nanoporosity networks on the shock properties.

Electrostatic Properties of Polymers Subjected to Atmospheric Pressure Plasma Treatment; Correlation of Experimental Results with Atomistic Modeling

NASA Technical Reports Server (NTRS)

Trigwell, S.; Boucher, D.; Calle, C. I.

2007-01-01

this study, PE, PTFE, PS and PMMA were exposed to a He+O2, APGD and pre and post treatment surface chemistries were analyzed by X-ray photoelectron spectroscopy and contact angle measurements. Semi-empirical and ab-initio calculations were performed to correlate the experimental results with sonic plausible molecular and electronic structure features of the oxidation process. For the PE and PS, significant surface oxidation showing C-O, C=O, and O-C=O bonding, and a decrease in the surface contact angles was observed. For the PTFE and PM MA, little change in the surface composition was observed. The molecular modeling calculations were performed on single and multiple oligomers and showed regardless of oxidation mechanism, e.g. -OH, =O or a combination thereof, experimentally observed levels of surface oxidation were unlikely to lead to a significant change in the electronic structure of PE and PS, and that the increased hydrophilic properties are the primary reason for the observed changes in its electrostatic behavior. Calculations for PTFE and PMMA argue strongly against significant oxidation of those materials, as confirmed by the XPS results.

Thermal conduction mechanisms in isotope-disordered boron nitride and carbon nanotubes

NASA Astrophysics Data System (ADS)

Savic, Ivana; Mingo, Natalio; Stewart, Derek

2009-03-01

We present first principles studies which determine dominant effects limiting the heat conduction in isotope-disordered boron nitride and carbon nanotubes [1]. Using an ab initio atomistic Green's function approach, we demonstrate that localization cannot be observed in the thermal conductivity measurements [1], and that diffusive scattering is the dominant mechanism which reduces the thermal conductivity [2]. We also give concrete predictions of the magnitude of the isotope effect on the thermal conductivities of carbon and boron nitride single-walled nanotubes [2]. We furthermore show that intershell scattering is not the main limiting mechanism for the heat flow through multi-walled boron nitride nanotubes [1], and that heat conduction restricted to a few shells leads to the low thermal conductivities experimentally measured [1]. We consequently successfully compare the results of our calculations [3] with the experimental measurements [1]. [1] C. W. Chang, A. M. Fennimore, A. Afanasiev, D. Okawa, T. Ikuno, H. Garcia, D. Li, A. Majumdar, A. Zettl, Phys. Rev. Lett. 2006, 97, 085901. [2] I. Savic, N. Mingo, D. A. Stewart, Phys. Rev. Lett. 2008, 101, 165502. [3] I. Savic, D. A. Stewart, N. Mingo, to be published.

Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport

PubMed Central

Blau, Samuel M.; Bennett, Doran I. G.; Kreisbeck, Christoph; Scholes, Gregory D.; Aspuru-Guzik, Alán

2018-01-01

The mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in 2D electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct excitation transport from the highest-energy to the lowest-energy pigments, bypassing a collection of intermediate states. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. We quantify the solvation dynamics of individual pigments using ab initio quantum mechanics/molecular mechanics (QM/MM) nuclear dynamics. Our atomistic spectral densities reproduce experimental observations ranging from absorption and fluorescence spectra to the timescales and selectivity of down-conversion observed in transient absorption measurements. We construct a general model for vibronic dimers and establish the parameter regimes of coherent and incoherent vibronic transport. We demonstrate that direct down-conversion in PC645 proceeds incoherently, enhanced by large reorganization energies and a broad collection of high-frequency vibrations. We suggest that a similar incoherent mechanism is appropriate across phycobiliproteins and represents a potential design principle for nanoscale control of EET. PMID:29588417

Impact of surface energy on the shock properties of granular explosives

NASA Astrophysics Data System (ADS)

Bidault, X.; Pineau, N.

