DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo

2013-08-01

A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

Neutron radiation damage studies in the structural materials of a 500 MWe fast breeder reactor using DPA cross-sections from ENDF / B-VII.1

NASA Astrophysics Data System (ADS)

Saha, Uttiyoarnab; Devan, K.; Bachchan, Abhitab; Pandikumar, G.; Ganesan, S.

2018-04-01

The radiation damage in the structural materials of a 500 MWe Indian prototype fast breeder reactor (PFBR) is re-assessed by computing the neutron displacement per atom (dpa) cross-sections from the recent nuclear data library evaluated by the USA, ENDF / B-VII.1, wherein revisions were taken place in the new evaluations of basic nuclear data because of using the state-of-the-art neutron cross-section experiments, nuclear model-based predictions and modern data evaluation techniques. An indigenous computer code, computation of radiation damage (CRaD), is developed at our centre to compute primary-knock-on atom (PKA) spectra and displacement cross-sections of materials both in point-wise and any chosen group structure from the evaluated nuclear data libraries. The new radiation damage model, athermal recombination-corrected displacement per atom (arc-dpa), developed based on molecular dynamics simulations is also incorporated in our study. This work is the result of our earlier initiatives to overcome some of the limitations experienced while using codes like RECOIL, SPECTER and NJOY 2016, to estimate radiation damage. Agreement of CRaD results with other codes and ASTM standard for Fe dpa cross-section is found good. The present estimate of total dpa in D-9 steel of PFBR necessitates renormalisation of experimental correlations of dpa and radiation damage to ensure consistency of damage prediction with ENDF / B-VII.1 library.

Opacity of iron, nickel, and copper plasmas in the x-ray wavelength range: Theoretical interpretation of 2p-3d absorption spectra

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

Blenski, T.; Loisel, G.; Poirier, M.

2011-09-15

This paper deals with theoretical studies on the 2p-3d absorption in iron, nickel, and copper plasmas related to LULI2000 (Laboratoire pour l'Utilisation des Lasers Intenses, 2000J facility) measurements in which target temperatures were of the order of 20 eV and plasma densities were in the range 0.004-0.01 g/cm{sup 3}. The radiatively heated targets were close to local thermodynamic equilibrium (LTE). The structure of 2p-3d transitions has been studied with the help of the statistical superconfiguration opacity code sco and with the fine-structure atomic physics codes hullac and fac. A new mixed version of the sco code allowing one to treatmore » part of the configurations by detailed calculation based on the Cowan's code rcg has been also used in these comparisons. Special attention was paid to comparisons between theory and experiment concerning the term features which cannot be reproduced by sco. The differences in the spin-orbit splitting and the statistical (thermal) broadening of the 2p-3d transitions have been investigated as a function of the atomic number Z. It appears that at the conditions of the experiment the role of the term and configuration broadening was different in the three analyzed elements, this broadening being sensitive to the atomic number. Some effects of the temperature gradients and possible non-LTE effects have been studied with the help of the radiative-collisional code scric. The sensitivity of the 2p-3d structures with respect to temperature and density in medium-Z plasmas may be helpful for diagnostics of LTE plasmas especially in future experiments on the {Delta}n=0 absorption in medium-Z plasmas for astrophysical applications.« less

A universal preconditioner for simulating condensed phase materials.

PubMed

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

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.

A universal preconditioner for simulating condensed phase materials

NASA Astrophysics Data System (ADS)

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-01

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

Configuration interaction in charge exchange spectra of tin and xenon

NASA Astrophysics Data System (ADS)

D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

2011-06-01

Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

Band structures of TiO2 doped with N, C and B*

PubMed Central

Xu, Tian-Hua; Song, Chen-Lu; Liu, Yong; Han, Gao-Rong

2006-01-01

This study on the band structures and charge densities of nitrogen (N)-, carbon (C)- and boron (B)-doped titanium dioxide (TiO2) by first-principles simulation with the CASTEP code (Segall et al., 2002) showed that the three 2p bands of impurity atom are located above the valence-band maximum and below the Ti 3d bands, and that along with the decreasing of impurity atomic number, the fluctuations become more intensive. We cannot observe obvious band-gap narrowing in our result. Therefore, the cause of absorption in visible light might be the isolated impurity atom 2p states in band-gap rather than the band-gap narrowing. PMID:16532532

Analysis of Crystallographic Structure of a Japanese Sword by the Pulsed Neutron Transmission Method

NASA Astrophysics Data System (ADS)

Kino, K.; Ayukawa, N.; Kiyanagi, Y.; Uchida, T.; Uno, S.; Grazzi, F.; Scherillo, A.

We measured two-dimensional transmission spectra of pulsed neutron beams for a Japanese sword sample. Atom density, crystalline size, and preferred orientation of crystals were obtained using the RITS code. The position dependence of the atomic density is consistent with the shape of the sample. The crystalline size is very small and shows position dependence, which is understood by the unique structure of Japanese swords. The preferred orientation has strong position dependence. Our study shows the usefulness of the pulsed neutron transmission method for cultural metal artifacts.

Multigrid based First-Principles Molecular Dynamics

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

Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

2017-06-01

MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

Simulation of Laser Cooling and Trapping in Engineering Applications

NASA Technical Reports Server (NTRS)

Ramirez-Serrano, Jaime; Kohel, James; Thompson, Robert; Yu, Nan; Lunblad, Nathan

2005-01-01

An advanced computer code is undergoing development for numerically simulating laser cooling and trapping of large numbers of atoms. The code is expected to be useful in practical engineering applications and to contribute to understanding of the roles that light, atomic collisions, background pressure, and numbers of particles play in experiments using laser-cooled and -trapped atoms. The code is based on semiclassical theories of the forces exerted on atoms by magnetic and optical fields. Whereas computer codes developed previously for the same purpose account for only a few physical mechanisms, this code incorporates many more physical mechanisms (including atomic collisions, sub-Doppler cooling mechanisms, Stark and Zeeman energy shifts, gravitation, and evanescent-wave phenomena) that affect laser-matter interactions and the cooling of atoms to submillikelvin temperatures. Moreover, whereas the prior codes can simulate the interactions of at most a few atoms with a resonant light field, the number of atoms that can be included in a simulation by the present code is limited only by computer memory. Hence, the present code represents more nearly completely the complex physics involved when using laser-cooled and -trapped atoms in engineering applications. Another advantage that the code incorporates is the possibility to analyze the interaction between cold atoms of different atomic number. Some properties that cold atoms of different atomic species have, like cross sections and the particular excited states they can occupy when interacting with each other and light fields, play important roles not yet completely understood in the new experiments that are under way in laboratories worldwide to form ultracold molecules. Other research efforts use cold atoms as holders of quantum information, and more recent developments in cavity quantum electrodynamics also use ultracold atoms to explore and expand new information-technology ideas. These experiments give a hint on the wide range of applications and technology developments that can be tackled using cold atoms and light fields. From more precise atomic clocks and gravity sensors to the development of quantum computers, there will be a need to completely understand the whole ensemble of physical mechanisms that play a role in the development of such technologies. The code also permits the study of the dynamic and steady-state operations of technologies that use cold atoms. The physical characteristics of lasers and fields can be time-controlled to give a realistic simulation of the processes involved such that the design process can determine the best control features to use. It is expected that with the features incorporated into the code it will become a tool for the useful application of ultracold atoms in engineering applications. Currently, the software is being used for the analysis and understanding of simple experiments using cold atoms, and for the design of a modular compact source of cold atoms to be used in future research and development projects. The results so far indicate that the code is a useful design instrument that shows good agreement with experimental measurements (see figure), and a Windows-based user-friendly interface is also under development.

Energy Levels and Oscillator Strengths for Ne-like Iron Ions

NASA Astrophysics Data System (ADS)

Zhong, J. Y.; Zhang, J.; Zhao, G.; Lu, X..

2004-02-01

Energy levels and oscillator strengths among the 27 fine-structure levels belonging to the (1s22s2)2p6, 2p53s, 2p53p and 2p53d configurations of neon-like iron ion have been calculated by using three atomic structure codes, RCN/RCG, AUTOSTRUCTURE (AS) and GRASP. The relativistic corrections of the wave functions are taken into account in RCN/RCG calculations. The results well agree with experimental and theoretical data wherever available. Finally the accuracy of three codes was analyzed.

Thermally activated decomposition of (Ga,Mn)As thin layer at medium temperature post growth annealing

NASA Astrophysics Data System (ADS)

Melikhov, Y.; Konstantynov, P.; Domagala, J.; Sadowski, J.; Chernyshova, M.; Wojciechowski, T.; Syryanyy, Y.; Demchenko, I. N.

2016-05-01

The redistribution of Mn atoms in Ga1-xMnxAs layer during medium-temperature annealing, 250-450 oC, by Mn K-edge X-ray absorption fine structure (XAFS) recorded at ALBA facility, was studied. For this purpose Ga1-xMnxAs thin layer with x=0.01 was grown on AlAs buffer layer deposited on GaAs(100) substrate by molecular beam epitaxy (MBE) followed by annealing. The examined layer was detached from the substrate using a “lift-off” procedure in order to eliminate elastic scattering in XAFS spectra. Fourier transform analysis of experimentally obtained EXAFS spectra allowed to propose a model which describes a redistribution/diffusion of Mn atoms in the host matrix. Theoretical XANES spectra, simulated using multiple scattering formalism (FEFF code) with the support of density functional theory (WIEN2k code), qualitatively describe the features observed in the experimental fine structure.

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.

Electron impact excitation of N IV: calculations with the DARC code and a comparison with ICFT results

NASA Astrophysics Data System (ADS)

Aggarwal, K. M.; Keenan, F. P.; Lawson, K. D.

2016-10-01

There have been discussions in the recent literature regarding the accuracy of the available electron impact excitation rates (equivalently effective collision strengths Υ) for transitions in Be-like ions. In the present paper we demonstrate, once again, that earlier results for Υ are indeed overestimated (by up to four orders of magnitude), for over 40 per cent of transitions and over a wide range of temperatures. To do this we have performed two sets of calculations for N IV, with two different model sizes consisting of 166 and 238 fine-structure energy levels. As in our previous work, for the determination of atomic structure the GRASP (General-purpose Relativistic Atomic Structure Package) is adopted and for the scattering calculations (the standard and parallelised versions of) the Dirac Atomic R-matrix Code (DARC) are employed. Calculations for collision strengths and effective collision strengths have been performed over a wide range of energy (up to 45 Ryd) and temperature (up to 2.0 × 106 K), useful for applications in a variety of plasmas. Corresponding results for energy levels, lifetimes and A-values for all E1, E2, M1 and M2 transitions among 238 levels of N IV are also reported.

Dirac R-matrix calculations of photoionization cross sections of Ni XII and atomic structure data of Ni XIII

NASA Astrophysics Data System (ADS)

Nazir, R. T.; Bari, M. A.; Bilal, M.; Sardar, S.; Nasim, M. H.; Salahuddin, M.

2017-02-01

We performed R-matrix calculations for photoionization cross sections of the two ground state configuration 3s23p5 (^2P^o3/2,1/2) levels and 12 excited states of Ni XII using relativistic Dirac Atomic R-matrix Codes (DARC) across the photon energy range between the ionizations thresholds of the corresponding states and well above the thresholds of the last level of the Ni XIII target ion. Generally, a good agreement is obtained between our results and the earlier theoretical photoionization cross sections. Moreover, we have used two independent fully relativistic GRASP and FAC codes to calculate fine-structure energy levels, wavelengths, oscillator strengths, transitions rates among the lowest 48 levels belonging to the configuration (3s23p4, 3s3p5, 3p6, 3s23p33d) in Ni XIII. Additionally, radiative lifetimes of all the excited states of Ni XIII are presented. Our results of the atomic structure of Ni XIII show good agreement with other theoretical and experimental results available in the literature. A good agreement is found between our calculated lifetimes and the experimental ones. Our present results are useful for plasma diagnostic of fusion and astrophysical plasmas.

A universal preconditioner for simulating condensed phase materials

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

Packwood, David; Ortner, Christoph, E-mail: c.ortner@warwick.ac.uk; Kermode, James, E-mail: j.r.kermode@warwick.ac.uk

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor ofmore » two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.« less

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Scalability improvements to NRLMOL for DFT calculations of large molecules

NASA Astrophysics Data System (ADS)

Diaz, Carlos Manuel

Advances in high performance computing (HPC) have provided a way to treat large, computationally demanding tasks using thousands of processors. With the development of more powerful HPC architectures, the need to create efficient and scalable code has grown more important. Electronic structure calculations are valuable in understanding experimental observations and are routinely used for new materials predictions. For the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for these calculations scale as N2, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure code hinder their efficient usage of these platforms. This thesis will present some developments to overcome these bottlenecks in order to study large systems. These developments, which are implemented in the NRLMOL electronic structure code, involve the use of sparse matrix storage formats and the use of linear algebra using sparse and distributed matrices. These developments along with other related development now allow ground state density functional calculations using up to 25,000 basis functions and the excited state calculations using up to 17,000 basis functions while utilizing all cores on a node. An example on a light-harvesting triad molecule is described. Finally, future plans to further improve the scalability will be presented.

C2x: A tool for visualisation and input preparation for CASTEP and other electronic structure codes

NASA Astrophysics Data System (ADS)

Rutter, M. J.

2018-04-01

The c2x code fills two distinct roles. Its first role is in acting as a converter between the binary format .check files from the widely-used CASTEP [1] electronic structure code and various visualisation programs. Its second role is to manipulate and analyse the input and output files from a variety of electronic structure codes, including CASTEP, ONETEP and VASP, as well as the widely-used 'Gaussian cube' file format. Analysis includes symmetry analysis, and manipulation arbitrary cell transformations. It continues to be under development, with growing functionality, and is written in a form which would make it easy to extend it to working directly with files from other electronic structure codes. Data which c2x is capable of extracting from CASTEP's binary checkpoint files include charge densities, spin densities, wavefunctions, relaxed atomic positions, forces, the Fermi level, the total energy, and symmetry operations. It can recreate .cell input files from checkpoint files. Volumetric data can be output in formats useable by many common visualisation programs, and c2x will itself calculate integrals, expand data into supercells, and interpolate data via combinations of Fourier and trilinear interpolation. It can extract data along arbitrary lines (such as lines between atoms) as 1D output. C2x is able to convert between several common formats for describing molecules and crystals, including the .cell format of CASTEP. It can construct supercells, reduce cells to their primitive form, and add specified k-point meshes. It uses the spglib library [2] to report symmetry information, which it can add to .cell files. C2x is a command-line utility, so is readily included in scripts. It is available under the GPL and can be obtained from http://www.c2x.org.uk. It is believed to be the only open-source code which can read CASTEP's .check files, so it will have utility in other projects.

ALICE: A non-LTE plasma atomic physics, kinetics and lineshape package

NASA Astrophysics Data System (ADS)

Hill, E. G.; Pérez-Callejo, G.; Rose, S. J.

2018-03-01

All three parts of an atomic physics, atomic kinetics and lineshape code, ALICE, are described. Examples of the code being used to model the emissivity and opacity of plasmas are discussed and interesting features of the code which build on the existing corpus of models are shown throughout.

Making Ordered DNA and Protein Structures from Computer-Printed Transparency Film Cut-Outs

ERIC Educational Resources Information Center

Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

2009-01-01

Instructions are given for building physical scale models of ordered structures of B-form DNA, protein [alpha]-helix, and parallel and antiparallel protein [beta]-pleated sheets made from colored computer printouts designed for transparency film sheets. Cut-outs from these sheets are easily assembled. Conventional color coding for atoms are used…

Calculations of the energy levels and oscillator strengths of the Ne-like Fe Ion (Fe XVII)

NASA Astrophysics Data System (ADS)

Zhong, Jia-yong; Zhang, Jie; Zhao, Gang; Lu, Xin

Energy levels and oscillator strengths among the 27 fine-structure levels belonging to the (ls 22s 2)2p 6, 2p 53s, 2p 53p and 2p 53d configurations of the neon-like iron ion have been calculated using three atomic structure codes RCN/RCG, AUTOSTRUCTURE (AS) and GRASP. Relativistic corrections of the wave functions are taken into account in the RCN/RCG calculation. The results agree well with the available experimental and theoretical data. The accuracy of the three codes is analysed.

Advanced Kr Atomic Structure and Ionization Kinetics for Pinches on ZR

NASA Astrophysics Data System (ADS)

Dasgupta, Arati; Clark, Robert; Giuliani, John; Ouart, Nick; Davis, Jack; Jones, Brent; Ampleford, Dave; Hansen, Stephanie

2011-10-01

High fluence photon sources above 10 keV are a challenge for HED plasmas. This motivates Kr atomic modeling as its K-shell radiation starts at 13 keV. We have developed atomic structure and collisional-radiatve data for the full K-and L-shell and much of the M-shell using the the state-of-the-art Flexible Atomic Code. All relevant atomic collisional and radiative processes that affect ionization balance and are necessary to accurately model the pinch dynamics and the spectroscopic details of the emitted radiation are included in constructing the model. This non-LTE CRE model will be used to generate synthetic spectra for fixed densities and temperatures relevant for Kr gas-puff simulations in ZR. Work supported by DOE/NNSA. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Analysis of soft x-ray emission spectra of laser-produced dysprosium, erbium and thulium plasmas

NASA Astrophysics Data System (ADS)

Sheil, John; Dunne, Padraig; Higashiguchi, Takeshi; Kos, Domagoj; Long, Elaine; Miyazaki, Takanori; O'Reilly, Fergal; O'Sullivan, Gerard; Sheridan, Paul; Suzuki, Chihiro; Sokell, Emma; White, Elgiva; Kilbane, Deirdre

2017-03-01

Soft x-ray emission spectra of dysprosium, erbium and thulium ions created in laser-produced plasmas were recorded with a flat-field grazing-incidence spectrometer in the 2.5-8 nm spectral range. The ions were produced using an Nd:YAG laser of 7 ns pulse duration and the spectra were recorded at various power densities. The experimental spectra were interpreted with the aid of the Cowan suite of atomic structure codes and the flexible atomic code. At wavelengths above 5.5 nm the spectra are dominated by overlapping n = 4 - n = 4 unresolved transition arrays from adjacent ion stages. Below 6 nm, n = 4 - n = 5 transitions also give rise to a series of interesting overlapping spectral features.

Effect on magnetic properties of germanium encapsulated C60 fullerene

NASA Astrophysics Data System (ADS)

Umran, Nibras Mossa; Kumar, Ranjan

2013-02-01

Structural and electronic properties of Gen(n = 1-4) doped C60 fullerene are investigated with ab initio density functional theory calculations by using an efficient computer code, known as SIESTA. The pseudopotentials are constructed using a Trouiller-Martins scheme, to describe the interaction of valence electrons with the atomic cores. In endohedral doped embedding of more germanium atoms complexes we have seen that complexes are stable and thereafter cage break down. We have also investigated that binding energy, electronic affinity increases and magnetic moment oscillating behavior as the number of semiconductor atoms in C60 fullerene goes on increasing.

Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.

PubMed

Schug, Alexander; Herges, Thomas; Verma, Abhinav; Lee, Kyu Hwan; Wenzel, Wolfgang

2005-12-09

The performances of three different stochastic optimization methods for all-atom protein structure prediction are investigated and compared. We use the recently developed all-atom free-energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp-cage protein (PDB-code 1L2Y) is folded with the stochastic tunneling method, a modified parallel tempering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.

The displacement effect of a fluorine atom in CaF2 on the band structure

NASA Astrophysics Data System (ADS)

Mir, A.; Zaoui, A.; Bensaid, D.

2018-05-01

We obtained the results for each configuration [100], [110] and [111] and each configuration contains two atoms of calcium and four fluorine atoms with lattice type B. This study was made by a code that is based on the DFT called wien2k. The results obtained are in good agreement with the experiment. For CaF2, an important variation of the fluoride ions concentration in CaF2 after displacement has been observed on the map of e-Density. The interpretation of the results is based on the existence of an important number of defects which are created by changing the atomic positions inside of sub lattice.

Use of Hilbert Curves in Parallelized CUDA code: Interaction of Interstellar Atoms with the Heliosphere

NASA Astrophysics Data System (ADS)

Destefano, Anthony; Heerikhuisen, Jacob

2015-04-01

Fully 3D particle simulations can be a computationally and memory expensive task, especially when high resolution grid cells are required. The problem becomes further complicated when parallelization is needed. In this work we focus on computational methods to solve these difficulties. Hilbert curves are used to map the 3D particle space to the 1D contiguous memory space. This method of organization allows for minimized cache misses on the GPU as well as a sorted structure that is equivalent to an octal tree data structure. This type of sorted structure is attractive for uses in adaptive mesh implementations due to the logarithm search time. Implementations using the Message Passing Interface (MPI) library and NVIDIA's parallel computing platform CUDA will be compared, as MPI is commonly used on server nodes with many CPU's. We will also compare static grid structures with those of adaptive mesh structures. The physical test bed will be simulating heavy interstellar atoms interacting with a background plasma, the heliosphere, simulated from fully consistent coupled MHD/kinetic particle code. It is known that charge exchange is an important factor in space plasmas, specifically it modifies the structure of the heliosphere itself. We would like to thank the Alabama Supercomputer Authority for the use of their computational resources.

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Effect of aluminum on the local structure of silicon in zeolites as studied by Si K edge X-ray absorption near-edge fine structure: spectra simulation with a non-muffin tin atomic background.