2018-01-01

This paper presents the first part of a two-fold molecular dynamics study of the impact of the granularity on the shock properties of high explosives. Recent experimental studies show that the granularity can have a substantial impact on the properties of detonation products {i.e., variations in the size distributions of detonation nanodiamonds [V. Pichot et al., Sci. Rep. 3, 2159 (2013)]}. These variations can have two origins: the surface energy, which is a priori enhanced from micro- to nano-scale, and the porosity induced by the granular structure. In this first report, we study the impact of the surface-energy contribution on the inert shock compression of TATB, TNT, α-RDX, and β-HMX nano-grains (triaminotrinitrobenzene, trinitrotoluene, hexogen and octogen, respectively). We compute the radius-dependent surface energy and combine it with an ab initio-based equation of state in order to obtain the resulting shock properties through the Rankine-Hugoniot relations. We find that the enhancement of the surface energy results in a moderate overheating under shock compression. This contribution is minor with respect to porosity, when compared to a simple macroscopic model. This result motivates further atomistic studies on the impact of nanoporosity networks on the shock properties.

Lewis Base Passivation of Hybrid Halide Perovskites Slows Electron-Hole Recombination: Time-Domain Ab Initio Analysis.

PubMed

Liu, Lihong; Fang, Wei-Hai; Long, Run; Prezhdo, Oleg V

2018-03-01

Nonradiative electron-hole recombination plays a key role in determining photon conversion efficiencies in solar cells. Experiments demonstrate significant reduction in the recombination rate upon passivation of methylammonium lead iodide perovskite with Lewis base molecules. Using nonadiabatic molecular dynamics combined with time-domain density functional theory, we find that the nonradiative charge recombination is decelerated by an order of magnitude upon adsorption of the molecules. Thiophene acts by the traditional passivation mechanism, forcing electron density away from the surface. In contrast, pyridine localizes the electron at the surface while leaving it energetically near the conduction band edge. This is because pyridine creates a stronger coordinative bond with a lead atom of the perovskite and has a lower energy unoccupied orbital compared with thiophene due to the more electronegative nitrogen atom relative to thiophene's sulfur. Both molecules reduce two-fold the nonadiabatic coupling and electronic coherence time. A broad range of vibrational modes couple to the electronic subsystem, arising from inorganic and organic components. The simulations reveal the atomistic mechanisms underlying the enhancement of the excited-state lifetime achieved by the perovskite passivation, rationalize the experimental results, and advance our understanding of charge-phonon dynamics in perovskite solar cells.

Atomistic modeling of metallic thin films by modified embedded atom method

NASA Astrophysics Data System (ADS)

Hao, Huali; Lau, Denvid

2017-11-01

Molecular dynamics simulation is applied to investigate the deposition process of metallic thin films. Eight metals, titanium, vanadium, iron, cobalt, nickel, copper, tungsten, and gold, are chosen to be deposited on the aluminum substrate. The second nearest-neighbor modified embedded atom method potential is adopted to predict their thermal and mechanical properties. When quantifying the screening parameters of the potential, the error for Young's modulus and coefficient of thermal expansion between the simulated results and the experimental measurements is less than 15%, demonstrating the reliability of the potential to predict metallic behaviors related to thermal and mechanical properties. A set of potential parameters which governs the interactions between aluminum and other metals in a binary system is also generated from ab initio calculation. The details of interfacial structures between the chosen films and substrate are successfully simulated with the help of these parameters. Our results indicate that the preferred orientation of film growth depends on the film crystal structure, and the inter-diffusion at the interface is correlated the cohesive energy parameter of potential for the binary system. Such finding provides an important basis to further understand the interfacial science, which contributes to the improvement of the mechanical properties, reliability and durability of films.

Thermodynamic integration based on classical atomistic simulations to determine the Gibbs energy of condensed phases: Calculation of the aluminum-zirconium system

NASA Astrophysics Data System (ADS)

Harvey, J.-P.; Gheribi, A. E.; Chartrand, P.

2012-12-01

In this work, an in silico procedure to generate a fully coherent set of thermodynamic properties obtained from classical molecular dynamics (MD) and Monte Carlo (MC) simulations is proposed. The procedure is applied to the Al-Zr system because of its importance in the development of high strength Al-Li alloys and of bulk metallic glasses. Cohesive energies of the studied condensed phases of the Al-Zr system (the liquid phase, the fcc solid solution, and various orthorhombic stoichiometric compounds) are calculated using the modified embedded atom model (MEAM) in the second-nearest-neighbor formalism (2NN). The Al-Zr MEAM-2NN potential is parameterized in this work using ab initio and experimental data found in the literature for the AlZr3-L12 structure, while its predictive ability is confirmed for several other solid structures and for the liquid phase. The thermodynamic integration (TI) method is implemented in a general MC algorithm in order to evaluate the absolute Gibbs energy of the liquid and the fcc solutions. The entropy of mixing calculated from the TI method, combined to the enthalpy of mixing and the heat capacity data generated from MD/MC simulations performed in the isobaric-isothermal/canonical (NPT/NVT) ensembles are used to parameterize the Gibbs energy function of all the condensed phases in the Al-rich side of the Al-Zr system in a CALculation of PHAse Diagrams (CALPHAD) approach. The modified quasichemical model in the pair approximation (MQMPA) and the cluster variation method (CVM) in the tetrahedron approximation are used to define the Gibbs energy of the liquid and the fcc solid solution respectively for their entire range of composition. Thermodynamic and structural data generated from our MD/MC simulations are used as input data to parameterize these thermodynamic models. A detailed analysis of the validity and transferability of the Al-Zr MEAM-2NN potential is presented throughout our work by comparing the predicted properties obtained from this formalism with available ab initio and experimental data for both liquid and solid phases.

Relating Ab Initio Mechanical Behavior of Intergranular Glassy Films in Γ-Si3N4 to Continuum Scales

NASA Astrophysics Data System (ADS)

Ouyang, L.; Chen, J.; Ching, W.; Misra, A.

2006-05-01

Nanometer thin intergranular glassy films (IGFs) form in polycrystalline ceramics during sintering at high temperatures. The structure and properties of these IGFs are significantly changed by doping with rare earth elements. We have performed highly accurate large-scale ab initio calculations of the mechanical properties of both undoped and Yittria doped (Y-IGF) model by theoretical uniaxial tensile experiments. Uniaxial strain was applied by incrementally stretching the super cell in one direction, while the other two dimensions were kept constant. At each strain, all atoms in the model were fully relaxed using Vienna Ab initio Simulation Package VASP. The relaxed model at a given strain serves as the starting position for the next increment of strain. This process is carried on until the total energy (TE) and stress data show that the "sample" is fully fractured. Interesting differences are seen between the stress-strain response of undoped and Y-doped models. For the undoped model, the stress-strain behavior indicates that the initial atomic structure of the IGF is such that there is negligible coupling between the x- and the y-z directions. However, once the behavior becomes non- linear the lateral stresses increase, indicating that the atomic structure evolves with loading [1]. To relate the ab initio calculations to the continuum scales we analyze the atomic-scale deformation field under this uniaxial loading [1]. The applied strain in the x-direction is mostly accommodated by the IGF part of the model and the crystalline part experiences almost negligible strain. As the overall strain on the sample is incrementally increased, the local strain field evolves such that locations proximal to the softer spots attract higher strains. As the load progresses, the strain concentration spots coalesce and eventually form persistent strain localization zone across the IGF. The deformation pattern obtained through ab initio calculations indicates that it is possible to construct discrete grain-scale models that may be used to bridge these calculations to the continuum scale for finite element analysis. Reference: 1. J. Chen, L. Ouyang, P. Rulis, A. Misra, W. Y. Ching, Phys. Rev. Lett. 95, 256103 (2005)

Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

2015-02-01

The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized gradient approximation for exchange-correlation. We caution, however, that simulations are mostly reliable at high T where ligand exchange is fast enough to yield thermodynamic averages over the timescales of the simulations.