PubMed

Bugaev, Lusegen A; Bokhoven, Jeroen A van; Khrapko, Valerii V

2009-04-09

Experimental Si K edge X-ray absorption near-edge fine structure (XANES) of zeolite faujasite, mordenite, and beta are interpreted by means of the FEFF8 code, replacing the theoretical atomic background mu(0) by a background that was extracted from an experimental spectrum. To some extent, this diminished the effect of the inaccuracy introduced by the MT potential and accounted for the intrinsic loss of photoelectrons. The agreement of the theoretical and experimental spectra at energies above the white lines enabled us to identify structural distortion around silicon, which occurs with increasing aluminum content. The Si K edge XANES spectra are very sensitive to slight distortions in the silicon coordination. Placing an aluminum atom on a nearest neighboring T site causes a distortion in the silicon tetrahedron, shortening one of the silicon-oxygen bonds relative to the other three.

Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

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

Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.

2010-05-15

The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes ofmore » laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).« less

First principles study of hydrogen adsorption on carbon nanowires.

NASA Astrophysics Data System (ADS)

Tapia, Alejandro; Aguilera, Luis; Murrieta, Gabriel; de Coss, Romeo

2007-03-01

Recently has been reported a new type of one-dimensional carbon structures. Carbon nanowires formed by a linear carbon-atom chain inside an armchair (5,5) carbon nanotube has been observed using high-resolution transmission electron microscopy. In the present work we have studied the changes in the electronic structure of a carbon nanowires and (5,5) single-walled carbon nanotubes (SWCN) when a hydrogen atom is adsorbed. We used the Density Functional Theory and the calculations where performed by the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the changes in the atomic structure, density of states (LDOS), and the local orbital population. We found charge transfer from the nanotube to the linear chain and the hydrogen atom, the electronic character of the chain and nanotube sub-systems in chain@SWCN is the same that in the corresponding isolated systems, chain or SWCN. But the hydrogen adsorption produced changes in the atomic estructure and the electronic properties. This research was supported by PRIORI-UADY under Grant No. FING-05-004 and Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grants No. 43830-F and 49985-J.

A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.

PubMed

Zhou, Weiqiang; Yan, Hong

2010-10-15

Protein-DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein-DNA complex are becoming available, the surface characteristics of the complex become an important research topic. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein-DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of -8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of -7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein-DNA interactions. The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm kenandzhou@hotmail.com.

Quality Scalability Aware Watermarking for Visual Content.

PubMed

Bhowmik, Deepayan; Abhayaratne, Charith

2016-11-01

Scalable coding-based content adaptation poses serious challenges to traditional watermarking algorithms, which do not consider the scalable coding structure and hence cannot guarantee correct watermark extraction in media consumption chain. In this paper, we propose a novel concept of scalable blind watermarking that ensures more robust watermark extraction at various compression ratios while not effecting the visual quality of host media. The proposed algorithm generates scalable and robust watermarked image code-stream that allows the user to constrain embedding distortion for target content adaptations. The watermarked image code-stream consists of hierarchically nested joint distortion-robustness coding atoms. The code-stream is generated by proposing a new wavelet domain blind watermarking algorithm guided by a quantization based binary tree. The code-stream can be truncated at any distortion-robustness atom to generate the watermarked image with the desired distortion-robustness requirements. A blind extractor is capable of extracting watermark data from the watermarked images. The algorithm is further extended to incorporate a bit-plane discarding-based quantization model used in scalable coding-based content adaptation, e.g., JPEG2000. This improves the robustness against quality scalability of JPEG2000 compression. The simulation results verify the feasibility of the proposed concept, its applications, and its improved robustness against quality scalable content adaptation. Our proposed algorithm also outperforms existing methods showing 35% improvement. In terms of robustness to quality scalable video content adaptation using Motion JPEG2000 and wavelet-based scalable video coding, the proposed method shows major improvement for video watermarking.

Estimations of Mo X-pinch plasma parameters on QiangGuang-1 facility by L-shell spectral analyses

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

Wu, Jian; Qiu, Aici; State Key Laboratory of Intense Pulsed Radiation Simulation and Effect, Northwest Institute of Nuclear Technology, Xi'an 710024

2013-08-15

Plasma parameters of molybdenum (Mo) X-pinches on the 1-MA QiangGuang-1 facility were estimated by L-shell spectral analysis. X-ray radiation from X-pinches had a pulsed width of 1 ns, and its spectra in 2–3 keV were measured with a time-integrated X-ray spectrometer. Relative intensities of spectral features were derived by correcting for the spectral sensitivity of the spectrometer. With an open source, atomic code FAC (flexible atomic code), ion structures, and various atomic radiative-collisional rates for O-, F-, Ne-, Na-, Mg-, and Al-like ionization stages were calculated, and synthetic spectra were constructed at given plasma parameters. By fitting the measured spectramore » with the modeled, Mo X-pinch plasmas on the QiangGuang-1 facility had an electron density of about 10{sup 21} cm{sup −3} and the electron temperature of about 1.2 keV.« less

Geophysical Plasmas and Atmospheric Modeling.

DTIC Science & Technology

1982-01-01

analysis of structuring observed in the STARFISH event and early time structure formation in the LWIR predicted for a standard event, (2) IR structure...for the LWIR problem, the SCORPIO code was coupled to a numerical module which describes the behavior of the Rayleigh-Taylor insta- bility, as discussed...the LWIR C1-14p) induced by sunlight and earthshine. Of the constituents in nuclear debris the uranium atom is of particular interest because it

A Real-Time All-Atom Structural Search Engine for Proteins

PubMed Central

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

2014-01-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

A real-time all-atom structural search engine for proteins.

PubMed

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

2014-07-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

NLTE opacity calculations: C-Si and C-Ge mixtures

NASA Astrophysics Data System (ADS)

Jarrah, W.; Benredjem, D.; Pain, J.-C.; Dubau, J.

2017-09-01

The opacity is an important issue in the knowledge of the radiative properties of ICF and astrophysical plasmas. We present the opacity of dopants (silicon, germanium) embedded in the ablator of some ICF capsules. In recent works, Hill and Rose calculated the opacity of silicon in LTE and non-LTE plasmas, while Minguez and co-workers focused on the opacity of carbon. We have used the Cowan code to calculate the atomic structure of carbon, silicon and germanium in various ionic stages. The cross-sections of atomic processes (collisional excitation, collisional ionization) are obtained by fitting the values given by the code FAC to the Van Regemorter-like formulas of Sampson and Zhang. A corrected Gaunt factor is then obtained. A collisional-radiative code was developed in order to obtain the ionic populations, the level populations and the opacity. Line broadening and line shift are taken into account. The ionization potential depression is included in our calculations. The effect of a radiation field on the opacity is examined.

TORUS: Radiation transport and hydrodynamics code

NASA Astrophysics Data System (ADS)

Harries, Tim

2014-04-01

TORUS is a flexible radiation transfer and radiation-hydrodynamics code. The code has a basic infrastructure that includes the AMR mesh scheme that is used by several physics modules including atomic line transfer in a moving medium, molecular line transfer, photoionization, radiation hydrodynamics and radiative equilibrium. TORUS is useful for a variety of problems, including magnetospheric accretion onto T Tauri stars, spiral nebulae around Wolf-Rayet stars, discs around Herbig AeBe stars, structured winds of O supergiants and Raman-scattered line formation in symbiotic binaries, and dust emission and molecular line formation in star forming clusters. The code is written in Fortran 2003 and is compiled using a standard Gnu makefile. The code is parallelized using both MPI and OMP, and can use these parallel sections either separately or in a hybrid mode.

Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

PubMed

Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

2011-11-14

The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

Spectroscopics database for warm Xenon and Iron in Astrophysics and Laboratory Astrophysics conditions

NASA Astrophysics Data System (ADS)

Busquet, Michel; Klapisch, Marcel; Bar-Shalom, Avi; Oreg, Josse

2010-11-01

The main contribution to spectral properties of astrophysics mixtures come often from Iron. On the other hand, in the so-called domain of ``Laboratory Astrophysics,'' where astrophysics phenomena are scaled down to the laboratory, Xenon (and Argon) are commonly used gases. At so called ``warm'' temperatures (T=5-50eV), L-shell Iron and M-shell Xenon present a very large number of spectral lines, originating from billions of levels. More often than not, Local Thermodynamical Equilibrium is assumed, leading to noticeable simplification of the computation. Nevertheless, complex and powerful atomic structure codes are required. We take benefit of powerful statistics and numerics, included in our atomic structure codes, STA[1] and HULLAC[2], to generate the required spectra. Recent improvements in both fields (statistics, numerics and convergence control) allow obtaining large databases (ro x T grid of > 200x200 points, and > 10000 frequencies) for temperature down to a few eV. We plan to port these improvements in the NLTE code SCROLL[3]. [1] A.Bar-Shalom, et al, Phys. Rev. A 40, 3183 (1989) [2] M.Busquet,et al, J.Phys. IV France 133, 973-975 (2006); A.Bar-Shalom, M.Klapisch, J.Oreg, J.Oreg, JQSRT 71, 169, (2001) [3] A.Bar-Shalom, et al, Phys. Rev. E 56, R70 (1997)

Mass-invariance of the iron enrichment in the hot haloes of massive ellipticals, groups, and clusters of galaxies

NASA Astrophysics Data System (ADS)

Mernier, F.; de Plaa, J.; Werner, N.; Kaastra, J. S.; Raassen, A. J. J.; Gu, L.; Mao, J.; Urdampilleta, I.; Truong, N.; Simionescu, A.

2018-05-01

X-ray measurements find systematically lower Fe abundances in the X-ray emitting haloes pervading groups (kT ≲ 1.7 keV) than in clusters of galaxies. These results have been difficult to reconcile with theoretical predictions. However, models using incomplete atomic data or the assumption of isothermal plasmas may have biased the best fit Fe abundance in groups and giant elliptical galaxies low. In this work, we take advantage of a major update of the atomic code in the spectral fitting package SPEX to re-evaluate the Fe abundance in 43 clusters, groups, and elliptical galaxies (the CHEERS sample) in a self-consistent analysis and within a common radius of 0.1r500. For the first time, we report a remarkably similar average Fe enrichment in all these systems. Unlike previous results, this strongly suggests that metals are synthesised and transported in these haloes with the same average efficiency across two orders of magnitude in total mass. We show that the previous metallicity measurements in low temperature systems were biased low due to incomplete atomic data in the spectral fitting codes. The reasons for such a code-related Fe bias, also implying previously unconsidered biases in the emission measure and temperature structure, are discussed.

The Electronic Structure of Transition Metal Coated Fullerenes

NASA Astrophysics Data System (ADS)

Patton, David C.; Pederson, Mark R.; Kaxiras, Efthimios

1998-03-01

Clusters composed of fullerene molecules with an outer shell of transition metal atoms in the composition C_60M_62 (M being a transition metal) have been produced with laser vaporisation techniques(F. Tast, N. Malinowski, S. Frank, M. Heinebrodt, I.M.L. Billas, and T. P. Martin, Z. Phys D 40), 351 (1997).. We have studied several of these very large systems with a parallel version of the all-electron NRLMOL cluster code. Optimized geometries of the metal encased fullerenes C_60Ti_62 and C_60V_62 are presented along with their HOMO-LUMO gaps, electron affinities, ionization energies, and cohesive energies. We compare the stability of these clusters to relaxed met-car structures (e.g. Ti_8C_12) and to relaxed rocksalt metal-carbide fragments (TiC)n with n=8 and 32. In addition to metal-coated fullerenes we consider the possibility of a trilayered structure consisting of a small shell of metal atoms enclosed by a metal coated fullerene. The nature of bonding in these systems is analyzed by studying the electronic charge distributions.

On fully three-dimensional resistive wall mode and feedback stabilization computationsa)

NASA Astrophysics Data System (ADS)

Strumberger, E.; Merkel, P.; Sempf, M.; Günter, S.

2008-05-01

Resistive walls, located close to the plasma boundary, reduce the growth rates of external kink modes to resistive time scales. For such slowly growing resistive wall modes, the stabilization by an active feedback system becomes feasible. The fully three-dimensional stability code STARWALL, and the feedback optimization code OPTIM have been developed [P. Merkel and M. Sempf, 21st IAEA Fusion Energy Conference 2006, Chengdu, China (International Atomic Energy Agency, Vienna, 2006, paper TH/P3-8] to compute the growth rates of resistive wall modes in the presence of nonaxisymmetric, multiply connected wall structures and to model the active feedback stabilization of these modes. In order to demonstrate the capabilities of the codes and to study the effect of the toroidal mode coupling caused by multiply connected wall structures, the codes are applied to test equilibria using the resistive wall structures currently under debate for ITER [M. Shimada et al., Nucl. Fusion 47, S1 (2007)] and ASDEX Upgrade [W. Köppendörfer et al., Proceedings of the 16th Symposium on Fusion Technology, London, 1990 (Elsevier, Amsterdam, 1991), Vol. 1, p. 208].

On fully three-dimensional resistive wall mode and feedback stabilization computations

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

Strumberger, E.; Merkel, P.; Sempf, M.

2008-05-15

Resistive walls, located close to the plasma boundary, reduce the growth rates of external kink modes to resistive time scales. For such slowly growing resistive wall modes, the stabilization by an active feedback system becomes feasible. The fully three-dimensional stability code STARWALL, and the feedback optimization code OPTIM have been developed [P. Merkel and M. Sempf, 21st IAEA Fusion Energy Conference 2006, Chengdu, China (International Atomic Energy Agency, Vienna, 2006, paper TH/P3-8] to compute the growth rates of resistive wall modes in the presence of nonaxisymmetric, multiply connected wall structures and to model the active feedback stabilization of these modes.more » In order to demonstrate the capabilities of the codes and to study the effect of the toroidal mode coupling caused by multiply connected wall structures, the codes are applied to test equilibria using the resistive wall structures currently under debate for ITER [M. Shimada et al., Nucl. Fusion 47, S1 (2007)] and ASDEX Upgrade [W. Koeppendoerfer et al., Proceedings of the 16th Symposium on Fusion Technology, London, 1990 (Elsevier, Amsterdam, 1991), Vol. 1, p. 208].« less

The MOLDY short-range molecular dynamics package

NASA Astrophysics Data System (ADS)

Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

2011-12-01

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

Energy levels and radiative rates for transitions in Cr-like Co IV and Ni V

NASA Astrophysics Data System (ADS)

Aggarwal, K. M.; Bogdanovich, P.; Karpuškienė, R.; Keenan, F. P.; Kisielius, R.; Stancalie, V.

2016-01-01

We report calculations of energy levels and radiative rates (A-values) for transitions in Cr-like Co IV and Ni V. The quasi-relativistic Hartree-Fock (QRHF) code is adopted for calculating the data although GRASP (general-purpose relativistic atomic structure package) and flexible atomic code (FAC) have also been employed for comparison purposes. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST for a majority of the levels. However, there are discrepancies for a few levels of up to 3%. The A-values are listed for all significantly contributing E1, E2 and M1 transitions, and the corresponding lifetimes reported, although unfortunately no previous theoretical or experimental results exist to compare with our data.

GAPD: a GPU-accelerated atom-based polychromatic diffraction simulation code.

PubMed

E, J C; Wang, L; Chen, S; Zhang, Y Y; Luo, S N

2018-03-01

GAPD, a graphics-processing-unit (GPU)-accelerated atom-based polychromatic diffraction simulation code for direct, kinematics-based, simulations of X-ray/electron diffraction of large-scale atomic systems with mono-/polychromatic beams and arbitrary plane detector geometries, is presented. This code implements GPU parallel computation via both real- and reciprocal-space decompositions. With GAPD, direct simulations are performed of the reciprocal lattice node of ultralarge systems (∼5 billion atoms) and diffraction patterns of single-crystal and polycrystalline configurations with mono- and polychromatic X-ray beams (including synchrotron undulator sources), and validation, benchmark and application cases are presented.

Charge exchange cross sections in slow collisions of Si3+ with Hydrogen atom

NASA Astrophysics Data System (ADS)

Joseph, Dwayne; Quashie, Edwin; Saha, Bidhan

2011-05-01

In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. Work supported by NSF CREST project (grant #0630370).

Density functional study of structural and electronic properties of Al{sub n}@C{sub 60}

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

Dhiman, Shobhna, E-mail: s-dhiman@hotmail.com; Kumar, Ranjan; Dharamvir, Keya

2014-04-24

Fullerene derivatives have been shown to make contributions in many types of applications. Ab initio investigation of structural and electronic properties of aluminum doped endohedral fullerene has been performed using numerical atomic orbital density functional theory. We have obtained ground state structures for Al{sub n}@C{sub 60} (n=1–10). Which shows that C{sub 60} molecule can accommodate maximum of nine aluminum atoms, for n > 9 the cage eventually break. Encapsulated large number of aluminum atoms leads to deformation of cage with diameter varies from 7.16Å to 7.95Å. Binding energy/Al atom is found to increase till n = 4 and after thatmore » it decreases with the number of Al atoms with a sudden increase for n=10 due to breakage of C{sub 60} cage and electronic affinity first increases till n=4 then it decreases up to n=9 with a sharp increase for n=10. Ionization potential also first increases and then decreases. Homo-Lumo gap decreases till n=3 with a sharp increase for n=4, after that it shows an oscillatory nature. The results obtained are consistent with available theoretical and experimental results. The ab-initio calculations were performed using SIESTA code with generalized gradient approximation (GGA)« less

An Essential Protein Repair Enzyme: Investigation of the Molecular Recognition Mechanism of Methionine Sulfoxide Reductase A

DTIC Science & Technology

2008-05-01

4 ). The three-dimensional spatial orientation of the atoms for these resolved solution structures (Protein Data Bank accession codes: 2gt3...Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 Å resolution . Struct. Fold. Des. 8: 1167 – 1178. 2 . Brot...sources (8). There is a 67% sequence identity between the E.coli and human MsrA ( 2 ). N-terminus C-terminus Figure 2 . Three-dimensional structure

The linearly scaling 3D fragment method for large scale electronic structure calculations

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

Zhao, Zhengji; Meza, Juan; Lee, Byounghak

2009-07-28

The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

The Linearly Scaling 3D Fragment Method for Large Scale Electronic Structure Calculations

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

Zhao, Zhengji; Meza, Juan; Lee, Byounghak

2009-06-26

The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

Relativistic opacities for astrophysical applications

DOE PAGES

Fontes, Christopher John; Fryer, Christopher Lee; Hungerford, Aimee L.; ...

2015-06-29

Here, we report on the use of the Los Alamos suite of relativistic atomic physics codes to generate radiative opacities for the modeling of astrophysically relevant plasmas under local thermodynamic equilibrium (LTE) conditions. The atomic structure calculations are carried out in fine-structure detail, including full configuration interaction. Three example applications are considered: iron opacities at conditions relevant to the base of the solar convection zone, nickel opacities for the modeling of stellar envelopes, and samarium opacities for the modeling of light curves produced by neutron star mergers. In the first two examples, comparisons are made between opacities that are generatedmore » with the fully and semi-relativistic capabilities in the Los Alamos suite of codes. As expected for these highly charged, iron-peak ions, the two methods produce reasonably similar results, providing confidence that the numerical methods have been correctly implemented. However, discrepancies greater than 10% are observed for nickel and investigated in detail. In the final application, the relativistic capability is used in a preliminary investigation of the complicated absorption spectrum associated with cold lanthanide elements.« less

3D RNA and functional interactions from evolutionary couplings

PubMed Central

Weinreb, Caleb; Riesselman, Adam; Ingraham, John B.; Gross, Torsten; Sander, Chris; Marks, Debora S.

2016-01-01

Summary Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules, and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions, e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by accelerating sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA. PMID:27087444

The Los Alamos suite of relativistic atomic physics codes

DOE PAGES

Fontes, C. J.; Zhang, H. L.; Jr, J. Abdallah; ...

2015-05-28

The Los Alamos SuitE of Relativistic (LASER) atomic physics codes is a robust, mature platform that has been used to model highly charged ions in a variety of ways. The suite includes capabilities for calculating data related to fundamental atomic structure, as well as the processes of photoexcitation, electron-impact excitation and ionization, photoionization and autoionization within a consistent framework. These data can be of a basic nature, such as cross sections and collision strengths, which are useful in making predictions that can be compared with experiments to test fundamental theories of highly charged ions, such as quantum electrodynamics. The suitemore » can also be used to generate detailed models of energy levels and rate coefficients, and to apply them in the collisional-radiative modeling of plasmas over a wide range of conditions. Such modeling is useful, for example, in the interpretation of spectra generated by a variety of plasmas. In this work, we provide a brief overview of the capabilities within the Los Alamos relativistic suite along with some examples of its application to the modeling of highly charged ions.« less

Calculated values of atomic oxygen fluences and solar exposure on selected surfaces of LDEF

NASA Technical Reports Server (NTRS)

Gillis, J. R.; Pippin, H. G.; Bourassa, R. J.; Gruenbaum, P. E.

1995-01-01

Atomic oxygen (AO) fluences and solar exposure have been modeled for selected hardware from the Long Duration Exposure Facility (LDEF). The atomic oxygen exposure was modeled using the microenvironment modeling code SHADOWV2. The solar exposure was modeled using the microenvironment modeling code SOLSHAD version 1.0.

Fast, clash-free RNA conformational morphing using molecular junctions

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

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

Fast, clash-free RNA conformational morphing using molecular junctions

DOE PAGES

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus; ...