ExoMol line list - XXI. Nitric Oxide (NO)

NASA Astrophysics Data System (ADS)

Wong, Andy; Yurchenko, Sergei N.; Bernath, Peter; Müller, Holger S. P.; McConkey, Stephanie; Tennyson, Jonathan

2017-09-01

Line lists for the X 2Π electronic ground state for the parent isotopologue of nitric oxide (14N16O) and five other major isotopologues (14N17O, 14N18O, 15N16O, 15N17O and 15N18O) are presented. The line lists are constructed using empirical energy levels (and line positions) and high-level ab initio intensities. The energy levels were obtained using a combination of two approaches, from an effective Hamiltonian and from solving the rovibronic Schrödinger equation variationally. The effective Hamiltonian model was obtained through a fit to the experimental line positions of NO available in the literature for all six isotopologues using the programs spfit and spcat. The variational model was built through a least squares fit of the ab initio potential and spin-orbit curves to the experimentally derived energies and experimental line positions of the main isotopologue only using the duo program. The ab initio potential energy, spin-orbit and dipole moment curves (PEC, SOC and DMC) are computed using high-level ab initio methods and the marvel method is used to obtain energies of NO from experimental transition frequencies. The line lists are constructed for each isotopologue based on the use of the most accurate energy levels and the ab initio DMC. Each line list covers a wavenumber range from 0 to 40 000 cm-1 with approximately 22 000 rovibronic states and 2.3-2.6 million transitions extending to Jmax = 184.5 and vmax = 51. Partition functions are also calculated up to a temperature of 5000 K. The calculated absorption line intensities at 296 K using these line lists show excellent agreement with those included in the HITRAN and HITEMP data bases. The computed NO line lists are the most comprehensive to date, covering a wider wavenumber and temperature range compared to both the HITRAN and HITEMP data bases. These line lists are also more accurate than those used in HITEMP. The full line lists are available from the CDS http://cdsarc.u-strasbg.fr and ExoMol www.exomol.com data bases; data will also be available from CDMS http://www.cdms.de.

Microscopic theory for coupled atomistic magnetization and lattice dynamics

NASA Astrophysics Data System (ADS)

Fransson, J.; Thonig, D.; Bessarab, P. F.; Bhattacharjee, S.; Hellsvik, J.; Nordström, L.

2017-12-01

A coupled atomistic spin and lattice dynamics approach is developed which merges the dynamics of these two degrees of freedom into a single set of coupled equations of motion. The underlying microscopic model comprises local exchange interactions between the electron spin and magnetic moment and the local couplings between the electronic charge and lattice displacements. An effective action for the spin and lattice variables is constructed in which the interactions among the spin and lattice components are determined by the underlying electronic structure. In this way, expressions are obtained for the electronically mediated couplings between the spin and lattice degrees of freedom, besides the well known interatomic force constants and spin-spin interactions. These former susceptibilities provide an atomistic ab initio description for the coupled spin and lattice dynamics. It is important to notice that this theory is strictly bilinear in the spin and lattice variables and provides a minimal model for the coupled dynamics of these subsystems and that the two subsystems are treated on the same footing. Questions concerning time-reversal and inversion symmetry are rigorously addressed and it is shown how these aspects are absorbed in the tensor structure of the interaction fields. By means of these results regarding the spin-lattice coupling, simple explanations of ionic dimerization in double-antiferromagnetic materials, as well as charge density waves induced by a nonuniform spin structure, are given. In the final parts, coupled equations of motion for the combined spin and lattice dynamics are constructed, which subsequently can be reduced to a form which is analogous to the Landau-Lifshitz-Gilbert equations for spin dynamics and a damped driven mechanical oscillator for the ionic motion. It is important to notice, however, that these equations comprise contributions that couple these descriptions into one unified formulation. Finally, Kubo-like expressions for the discussed exchanges in terms of integrals over the electronic structure and, moreover, analogous expressions for the damping within and between the subsystems are provided. The proposed formalism and types of couplings enable a step forward in the microscopic first principles modeling of coupled spin and lattice quantities in a consistent format.