2017-03-13

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

Comparisons of laboratory wavelength measurements with theoretical calculations for neon-like through lithium-like argon, sulfur, and silicon

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

Lepson, J K; Beiersdorfer, P; Behar, E

Atomic structure codes have a difficult time accurately calculating the wavelengths of many-electron ions without the benefit of laboratory measurements. This is especially true for wavelengths of lines in the extreme ultraviolet and soft x-ray regions. We are using the low-energy capability of the Livermore electron beam ion traps to compile a comprehensive catalog of astrophysically relevant emission lines in support of satellite x-ray observations. Our database includes wavelength measurements, relative intensities, and line assignments, and is compared to a full set of calculations using the Hebrew University - Lawrence Livermore Atomic Code (HULLAC). Mean deviation of HULLAC calculations frommore » our measured wavelength values is highest for L-shell transitions of neon-like ions and lowest for lithium-like ions, ranging from a mean deviation of over 0.5 {angstrom} for Si V to 12 m{angstrom} in Ar XVI.« less

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV

NASA Astrophysics Data System (ADS)

Aggarwal, Kanti M.; Keenan, Francis P.

2013-04-01

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV. The grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths, and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are provided for all 49 levels of the above five ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 108 K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, particularly for some forbidden transitions, are also discussed. Finally, discrepancies between the present results for effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions.

A first principles study of the electronic structure, elastic and thermal properties of UB2

NASA Astrophysics Data System (ADS)

Jossou, Ericmoore; Malakkal, Linu; Szpunar, Barbara; Oladimeji, Dotun; Szpunar, Jerzy A.

2017-07-01

Uranium diboride (UB2) has been widely deployed for refractory use and is a proposed material for Accident Tolerant Fuel (ATF) due to its high thermal conductivity. However, the applicability of UB2 towards high temperature usage in a nuclear reactor requires the need to investigate the thermomechanical properties, and recent studies have failed in highlighting applicable properties. In this work, we present an in-depth theoretical outlook of the structural and thermophysical properties of UB2, including but not limited to elastic, electronic and thermal transport properties. These calculations were performed within the framework of Density Functional Theory (DFT) + U approach, using Quantum ESPRESSO (QE) code considering the addition of Coulomb correlations on the uranium atom. The phonon spectra and elastic constant analysis show the dynamic and mechanical stability of UB2 structure respectively. The electronic structure of UB2 was investigated using full potential linear augmented plane waves plus local orbitals method (FP-LAPW+lo) as implemented in WIEN2k code. The absence of a band gap in the total and partial density of states confirms the metallic nature while the valence electron density plot reveals the presence of covalent bond between adjacent B-B atoms. We predicted the lattice thermal conductivity (kL) by solving Boltzmann Transport Equation (BTE) using ShengBTE. The second order harmonic and third-order anharmonic interatomic force constants required as input to ShengBTE was calculated using the Density-functional perturbation theory (DFPT). However, we predicted the electronic thermal conductivity (kel) using Wiedemann-Franz law as implemented in Boltztrap code. We also show that the sound velocity along 'a' and 'c' axes exhibit high anisotropy, which accounts for the anisotropic thermal conductivity of UB2.

Group-sparse representation with dictionary learning for medical image denoising and fusion.

PubMed

Li, Shutao; Yin, Haitao; Fang, Leyuan

2012-12-01

Recently, sparse representation has attracted a lot of interest in various areas. However, the standard sparse representation does not consider the intrinsic structure, i.e., the nonzero elements occur in clusters, called group sparsity. Furthermore, there is no dictionary learning method for group sparse representation considering the geometrical structure of space spanned by atoms. In this paper, we propose a novel dictionary learning method, called Dictionary Learning with Group Sparsity and Graph Regularization (DL-GSGR). First, the geometrical structure of atoms is modeled as the graph regularization. Then, combining group sparsity and graph regularization, the DL-GSGR is presented, which is solved by alternating the group sparse coding and dictionary updating. In this way, the group coherence of learned dictionary can be enforced small enough such that any signal can be group sparse coded effectively. Finally, group sparse representation with DL-GSGR is applied to 3-D medical image denoising and image fusion. Specifically, in 3-D medical image denoising, a 3-D processing mechanism (using the similarity among nearby slices) and temporal regularization (to perverse the correlations across nearby slices) are exploited. The experimental results on 3-D image denoising and image fusion demonstrate the superiority of our proposed denoising and fusion approaches.

Protein and gene structure of a blue laccase from Pleurotus ostreatus1.

PubMed Central

Giardina, P; Palmieri, G; Scaloni, A; Fontanella, B; Faraco, V; Cennamo, G; Sannia, G

1999-01-01

A new laccase isoenzyme (POXA1b, where POX is phenol oxidase), produced by Pleurotus ostreatus in cultures supplemented with copper sulphate, has been purified and fully characterized. The main characteristics of this protein (molecular mass in native and denaturing conditions, pI and catalytic properties) are almost identical to the previously studied laccase POXA1w. However, POXA1b contains four copper atoms per molecule instead of one copper, two zinc and one iron atom per molecule of POXA1w. Furthermore, POXA1b shows an unusually high stability at alkaline pH. The gene and cDNA coding for POXA1b have been cloned and sequenced. The gene coding sequence contains 1599 bp, interrupted by 15 introns. Comparison of the structure of the poxa1b gene with the two previously studied P. ostreatus laccase genes (pox1 and poxc) suggests that these genes belong to two different subfamilies. The amino acid sequence of POXA1b deduced from the cDNA sequence has been almost completely verified by means of matrix-assisted laser desorption ionization MS. It has been demonstrated that three out of six putative glycosylation sites are post-translationally modified and the structure of the bound glycosidic moieties has been determined, whereas two other putative glycosylation sites are unmodified. PMID:10417329

Recent advances in the structure elucidation of small organic molecules by the LSD software.

PubMed

Plainchont, Bertrand; de Paulo Emerenciano, Vicente; Nuzillard, Jean-Marc

2013-08-01

The LSD software proposes the structures of small organic molecules that fit with structural constraints from 1D and 2D NMR spectroscopy. Its initial design introduced limits that needed to be eliminated to extend its scope and help its users choose the most likely structure among those proposed. The LSD software code has been improved, so that it recognizes a wider set of atom types to build molecules. More flexibility has been given in the interpretation of 2D NMR data, including the automatic detection of very long-range correlations. A program named pyLSD was written to deal with problems in which atom types are ambiguously defined. It also provides a (13)C NMR chemical shift-based solution ranking algorithm. PyLSD was able to propose the correct structure of hexacyclinol, a natural product whose structure determination has been highly controversal. The solution was ranked first within a list of ten structures that were produced by pyLSD from the literature NMR data. The structure of an aporphin natural product was determined by pyLSD, taking advantage of the possibility of handling electrically charged atoms. The structure generation of the insect antifeedant azadirachtin by LSD was reinvestigated by pyLSD, considering that three (13)C resonances did not lead to univocal hybridization states. Copyright © 2013 John Wiley & Sons, Ltd.

First principles study of NH3 adsorption on carbon nanowires

NASA Astrophysics Data System (ADS)

Tapia, Jorge-Alejandro; Sanchez, Alvaro-Daniel; Acosta, Cesar; Canto, Gabriel

2009-03-01

Recently has been reported a new type of one-dimensional carbon structures. Carbon nanowires formed by a linear carbon-atom chain inside an armchair (5,5) carbon nanotube has been observed using high-resolution transmission electron microscopy. Theoretical and experimental studies of the NH3 adsorption in the carbon nanotubes report changes in the electronic properties of the carbon nanotubes. In the present work we have studied the electronic and structure properties of carbon nanowires (chain@SWCNT) when NH3 atoms are adsorbed. We used the Density Functional Theory and the calculations where performed by the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the changes in the atomic structure and density of states (DOS). We found that the electronic character of the carbon chain of the chain@SWCNT system, can be modulate by NH3 adsorption. This research was supported by SEP under Grant No. PROMEP/103.5/07/2595 and the Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grants No. 82497 and 60534.

Electronic stopping in oxides beyond Bragg additivity

NASA Astrophysics Data System (ADS)

Sigmund, P.; Schinner, A.

2018-01-01

We present stopping cross sections calculated by our PASS code for several ions in metal oxides and SiO2 over a wide energy range. Input takes into account changes in the valence structure by assigning two additional electrons to the 2p shell of oxygen and removing the appropriate number of electrons from the outer shells of the metal atom. Results are compared with tabulated experimental values and with two versions of Bragg's additivity rule. Calculated stopping cross sections are applied in testing a recently-proposed scaling rule, which relates the stopping cross section to the number of oxygen atoms per molecule.

SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

2017-10-01

As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

NASA Astrophysics Data System (ADS)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

PubMed

Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-16

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Analysis of unresolved transition arrays in XUV spectral region from highly charged lead ions produced by subnanosecond laser pulse

NASA Astrophysics Data System (ADS)

Wu, Tao; Higashiguchi, Takeshi; Li, Bowen; Arai, Goki; Hara, Hiroyuki; Kondo, Yoshiki; Miyazaki, Takanori; Dinh, Thanh-Hung; O'Reilly, Fergal; Sokell, Emma; O'Sullivan, Gerry

2017-02-01

Soft x-ray and extreme ultraviolet (XUV) spectra from lead (Pb, Z=82) laser-produced plasmas (LPPs) were measured in the 1.0-7.0 nm wavelength region employing a 150-ps, 1064-nm Nd:YAG laser with focused power densities in the range from 3.1×1013 W/cm2 to 1.4×1014 W/cm2. The flexible atomic code (FAC) and the Cowan's suite of atomic structure codes were applied to compute and explain the radiation properties of the lead spectra observed. The most prominent structure in the spectra is a broad double peak, which is produced by Δn=0, n=4-4 and Δn=1, n=4-5 transition arrays emitted from highly charged lead ions. The emission characteristics of Δn=1, n=4-5 transitions were investigated by the use of the unresolved transition arrays (UTAs) model. Numerous new spectral features generated by Δn=1, n=4-5 transitions in ions from Pb21+ to Pb45+ are discerned with the aid of the results from present computations as well as consideration of previous theoretical predictions and experimental data.

Statistical dielectronic recombination rates for multielectron ions in plasma

NASA Astrophysics Data System (ADS)

Demura, A. V.; Leont'iev, D. S.; Lisitsa, V. S.; Shurygin, V. A.

2017-10-01

We describe the general analytic derivation of the dielectronic recombination (DR) rate coefficient for multielectron ions in a plasma based on the statistical theory of an atom in terms of the spatial distribution of the atomic electron density. The dielectronic recombination rates for complex multielectron tungsten ions are calculated numerically in a wide range of variation of the plasma temperature, which is important for modern nuclear fusion studies. The results of statistical theory are compared with the data obtained using level-by-level codes ADPAK, FAC, HULLAC, and experimental results. We consider different statistical DR models based on the Thomas-Fermi distribution, viz., integral and differential with respect to the orbital angular momenta of the ion core and the trapped electron, as well as the Rost model, which is an analog of the Frank-Condon model as applied to atomic structures. In view of its universality and relative simplicity, the statistical approach can be used for obtaining express estimates of the dielectronic recombination rate coefficients in complex calculations of the parameters of the thermonuclear plasmas. The application of statistical methods also provides information for the dielectronic recombination rates with much smaller computer time expenditures as compared to available level-by-level codes.

MEAM interatomic force calculation subroutine for LAMMPS

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

Stukowski, A.

2010-10-25

Interatomic force and energy calculation subroutine tobe used with the molecular dynamics simulation code LAMMPS (Ref a.). The code evaluates the total energy and atomic forces (energy gradient) according to cubic spine-based variant (Ref b.) of the Modified Embedded Atom Method (MEAM).

CRITIC2: A program for real-space analysis of quantum chemical interactions in solids

NASA Astrophysics Data System (ADS)

Otero-de-la-Roza, A.; Johnson, Erin R.; Luaña, Víctor

2014-03-01

We present CRITIC2, a program for the analysis of quantum-mechanical atomic and molecular interactions in periodic solids. This code, a greatly improved version of the previous CRITIC program (Otero-de-la Roza et al., 2009), can: (i) find critical points of the electron density and related scalar fields such as the electron localization function (ELF), Laplacian, … (ii) integrate atomic properties in the framework of Bader’s Atoms-in-Molecules theory (QTAIM), (iii) visualize non-covalent interactions in crystals using the non-covalent interactions (NCI) index, (iv) generate relevant graphical representations including lines, planes, gradient paths, contour plots, atomic basins, … and (v) perform transformations between file formats describing scalar fields and crystal structures. CRITIC2 can interface with the output produced by a variety of electronic structure programs including WIEN2k, elk, PI, abinit, Quantum ESPRESSO, VASP, Gaussian, and, in general, any other code capable of writing the scalar field under study to a three-dimensional grid. CRITIC2 is parallelized, completely documented (including illustrative test cases) and publicly available under the GNU General Public License. Catalogue identifier: AECB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 11686949 No. of bytes in distributed program, including test data, etc.: 337020731 Distribution format: tar.gz Programming language: Fortran 77 and 90. Computer: Workstations. Operating system: Unix, GNU/Linux. Has the code been vectorized or parallelized?: Shared-memory parallelization can be used for most tasks. Classification: 7.3. Catalogue identifier of previous version: AECB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 157 Nature of problem: Analysis of quantum-chemical interactions in periodic solids by means of atoms-in-molecules and related formalisms. Solution method: Critical point search using Newton’s algorithm, atomic basin integration using bisection, qtree and grid-based algorithms, diverse graphical representations and computation of the non-covalent interactions index on a three-dimensional grid. Additional comments: !!!!! The distribution file for this program is over 330 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: Variable, depending on the crystal and the source of the underlying scalar field.

A Monte Carlo calculation model of electronic portal imaging device for transit dosimetry through heterogeneous media

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

Yoon, Jihyung; Jung, Jae Won, E-mail: jungj@ecu.edu; Kim, Jong Oh

2016-05-15

Purpose: To develop and evaluate a fast Monte Carlo (MC) dose calculation model of electronic portal imaging device (EPID) based on its effective atomic number modeling in the XVMC code. Methods: A previously developed EPID model, based on the XVMC code by density scaling of EPID structures, was modified by additionally considering effective atomic number (Z{sub eff}) of each structure and adopting a phase space file from the EGSnrc code. The model was tested under various homogeneous and heterogeneous phantoms and field sizes by comparing the calculations in the model with measurements in EPID. In order to better evaluate themore » model, the performance of the XVMC code was separately tested by comparing calculated dose to water with ion chamber (IC) array measurement in the plane of EPID. Results: In the EPID plane, calculated dose to water by the code showed agreement with IC measurements within 1.8%. The difference was averaged across the in-field regions of the acquired profiles for all field sizes and phantoms. The maximum point difference was 2.8%, affected by proximity of the maximum points to penumbra and MC noise. The EPID model showed agreement with measured EPID images within 1.3%. The maximum point difference was 1.9%. The difference dropped from the higher value of the code by employing the calibration that is dependent on field sizes and thicknesses for the conversion of calculated images to measured images. Thanks to the Z{sub eff} correction, the EPID model showed a linear trend of the calibration factors unlike those of the density-only-scaled model. The phase space file from the EGSnrc code sharpened penumbra profiles significantly, improving agreement of calculated profiles with measured profiles. Conclusions: Demonstrating high accuracy, the EPID model with the associated calibration system may be used for in vivo dosimetry of radiation therapy. Through this study, a MC model of EPID has been developed, and their performance has been rigorously investigated for transit dosimetry.« less

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of Mn K -edge XANES data

NASA Astrophysics Data System (ADS)

Monesi, C.; Meneghini, C.; Bardelli, F.; Benfatto, M.; Mobilio, S.; Manju, U.; Sarma, D. D.

2005-11-01

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K -edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3 . The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K -edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Master equation theory applied to the redistribution of polarized radiation in the weak radiation field limit. V. The two-term atom

NASA Astrophysics Data System (ADS)

Bommier, Véronique

2017-11-01

Context. In previous papers of this series, we presented a formalism able to account for both statistical equilibrium of a multilevel atom and coherent and incoherent scatterings (partial redistribution). Aims: This paper provides theoretical expressions of the redistribution function for the two-term atom. This redistribution function includes both coherent (RII) and incoherent (RIII) scattering contributions with their branching ratios. Methods: The expressions were derived by applying the formalism outlined above. The statistical equilibrium equation for the atomic density matrix is first formally solved in the case of the two-term atom with unpolarized and infinitely sharp lower levels. Then the redistribution function is derived by substituting this solution for the expression of the emissivity. Results: Expressions are provided for both magnetic and non-magnetic cases. Atomic fine structure is taken into account. Expressions are also separately provided under zero and non-zero hyperfine structure. Conclusions: Redistribution functions are widely used in radiative transfer codes. In our formulation, collisional transitions between Zeeman sublevels within an atomic level (depolarizing collisions effect) are taken into account when possible (I.e., in the non-magnetic case). However, the need for a formal solution of the statistical equilibrium as a preliminary step prevents us from taking into account collisional transfers between the levels of the upper term. Accounting for these collisional transfers could be done via a numerical solution of the statistical equilibrium equation system.

High-Throughput Characterization of Porous Materials Using Graphics Processing Units

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

Kim, Jihan; Martin, Richard L.; Rübel, Oliver

We have developed a high-throughput graphics processing units (GPU) code that can characterize a large database of crystalline porous materials. In our algorithm, the GPU is utilized to accelerate energy grid calculations where the grid values represent interactions (i.e., Lennard-Jones + Coulomb potentials) between gas molecules (i.e., CHmore » $$_{4}$$ and CO$$_{2}$$) and material's framework atoms. Using a parallel flood fill CPU algorithm, inaccessible regions inside the framework structures are identified and blocked based on their energy profiles. Finally, we compute the Henry coefficients and heats of adsorption through statistical Widom insertion Monte Carlo moves in the domain restricted to the accessible space. The code offers significant speedup over a single core CPU code and allows us to characterize a set of porous materials at least an order of magnitude larger than ones considered in earlier studies. For structures selected from such a prescreening algorithm, full adsorption isotherms can be calculated by conducting multiple grand canonical Monte Carlo simulations concurrently within the GPU.« less

Energy Levels and Radiative Rates for Transitions in F-like Sc XIII and Ne-like Sc XII and Y XXX

NASA Astrophysics Data System (ADS)

Aggarwal, Kanti

2018-05-01

Energy levels, radiative rates and lifetimes are reported for F-like Sc~XIII and Ne-like Sc~XII and Y~XXX for which the general-purpose relativistic atomic structure package ({\\sc grasp}) has been adopted. For all three ions limited data exist in the literature but comparisons have been made wherever possible to assess the accuracy of the calculations. In the present work the lowest 102, 125 and 139 levels have been considered for the respective ions. Additionally, calculations have also been performed with the flexible atomic code ({\\sc fac}) to (particularly) confirm the accuracy of energy levels.

Atomic structure calculations and identification of EUV and SXR spectral lines in Sr XXX

NASA Astrophysics Data System (ADS)

Goyal, Arun; Khatri, Indu; Aggarwal, Sunny; Singh, A. K.; Mohan, Man

2015-08-01

We report an extensive theoretical study of atomic data for Sr XXX in a wide range with L-shell electron excitations to the M-shell. We have calculated energy levels, wave-function compositions and lifetimes for lowest 113 fine structure levels and wavelengths of an extreme Ultraviolet (EUV) and soft X-ray (SXR) transitions. We have employed multi-configuration Dirac Fock method (MCDF) approach within the framework of Dirac-Coulomb Hamiltonian including quantum electrodynamics (QED) and Breit corrections. We have also presented the radiative data for electric and magnetic dipole (E1, M1) and quadrupole (E2, M2) transitions from the ground state. We have made comparisons with available energy levels compiled by NIST and achieve good agreement. But due to inadequate data in the literature, analogous relativistic distorted wave calculations have also been performed using flexible atomic code (FAC) to assess the reliability and accuracy of our results. Additionally, we have provided new atomic data for Sr XXX which is not published elsewhere in the literature and we believe that our results may be beneficial in fusion plasma research and astrophysical investigations and applications.

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

PubMed

Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

2009-07-02

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently.

The Emergence of Atomic-Level Structural Information for Ordered Metal-Solution Interfaces: Some Recent Contributions from In-Situ Infrared Spectroscopy and Scanning Tunneling Microscopy

DTIC Science & Technology

1992-02-28

Distribution/ Availabilit Codes jAval’ an~d/or Dist Speoial (19. cont.) reconstruction at gold-aqueous interfaces. All three low-index gold surfaces are...uncharged (vide supra). This difference may well be due to the influence of the interfacial water , or conceivably to adsorbed perchlorate anions. Both Au

GPU acceleration of the Locally Selfconsistent Multiple Scattering code for first principles calculation of the ground state and statistical physics of materials

NASA Astrophysics Data System (ADS)

Eisenbach, Markus; Larkin, Jeff; Lutjens, Justin; Rennich, Steven; Rogers, James H.

2017-02-01

The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn-Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. We present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. We reimplement the scattering matrix calculation for GPUs with a block matrix inversion algorithm that only uses accelerator memory. Using the Cray XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code.

GPU acceleration of the Locally Selfconsistent Multiple Scattering code for first principles calculation of the ground state and statistical physics of materials

DOE PAGES

Eisenbach, Markus; Larkin, Jeff; Lutjens, Justin; ...

2016-07-12

The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn–Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. In this paper, we present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. We reimplement the scattering matrix calculation for GPUs with a block matrix inversion algorithm that only uses accelerator memory. Finally, using the Craymore » XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code.« less

Multi-scale modeling of irradiation effects in spallation neutron source materials

NASA Astrophysics Data System (ADS)

Yoshiie, T.; Ito, T.; Iwase, H.; Kaneko, Y.; Kawai, M.; Kishida, I.; Kunieda, S.; Sato, K.; Shimakawa, S.; Shimizu, F.; Hashimoto, S.; Hashimoto, N.; Fukahori, T.; Watanabe, Y.; Xu, Q.; Ishino, S.

2011-07-01

Changes in mechanical property of Ni under irradiation by 3 GeV protons were estimated by multi-scale modeling. The code consisted of four parts. The first part was based on the Particle and Heavy-Ion Transport code System (PHITS) code for nuclear reactions, and modeled the interactions between high energy protons and nuclei in the target. The second part covered atomic collisions by particles without nuclear reactions. Because the energy of the particles was high, subcascade analysis was employed. The direct formation of clusters and the number of mobile defects were estimated using molecular dynamics (MD) and kinetic Monte-Carlo (kMC) methods in each subcascade. The third part considered damage structural evolutions estimated by reaction kinetic analysis. The fourth part involved the estimation of mechanical property change using three-dimensional discrete dislocation dynamics (DDD). Using the above four part code, stress-strain curves for high energy proton irradiated Ni were obtained.

Polarization-dependent atomic dipole traps behind a circular aperture for neutral-atom quantum computing

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

Gillen-Christandl, Katharina; Copsey, Bert D.

2011-02-15

The neutral-atom quantum computing community has successfully implemented almost all necessary steps for constructing a neutral-atom quantum computer. We present computational results of a study aimed at solving the remaining problem of creating a quantum memory with individually addressable sites for quantum computing. The basis of this quantum memory is the diffraction pattern formed by laser light incident on a circular aperture. Very close to the aperture, the diffraction pattern has localized bright and dark spots that can serve as red-detuned or blue-detuned atomic dipole traps. These traps are suitable for quantum computing even for moderate laser powers. In particular,more » for moderate laser intensities ({approx}100 W/cm{sup 2}) and comparatively small detunings ({approx}1000-10 000 linewidths), trap depths of {approx}1 mK and trap frequencies of several to tens of kilohertz are achieved. Our results indicate that these dipole traps can be moved by tilting the incident laser beams without significantly changing the trap properties. We also explored the polarization dependence of these dipole traps. We developed a code that calculates the trapping potential energy for any magnetic substate of any hyperfine ground state of any alkali-metal atom for any laser detuning much smaller than the fine-structure splitting for any given electric field distribution. We describe details of our calculations and include a summary of different notations and conventions for the reduced matrix element and how to convert it to SI units. We applied this code to these traps and found a method for bringing two traps together and apart controllably without expelling the atoms from the trap and without significant tunneling probability between the traps. This approach can be scaled up to a two-dimensional array of many pinholes, forming a quantum memory with single-site addressability, in which pairs of atoms can be brought together and apart for two-qubit gates for quantum computing.« less

GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations.

PubMed

Maia, Julio Daniel Carvalho; Urquiza Carvalho, Gabriel Aires; Mangueira, Carlos Peixoto; Santana, Sidney Ramos; Cabral, Lucidio Anjos Formiga; Rocha, Gerd B

2012-09-11

In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our modifications consisted of using a combination of highly optimized linear algebra libraries for both CPU (LAPACK and BLAS from Intel MKL) and GPU (MAGMA and CUBLAS) to hasten time-consuming parts of MOPAC such as the pseudodiagonalization, full diagonalization, and density matrix assembling. We have shown that it is possible to obtain large speedups just by using CPU serial linear algebra libraries in the MOPAC code. As a special case, we show a speedup of up to 14 times for a methanol simulation box containing 2400 atoms and 4800 basis functions, with even greater gains in performance when using multithreaded CPUs (2.1 times in relation to the single-threaded CPU code using linear algebra libraries) and GPUs (3.8 times). This degree of acceleration opens new perspectives for modeling larger structures which appear in inorganic chemistry (such as zeolites and MOFs), biochemistry (such as polysaccharides, small proteins, and DNA fragments), and materials science (such as nanotubes and fullerenes). In addition, we believe that this parallel (GPU-GPU) MOPAC code will make it feasible to use semiempirical methods in lengthy molecular simulations using both hybrid QM/MM and QM/QM potentials.

Roothaan's approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior.

PubMed

Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge

2015-07-21

In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.

Roothaan’s approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior

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

Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.

2015-07-21

In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energiesmore » always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.« less

[Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations

NASA Technical Reports Server (NTRS)

Poltev, V. I.; Bruskov, V. I.; Shuliupina, N. V.; Rein, R.; Shibata, M.; Ornstein, R.; Miller, J.

1993-01-01

The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.

Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats

NASA Astrophysics Data System (ADS)

Ghiringhelli, Luca M.; Carbogno, Christian; Levchenko, Sergey; Mohamed, Fawzi; Huhs, Georg; Lüders, Martin; Oliveira, Micael; Scheffler, Matthias

2017-11-01

With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is standardization, which means using consistent and unique conventions for, e.g., units, zero base lines, and file formats. There are two main strategies to achieve this goal. One accepts the heterogeneous nature of the community, which comprises scientists from physics, chemistry, bio-physics, and materials science, by complying with the diverse ecosystem of computer codes and thus develops "converters" for the input and output files of all important codes. These converters then translate the data of each code into a standardized, code-independent format. The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs, outputs, and restart files, directly into the same code-independent format. In this perspective paper, we present both strategies and argue that they can and should be regarded as complementary, if not even synergetic. The represented appropriate format and conventions were agreed upon by two teams, the Electronic Structure Library (ESL) of the European Center for Atomic and Molecular Computations (CECAM) and the NOvel MAterials Discovery (NOMAD) Laboratory, a European Centre of Excellence (CoE). A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations.

Atomic Physics Effects on Convergent, Child-Langmuir Ion Flow between Nearly Transparent Electrodes

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

Santarius, John F.; Emmert, Gilbert A.

Research during this project at the University of Wisconsin Fusion Technology Institute (UW FTI) on ion and neutral flow through an arbitrary, monotonic potential difference created by nearly transparent electrodes accomplished the following: (1) developed and implemented an integral equation approach for atomic physics effects in helium plasmas; (2) extended the analysis to coupled integral equations that treat atomic and molecular deuterium ions and neutrals; (3) implemented the key deuterium and helium atomic and molecular cross sections; (4) added negative ion production and related cross sections; and (5) benchmarked the code against experimental results. The analysis and codes treat themore » species D0, D20, D+, D2+, D3+, D and, separately at present, He0 and He+. Extensions enhanced the analysis and related computer codes to include He++ ions plus planar and cylindrical geometries.« less

Protein-protein interaction specificity is captured by contact preferences and interface composition.

PubMed

Nadalin, Francesca; Carbone, Alessandra

2018-02-01

Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. alessandra.carbone@lip6.fr. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Nondestructive imaging of atomically thin nanostructures buried in silicon

PubMed Central

Gramse, Georg; Kölker, Alexander; Lim, Tingbin; Stock, Taylor J. Z.; Solanki, Hari; Schofield, Steven R.; Brinciotti, Enrico; Aeppli, Gabriel; Kienberger, Ferry; Curson, Neil J.

2017-01-01

It is now possible to create atomically thin regions of dopant atoms in silicon patterned with lateral dimensions ranging from the atomic scale (angstroms) to micrometers. These structures are building blocks of quantum devices for physics research and they are likely also to serve as key components of devices for next-generation classical and quantum information processing. Until now, the characteristics of buried dopant nanostructures could only be inferred from destructive techniques and/or the performance of the final electronic device; this severely limits engineering and manufacture of real-world devices based on atomic-scale lithography. Here, we use scanning microwave microscopy (SMM) to image and electronically characterize three-dimensional phosphorus nanostructures fabricated via scanning tunneling microscope–based lithography. The SMM measurements, which are completely nondestructive and sensitive to as few as 1900 to 4200 densely packed P atoms 4 to 15 nm below a silicon surface, yield electrical and geometric properties in agreement with those obtained from electrical transport and secondary ion mass spectroscopy for unpatterned phosphorus δ layers containing ~1013 P atoms. The imaging resolution was 37 ± 1 nm in lateral and 4 ± 1 nm in vertical directions, both values depending on SMM tip size and depth of dopant layers. In addition, finite element modeling indicates that resolution can be substantially improved using further optimized tips and microwave gradient detection. Our results on three-dimensional dopant structures reveal reduced carrier mobility for shallow dopant layers and suggest that SMM could aid the development of fabrication processes for surface code quantum computers. PMID:28782006

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

DOE PAGES

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.; ...

2018-04-19

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

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

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

Track structure in radiation biology: theory and applications.

PubMed

Nikjoo, H; Uehara, S; Wilson, W E; Hoshi, M; Goodhead, D T

1998-04-01

A brief review is presented of the basic concepts in track structure and the relative merit of various theoretical approaches adopted in Monte-Carlo track-structure codes are examined. In the second part of the paper, a formal cluster analysis is introduced to calculate cluster-distance distributions. Total experimental ionization cross-sections were least-square fitted and compared with the calculation by various theoretical methods. Monte-Carlo track-structure code Kurbuc was used to examine and compare the spectrum of the secondary electrons generated by using functions given by Born-Bethe, Jain-Khare, Gryzinsky, Kim-Rudd, Mott and Vriens' theories. The cluster analysis in track structure was carried out using the k-means method and Hartigan algorithm. Data are presented on experimental and calculated total ionization cross-sections: inverse mean free path (IMFP) as a function of electron energy used in Monte-Carlo track-structure codes; the spectrum of secondary electrons generated by different functions for 500 eV primary electrons; cluster analysis for 4 MeV and 20 MeV alpha-particles in terms of the frequency of total cluster energy to the root-mean-square (rms) radius of the cluster and differential distance distributions for a pair of clusters; and finally relative frequency distribution for energy deposited in DNA, single-strand break and double-strand breaks for 10MeV/u protons, alpha-particles and carbon ions. There are a number of Monte-Carlo track-structure codes that have been developed independently and the bench-marking presented in this paper allows a better choice of the theoretical method adopted in a track-structure code to be made. A systematic bench-marking of cross-sections and spectra of the secondary electrons shows differences between the codes at atomic level, but such differences are not significant in biophysical modelling at the macromolecular level. Clustered-damage evaluation shows: that a substantial proportion of dose ( 30%) is deposited by low-energy electrons; the majority of DNA damage lesions are of simple type; the complexity of damage increases with increased LET, while the total yield of strand breaks remains constant; and at high LET values nearly 70% of all double-strand breaks are of complex type.

Scalable and portable visualization of large atomistic datasets

NASA Astrophysics Data System (ADS)

Sharma, Ashish; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2004-10-01

A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data minimization, and levels-of-detail for minimal rendering Restrictions on the complexity of the problem: None Typical running time: The program is interactive in its execution Unusual features of the program: None References: The conceptual foundation and subsequent implementation of the algorithms are found in [A. Sharma, A. Nakano, R.K. Kalia, P. Vashishta, S. Kodiyalam, P. Miller, W. Zhao, X.L. Liu, T.J. Campbell, A. Haas, Presence—Teleoperators and Virtual Environments 12 (1) (2003)].

Computational Investigation of Graphene-Carbon Nanotube-Polymer Composite

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Roth, Michael; Todde, Guido; Subramanian, Gopinath; Shukla, Manoj; Univ of Southern Mississippi Collaboration; US Army Engineer Research; Development Center 3909 Halls Ferry Road Vicksburg, MS 39180, USA Collaboration

Graphene is a single atom thick two dimensional carbon sheet where sp2 -hybridized carbon atoms are arranged in a honeycomb structure. The functionalization of graphene and carbon nanotubes (CNTs) with polymer is a route for developing high performance nanocomposite materials. We study the interfacial interactions among graphene, CNT, and Nylon 6 polymer using computational methods based on density functional theory (DFT) and empirical force-field. Our DFT calculations are carried out using Quantum-ESPRESSO electronic structure code with van der Waals functional (vdW-DF2), whereas the empirical calculations are performed using LAMMPS with the COMPASS force-field. Our results demonstrated that the interactions between (8,8) CNT and graphene, and between CNT/graphene and Nylon 6 consist mostly of van der Waals type. The computed Young's moduli indicated that the mechanical properties of carbon nanostructures are enhanced by their interactions with polymer. The presence of Stone-Wales (SW) defects lowered the Young's moduli of carbon nanostructures.

Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

PubMed

Ivanciuc, Ovidiu

2013-06-01

Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

How localized is ``local?'' Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory

NASA Astrophysics Data System (ADS)

Havu, Vile; Blum, Volker; Scheffler, Matthias

2007-03-01

Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO's can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ˜tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,^1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc<= 3å have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome

NASA Astrophysics Data System (ADS)

Chwastyk, Mateusz; Poma Bernaola, Adolfo; Cieplak, Marek

2015-07-01

We propose to improve and simplify protein refinement procedures through consideration of which pairs of amino acid residues should form native contacts. We first consider 11 330 proteins from the CATH database to determine statistical distributions of contacts associated with a given type of amino acid. The distributions are set across the distances between the α-C atoms that are in contact. Based on this data, we determine typical radii of effective spheres that can be placed on the α-C atoms in order to reconstruct the distribution of the contact lengths. This is done by checking for overlaps with enlarged van der Waals spheres associated with heavy atoms on other amino acids. The resulting contacts can be used to identify non-native contacts that may arise during the time evolution of structure-based models. Here, the radii are used to guide reconstruction of nine missing side chains in a type I cohesin domain with the Protein Data Bank code 1AOH. We first identify the likely missing contacts and then sculpt the corresponding side chains by standard refinement tools to achieve consistency with the expected contact map. One ambiguity in refinement is resolved by determining all-atom conformational energies.

Numerical Studies of Impurities in Fusion Plasmas

DOE R&D Accomplishments Database

Hulse, R. A.

1982-09-01

The coupled partial differential equations used to describe the behavior of impurity ions in magnetically confined controlled fusion plasmas require numerical solution for cases of practical interest. Computer codes developed for impurity modeling at the Princeton Plasma Physics Laboratory are used as examples of the types of codes employed for this purpose. These codes solve for the impurity ionization state densities and associated radiation rates using atomic physics appropriate for these low-density, high-temperature plasmas. The simpler codes solve local equations in zero spatial dimensions while more complex cases require codes which explicitly include transport of the impurity ions simultaneously with the atomic processes of ionization and recombination. Typical applications are discussed and computational results are presented for selected cases of interest.

Parallelization of the FLAPW method

NASA Astrophysics Data System (ADS)

Canning, A.; Mannstadt, W.; Freeman, A. J.

2000-08-01

The FLAPW (full-potential linearized-augmented plane-wave) method is one of the most accurate first-principles methods for determining structural, electronic and magnetic properties of crystals and surfaces. Until the present work, the FLAPW method has been limited to systems of less than about a hundred atoms due to the lack of an efficient parallel implementation to exploit the power and memory of parallel computers. In this work, we present an efficient parallelization of the method by division among the processors of the plane-wave components for each state. The code is also optimized for RISC (reduced instruction set computer) architectures, such as those found on most parallel computers, making full use of BLAS (basic linear algebra subprograms) wherever possible. Scaling results are presented for systems of up to 686 silicon atoms and 343 palladium atoms per unit cell, running on up to 512 processors on a CRAY T3E parallel supercomputer.

Abstract ID: 176 Geant4 implementation of inter-atomic interference effect in small-angle coherent X-ray scattering for materials of medical interest.

PubMed

Paternò, Gianfranco; Cardarelli, Paolo; Contillo, Adriano; Gambaccini, Mauro; Taibi, Angelo

2018-01-01

Advanced applications of digital mammography such as dual-energy and tomosynthesis require multiple exposures and thus deliver higher dose compared to standard mammograms. A straightforward manner to reduce patient dose without affecting image quality would be removal of the anti-scatter grid, provided that the involved reconstruction algorithms are able to take the scatter figure into account [1]. Monte Carlo simulations are very well suited for the calculation of X-ray scatter distribution and can be used to integrate such information within the reconstruction software. Geant4 is an open source C++ particle tracking code widely used in several physical fields, including medical physics [2,3]. However, the coherent scattering cross section used by the standard Geant4 code does not take into account the influence of molecular interference. According to the independent atomic scattering approximation (the so-called free-atom model), coherent radiation is indistinguishable from primary radiation because its angular distribution is peaked in the forward direction. Since interference effects occur between x-rays scattered by neighbouring atoms in matter, it was shown experimentally that the scatter distribution is affected by the molecular structure of the target, even in amorphous materials. The most important consequence is that the coherent scatter distribution is not peaked in the forward direction, and the position of the maximum is strongly material-dependent [4]. In this contribution, we present the implementation of a method to take into account inter-atomic interference in small-angle coherent scattering in Geant4, including a dedicated data set of suitable molecular form factor values for several materials of clinical interest. Furthermore, we present scatter images of simple geometric phantoms in which the Rayleigh contribution is rigorously evaluated. Copyright © 2017.

The Potential of Micro Electro Mechanical Systems and Nanotechnology for the U.S. Army

DTIC Science & Technology

2001-05-01

Quantitative Structure Activity Relationship ( QSAR ) model . The QSAR model calculates the proper composition of the polymer-carbon black matrix...example, the BEI Gyrochip Model QRS11 from Systron Donner Inertial Division has a startup time of less than 1 second, a Mean Time Between Failure (MTBF... modeling from many equations per atom to a few lines of code. This approach is amenable to parallel processing. Nevertheless, their programs require

Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3.

PubMed

Stashans, Arvids; Chamba, Gaston; Pinto, Henry

2008-02-01

The electronic structure, chemical bonding, geometry, and effects produced by Sr-doping in CaCO(3) have been studied on the basis of density-functional theory using the VASP simulation package and molecular-orbital theory utilizing the CLUSTERD computer code. Two calcium carbonate structures which occur naturally in anhydrous crystalline forms, calcite and aragonite, were considered in the present investigation. The obtained diagrams of density of states show similar patterns for both materials. The spatial structures are computed and analyzed in comparison to the available experimental data. The electronic properties and atomic displacements because of the trace element Sr-incorporation are discussed in a comparative manner for the two crystalline structures. (c) 2007 Wiley Periodicals, Inc.

Porting LAMMPS to GPUs.

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

Brown, William Michael; Plimpton, Steven James; Wang, Peng

2010-03-01

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

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 MD simulations of geomaterials with ~1000 atoms

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2009-12-01

In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in SIESTA in accordance with calculations from CRYSTAL as a check on feasibility. Results are reported here that suggest SIESTA may indeed be useful to model silicate liquids at very high T and P.

Collisional-radiative modeling of tungsten at temperatures of 1200–2400 eV

DOE PAGES

Colgan, James; Fontes, Christopher; Zhang, Honglin; ...

2015-04-30

We discuss new collisional-radiative modeling calculations of tungsten at moderate temperatures of 1200 to 2400 eV. Such plasma conditions are relevant to ongoing experimental work at ASDEX Upgrade and are expected to be relevant for ITER. Our calculations are made using the Los Alamos National Laboratory (LANL) collisional-radiative modeling ATOMIC code. These calculations formed part of a submission to the recent NLTE-8 workshop that was held in November 2013. This series of workshops provides a forum for detailed comparison of plasma and spectral quantities from NLTE collisional-radiative modeling codes. We focus on the LANL ATOMIC calculations for tungsten that weremore » submitted to the NLTE-8 workshop and discuss different models that were constructed to predict the tungsten emission. In particular, we discuss comparisons between semi-relativistic configuration-average and fully relativistic configuration-average calculations. As a result, we also present semi-relativistic calculations that include fine-structure detail, and discuss the difficult problem of ensuring completeness with respect to the number of configurations included in a CR calculation.« less

MCNP6.1 simulations for low-energy atomic relaxation: Code-to-code comparison with GATEv7.2, PENELOPE2014, and EGSnrc

NASA Astrophysics Data System (ADS)

Jung, Seongmoon; Sung, Wonmo; Lee, Jaegi; Ye, Sung-Joon

2018-01-01

Emerging radiological applications of gold nanoparticles demand low-energy electron/photon transport calculations including details of an atomic relaxation process. Recently, MCNP® version 6.1 (MCNP6.1) has been released with extended cross-sections for low-energy electron/photon, subshell photoelectric cross-sections, and more detailed atomic relaxation data than the previous versions. With this new feature, the atomic relaxation process of MCNP6.1 has not been fully tested yet with its new physics library (eprdata12) that is based on the Evaluated Atomic Data Library (EADL). In this study, MCNP6.1 was compared with GATEv7.2, PENELOPE2014, and EGSnrc that have been often used to simulate low-energy atomic relaxation processes. The simulations were performed to acquire both photon and electron spectra produced by interactions of 15 keV electrons or photons with a 10-nm-thick gold nano-slab. The photon-induced fluorescence X-rays from MCNP6.1 fairly agreed with those from GATEv7.2 and PENELOPE2014, while the electron-induced fluorescence X-rays of the four codes showed more or less discrepancies. A coincidence was observed in the photon-induced Auger electrons simulated by MCNP6.1 and GATEv7.2. A recent release of MCNP6.1 with eprdata12 can be used to simulate the photon-induced atomic relaxation.

Electronic Structure Calculation of Permanent Magnets using the KKR Green's Function Method

NASA Astrophysics Data System (ADS)

Doi, Shotaro; Akai, Hisazumi

2014-03-01

Electronic structure and magnetic properties of permanent magnetic materials, especially Nd2Fe14B, are investigated theoretically using the KKR Green's function method. Important physical quantities in magnetism, such as magnetic moment, Curie temperature, and anisotropy constant, which are obtained from electronics structure calculations in both cases of atomic-sphere-approximation and full-potential treatment, are compared with past band structure calculations and experiments. The site preference of heavy rare-earth impurities are also evaluated through the calculation of formation energy with the use of coherent potential approximations. Further, the development of electronic structure calculation code using the screened KKR for large super-cells, which is aimed at studying the electronic structure of realistic microstructures (e.g. grain boundary phase), is introduced with some test calculations.