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer

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

Daily, Michael D.; Baer, Marcel D.; Mundy, Christopher J.

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids usingmore » a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical forcefield (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through sidechain-sidechain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described. MDD was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. Research was funded by the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. MDB acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Material & Engineering. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

PubMed

Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J

2013-02-28

A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

NASA Astrophysics Data System (ADS)

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

2018-05-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

The hydrogen abstraction reaction O({sup 3}P) + CH{sub 4}: A new analytical potential energy surface based on fit to ab initio calculations

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

González-Lavado, Eloisa; Corchado, Jose C.; Espinosa-Garcia, Joaquin, E-mail: joaquin@unex.es

2014-02-14

Based exclusively on high-level ab initio calculations, a new full-dimensional analytical potential energy surface (PES-2014) for the gas-phase reaction of hydrogen abstraction from methane by an oxygen atom is developed. The ab initio information employed in the fit includes properties (equilibrium geometries, relative energies, and vibrational frequencies) of the reactants, products, saddle point, points on the reaction path, and points on the reaction swath, taking especial caution respecting the location and characterization of the intermediate complexes in the entrance and exit channels. By comparing with the reference results we show that the resulting PES-2014 reproduces reasonably well the whole setmore » of ab initio data used in the fitting, obtained at the CCSD(T) = FULL/aug-cc-pVQZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical surface we perform an extensive dynamics study using quasi-classical trajectory calculations, comparing the results with recent experimental and theoretical data. The excitation function increases with energy (concave-up) reproducing experimental and theoretical information, although our values are somewhat larger. The OH rotovibrational distribution is cold in agreement with experiment. Finally, our results reproduce experimental backward scattering distribution, associated to a rebound mechanism. These results lend confidence to the accuracy of the new surface, which substantially improves the results obtained with our previous surface (PES-2000) for the same system.« less

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

NASA Astrophysics Data System (ADS)

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

2018-03-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

Accurate double many-body expansion potential energy surface of HS2A2A‧) by scaling the external correlation

NASA Astrophysics Data System (ADS)

Lu-Lu, Zhang; Yu-Zhi, Song; Shou-Bao, Gao; Yuan, Zhang; Qing-Tian, Meng

2016-05-01

A globally accurate single-sheeted double many-body expansion potential energy surface is reported for the first excited state of HS2 by fitting the accurate ab initio energies, which are calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set. By using the double many-body expansion-scaled external correlation method, such calculated ab initio energies are then slightly corrected by scaling their dynamical correlation. A grid of 2767 ab initio energies is used in the least-square fitting procedure with the total root-mean square deviation being 1.406 kcal·mol-1. The topographical features of the HS2(A2A‧) global potential energy surface are examined in detail. The attributes of the stationary points are presented and compared with the corresponding ab initio results as well as experimental and other theoretical data, showing good agreement. The resulting potential energy surface of HS2(A2A‧) can be used as a building block for constructing the global potential energy surfaces of larger S/H molecular systems and recommended for dynamic studies on the title molecular system. Project supported by the National Natural Science Foundation of China (Grant No. 11304185), the Taishan Scholar Project of Shandong Province, China, the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014AM022), the Shandong Province Higher Educational Science and Technology Program, China (Grant No. J15LJ03), the China Postdoctoral Science Foundation (Grant No. 2014M561957), and the Post-doctoral Innovation Project of Shandong Province, China (Grant No. 201402013).

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations.

PubMed

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A; Ferreira, Rafaela Salgado

2018-05-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC 50  = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

PubMed

Zhang, Dawei; Liu, Chungen

2016-04-12

The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems.

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.