An X-Ray Analysis Database of Photoionization Cross Sections Including Variable Ionization

NASA Technical Reports Server (NTRS)

Wang, Ping; Cohen, David H.; MacFarlane, Joseph J.; Cassinelli, Joseph P.

1997-01-01

Results of research efforts in the following areas are discussed: review of the major theoretical and experimental data of subshell photoionization cross sections and ionization edges of atomic ions to assess the accuracy of the data, and to compile the most reliable of these data in our own database; detailed atomic physics calculations to complement the database for all ions of 17 cosmically abundant elements; reconciling the data from various sources and our own calculations; and fitting cross sections with functional approximations and incorporating these functions into a compact computer code.Also, efforts included adapting an ionization equilibrium code, tabulating results, and incorporating them into the overall program and testing the code (both ionization equilibrium and opacity codes) with existing observational data. The background and scientific applications of this work are discussed. Atomic physics cross section models and calculations are described. Calculation results are compared with available experimental data and other theoretical data. The functional approximations used for fitting cross sections are outlined and applications of the database are discussed.

Numerical optimization of a picosecond pulse driven Ni-like Nb x-ray laser at 20.3 nm

NASA Astrophysics Data System (ADS)

Lu, X.; Zhong, J. Y.; Li, Y. J.; Zhang, J.

2003-07-01

Detailed simulations of a Ni-like Nb x-ray laser pumped by a nanosecond prepulse followed by a picosecond main pulse are presented. The atomic physics data are obtained using the Cowan code [R. D. Cowan, The Theory of Atomic Structure and Spectra (University of California Press, Berkeley, CA, 1981)]. The optimization calculations are performed in terms of the intensity of prepulse and the time delay between the prepulse and the main pulse. A high gain over 150 cm-1 is obtained for the optimized drive pulse configuration. The ray-tracing calculations suggest that the total pump energy for a saturated x-ray laser can be reduced to less than 1 J.

On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

PubMed

Noel, Yves; D'arco, Philippe; Demichelis, Raffaella; Zicovich-Wilson, Claudio M; Dovesi, Roberto

2010-03-01

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented. (c) 2009 Wiley Periodicals, Inc.

CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes.

PubMed

Calvello, Simone; Piccardo, Matteo; Rao, Shashank Vittal; Soncini, Alessandro

2018-03-05

We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin-orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree-Fock (CAHF) algorithm for the determination of 4f quasi-atomic active orbitals common to all multi-electron spin manifolds contributing to the ground spin-orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi-Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem-specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state-of-the-art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres, represents a more time-efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non-perturbative spin-orbit coupling effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Noncontiguous atom matching structural similarity function.

PubMed

Teixeira, Ana L; Falcao, Andre O

2013-10-28

Measuring similarity between molecules is a fundamental problem in cheminformatics. Given that similar molecules tend to have similar physical, chemical, and biological properties, the notion of molecular similarity plays an important role in the exploration of molecular data sets, query-retrieval in molecular databases, and in structure-property/activity modeling. Various methods to define structural similarity between molecules are available in the literature, but so far none has been used with consistent and reliable results for all situations. We propose a new similarity method based on atom alignment for the analysis of structural similarity between molecules. This method is based on the comparison of the bonding profiles of atoms on comparable molecules, including features that are seldom found in other structural or graph matching approaches like chirality or double bond stereoisomerism. The similarity measure is then defined on the annotated molecular graph, based on an iterative directed graph similarity procedure and optimal atom alignment between atoms using a pairwise matching algorithm. With the proposed approach the similarities detected are more intuitively understood because similar atoms in the molecules are explicitly shown. This noncontiguous atom matching structural similarity method (NAMS) was tested and compared with one of the most widely used similarity methods (fingerprint-based similarity) using three difficult data sets with different characteristics. Despite having a higher computational cost, the method performed well being able to distinguish either different or very similar hydrocarbons that were indistinguishable using a fingerprint-based approach. NAMS also verified the similarity principle using a data set of structurally similar steroids with differences in the binding affinity to the corticosteroid binding globulin receptor by showing that pairs of steroids with a high degree of similarity (>80%) tend to have smaller differences in the absolute value of binding activity. Using a highly diverse set of compounds with information about the monoamine oxidase inhibition level, the method was also able to recover a significantly higher average fraction of active compounds when the seed is active for different cutoff threshold values of similarity. Particularly, for the cutoff threshold values of 86%, 93%, and 96.5%, NAMS was able to recover a fraction of actives of 0.57, 0.63, and 0.83, respectively, while the fingerprint-based approach was able to recover a fraction of actives of 0.41, 0.40, and 0.39, respectively. NAMS is made available freely for the whole community in a simple Web based tool as well as the Python source code at http://nams.lasige.di.fc.ul.pt/.

First principles calculations of the magnetic and hyperfine properties of Fe/N/Fe and Fe/O/Fe multilayers in the ground state of cohesive energy

NASA Astrophysics Data System (ADS)

dos Santos, A. V.; Samudio Pérez, C. A.; Muenchen, D.; Anibele, T. P.

2015-01-01

The ground state properties of Fe/N/Fe and Fe/O/Fe multilayers were investigated using the first principles calculations. The calculations were performed using the Linearized Augmented Plane Wave (LAPW) method implemented in the Wien2k code. A supercell consisting of one layer of nitride (or oxide) between two layers of Fe in the bcc structure was used to model the structure of the multilayer. The research in new materials also stimulated theoretical and experimental studies of iron-based nitrides due to their variety of structural and magnetic properties for the potential applications as in high strength steels and for high corrosion resistance. It is obvious from many reports that magnetic iron nitrides such as γ-Fe4N and α-Fe16N2 have interesting magnetic properties, among these a high magnetisation saturation and a high density crimp. However, although Fe-N films and multilayers have many potential applications, they can be produced in many ways and are being extensively studied from the theoretical point of view there is no detailed knowledge of their electronic structure. Clearly, efforts to understand the influence of the nitrogen atoms on the entire electronic structure are needed as to correctly interpret the observed changes in the magnetic properties when going from Fe-N bulk compounds to multilayer structures. Nevertheless, the N atoms are not solely responsible for electronics alterations in solid compounds. Theoretical results showed that Fe4X bulk compounds, where X is a variable atom with increasing atomic number (Z), the nature of bonding between X and adjacent Fe atoms changes from more covalent to more ionic and the magnetic moments of Fe also increase for Z=7, i.e. N. This is an indicative that atoms with a Z number higher than 7, i.e., O, can produce several new alterations in the entire magnetic properties of Fe multilayers. This paper presents the first results of an ab-initio electronic structure calculations, performed for Fe-N and Fe-O multilayers. Firstly, the formation energy and the cohesive energy of the multilayers are discussed. For optimised values, the cohesive energy of the multilayers to obtain the lattice parameters at the equilibrium ground state was used, i.e. a new methodology for this calculus was applied. Secondly, the magnetic properties and hyperfine interactions (magnetic field, electric field gradient and the isomer shift) of the iron atoms of the multilayers are discussed.

Vanadium fine-structure K-shell electron impact ionization cross sections for fast-electron diagnostic in laser–solid experiments

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

Palmeri, P., E-mail: patrick.palmeri@umons.ac.be; Quinet, P., E-mail: pascal.quinet@umons.ac.be; IPNAS, Université de Liège, B-4000 Liège

2015-09-15

The K-shell electron impact ionization (EII) cross section, along with the K-shell fluorescence yield, is one of the key atomic parameters for fast-electron diagnostic in laser–solid experiments through the K-shell emission cross section. In addition, in a campaign dedicated to the modeling of the K lines of astrophysical interest (Palmeri et al. (2012)), the K-shell fluorescence yields for the K-vacancy fine-structure atomic levels of all the vanadium isonuclear ions have been calculated. In this study, the K-shell EII cross sections connecting the ground and the metastable levels of the parent vanadium ions to the daughter ions K-vacancy levels considered in Palmerimore » et al. (2012) have been determined. The relativistic distorted-wave (DW) approximation implemented in the FAC atomic code has been used for the incident electron kinetic energies up to 20 times the K-shell threshold energies. Moreover, the resulting DW cross sections have been extrapolated at higher energies using the asymptotic behavior of the modified relativistic binary encounter Bethe model (MRBEB) of Guerra et al. (2012) with the density-effect correction proposed by Davies et al. (2013)« less

Turning limited experimental information into 3D models of RNA.

PubMed

Flores, Samuel Coulbourn; Altman, Russ B

2010-09-01

Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of significantly larger structures.

REU in Physics at Kansas State University--- an Evolving Program

NASA Astrophysics Data System (ADS)

Corwin, Kristan; Glymour, Bruce; Lara, Amy; Weaver, Larry; Zollman, Dean

2009-03-01

The REU site in the Physics Department at Kansas State University, funded by NSF for 13 years between 1992 and 2007, originally focused on atomic collision physics. Now the theme has broadened to include laser-matter interactions on atomic and nanoscales, and an ethics component is incorporated. Students study how atoms and molecules interact with ultra-fast optical and x-ray pulses, reveal the structure of nanoparticle crystallization and gel formation with scattered laser light, and develop computer codes for atomic interactions in Bose-Einstein condensates and nanoparticle self-assembly from lattices to gels; some have traveled to Japan for neutrino experiments. The students we select come primarily from smaller colleges and universities in the Midwest where research opportunities are limited. Prof. Weaver, who has served as PI since 1992, facilitates their transition from a teaching to research environment through lectures and individual interactions. Our program is in a period of transition. While Prof. Weaver continues to be the ``impedance match'' between students and mentors, other leadership roles are gradually being assumed by a team of faculty members who strive to preserve the intimacy and excellence of the program.

Atomic structure calculations for F-like tungsten

NASA Astrophysics Data System (ADS)

Sunny, Aggarwal

2014-09-01

Energy levels, wavefunction compositions and lifetimes have been computed for all levels of 1s22s22p5, 1s22s2p6, 1s22s22p43s, 1s22s22p43p, and 1s22s22p43d configurations in highly charged F-like tungsten ion. The multiconfigurational Dirac—Fock method (MCDF) is adopted to generate the wavefunctions. We have also presented the transition wavelengths, oscillator strengths, transition probabilities, and line strengths for the electric dipole (E1) and magnetic quadrupole (M2) transition from the 1s22s22p5 ground configuration. We have performed parallel calculations with the flexible atomic code (FAC) for comparing the atomic data. The reliability of present data is assessed by comparison with other theoretical and experimental data available in the literature. Good agreement is found between our results and those obtained using different approaches confirm the quality of our results. Additionally, we have predicted some new atomic data for F-like W that were not available so far and may be important for plasma diagnostic analysis in fusion plasma.

The crystal structure of the new ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2)

NASA Astrophysics Data System (ADS)

Fedyna, L. O.; Bodak, O. I.; Fedorchuk, A. O.; Tokaychuk, Ya. O.

2005-06-01

New ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2) was synthesized and its crystal structure was determined by direct methods from X-ray powder diffraction data (diffractometer DRON-3M, Cu Kα-radiation, R=6.99%,R=12.27%,R=11.55%). The compound crystallizes with the own cubic structure type: space group F 4¯ 3m, Pearson code cF272, a=16.6150(2) Å,Z=8. The structure of the Dy 3Cu 20Sb 11-x ( x≈2) can be obtained from the structure type BaHg 11 by doubling of the lattice parameter and subtraction of 16 atoms. The studied structure was compared with the structures of known compounds, which crystallize in the same space group with similar cell parameters.

PDB-Explorer: a web-based interactive map of the protein data bank in shape space.

PubMed

Jin, Xian; Awale, Mahendra; Zasso, Michaël; Kostro, Daniel; Patiny, Luc; Reymond, Jean-Louis

2015-10-23

The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB. ᅟ

Exploring the Ability of a Coarse-grained Potential to Describe the Stress-strain Response of Glassy Polystyrene

DTIC Science & Technology

2012-10-01

using the open-source code Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) (http://lammps.sandia.gov) (23). The commercial...parameters are proprietary and cannot be ported to the LAMMPS 4 simulation code. In our molecular dynamics simulations at the atomistic resolution, we...IBI iterative Boltzmann inversion LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator MAPS Materials Processes and Simulations MS

IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection

PubMed Central

Moal, Iain H.; Barradas-Bautista, Didier; Jiménez-García, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A.; Fernández-Recio, Juan

2018-01-01

Motivation In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. Results Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. Availability IRaPPA has been implemented in the SwarmDock server (http://bmm.crick.ac.uk/~SwarmDock/), pyDock server (http://life.bsc.es/pid/pydockrescoring/) and ZDOCK server (http://zdock.umassmed.edu/), with code available on request. PMID:28200016

Programming the Assembly of Unnatural Materials with Nucleic Acids

NASA Astrophysics Data System (ADS)

Mirkin, Chad

Nature directs the assembly of enormously complex and highly functional materials through an encoded class of biomolecules, nucleic acids. The establishment of a similarly programmable code for the construction of synthetic, unnatural materials would allow researchers to impart functionality by precisely positioning all material components. Although it is exceedingly difficult to control the complex interactions between atomic and molecular species in such a manner, interactions between nanoscale components can be directed through the ligands attached to their surface. Our group has shown that nucleic acids can be used as highly programmable surface ligands to control the spacing and symmetry of nanoparticle building blocks in structurally sophisticated and functional materials. These nucleic acids function as programmable ``bonds'' between nanoparticle ``atoms,'' analogous to a nanoscale genetic code for assembling materials. The sequence and length tunability of nucleic acid bonds has allowed us to define a powerful set of design rules for the construction of nanoparticle superlattices with more than 30 unique lattice symmetries, tunable defect structures and interparticle spacings, and several well-defined crystal habits. Further, the nature of the nucleic acid bond enables an additional level of structural control: temporal regulation of dynamic material response to external biomolecular and chemical stimuli. This control allows for the reversible transformation between thermodynamic states with different crystal symmetries, particle stoichiometries, thermal stabilities, and interparticle spacings on demand. Notably, our unique genetic approach affords functional nanoparticle architectures that, among many other applications, can be used to systematically explore and manipulate optoelectronic material properties, such as tunable interparticle plasmonic interactions, microstructure-directed energy emission, and coupled plasmonic and photonic modes.

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

PubMed

Willighagen, Egon L; Mayfield, John W; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš; Rojas-Chertó, Miquel; Spjuth, Ola; Torrance, Gilleain; Evelo, Chris T; Guha, Rajarshi; Steinbeck, Christoph

2017-06-06

The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. Graphical abstract CDK 2.0 provides new features and improved performance.

77 FR 133 - In the Matter of Connecticut Yankee Atomic Power Company; Northeast Utilities; NSTAR (Haddam Neck...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-03

... the Matter of Connecticut Yankee Atomic Power Company; Northeast Utilities; NSTAR (Haddam Neck Plant); Order Approving Application Regarding Proposed Merger I Connecticut Yankee Atomic Power Company..., pursuant to Section 184 of the Atomic Energy Act of 1954, as amended (AEA), and Title 10 of the Code of...

Detailed numerical simulations of laser cooling processes

NASA Technical Reports Server (NTRS)

Ramirez-Serrano, J.; Kohel, J.; Thompson, R.; Yu, N.

2001-01-01

We developed a detailed semiclassical numerical code of the forces applied on atoms in optical and magnetic fields to increase the understanding of the different roles that light, atomic collisions, background pressure, and number of particles play in experiments with laser cooled and trapped atoms.

Quantum nonlinear optics without photons

NASA Astrophysics Data System (ADS)

Stassi, Roberto; Macrı, Vincenzo; Kockum, Anton Frisk; Di Stefano, Omar; Miranowicz, Adam; Savasta, Salvatore; Nori, Franco

2017-08-01

Spontaneous parametric down-conversion is a well-known process in quantum nonlinear optics in which a photon incident on a nonlinear crystal spontaneously splits into two photons. Here we propose an analogous physical process where one excited atom directly transfers its excitation to a pair of spatially separated atoms with probability approaching 1. The interaction is mediated by the exchange of virtual rather than real photons. This nonlinear atomic process is coherent and reversible, so the pair of excited atoms can transfer the excitation back to the first one: the atomic analog of sum-frequency generation of light. The parameters used to investigate this process correspond to experimentally demonstrated values in ultrastrong circuit quantum electrodynamics. This approach can be extended to realize other nonlinear interatomic processes, such as four-atom mixing, and is an attractive architecture for the realization of quantum devices on a chip. We show that four-qubit mixing can efficiently implement quantum repetition codes and, thus, can be used for error-correction codes.

K-shell X-ray transition energies of multi-electron ions of silicon and sulfur

NASA Astrophysics Data System (ADS)

Beiersdorfer, P.; Brown, G. V.; Hell, N.; Santana, J. A.

2017-10-01

Prompted by the detection of K-shell absorption or emission features in the spectra of plasma surrounding high mass X-ray binaries and black holes, recent measurements using the Livermore electron beam ion trap have focused on the energies of the n = 2 to n = 1 K-shell transitions in the L-shell ions of lithiumlike through fluorinelike silicon and sulfur. In parallel, we have made calculations of these transitions using the Flexible Atomic Code and the multi-reference Møller-Plesset (MRMP) atomic physics code. Using this code we have attempted to produce sets of theoretical atomic data with spectroscopic accuracy for all the L-shell ions of silicon and sulfur. We present results of our calculations for oxygenlike and fluorinelike silicon and compare them to the recent electron beam ion trap measurements as well as previous calculations.

Tartarus: A relativistic Green's function quantum average atom code

DOE PAGES

Gill, Nathanael Matthew; Starrett, Charles Edward

2017-06-28

A relativistic Green’s Function quantum average atom model is implemented in the Tartarus code for the calculation of equation of state data in dense plasmas. We first present the relativistic extension of the quantum Green’s Function average atom model described by Starrett [1]. The Green’s Function approach addresses the numerical challenges arising from resonances in the continuum density of states without the need for resonance tracking algorithms or adaptive meshes, though there are still numerical challenges inherent to this algorithm. We discuss how these challenges are addressed in the Tartarus algorithm. The outputs of the calculation are shown in comparisonmore » to PIMC/DFT-MD simulations of the Principal Shock Hugoniot in Silicon. Finally, we also present the calculation of the Hugoniot for Silver coming from both the relativistic and nonrelativistic modes of the Tartarus code.« less

K-shell X-ray transition energies of multi-electron ions of silicon and sulfur

DOE PAGES

Beiersdorfer, P.; Brown, G. V.; Hell, N.; ...

2017-04-20

Prompted by the detection of K-shell absorption or emission features in the spectra of plasma surrounding high mass X-ray binaries and black holes, recent measurements using the Livermore electron beam ion trap have focused on the energies of the n = 2 to n = 1 K-shell transitions in the L-shell ions of lithiumlike through fluorinelike silicon and sulfur. In parallel, we have made calculations of these transitions using the Flexible Atomic Code and the multi-reference Møller-Plesset (MRMP) atomic physics code. Using this code we have attempted to produce sets of theoretical atomic data with spectroscopic accuracy for all themore » L-shell ions of silicon and sulfur. Here, we present results of our calculations for oxygenlike and fluorinelike silicon and compare them to the recent electron beam ion trap measurements as well as previous calculations.« less

Tartarus: A relativistic Green's function quantum average atom code

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

Gill, Nathanael Matthew; Starrett, Charles Edward

A relativistic Green’s Function quantum average atom model is implemented in the Tartarus code for the calculation of equation of state data in dense plasmas. We first present the relativistic extension of the quantum Green’s Function average atom model described by Starrett [1]. The Green’s Function approach addresses the numerical challenges arising from resonances in the continuum density of states without the need for resonance tracking algorithms or adaptive meshes, though there are still numerical challenges inherent to this algorithm. We discuss how these challenges are addressed in the Tartarus algorithm. The outputs of the calculation are shown in comparisonmore » to PIMC/DFT-MD simulations of the Principal Shock Hugoniot in Silicon. Finally, we also present the calculation of the Hugoniot for Silver coming from both the relativistic and nonrelativistic modes of the Tartarus code.« less

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

PubMed

Wohlin, Åsa

2015-03-21

The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

An efficient dictionary learning algorithm and its application to 3-D medical image denoising.

PubMed

Li, Shutao; Fang, Leyuan; Yin, Haitao

2012-02-01

In this paper, we propose an efficient dictionary learning algorithm for sparse representation of given data and suggest a way to apply this algorithm to 3-D medical image denoising. Our learning approach is composed of two main parts: sparse coding and dictionary updating. On the sparse coding stage, an efficient algorithm named multiple clusters pursuit (MCP) is proposed. The MCP first applies a dictionary structuring strategy to cluster the atoms with high coherence together, and then employs a multiple-selection strategy to select several competitive atoms at each iteration. These two strategies can greatly reduce the computation complexity of the MCP and assist it to obtain better sparse solution. On the dictionary updating stage, the alternating optimization that efficiently approximates the singular value decomposition is introduced. Furthermore, in the 3-D medical image denoising application, a joint 3-D operation is proposed for taking the learning capabilities of the presented algorithm to simultaneously capture the correlations within each slice and correlations across the nearby slices, thereby obtaining better denoising results. The experiments on both synthetically generated data and real 3-D medical images demonstrate that the proposed approach has superior performance compared to some well-known methods. © 2011 IEEE

Application of x-ray absorption fine structure (XAFS) to local-order analysis in Fe-Cr maghemite-like materials

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

Montero-Cabrera, M. E., E-mail: elena.montero@cimav.edu.mx; Fuentes-Cobas, L. E.; Macías-Ríos, E.

2015-07-23

The maghemite-like oxide system γ-Fe{sub 2-x}Cr{sub x}O{sub 3} (x=0.75, 1 and 1.25) was studied by X-ray absorption fine structure (XAFS) and by synchrotron radiation X-ray diffraction (XRD). Measurements were performed at the Stanford Synchrotron Radiation Lightsource at room temperature, at beamlines 2-1, 2-3 and 4-3. High-resolution XRD patterns were processed by means of the Rietveld method. In cases of atoms being neighbors in the Periodic Table, the order/disorder degree of the considered solutions is indiscernible by “normal” (absence of “anomalous scattering”) diffraction experiments. Thus, maghemite-like materials were investigated by XAFS in both Fe and Cr K-edges to clarify, via short-rangemore » structure characterization, the local ordering of the investigated system. Athena and Artemis graphic user interfaces for IFEFFIT and FEFF8.4 codes were employed for XAFS spectra interpretation. Pre-edge decomposition and theoretical modeling of X-ray absorption near edge structure (XANES) transitions were performed. By analysis of the Cr K-edge XANES, it has been confirmed that Cr is located in an octahedral environment. Fitting of the extended X-ray absorption fine structure (EXAFS) spectra was performed under the consideration that the central atom of Fe is allowed to occupy octa- and tetrahedral positions, while Cr occupies only octahedral ones. Coordination number of neighboring atoms, interatomic distances and their quadratic deviation average were determined for x=1, by fitting simultaneously the EXAFS spectra of both Fe and Cr K-edges. The results of fitting the experimental spectra with theoretical standards showed that the cation vacancies tend to follow a regular pattern within the structure of the iron-chromium maghemite (FeCrO{sub 3})« less

Ab initio MD simulations of Mg2SiO4 liquid at high pressures and temperatures relevant to the Earth's mantle

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2010-12-01

Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental zero-pressure volume of forsterite under static conditions (Stixrude and Lithgow-Bertollini 2005). Results are reported here that show SIESTA calculations of T and P on densities in the range of 2.7 - 5.0 g/cc of liquid Mg2SiO4 are similar to the VASP calculations of DeKoker et al. (2008), which used the same functional. This opens the possibility of conducting fast /emph{ab initio} MD simulations of geomaterials with a hundreds of atoms.

A computer code for calculations in the algebraic collective model of the atomic nucleus

NASA Astrophysics Data System (ADS)

Welsh, T. A.; Rowe, D. J.

2016-03-01

A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1 , 1) × SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functions of the model's quadrupole moments qˆM and are at most quadratic in the corresponding conjugate momenta πˆN (- 2 ≤ M , N ≤ 2). The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [ π ˆ ⊗ q ˆ ⊗ π ˆ ] 0 and [ π ˆ ⊗ π ˆ ] LM. The code is made efficient by use of an analytical expression for the needed SO(5)-reduced matrix elements, and use of SO(5) ⊃ SO(3) Clebsch-Gordan coefficients obtained from precomputed data files provided with the code.

The role of configuration interaction in the LTE opacity of Fe

NASA Astrophysics Data System (ADS)

Colgan, James; Kilcrease, David; Magee, Norm; Armstrong, Gregory; Abdallah, Joe; Sherrill, Manolo; Fontes, Christopher; Zhang, Honglin; Hakel, Peter

2013-05-01

The Los Alamos National Laboratory code ATOMIC has been recently used to generate a series of local-thermodynamic-equilibrium (LTE) light element opacities for the elements H through Ne. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. Recent efforts have resulted in comprehensive new calculations of the opacity of Fe. In this presentation we explore the role of configuration interaction (CI) in the Fe opacity, and show where CI influences the monochromatic opacity. We present such comparisons for conditions of astrophysical interest. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.

DAGON: a 3D Maxwell-Bloch code

NASA Astrophysics Data System (ADS)

Oliva, Eduardo; Cotelo, Manuel; Escudero, Juan Carlos; González-Fernández, Agustín.; Sanchís, Alberto; Vera, Javier; Vicéns, Sergio; Velarde, Pedro

2017-05-01

The amplification of UV radiation and high order harmonics (HOH) in plasmas is a subject of raising interest due to its different potential applications in several fields like environment and security (detection at distance), biology, materials science and industry (3D imaging) and atomic and plasma physics (pump-probe experiments). In order to develop these sources, it is necessary to properly understand the amplification process. Being the plasma an inhomogeneous medium which changes with time, it is desirable to have a full time-dependent 3D description of the interaction of UV and XUV radiation with plasmas. For these reasons, at the Instituto de Fusíon Nuclear we have developed DAGON, a 3D Maxwell-Bloch code capable of studying the full spationtemporal structure of the amplification process abovementioned.

The Disk of 48 Lib Revealed by NPOI

NASA Astrophysics Data System (ADS)

Lembryk, Ludwik; Tycner, C.; Sigut, A.; Zavala, R. T.

2013-01-01

We present a study of the disk around the Be star 48 Lib, where NLTE numerical disk models are being compared to the spectral and interferometric data to constrain the physical properties of the inner disk structure. The computational models are generated using the BEDISK code, which accounts for heating and cooling of various atoms in the disk and assumes solar chemical composition. A large set of self-consistent disk models produced with the BEDISK code is in turn used to generate synthetic spectra and images assuming a wide range of inclination angles using the BERAY code. The aim of this project is to constrain the physical properties as well as the inclination angles using both spectroscopic and interferometric data. The interferometric data were obtained using the Naval Precision Optical Interferometer (NPOI), with the focus on Hydrogen Balmer-alpha emission, which is the strongest emission line present due to the circumstellar structure. Because 48 Lib shows clear asymmetric spectral lines, we discuss how we model the asymmetric peaks of the Halpha line by combining two models computed with different density structures. The corresponding synthetic images of these combined density structures are then Fourier transformed and compared to the interferometric data. This numerical strategy has the potential to easily model the commonly observed variation of the ratio of the violet-to-red (V/R ratio) emission peaks and constrain the long-term variability associated with the disk of 48 Lib as well as other emission-line stars that show similar variability.

Atomic structure considerations for the low-temperature opacity of Sn

DOE PAGES

Colgan, J.; Kilcrease, D. P.; Abdallah, J.; ...

2017-03-31

Here, we have begun a preliminary investigation into the opacity of Sn at low temperatures (< 50 eV). The emissivity and opacity of Sn is a crucial factor in determining the utility of Sn in EUV lithography, with numerous industrial implications. To this end, we have been exploring the accuracy of some approximations used in opacity models for the relevant ion stages of Sn (neutral through ~ 18 times ionized). We also find that the use of intermediate-coupling, as compared to full configuration-interaction, is not adequate to obtain accurate line positions of the important bound-bound transitions in Sn. One requiresmore » full configuration-interaction to properly describe the strong mixing between the various n=4 sub-shells that give rise to the Δn= 0 transitions that dominate the opacity spectrum at low temperatures. Furthermore, since calculations that include full configuration-interaction for large numbers of configurations quickly become computationally prohibitive, we have explored hybrid calculations, in which full configuration-interaction is retained for the most important transitions, while intermediate-coupling is employed for all other transitions. After extensive exploration of the atomic structure properties, local-thermodynamic-equilibrium (LTE) opacities are generated using the ATOMIC code at selected temperatures and densities and compared to experiment.« less

Atomic structure considerations for the low-temperature opacity of Sn

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

Colgan, J.; Kilcrease, D. P.; Abdallah, J.

Here, we have begun a preliminary investigation into the opacity of Sn at low temperatures (< 50 eV). The emissivity and opacity of Sn is a crucial factor in determining the utility of Sn in EUV lithography, with numerous industrial implications. To this end, we have been exploring the accuracy of some approximations used in opacity models for the relevant ion stages of Sn (neutral through ~ 18 times ionized). We also find that the use of intermediate-coupling, as compared to full configuration-interaction, is not adequate to obtain accurate line positions of the important bound-bound transitions in Sn. One requiresmore » full configuration-interaction to properly describe the strong mixing between the various n=4 sub-shells that give rise to the Δn= 0 transitions that dominate the opacity spectrum at low temperatures. Furthermore, since calculations that include full configuration-interaction for large numbers of configurations quickly become computationally prohibitive, we have explored hybrid calculations, in which full configuration-interaction is retained for the most important transitions, while intermediate-coupling is employed for all other transitions. After extensive exploration of the atomic structure properties, local-thermodynamic-equilibrium (LTE) opacities are generated using the ATOMIC code at selected temperatures and densities and compared to experiment.« less

Copper fine-structure K-shell electron impact ionization cross sections for fast-electron diagnostic in laser-solid experiments

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

Palmeri, P., E-mail: patrick.palmeri@umons.ac.be; Quinet, P., E-mail: pascal.quinet@umons.ac.be; IPNAS, Université de Liège, B-4000 Liège

2015-03-15

The K-shell electron impact ionization (EII) cross section, along with the K-shell fluorescence yield, is one of the key atomic parameters for fast-electron diagnostic in laser-solid experiments through the K-shell emission cross section. In addition, copper is a material that has been often used in those experiments because it has a maximum total K-shell emission yield. Furthermore, in a campaign dedicated to the modeling of the K lines of astrophysical interest (Palmeri et al., 2012), the K-shell fluorescence yields for the K-vacancy fine-structure atomic levels of all the copper isonuclear ions have been calculated. In this study, the K-shell EII crossmore » sections connecting the ground and the metastable levels of the parent copper ions to the daughter ions K-vacancy levels considered in Palmeri et al. (2012) have been determined. The relativistic distorted-wave (DW) approximation implemented in the FAC atomic code has been used for the incident electron kinetic energies up to 10 times the K-shell threshold energies. Moreover, the resulting DW cross sections have been extrapolated at higher energies using the asymptotic form proposed by Davies et al. (2013)« less

Quaternionic representation of the genetic code.

PubMed

Carlevaro, C Manuel; Irastorza, Ramiro M; Vericat, Fernando

2016-03-01

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Current and anticipated uses of thermal hydraulic codes at the Japan Atomic Energy Research Institute

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

Akimoto, Hajime; Kukita; Ohnuki, Akira

1997-07-01

The Japan Atomic Energy Research Institute (JAERI) is conducting several research programs related to thermal-hydraulic and neutronic behavior of light water reactors (LWRs). These include LWR safety research projects, which are conducted in accordance with the Nuclear Safety Commission`s research plan, and reactor engineering projects for the development of innovative reactor designs or core/fuel designs. Thermal-hydraulic and neutronic codes are used for various purposes including experimental analysis, nuclear power plant (NPP) safety analysis, and design assessment.

A Nonlinear Model for Fuel Atomization in Spray Combustion

NASA Technical Reports Server (NTRS)

Liu, Nan-Suey (Technical Monitor); Ibrahim, Essam A.; Sree, Dave

2003-01-01

Most gas turbine combustion codes rely on ad-hoc statistical assumptions regarding the outcome of fuel atomization processes. The modeling effort proposed in this project is aimed at developing a realistic model to produce accurate predictions of fuel atomization parameters. The model involves application of the nonlinear stability theory to analyze the instability and subsequent disintegration of the liquid fuel sheet that is produced by fuel injection nozzles in gas turbine combustors. The fuel sheet is atomized into a multiplicity of small drops of large surface area to volume ratio to enhance the evaporation rate and combustion performance. The proposed model will effect predictions of fuel sheet atomization parameters such as drop size, velocity, and orientation as well as sheet penetration depth, breakup time and thickness. These parameters are essential for combustion simulation codes to perform a controlled and optimized design of gas turbine fuel injectors. Optimizing fuel injection processes is crucial to improving combustion efficiency and hence reducing fuel consumption and pollutants emissions.

Predicting activity approach based on new atoms similarity kernel function.

PubMed

Abu El-Atta, Ahmed H; Moussa, M I; Hassanien, Aboul Ella

2015-07-01

Drug design is a high cost and long term process. To reduce time and costs for drugs discoveries, new techniques are needed. Chemoinformatics field implements the informational techniques and computer science like machine learning and graph theory to discover the chemical compounds properties, such as toxicity or biological activity. This is done through analyzing their molecular structure (molecular graph). To overcome this problem there is an increasing need for algorithms to analyze and classify graph data to predict the activity of molecules. Kernels methods provide a powerful framework which combines machine learning with graph theory techniques. These kernels methods have led to impressive performance results in many several chemoinformatics problems like biological activity prediction. This paper presents a new approach based on kernel functions to solve activity prediction problem for chemical compounds. First we encode all atoms depending on their neighbors then we use these codes to find a relationship between those atoms each other. Then we use relation between different atoms to find similarity between chemical compounds. The proposed approach was compared with many other classification methods and the results show competitive accuracy with these methods. Copyright © 2015 Elsevier Inc. All rights reserved.

Wavelengths and energy levels for the Zn I isoelectronic sequence Sn{sup 20+} through U{sup 62+}

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

Brown, C.M.; Seely, J.F.; Kania, D.R.

Calculated and experimentally determined transition energies are presented for the Zn I isoelectronic sequence for the elements with atomic numbers Z = 50-92. The excitation energies were calculated for the 84 levels belonging to the 10 configurations of the type 4l4l{prime} by using the Hebrew University Lawrence Livermore Atomic Code (HULLAC). The analysis of the energy level structure along the isoelectronic sequence accounted for 20 avoided level crossings. The differences between the calculated and experimental transition energies were determined for 16 transitions, and the excitation energies of the levels belonging to the 4s4p, 4p{sup 2}, 4s4d, and 4s4f configurations weremore » derived from the semiempirically corrected transition energies. 16 refs., 3 figs., 1 tab.« less

Energy levels and radiative rates for Ne-like ions from Cu to Ga

NASA Astrophysics Data System (ADS)

Singh, Narendra; Aggarwal, Sunny

2017-11-01

Energy levels, lifetimes and wave function compositions are computed for 127 fine structural levels in Ne-like ions (Z=29{-}31). Configuration interaction has been included among 51 configurations (generating 1016 levels) and multiconfigurational Dirac-Fock method is used to generate the wave functions. Similar calculations have also been performed using the fully relativistic flexible atomic code (FAC). Transition wavelength, oscillator strength, transition probabilities and line strength are reported for electric dipole (E1), electric quadrupole (E2), magnetic dipole (M1) and magnetic quadrupole (M2) transitions from the ground level. We compared our calculated results with the available data in the literature. The calculated results are found to be in close agreement with the previous results. Further, we predict some new atomic data which may be important for plasma diagnostics.

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

Theoretical Study of Radiation from a Broad Range of Impurity Ions for Magnetic Fusion Diagnostics

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

Safronova, Alla

Spectroscopy of radiation emitted by impurities plays an important role in the study of magnetically confined fusion plasmas. The measurements of these impurities are crucial for the control of the general machine conditions, for the monitoring of the impurity levels, and for the detection of various possible fault conditions. Low-Z impurities, typically present in concentrations of 1%, are lithium, beryllium, boron, carbon, and oxygen. Some of the common medium-Z impurities are metals such as iron, nickel, and copper, and high-Z impurities, such as tungsten, are present in smaller concentrations of 0.1% or less. Despite the relatively small concentration numbers, themore » aforementioned impurities might make a substantial contribution to radiated power, and also influence both plasma conditions and instruments. A detailed theoretical study of line radiation from impurities that covers a very broad spectral range from less than 1 Å to more than 1000 Å has been accomplished and the results were applied to the LLNL Electron Beam Ion Trap (EBIT) and the Sustained Spheromak Physics Experiment (SSPX) and to the National Spherical Torus Experiment (NSTX) at Princeton. Though low- and medium-Z impurities were also studied, the main emphasis was made on the comprehensive theoretical study of radiation from tungsten using different state-of-the-art atomic structure codes such as Relativistic Many-Body Perturbation Theory (RMBPT). The important component of this research was a comparison of the results from the RMBPT code with other codes such as the Multiconfigurational Hartree–Fock developed by Cowan (COWAN code) and the Multiconfiguration Relativistic Hebrew University Lawrence Atomic Code (HULLAC code), and estimation of accuracy of calculations. We also have studied dielectronic recombination, an important recombination process for fusion plasma, for variety of highly and low charged tungsten ions using COWAN and HULLAC codes. Accurate DR rate coefficients are needed for describing the ionization balance of plasmas, which in turn determines the lines contributing to the spectral emission and the radiative power loss. In particular, we have calculated relativistic atomic data and corresponding dielectronic satellite spectra of highly ionized W ions, such as, for example, Li-like W (with the shortest wavelength of x-ray radiation of about 0.2 Å) that might exist in ITER core plasmas at very high temperatures of 30-40 keV. In addition, we have completed relativistic calculations of low ionized W ions from Lu-like (W3+) to Er-like (W6+) and for Sm-like(W12+) and Pm-like (W13+) that cover a spectral range from few hundred to thousand Å and are more relevant to the edge plasma diagnostics in tokamak.« less

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

NASA Astrophysics Data System (ADS)

Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

2010-12-01

Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

Modification of the band offset in boronitrene

NASA Astrophysics Data System (ADS)

Obodo, K. O.; Andrew, R. C.; Chetty, N.

2011-10-01

Using density functional methods within the generalized gradient approximation implemented in the Quantum Espresso codes, we modify the band offset in a single layer of boronitrene by substituting a double line of carbon atoms. This effectively introduces a line of dipoles at the interface. We considered various junctions of this system within the zigzag and armchair orientations. Our results show that the “zigzag-short” structure is energetically most stable, with a formation energy of 0.502 eV and with a band offset of 1.51 eV. The “zigzag-long” structure has a band offset of 1.99 eV. The armchair structures are nonpolar, while the zigzag-single structures show a charge accumulation for the C-substituted B and charge depletion for the C-substituted N at the junction. Consequently there is no shifting of the bands.

Tornado and extreme wind design criteria for nuclear power plants

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

None

1973-12-01

Nuclear power plant design criteria for tornadoes and extreme winds are presented. Data, formulas, and procedures for determining maximum wind loading on structures and parts of structures are included. Extreme wind loading is applied to structures using methods and procedures consistent with ANSI Building Code A58.1- 1972. The design wind velocities specified generally exceed 100-year recurrent interval winds. Tornado wind loading is applied to structures using procedures paralleling those for extrene winds with additional criteria resulting from the atmospheric pressure change accompanying tornadoes and tornado missile inipact effects. Tornado loading for the 48 contiguous United States is specified for twomore » major zones separated by the Continental Divide. A cross reference listing items related to Atomic Energy Commission Safety Analysis Report format is provided. Development supporting tornado criteria is included. (auth)« less

Structural basis of peptide recognition by the angiotensin-1 converting enzyme homologue AnCE from Drosophila melanogaster

PubMed Central

Akif, Mohd; Masuyer, Geoffrey; Bingham, Richard J; Sturrock, Edward D; Isaac, R Elwyn; Acharya, K Ravi

2012-01-01

Human somatic angiotensin-1 converting enzyme (ACE) is a zinc-dependent exopeptidase, that catalyses the conversion of the decapeptide angiotensin I to the octapeptide angiotensin II, by removing a C-terminal dipeptide. It is the principal component of the renin-angiotensin–aldosterone system that regulates blood pressure. Hence it is an important therapeutic target for the treatment of hypertension and cardiovascular disorders. Here, we report the structures of an ACE homologue from Drosophila melanogaster (AnCE; a proven structural model for the more complex human ACE) co-crystallized with mammalian peptide substrates (bradykinin, Thr6–bradykinin, angiotensin I and a snake venom peptide inhibitor, bradykinin-potentiating peptide-b). The structures determined at 2-Å resolution illustrate that both angiotensin II (the cleaved product of angiotensin I by AnCE) and bradykinin-potentiating peptide-b bind in an analogous fashion at the active site of AnCE, but also exhibit significant differences. In addition, the binding of Arg–Pro–Pro, the cleavage product of bradykinin and Thr6– bradykinin, provides additional detail of the general peptide binding in AnCE. Thus the new structures of AnCE complexes presented here improves our understanding of the binding of peptides and the mechanism by which peptides inhibit this family of enzymes. Database The atomic coordinates and structure factors for AnCE–Ang II (code 4AA1), AnCE–BPPb (code 4AA2), AnCE–BK (code 4ASQ) and AnCE–Thr6–BK (code 4ASR) complexes have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/) Structured digital abstract AnCE cleaves Ang I by enzymatic study (View interaction) Bradykinin and AnCE bind by x-ray crystallography (View interaction) BPP and AnCE bind by x-ray crystallography (View interaction) AnCE cleaves Bradykinin by enzymatic study (View interaction) Ang II and AnCE bind by x-ray crystallography (View interaction) PMID:23082758

A study to compute integrated dpa for neutron and ion irradiation environments using SRIM-2013

NASA Astrophysics Data System (ADS)

Saha, Uttiyoarnab; Devan, K.; Ganesan, S.