PubMed

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. Copyright 2008 Wiley Periodicals, Inc.

Theoretical determination of molecular structure and conformation. Part X. Geometry and puckering potential of azetidine, (CH 2) 3NH, combination of electron diffraction and ab initio studies

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.

1981-09-01

Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.

Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

NASA Astrophysics Data System (ADS)

Makhov, Dmitry V.; Symonds, Christopher; Fernandez-Alberti, Sebastian; Shalashilin, Dmitrii V.

2017-08-01

The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique which allows treatment of a large number of quantum nuclear degrees of freedom. This paper presents a review of MCE and its recent applications, providing a summary of the formalisms, including its ab initio direct dynamics versions and also giving a summary of recent results. Firstly, we describe the Multiconfigurational Ehrenfest version 2 (MCEv2) method and its applicability to direct dynamics and report new calculations which show that the approach converges to the exact result in model systems with tens of degrees of freedom. Secondly, we review previous ;on the fly; ab initio Multiple Cloning (AIMC-MCE) MCE dynamics results obtained for systems of a similar size, in which the calculations treat every electron and every nucleus of a polyatomic molecule on a fully quantum basis. We also review the Time Dependent Diabatic Basis (TDDB) version of the technique and give an example of its application. We summarise the details of the sampling techniques and interpolations used for calculation of the matrix elements, which make our approach efficient. Future directions of work are outlined.

Ab initio study of the structure and dynamics of bulk liquid Fe

NASA Astrophysics Data System (ADS)

Marqués, M.; González, L. E.; González, D. J.

2015-10-01

Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

A new ab initio potential energy surface of LiClH (1A') system and quantum dynamics calculation for Li + HCl (v = 0, j = 0-2) → LiCl + H reaction

NASA Astrophysics Data System (ADS)

Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying

2017-04-01

A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.

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.

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory.

PubMed

Frandsen, Benjamin A; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J; Staunton, Julie B; Billinge, Simon J L

2016-05-13

We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ∼1  nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

Thermodynamic properties by equation of state and from Ab initio molecular dynamics of liquid potassium under pressure

NASA Astrophysics Data System (ADS)

Li, Huaming; Tian, Yanting; Sun, Yongli; Li, Mo; Nonequilibrium materials; physics Team; Computational materials science Team

In this work, we apply a general equation of state of liquid and Ab initio molecular-dynamics method to study thermodynamic properties in liquid potassium under high pressure. Isothermal bulk modulus and molar volume of molten sodium are calculated within good precision as compared with the experimental data. The calculated internal energy data and the calculated values of isobaric heat capacity of molten potassium show the minimum along the isothermal lines as the previous result obtained in liquid sodium. The expressions for acoustical parameter and nonlinearity parameter are obtained based on thermodynamic relations from the equation of state. Both parameters for liquid potassium are calculated under high pressure along the isothermal lines by using the available thermodynamic data and numeric derivations. Furthermore, Ab initio molecular-dynamics simulations are used to calculate some thermodynamic properties of liquid potassium along the isothermal lines. Scientific Research Starting Foundation from Taiyuan university of Technology, Shanxi Provincial government (``100-talents program''), China Scholarship Council and National Natural Science Foundation of China (NSFC) under Grant No. 51602213.

Electron transport in extended carbon-nanotube/metal contacts: Ab initio based Green function method

NASA Astrophysics Data System (ADS)

Fediai, Artem; Ryndyk, Dmitry A.; Cuniberti, Gianaurelio

2015-04-01

We have developed a new method that is able to predict the electrical properties of the source and drain contacts in realistic carbon nanotube field effect transistors (CNTFETs). It is based on large-scale ab initio calculations combined with a Green function approach. For the first time, both internal and external parts of a realistic CNT-metal contact are taken into account at the ab initio level. We have developed the procedure allowing direct calculation of the self-energy for an extended contact. Within the method, it is possible to calculate the transmission coefficient through a contact of both finite and infinite length; the local density of states can be determined in both free and embedded CNT segments. We found perfect agreement with the experimental data for Pd and Al contacts. We have explained why CNTFETs with Pd electrodes are p -type FETs with ohmic contacts, which can carry current close to the ballistic limit (provided contact length is large enough), whereas in CNT-Al contacts transmission is suppressed to a significant extent, especially for holes.