2018-05-01

Displacements per atom (dpa), estimated based on the standard Norgett-Robinson-Torrens (NRT) model, is used for assessing radiation damage effects in fast reactor materials. A computer code CRaD has been indigenously developed towards establishing the infrastructure to perform improved radiation damage studies in Indian fast reactors. We propose a method for computing multigroup neutron NRT dpa cross sections based on SRIM-2013 simulations. In this method, for each neutron group, the recoil or primary knock-on atom (PKA) spectrum and its average energy are first estimated with CRaD code from ENDF/B-VII.1. This average PKA energy forms the input for SRIM simulation, wherein the recoil atom is taken as the incoming ion on the target. The NRT-dpa cross section of iron computed with "Quick" Kinchin-Pease (K-P) option of SRIM-2013 is found to agree within 10% with the standard NRT-dpa values, if damage energy from SRIM simulation is used. SRIM-2013 NRT-dpa cross sections applied to estimate the integrated dpa for Fe, Cr and Ni are in good agreement with established computer codes and data. A similar study carried out for polyatomic material, SiC, shows encouraging results. In this case, it is observed that the NRT approach with average lattice displacement energy of 25 eV coupled with the damage energies from the K-P option of SRIM-2013 gives reliable displacement cross sections and integrated dpa for various reactor spectra. The source term of neutron damage can be equivalently determined in the units of dpa by simulating self-ion bombardment. This shows that the information of primary recoils obtained from CRaD can be reliably applied to estimate the integrated dpa and damage assessment studies in accelerator-based self-ion irradiation experiments of structural materials. This study would help to advance the investigation of possible correlations between the damages induced by ions and reactor neutrons.

TiS2 and ZrS2 single- and double-wall nanotubes: first-principles study.

PubMed

Bandura, Andrei V; Evarestov, Robert A

2014-02-15

Hybrid density functional theory has been applied for investigations of the electronic and atomic structure of bulk phases, nanolayers, and nanotubes based on titanium and zirconium disulfides. Calculations have been performed on the basis of the localized atomic functions by means of the CRYSTAL-2009 computer code. The full optimization of all atomic positions in the regarded systems has been made to study the atomic relaxation and to determine the most favorable structures. The different layered and isotropic bulk phases have been considered as the possible precursors of the nanotubes. Calculations on single-walled TiS2 and ZrS2 nanotubes confirmed that the nanotubes obtained by rolling up the hexagonal crystalline layers with octahedral 1T morphology are the most stable. The strain energy of TiS2 and ZrS2 nanotubes is small, does not depend on the tube chirality, and approximately obeys to D(-2) law (D is nanotube diameter) of the classical elasticity theory. It is greater than the strain energy of the similar TiO2 and ZrO2 nanotubes; however, the formation energy of the disulfide nanotubes is considerably less than the formation energy of the dioxide nanotubes. The distance and interaction energy between the single-wall components of the double-wall nanotubes is proved to be close to the distance and interaction energy between layers in the layered crystals. Analysis of the relaxed nanotube shape using radial coordinate of the metal atoms demonstrates a small but noticeable deviation from completely cylindrical cross-section of the external walls in the armchair-like double-wall nanotubes. Copyright © 2013 Wiley Periodicals, Inc.

Atomic structure of the Y complex of the nuclear pore

DOE PAGES

Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; ...

2015-03-30

The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved coremore » of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.« less

SKIRT: Hybrid parallelization of radiative transfer simulations

NASA Astrophysics Data System (ADS)

Verstocken, S.; Van De Putte, D.; Camps, P.; Baes, M.

2017-07-01

We describe the design, implementation and performance of the new hybrid parallelization scheme in our Monte Carlo radiative transfer code SKIRT, which has been used extensively for modelling the continuum radiation of dusty astrophysical systems including late-type galaxies and dusty tori. The hybrid scheme combines distributed memory parallelization, using the standard Message Passing Interface (MPI) to communicate between processes, and shared memory parallelization, providing multiple execution threads within each process to avoid duplication of data structures. The synchronization between multiple threads is accomplished through atomic operations without high-level locking (also called lock-free programming). This improves the scaling behaviour of the code and substantially simplifies the implementation of the hybrid scheme. The result is an extremely flexible solution that adjusts to the number of available nodes, processors and memory, and consequently performs well on a wide variety of computing architectures.

Modeling the heating and atomic kinetics of a photoionized neon plasma experiment

NASA Astrophysics Data System (ADS)

Lockard, Tom E.

Motivated by gas cell photoionized plasma experiments performed by our group at the Z facility of Sandia National Laboratories, we discuss in this dissertation a modeling study of the heating and ionization of the plasma for conditions characteristic of these experiments. Photoionized plasmas are non-equilibrium systems driven by a broadband x-ray radiation flux. They are commonly found in astrophysics but rarely seen in the laboratory. Several modeling tools have been employed: (1) a view-factor computer code constrained with side x-ray power and gated monochromatic image measurements of the z-pinch radiation, to model the time-history of the photon-energy resolved x-ray flux driving the photoionized plasma, (2) a Boltzmann self-consistent electron and atomic kinetics model to simulate the electron distribution function and configuration-averaged atomic kinetics, (3) a radiation-hydrodynamics code with inline non-equilibrium atomic kinetics to perform a comprehensive numerical simulation of the experiment and plasma heating, and (4) steady-state and time-dependent collisional-radiative atomic kinetics calculations with fine-structure energy level description to assess transient effects in the ionization and charge state distribution of the plasma. The results indicate that the photon-energy resolved x-ray flux impinging on the front window of the gas cell is very well approximated by a linear combination of three geometrically-diluted Planckian distributions. Knowledge of the spectral details of the x-ray drive turned out to be important for the heating and ionization of the plasma. The free electrons in the plasma thermalize quickly relative to the timescales associated with the time-history of the x-ray drive and the plasma atomic kinetics. Hence, electrons are well described by a Maxwellian energy distribution of a single temperature. This finding is important to support the application of a radiation-hydrodynamic model to simulate the experiment. It is found that the computed plasma heating compares well with experimental observation when the effects of the windows, hydrodynamics, and non-equilbirium neon emissivity and opacity are employed. The atomic kinetics shows significant time-dependent effects because the timescale of the x-ray drive is too short compared to that of the photoionization process. These modeling and simulation results are important to test theory and modeling assumptions and approximations, and also to provide guidance on data interpretation and analysis.

Examination of total cross section resonance structure of niobium and silicon in neutron transmission experiments

NASA Astrophysics Data System (ADS)

Andrianova, Olga; Lomakov, Gleb; Manturov, Gennady

2017-09-01

The neutron transmission experiments are one of the main sources of information about the neutron cross section resonance structure and effect in the self-shielding. Such kind of data for niobium and silicon nuclides in energy range 7 keV to 3 MeV can be obtained from low-resolution transmission measurements performed earlier in Russia (with samples of 0.027 to 0.871 atom/barn for niobium and 0.076 to 1.803 atom/barn for silicon). A significant calculation-to-experiment discrepancy in energy range 100 to 600 keV and 300 to 800 keV for niobium and silicon, respectively, obtained using the evaluated nuclear data library ROSFOND, were found. The EVPAR code was used for estimation the average resonance parameters in energy range 7 to 600 keV for niobium. For silicon a stochastic optimization method was used to modify the resolved resonance parameters in energy range 300 to 800 keV. The improved ROSFOND evaluated nuclear data files were tested in calculation of ICSBEP integral benchmark experiments.

Cd{sub 0.9375}Mn{sub 0.0625}S diluted magnetic semiconductor: A DFT study

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

Rani, Anita; Kaur, Kulwinder; Kumar, Ranjan, E-mail: ranianita64@gmail.com

We studied the spin polarized electronic band structures and magnetic properties of the diluted magnetic semiconductor Cd{sub 1-x}Mn{sub x}S in Zinc Blende phase (B3) with 0.0625 Mn by using ab initio method. The calculations were performed by using Density Functional Theory as implemented in the Spanish Initiative for Electronic Simulations with Thousands of Atoms code using local density approximation (LDA). Calculated electronic band structures and magnetic properties of Cd{sub 1-x}Mn{sub x}S are discussed in terms of contribution of Mn 3d{sup 5} 4s{sup 2}, Cd 4d{sup 10} 5s{sup 2}, S 3s{sup 2} 3p{sup 4} orbitals. The total magnetic moment is foundmore » to be 5.00 µb for Cd{sub 1−x}Mn{sub x}S at x=0.0625. This value indicate that Mn atom adds no hole carrier to the perfect CdS crystal. We found that Mn doped systems are ferromagnetic. Calculated results are in good agreement with previous studies.« less

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files.

PubMed

Lütteke, Thomas; von der Lieth, Claus-W

2004-06-04

Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. Unfortunately, no software is currently available which aligns the 3D information with the reported assignments. It is the aim of this work to fill this gap. The pdb-care program http://www.glycosciences.de/tools/pdb-care/ is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported. Frequent use of pdb-care will help to improve the quality of carbohydrate data contained in the PDB. Automatic assignment of carbohydrate structures contained in PDB entries will enable the cross-linking of glycobiology resources with genomic and proteomic data collections.

Nuclear Analysis

NASA Technical Reports Server (NTRS)

Clement, J. D.; Kirby, K. D.

1973-01-01

Exploratory calculations were performed for several gas core breeder reactor configurations. The computational method involved the use of the MACH-1 one dimensional diffusion theory code and the THERMOS integral transport theory code for thermal cross sections. Computations were performed to analyze thermal breeder concepts and nonbreeder concepts. Analysis of breeders was restricted to the (U-233)-Th breeding cycle, and computations were performed to examine a range of parameters. These parameters include U-233 to hydrogen atom ratio in the gaseous cavity, carbon to thorium atom ratio in the breeding blanket, cavity size, and blanket size.

GPU Acceleration of the Locally Selfconsistent Multiple Scattering Code for First Principles Calculation of the Ground State and Statistical Physics of Materials

NASA Astrophysics Data System (ADS)

Eisenbach, Markus

The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn-Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. We present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. Using the Cray XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code. This work has been sponsored by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Material Sciences and Engineering Division and by the Office of Advanced Scientific Computing. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

Simulated Raman Spectral Analysis of Organic Molecules

NASA Astrophysics Data System (ADS)

Lu, Lu

The advent of the laser technology in the 1960s solved the main difficulty of Raman spectroscopy, resulted in simplified Raman spectroscopy instruments and also boosted the sensitivity of the technique. Up till now, Raman spectroscopy is commonly used in chemistry and biology. As vibrational information is specific to the chemical bonds, Raman spectroscopy provides fingerprints to identify the type of molecules in the sample. In this thesis, we simulate the Raman Spectrum of organic and inorganic materials by General Atomic and Molecular Electronic Structure System (GAMESS) and Gaussian, two computational codes that perform several general chemistry calculations. We run these codes on our CPU-based high-performance cluster (HPC). Through the message passing interface (MPI), a standardized and portable message-passing system which can make the codes run in parallel, we are able to decrease the amount of time for computation and increase the sizes and capacities of systems simulated by the codes. From our simulations, we will set up a database that allows search algorithm to quickly identify N-H and O-H bonds in different materials. Our ultimate goal is to analyze and identify the spectra of organic matter compositions from meteorites and compared these spectra with terrestrial biologically-produced amino acids and residues.

Detonation of Meta-stable Clusters

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

Kuhl, Allen; Kuhl, Allen L.; Fried, Laurence E.

2008-05-31

We consider the energy accumulation in meta-stable clusters. This energy can be much larger than the typical chemical bond energy (~;;1 ev/atom). For example, polymeric nitrogen can accumulate 4 ev/atom in the N8 (fcc) structure, while helium can accumulate 9 ev/atom in the excited triplet state He2* . They release their energy by cluster fission: N8 -> 4N2 and He2* -> 2He. We study the locus of states in thermodynamic state space for the detonation of such meta-stable clusters. In particular, the equilibrium isentrope, starting at the Chapman-Jouguet state, and expanding down to 1 atmosphere was calculated with the Cheetahmore » code. Large detonation pressures (3 and 16 Mbar), temperatures (12 and 34 kilo-K) and velocities (20 and 43 km/s) are a consequence of the large heats of detonation (6.6 and 50 kilo-cal/g) for nitrogen and helium clusters respectively. If such meta-stable clusters could be synthesized, they offer the potential for large increases in the energy density of materials.« less

GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments.

PubMed

Groß, Lynn; Herrmann, Carmen

2016-09-30

Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Quantitative analysis of vacuum-ultraviolet radiation from nanosecond laser-zinc interaction

NASA Astrophysics Data System (ADS)

Parchamy, Homaira; Szilagyi, John; Masnavi, Majid; Richardson, Martin

2018-07-01

The paper reports measurements of the vacuum-ultraviolet spectral irradiances of a flat zinc target over a wavelength region of 124-164 nm generated by 10 and 60 ns duration low-intensities, 5 ×109 - 3 ×1010 W cm-2, 1.06 μm wavelength laser pulses. Maximum radiation conversion efficiencies of 2.5%/2πsr and 0.8%/2πsr were measured for 60 and 10 ns laser pulses at the intensities of 5 ×109 and 1.4 ×1010 W cm-2, respectively. Atomic structure calculations using a relativistic configuration-interaction, flexible atomic code and a developed non-local thermodynamic equilibrium population kinetics model in comparison to the experimental spectra detected by the Seya-Namioka type monochromator reveal the strong broadband experimental emission originates mainly from 3d94p-3d94s, 3d94d-3d94p and 3d84p-3d84s, 3d84d-3d84p unresolved-transition arrays of double and triple ionized zinc, respectively. Two-dimensional radiation-hydrodynamics code is used to investigate time-space plasma evolution and spectral radiation of a 10 ns full-width-at-half-maximum Gaussian laser pulse-zinc interaction.

Silicon Nitride Equation of State

NASA Astrophysics Data System (ADS)

Swaminathan, Pazhayannur; Brown, Robert

2015-06-01

This report presents the development a global, multi-phase equation of state (EOS) for the ceramic silicon nitride (Si3N4) . Structural forms include amorphous silicon nitride normally used as a thin film and three crystalline polymorphs. Crystalline phases include hexagonal α-Si3N4, hexagonalβ-Si3N4, and the cubic spinel c-Si3N4. Decomposition at about 1900 °C results in a liquid silicon phase and gas phase products such as molecular nitrogen, atomic nitrogen, and atomic silicon. The silicon nitride EOS was developed using EOSPro which is a new and extended version of the PANDA II code. Both codes are valuable tools and have been used successfully for a variety of material classes. Both PANDA II and EOSPro can generate a tabular EOS that can be used in conjunction with hydrocodes. The paper describes the development efforts for the component solid phases and presents results obtained using the EOSPro phase transition model to investigate the solid-solid phase transitions in relation to the available shock data. Furthermore, the EOSPro mixture model is used to develop a model for the decomposition products and then combined with the single component solid models to study the global phase diagram. Sponsored by the NASA Goddard Space Flight Center Living With a Star program office.

Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized System Dynamics

NASA Astrophysics Data System (ADS)

Ho, Phay; Knight, Christopher; Bostedt, Christoph; Young, Linda; Tegze, Miklos; Faigel, Gyula

2016-05-01

We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

Ignition and combustion characteristics of metallized propellants

NASA Technical Reports Server (NTRS)

Mueller, D. C.; Turns, Stephen R.

1992-01-01

During this reporting period, theoretical work on the secondary atomization process was continued and the experimental apparatus was improved. A one-dimensional model of a rocket combustor, incorporating multiple droplet size classes, slurry combustion, secondary atomization, radiation heat transfer, and two-phase slip between slurry droplets and the gas flow was derived and a computer code was written to implement this model. The STANJAN chemical equilibrium solver was coupled with this code to yield gas temperature, density, and composition as functions of axial location. Preliminary results indicate that the model is performing correctly, given current model assumptions. Radiation heat transfer in the combustion chamber is treated as an optically-thick participating media problem requiring a solution of the radiative transfer equation. A cylindrical P sub 1 approximation was employed to yield an analytical expression for chamber-wall heat flux at each axial location. The code exercised to determine the effects of secondary atomization intensity, defined as the number of secondary drops produced per initial drop, on chamber burnout distance and final Al2O3 agglomerate diameter. These results indicate that only weak secondary atomization is required to significantly reduce these two parameters. Stronger atomization intensities were found to yield decreasing marginal benefits. The experimental apparatus was improved to reduce building vibration effects on the optical system alignment. This was accomplished by mounting the burner and the transmitting/receiving optics on a single frame supported by vibration-isolation legs. Calibration and shakedown tests indicate that vibration problems were eliminated and that the system is performing correctly.

Ion channeling study of defects in compound crystals using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Turos, A.; Jozwik, P.; Nowicki, L.; Sathish, N.

2014-08-01

Ion channeling is a well-established technique for determination of structural properties of crystalline materials. Defect depth profiles have been usually determined basing on the two-beam model developed by Bøgh (1968) [1]. As long as the main research interest was focused on single element crystals it was considered as sufficiently accurate. New challenge emerged with growing technological importance of compound single crystals and epitaxial heterostructures. Overlap of partial spectra due to different sublattices and formation of complicated defect structures makes the two beam method hardly applicable. The solution is provided by Monte Carlo computer simulations. Our paper reviews principal aspects of this approach and the recent developments in the McChasy simulation code. The latter made it possible to distinguish between randomly displaced atoms (RDA) and extended defects (dislocations, loops, etc.). Hence, complex defect structures can be characterized by the relative content of these two components. The next refinement of the code consists of detailed parameterization of dislocations and dislocation loops. Defect profiles for variety of compound crystals (GaN, ZnO, SrTiO3) have been measured and evaluated using the McChasy code. Damage accumulation curves for RDA and extended defects revealed non monotonous defect buildup with some characteristic steps. Transition to each stage is governed by the different driving force. As shown by the complementary high resolution XRD measurements lattice strain plays here the crucial role and can be correlated with the concentration of extended defects.

PAREMD: A parallel program for the evaluation of momentum space properties of atoms and molecules

NASA Astrophysics Data System (ADS)

Meena, Deep Raj; Gadre, Shridhar R.; Balanarayan, P.

2018-03-01

The present work describes a code for evaluating the electron momentum density (EMD), its moments and the associated Shannon information entropy for a multi-electron molecular system. The code works specifically for electronic wave functions obtained from traditional electronic structure packages such as GAMESS and GAUSSIAN. For the momentum space orbitals, the general expression for Gaussian basis sets in position space is analytically Fourier transformed to momentum space Gaussian basis functions. The molecular orbital coefficients of the wave function are taken as an input from the output file of the electronic structure calculation. The analytic expressions of EMD are evaluated over a fine grid and the accuracy of the code is verified by a normalization check and a numerical kinetic energy evaluation which is compared with the analytic kinetic energy given by the electronic structure package. Apart from electron momentum density, electron density in position space has also been integrated into this package. The program is written in C++ and is executed through a Shell script. It is also tuned for multicore machines with shared memory through OpenMP. The program has been tested for a variety of molecules and correlated methods such as CISD, Møller-Plesset second order (MP2) theory and density functional methods. For correlated methods, the PAREMD program uses natural spin orbitals as an input. The program has been benchmarked for a variety of Gaussian basis sets for different molecules showing a linear speedup on a parallel architecture.

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.

PubMed

Berger, Daniel; Logsdail, Andrew J; Oberhofer, Harald; Farrow, Matthew R; Catlow, C Richard A; Sherwood, Paul; Sokol, Alexey A; Blum, Volker; Reuter, Karsten

2014-07-14

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework

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

Berger, Daniel, E-mail: daniel.berger@ch.tum.de; Oberhofer, Harald; Reuter, Karsten

2014-07-14

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capabilitymore » by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO{sub 2}(110)« less

Sheet, ligament and droplet formation in swirling primary atomization

NASA Astrophysics Data System (ADS)

Shao, Changxiao; Luo, Kun; Chai, Min; Fan, Jianren

2018-04-01

We report direct numerical simulations of swirling liquid atomization to understand the physical mechanism underlying the sheet breakup of a non-turbulent liquid swirling jet which lacks in-depth investigation. The volume-of-fluid (VOF) method coupled with adapted mesh refinement (AMR) technique in GERRIS code is employed in the present simulation. The mechanisms of sheet, ligament and droplet formation are investigated. It is observed that the olive-shape sheet structure is similar to the experimental result qualitatively. The numerical results show that surface tension, pressure difference and swirling effect contribute to the contraction and extension of liquid sheet. The ligament formation is partially at the sheet rim or attributed to the extension of liquid hole. Especially, the movement of hairpin vortex exerts by an anti-radial direction force to the sheet surface and leads to the sheet thinness. In addition, droplet formation is attributed to breakup of ligament and central sheet.

Wavelengths and energy levels for the Zn I isoelectronic sequence Ga[sup 1+] through Xe[sup 24+

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

Seely, J.F.; Bar-Shalom, A.

Calculated and experimentally determined transition energies were compared for the Zn I isoelectronic sequence for the elements with atomic numbers Z = 31-54. Using the Hebrew Univ. Lawrence Livermore Atomic Code, the excitation energies were calculated for the 109 levels belonging to the lowest 16 configurations of the types 4/4/[prime] and 4/5/[prime]. The analysis of the energy-level structure along the isoelectronic sequence accounted for a number of avoided level crossings. The differences between the calculated and experimental transition energies were determined for 24 transitions among the 4s[sup 2], 4s4p, 4p[sup 2], 4s4d, and 4s4f configurations. Wavelengths were predicted for previouslymore » unobserved transitions in the highly charged ions. 15 refs., 4 figs., 3 tabs.« less

Analysis of neutron spectrum effects on primary damage in tritium breeding blankets

NASA Astrophysics Data System (ADS)

Choi, Yong Hee; Joo, Han Gyu

2012-07-01

The effect of neutron spectrum on primary damages in a structural material of a tritium breeding blanket is investigated with a newly established recoil spectrum estimation system. First, a recoil spectrum generation code is developed to obtain the energy spectrum of primary knock-on atoms (PKAs) for a given neutron spectrum utilizing the latest ENDF/B data. Secondly, a method for approximating the high energy tail of the recoil spectrum is introduced to avoid expensive molecular dynamics calculations for high energy PKAs using the concept of recoil energy of the secondary knock-on atoms originated by the INtegration of CAScades (INCAS) model. Thirdly, the modified spectrum is combined with a set of molecular dynamics calculation results to estimate the primary damage parameters such as the number of surviving point defects. Finally, the neutron spectrum is varied by changing the material of the spectral shifter and the result in primary damage parameters is examined.