Chiral self-recognition: direct spectroscopic detection of the homochiral and heterochiral dimers of propylene oxide in the gas phase.

PubMed

Su, Zheng; Borho, Nicole; Xu, Yunjie

2006-12-27

In this report, we describe rotational spectroscopic and high-level ab initio studies of the 1:1 chiral molecular adduct of propylene oxide dimer. The complexes are bound by weak secondary hydrogen bonds, that is, the O(epoxy)...H-C noncovalent interactions. Six homochiral and six heterochiral conformers were predicted to be the most stable configurations where each monomer acts as a proton acceptor and a donor simultaneously, forming two six- or five-membered intermolecular hydrogen-bonded rings. Rotational spectra of six, that is, three homochiral and heterochiral conformer pairs, out of the eight conformers that were predicted to have sufficiently large permanent electric dipole moments were measured and analyzed. The relative conformational stability order and the signs of the chiral recognition energies of the six conformers were determined experimentally and were compared to the ab initio computational results. The experimental observations and the ab initio calculations suggest that the concerted effort of these weak secondary hydrogen bonds can successfully lock the subunits in a particular orientation and that the overall binding strength is comparable to a classic hydrogen bond.

A new ab initio potential energy surface for the Ne-H 2 interaction

NASA Astrophysics Data System (ADS)

Lique, François

2009-03-01

A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

Exchange coupling and magnetic anisotropy in a family of bipyrimidyl radical-bridged dilanthanide complexes: density functional theory and ab initio calculations.

PubMed

Zhang, Yi-Quan; Luo, Cheng-Lin; Zhang, Qiang

2014-05-05

The origin of the magnetic anisotropy energy barriers in a series of bpym(-) (bpym = 2,2'-bipyrimidine) radical-bridged dilanthanide complexes [(Cp*2Ln)2(μ-bpym)](+) [Cp* = pentamethylcyclopentadienyl; Ln = Gd(III) (1), Tb(III) (2), Dy(III) (3), Ho(III) (4), Er(III) (5)] has been explored using density functional theory (DFT) and ab initio methods. DFT calculations show that the exchange coupling between the two lanthanide ions for each complex is very weak, but the antiferromagnetic Ln-bpym(-) couplings are strong. Ab initio calculations show that the effective energy barrier of 2 or 3 mainly comes from the contribution of a single Tb(III) or Dy(III) fragment, which is only about one third of a single Ln energy barrier. For 4 or 5, however, both of the two Ho(III) or Er(III) fragments contribute to the total energy barrier. Thus, it is insufficient to only increase the magnetic anisotropy energy barrier of a single Ln ion, while enhancing the Ln-bpym(-) couplings is also very important. Copyright © 2014 Wiley Periodicals, Inc.

A Toolbox for Ab Initio 3-D Reconstructions in Single-particle Electron Microscopy

PubMed Central

Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S

2010-01-01

Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a “toolbox” of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map. PMID:20018246

Substituent Inductive Effects on the Electrochemical Oxidation of Flavonoids Studied by Square Wave Voltammetry and Ab Initio Calculations.

PubMed

Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo

2016-10-27

Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.

Structural phase transition of BeTe: an ab initio molecular dynamics study.

PubMed

Alptekin, Sebahaddin

2017-08-11

Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results. Graphical abstract The energy-volume relation and ZB phase for the BeTe.

Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

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

Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine

Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less

Comparative study of ab initio nonradiative recombination rate calculations under different formalisms

NASA Astrophysics Data System (ADS)

Shi, Lin; Xu, Ke; Wang, Lin-Wang

2015-05-01

Nonradiative carrier recombination is of both great applied and fundamental importance, but the correct ab initio approaches to calculate it remain to be inconclusive. Here we used five different approximations to calculate the nonradiative carrier recombinations of two complex defect structures GaP :Z nGa-OP and GaN :Z nGa-VN , and compared the results with experiments. In order to apply different multiphonon assisted electron transition formalisms, we have calculated the electron-phonon coupling constants by ab initio density functional theory for all phonon modes. Compared with different methods, the capture coefficients calculated by the static coupling theory are 4.30 ×10-8 and 1.46 ×10-7c m3/s for GaP :Z nGa-OP and GaN :Z nGa-VN , which are in good agreement with the experiment results, (4-1+2) ×10-8 and 3.0 ×10-7c m3/s , respectively. We also provided arguments for why the static coupling theory should be used to calculate the nonradiative decays of semiconductors.

Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only).

PubMed

Domain, C; Olsson, P; Becquart, C S; Legris, A; Guillemoles, J F

2008-02-13

Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency.

Conformational properties and electronic structure of tetrahydrotetrazines studied by photoelectron spectroscopy and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Muchall, Heidi M.; Rademacher, Paul

1997-11-01

The photoelectron (PE) spectra of tetrahydro-1,2,3,4-tetrazines 1 and 2 and tetrahydro-1,2,4,5-tetrazines 3-5 have been recorded and their conformations have been investigated by ab initio SCF calculations. While v-tetrazine 2 is planar, tetrazines 1 and 3-5 each possess two low-energy conformations, according to ab initio HF and Becke3LYP methods. Attempts to assign ionization potentials to molecular orbitals obtained by semiempirical PM3 calculations indicate that this method is not suited for the compounds studied. Best results were obtained when the ab initio hybrid method Becke3LYP of the density functional theory was employed. Two conformers of 1 and 3-5 are present in the gas phase and their PE spectra are superimposed one upon the other. For v-tetrazine 1, ionizations arising from half-chair and unsymmetrical boat conformers have similar energies and cannot be separated in the PE spectrum. For s-tetrazine 3, on the other hand, the spectrum clearly shows different ionizations of both half-chairs, 3ee and 3ae.

Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

NASA Astrophysics Data System (ADS)

Ylikantola, A.; Linnanto, J.; Knuutinen, J.; Oravilahti, A.; Toivakka, M.

2013-07-01

The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree-Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree-Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree-Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

Equilibrium and Dynamics Properties of Poly(oxyethylene) Melts and Related Poly(alkylethers) from Simulations and Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

1994-01-01

Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.

Verification of Anderson superexchange in MnO via magnetic pair distribution function analysis and ab initio theory

DOE PAGES

Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine; ...

2016-05-11

Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less

Ab initio calculations and kinetic modeling of thermal conversion of methyl chloride: implications for gasification of biomass.

PubMed

Singla, Mallika; Rasmussen, Morten Lund; Hashemi, Hamid; Wu, Hao; Glarborg, Peter; Pelucchi, Matteo; Faravelli, Tiziano; Marshall, Paul

2018-04-25

Limitations in current hot gas cleaning methods for chlorine species from biomass gasification may be a challenge for end use such as gas turbines, engines, and fuel cells, all requiring very low levels of chlorine. During devolatilization of biomass, chlorine is released partly as methyl chloride. In the present work, the thermal conversion of CH3Cl under gasification conditions was investigated. A detailed chemical kinetic model for pyrolysis and oxidation of methyl chloride was developed and validated against selected experimental data from the literature. Key reactions of CH2Cl with O2 and C2H4 for which data are scarce were studied by ab initio methods. The model was used to analyze the fate of methyl chloride in gasification processes. The results indicate that CH3Cl emissions will be negligible for most gasification technologies, but could be a concern for fluidized bed gasifiers, in particular in low-temperature gasification. The present work illustrates how ab initio theory and chemical kinetic modeling can help to resolve emission issues for thermal processes in industrial scale.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.