Simultaneous estimation of plasma parameters from spectroscopic data of neutral helium using least square fitting of CR-model

NASA Astrophysics Data System (ADS)

Jain, Jalaj; Prakash, Ram; Vyas, Gheesa Lal; Pal, Udit Narayan; Chowdhuri, Malay Bikas; Manchanda, Ranjana; Halder, Nilanjan; Choyal, Yaduvendra

2015-12-01

In the present work an effort has been made to estimate the plasma parameters simultaneously like—electron density, electron temperature, ground state atom density, ground state ion density and metastable state density from the observed visible spectra of penning plasma discharge (PPD) source using least square fitting. The analysis is performed for the prominently observed neutral helium lines. The atomic data and analysis structure (ADAS) database is used to provide the required collisional-radiative (CR) photon emissivity coefficients (PECs) values under the optical thin plasma condition in the analysis. With this condition the estimated plasma temperature from the PPD is found rather high. It is seen that the inclusion of opacity in the observed spectral lines through PECs and addition of diffusion of neutrals and metastable state species in the CR-model code analysis improves the electron temperature estimation in the simultaneous measurement.

Relaxation of Actinide Surfaces: An All Electron Study

NASA Astrophysics Data System (ADS)

Atta-Fynn, Raymond; Dholabhai, Pratik; Ray, Asok

2006-10-01

Fully relativistic full potential density functional calculations with a linearized augmented plane wave plus local orbitals basis (LAPW + lo) have been performed to investigate the relaxations of heavy actinide surfaces, namely the (111) surface of fcc δ-Pu and the (0001) surface of dhcp Am using WIEN2k. This code uses the LAPW + lo method with the unit cell divided into non-overlapping atom-centered spheres and an interstitial region. The APW+lo basis is used to describe all s, p, d, and f states and LAPW basis to describe all higher angular momentum states. Each surface was modeled by a three-layer periodic slab separated by 60 Bohr vacuum with four atoms per surface unit cell. In general, we have found a contraction of the interlayer separations for both Pu and Am. We will report, in detail, the electronic and geometric structures of the relaxed surfaces and comparisons with the respective non-relaxed surfaces.

Resonant scattering as a sensitive diagnostic of current collisional plasma models

NASA Astrophysics Data System (ADS)

Ogorzalek, Anna; Zhuravleva, Irina; Allen, Steven W.; Pinto, Ciro; Werner, Norbert; Mantz, Adam; Canning, Rebecca; Fabian, Andrew C.; Kaastra, Jelle S.; de Plaa, Jelle

2017-08-01

Resonant scattering is a subtle process that suppresses fluxes of some of the brightest optically thick X-ray emission lines produced by collisional plasmas in galaxy clusters and massive early-type galaxies. The amplitude of the effect depends on the turbulent structure of the hot gas, making it a sensitive velocity probe. It is therefore crucial to properly model this effect in order to correctly interpret high resolution X-ray spectra. Our measurements of resonant scattering with XMM-Newton Reflection Grating Spectrometer in giant elliptical galaxies and with Hitomi in the center of Perseus Cluster show that the potentially rich inference from this effect is limited by the uncertainties in the atomic data underlying plasma codes such as APEC and SPEX. Typically, the effect is of the order of 10-20%, while the discrepancy between the two codes is of similar order or even higher. Precise knowledge of the emissivity and oscillator strengths of lines emitted by Fe XVII and Fe XXV, as well as their respective uncertainties propagated through plasma codes are key to understanding gas dynamics and microphysics in giant galaxies and cluster ICM, respectively. This is especially crucial for massive ellipticals, where sub-eV resolution would be needed to measure line broadening precisely, making resonant scattering an important velocity diagnostic in these systems for the foreseeable future. In this poster, I will summarize current status of resonant scattering measurements and show how they depend on the assumed atomic data. I will also discuss which improvements are essential to maximize scientific inference from future high resolution X-ray spectra.

Classification of melanoma lesions using sparse coded features and random forests

NASA Astrophysics Data System (ADS)

Rastgoo, Mojdeh; Lemaître, Guillaume; Morel, Olivier; Massich, Joan; Garcia, Rafael; Meriaudeau, Fabrice; Marzani, Franck; Sidibé, Désiré

2016-03-01

Malignant melanoma is the most dangerous type of skin cancer, yet it is the most treatable kind of cancer, conditioned by its early diagnosis which is a challenging task for clinicians and dermatologists. In this regard, CAD systems based on machine learning and image processing techniques are developed to differentiate melanoma lesions from benign and dysplastic nevi using dermoscopic images. Generally, these frameworks are composed of sequential processes: pre-processing, segmentation, and classification. This architecture faces mainly two challenges: (i) each process is complex with the need to tune a set of parameters, and is specific to a given dataset; (ii) the performance of each process depends on the previous one, and the errors are accumulated throughout the framework. In this paper, we propose a framework for melanoma classification based on sparse coding which does not rely on any pre-processing or lesion segmentation. Our framework uses Random Forests classifier and sparse representation of three features: SIFT, Hue and Opponent angle histograms, and RGB intensities. The experiments are carried out on the public PH2 dataset using a 10-fold cross-validation. The results show that SIFT sparse-coded feature achieves the highest performance with sensitivity and specificity of 100% and 90.3% respectively, with a dictionary size of 800 atoms and a sparsity level of 2. Furthermore, the descriptor based on RGB intensities achieves similar results with sensitivity and specificity of 100% and 71.3%, respectively for a smaller dictionary size of 100 atoms. In conclusion, dictionary learning techniques encode strong structures of dermoscopic images and provide discriminant descriptors.

Assessment of current atomic scale modelling methods for the investigation of nuclear fuels under irradiation: Example of uranium dioxide

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

Bertolus, Marjorie; Krack, Matthias; Freyss, Michel

Multiscale approaches are developed to build more physically based kinetic and mechanical mesoscale models to enhance the predictive capability of fuel performance codes and increase the efficiency of the development of the safer and more innovative nuclear materials needed in the future. Atomic scale methods, and in particular electronic structure and empirical potential methods, form the basis of this multiscale approach. It is therefore essential to know the accuracy of the results computed at this scale if we want to feed them into higher scale models. We focus here on the assessment of the description of interatomic interactions in uraniummore » dioxide using on the one hand electronic structure methods, in particular in the density functional theory (DFT) framework and on the other hand empirical potential methods. These two types of methods are complementary, the former enabling to get results from a minimal amount of input data and further insight into the electronic and magnetic properties, while the latter are irreplaceable for studies where a large number of atoms needs to be considered. We consider basic properties as well as specific ones, which are important for the description of nuclear fuel under irradiation. These are especially energies, which are the main data passed to higher scale models. We limit ourselves to uranium dioxide.« less

Atomistic structures of nano-engineered SiC and radiation-induced amorphization resistance

NASA Astrophysics Data System (ADS)

Imada, Kenta; Ishimaru, Manabu; Sato, Kazuhisa; Xue, Haizhou; Zhang, Yanwen; Shannon, Steven; Weber, William J.

2015-10-01

Nano-engineered 3C-SiC thin films, which possess columnar structures with high-density stacking faults and twins, were irradiated with 2 MeV Si ions at cryogenic and room temperatures. From cross-sectional transmission electron microscopy observations in combination with Monte Carlo simulations based on the Stopping and Range of Ions in Matter code, it was found that their amorphization resistance is six times greater than bulk crystalline SiC at room temperature. High-angle bright-field images taken by spherical aberration corrected scanning transmission electron microscopy revealed that the distortion of atomic configurations is localized near the stacking faults. The resultant strain field probably contributes to the enhancement of radiation tolerance of this material.

A domain specific language for performance portable molecular dynamics algorithms

NASA Astrophysics Data System (ADS)

Saunders, William Robert; Grant, James; Müller, Eike Hermann

2018-03-01

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

X-Ray, EUV, UV and Optical Emissivities of Astrophysical Plasmas

NASA Technical Reports Server (NTRS)

Raymond, John C.; West, Donald (Technical Monitor)

2000-01-01

This grant primarily covered the development of the thermal X-ray emission model code called APEC, which is meant to replace the Raymond and Smith (1977) code. The new code contains far more spectral lines and a great deal of updated atomic data. The code is now available (http://hea-www.harvard.edu/APEC), though new atomic data is still being added, particularly at longer wavelengths. While initial development of the code was funded by this grant, current work is carried on by N. Brickhouse, R. Smith and D. Liedahl under separate funding. Over the last five years, the grant has provided salary support for N. Brickhouse, R. Smith, a summer student (L. McAllister), an SAO predoctoral fellow (A. Vasquez), and visits by T. Kallman, D. Liedahl, P. Ghavamian, J.M. Laming, J. Li, P. Okeke, and M. Martos. In addition to the code development, the grant supported investigations into X-ray and UV spectral diagnostics as applied to shock waves in the ISM, accreting black holes and white dwarfs, and stellar coronae. Many of these efforts are continuing. Closely related work on the shock waves and coronal mass ejections in the solar corona has grown out of the efforts supported by the grant.

On the importance of local orbitals using second energy derivatives for d and f electrons

NASA Astrophysics Data System (ADS)

Karsai, Ferenc; Tran, Fabien; Blaha, Peter

2017-11-01

The all-electron linearized augmented plane wave (LAPW) methods are among the most accurate to solve the Kohn-Sham equations of density functional theory for periodic solids. In the LAPW methods, the unit cell is partitioned into spheres surrounding the atoms, inside which the wave functions are expanded into spherical harmonics, and the interstitial region, where the wave functions are expanded in Fourier series. Recently, Michalicek et al. (2013) reported an analysis of the so-called linearization error, which is inherent to the basis functions inside the spheres, and advocated the use of local orbital basis functions involving the second energy derivative of the radial part (HDLO). In the present work, we report the implementation of such basis functions into the WIEN2k code, and discuss in detail the improvement in terms of accuracy. From our tests, which involve atoms from the whole periodic table, it is concluded that for ground-state properties (e.g., equilibrium volume) the use of HDLO is necessary only for atoms with d or f electrons in the valence and large atomic spheres. For unoccupied states which are not too high above the Fermi energy, HDLO systematically improve the band structure, which may be of importance for the calculation of optical properties.

IAEA activities on atomic, molecular and plasma-material interaction data for fusion

NASA Astrophysics Data System (ADS)

Braams, Bastiaan J.; Chung, Hyun-Kyung

2013-09-01

The IAEA Atomic and Molecular Data Unit (http://www-amdis.iaea.org/) aims to provide internationally evaluated and recommended data for atomic, molecular and plasma-material interaction (A+M+PMI) processes in fusion research. The Unit organizes technical meetings and coordinates an A+M Data Centre Network (DCN) and a Code Centre Network (CCN). In addition the Unit organizes Coordinated Research Projects (CRPs), for which the objectives are mixed between development of new data and evaluation and recommendation of existing data. In the area of A+M data we are placing new emphasis in our meeting schedule on data evaluation and especially on uncertainties in calculated cross section data and the propagation of uncertainties through structure data and fundamental cross sections to effective rate coefficients. Following a recent meeting of the CCN it is intended to use electron scattering on Be, Ne and N2 as exemplars for study of uncertainties and uncertainty propagation in calculated data; this will be discussed further at the presentation. Please see http://www-amdis.iaea.org/CRP/ for more on our active and planned CRPs, which are concerned with atomic processes in core and edge plasma and with plasma interaction with beryllium-based surfaces and with irradiated tungsten.

Remote state preparation through hyperentangled atomic states

NASA Astrophysics Data System (ADS)

Nawaz, Mehwish; ul-Islam, Rameez-; Ikram, Manzoor

2018-04-01

Hyperentangled states have enhanced channel capacity in quantum processing and have yielded` evident increased communication speed in quantum informatics as a consequence of excessively high information content coded over each quantum entity. In the present article, we intend to demonstrate this fact by utilizing atomic states simultaneously entangled both in internal as well as external degrees of freedom, i.e. the de Broglie motion for remote state preparation (RSP). The results clearly demonstrate that we can efficiently communicate two bit information while manipulating only a single quantum subsystem. The states are prepared and manipulated using atomic Bragg diffraction as well as Ramsey interferometry, both of which are now considered as standard, state of the art tools based on cavity quantum electrodynamics. Since atomic Bragg diffraction is a large interaction time regime and produces spatially well separated, decoherence resistant outputs, the schematics presented here for the RSP offer important perspectives on efficient detection as well as unambiguous information coding and readout. The article summarizes the experimental feasibility of the proposal, culminating with a brief discussion.

Development of Spectral and Atomic Models for Diagnosing Energetic Particle Characteristics in Fast Ignition Experiments

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

MacFarlane, Joseph J.; Golovkin, I. E.; Woodruff, P. R.

2009-08-07

This Final Report summarizes work performed under DOE STTR Phase II Grant No. DE-FG02-05ER86258 during the project period from August 2006 to August 2009. The project, “Development of Spectral and Atomic Models for Diagnosing Energetic Particle Characteristics in Fast Ignition Experiments,” was led by Prism Computational Sciences (Madison, WI), and involved collaboration with subcontractors University of Nevada-Reno and Voss Scientific (Albuquerque, NM). In this project, we have: Developed and implemented a multi-dimensional, multi-frequency radiation transport model in the LSP hybrid fluid-PIC (particle-in-cell) code [1,2]. Updated the LSP code to support the use of accurate equation-of-state (EOS) tables generated by Prism’smore » PROPACEOS [3] code to compute more accurate temperatures in high energy density physics (HEDP) plasmas. Updated LSP to support the use of Prism’s multi-frequency opacity tables. Generated equation of state and opacity data for LSP simulations for several materials being used in plasma jet experimental studies. Developed and implemented parallel processing techniques for the radiation physics algorithms in LSP. Benchmarked the new radiation transport and radiation physics algorithms in LSP and compared simulation results with analytic solutions and results from numerical radiation-hydrodynamics calculations. Performed simulations using Prism radiation physics codes to address issues related to radiative cooling and ionization dynamics in plasma jet experiments. Performed simulations to study the effects of radiation transport and radiation losses due to electrode contaminants in plasma jet experiments. Updated the LSP code to generate output using NetCDF to provide a better, more flexible interface to SPECT3D [4] in order to post-process LSP output. Updated the SPECT3D code to better support the post-processing of large-scale 2-D and 3-D datasets generated by simulation codes such as LSP. Updated atomic physics modeling to provide for more comprehensive and accurate atomic databases that feed into the radiation physics modeling (spectral simulations and opacity tables). Developed polarization spectroscopy modeling techniques suitable for diagnosing energetic particle characteristics in HEDP experiments. A description of these items is provided in this report. The above efforts lay the groundwork for utilizing the LSP and SPECT3D codes in providing simulation support for DOE-sponsored HEDP experiments, such as plasma jet and fast ignition physics experiments. We believe that taken together, the LSP and SPECT3D codes have unique capabilities for advancing our understanding of the physics of these HEDP plasmas. Based on conversations early in this project with our DOE program manager, Dr. Francis Thio, our efforts emphasized developing radiation physics and atomic modeling capabilities that can be utilized in the LSP PIC code, and performing radiation physics studies for plasma jets. A relatively minor component focused on the development of methods to diagnose energetic particle characteristics in short-pulse laser experiments related to fast ignition physics. The period of performance for the grant was extended by one year to August 2009 with a one-year no-cost extension, at the request of subcontractor University of Nevada-Reno.« less

Summary Report of a Specialized Workshop on Nuclear Structure and Decay Data (NSDD) Evaluations

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

Nichols, Alan L.; Dimitrious, P.; Kondev, F. G.

2015-04-27

A three-day specialised workshop on Nuclear Structure and Decay Data Evaluations was organised and held at the headquarters of the International Atomic Energy Agency in Vienna, Austria, from 27 to 29 April 2015. This workshop covered a wide range of important topics and issues addressed when evaluating and maintaining the Evaluated Nuclear Structure Data File (ENSDF). The primary aim was to improve evaluators’ abilities to identify and understand the most appropriate evaluation processes to adopt in the formulation of individual ENSDF data sets. Participants assessed and reviewed existing policies, procedures and codes, and round-table discussions included the debate and resolutionmore » of specific difficulties experienced by ENSDF evaluators (i.e., all workshop participants). The contents of this report constitute a record of this workshop, based on the presentations and subsequent discussions.« less

Relativistic R -matrix calculations for the electron-impact excitation of neutral molybdenum

NASA Astrophysics Data System (ADS)

Smyth, R. T.; Johnson, C. A.; Ennis, D. A.; Loch, S. D.; Ramsbottom, C. A.; Ballance, C. P.

2017-10-01

A recent PISCES-B Mod experiment [Nishijima et al., J. Phys. B 43, 225701 (2010), 10.1088/0953-4075/43/22/225701] has revealed up to a factor of 5 discrepancy between measurement and the two existing theoretical models [Badnell et al., J. Phys. B 29, 3683 (1996), 10.1088/0953-4075/29/16/014; Bartschat et al., J. Phys. B 35, 2899 (2002), 10.1088/0953-4075/35/13/305], providing important diagnostics for Mo i. In the following paper we address this issue by employing a relativistic atomic structure and R -matrix scattering calculations to improve upon the available models for future applications and benchmark results against a recent Compact Toroidal Hybrid experiment [Hartwell et al., Fusion Sci. Technol. 72, 76 (2017), 10.1080/15361055.2017.1291046]. We determine the atomic structure of Mo i using grasp0, which implements the multiconfigurational Dirac-Fock method. Fine structure energies and radiative transition rates are presented and compared to existing experimental and theoretical values. The electron-impact excitation of Mo i is investigated using the relativistic R -matrix method and the parallel versions of the Dirac atomic R -matrix codes. Electron-impact excitation cross sections are presented and compared to the few available theoretical cross sections. Throughout, our emphasis is on improving the results for the z 1,2,3o5P →a S52,z 2,3,4o7P → a S73 and y 2,3,4o7P → a S73 electric dipole transitions of particular relevance for diagnostic work.

Fine-structure excitation of Fe II and Fe III due to collisions with electrons

NASA Astrophysics Data System (ADS)

Wan, Yier; Qi, Yueying; Favreau, Connor; Loch, Stuart; Stancil, P.; Ballance, Connor; McLaughlin, Brendan

2018-06-01

Atomic data of iron peak elements are of great importance in astronomical observations. Among all the ionization stages of iron, Fe II and Fe III are of particular importance because of the high cosmic abundance, relatively low ionization potential and complex open d-shell atomic structure. Fe II and Fe III emission are observed from nearly all classes of astronomical objects over a wide spectral range from the infrared to the ultraviolet. To meaningfully interpret these spectra, astronomers have to employ highly complex modeling codes with reliable collision data to simulate the astrophysical observations. The major aim of this work is to provide reliable atomic data for diagnostics. We present new collision strengths and effective collisions for electron impact excitation of Fe II and Fe III for the forbidden transitions among the fine-structure levels of the ground terms. A very fine energy mesh is used for the collision strengths and the effective collision strengths are calculated over a wide range of electron temperatures of astrophysical importance (10-2000 K). The configuration interaction state wave functions are generated with a scaled Thomas-Fermi-Dirac-Amaldi (TFDA) potential, while the R-matrix plus intermediate coupling frame transformation (ICFT), Breit-Pauli R-matrix and Dirac R-matrix packages are used to obtain collision strengths. Influences of the different methods and configuration expansions on the collisional data are discussed. Comparison is made with earlier theoretical work and differences are found to occur at the low temperatures considered here.This work was funded by NASA grant NNX15AE47G.

Development of Safety Assessment Code for Decommissioning of Nuclear Facilities

NASA Astrophysics Data System (ADS)

Shimada, Taro; Ohshima, Soichiro; Sukegawa, Takenori

A safety assessment code, DecDose, for decommissioning of nuclear facilities has been developed, based on the experiences of the decommissioning project of Japan Power Demonstration Reactor (JPDR) at Japan Atomic Energy Research Institute (currently JAEA). DecDose evaluates the annual exposure dose of the public and workers according to the progress of decommissioning, and also evaluates the public dose at accidental situations including fire and explosion. As for the public, both the internal and the external doses are calculated by considering inhalation, ingestion, direct radiation from radioactive aerosols and radioactive depositions, and skyshine radiation from waste containers. For external dose for workers, the dose rate from contaminated components and structures to be dismantled is calculated. Internal dose for workers is calculated by considering dismantling conditions, e.g. cutting speed, cutting length of the components and exhaust velocity. Estimation models for dose rate and staying time were verified by comparison with the actual external dose of workers which were acquired during JPDR decommissioning project. DecDose code is expected to contribute the safety assessment for decommissioning of nuclear facilities.

Investigation of plasma behavior during noble gas injection in the end-cell of GAMMA 10/PDX by using the multi-fluid code ‘LINDA’

NASA Astrophysics Data System (ADS)

Islam, M. S.; Nakashima, Y.; Hatayama, A.

2017-12-01

The linear divertor analysis with fluid model (LINDA) code has been developed in order to simulate plasma behavior in the end-cell of linear fusion device GAMMA 10/PDX. This paper presents the basic structure and simulated results of the LINDA code. The atomic processes of hydrogen and impurities have been included in the present model in order to investigate energy loss processes and mechanism of plasma detachment. A comparison among Ar, Kr and Xe shows that Xe is the most effective gas on the reduction of electron and ion temperature. Xe injection leads to strong reduction in the temperature of electron and ion. The energy loss terms for both the electron and the ion are enhanced significantly during Xe injection. It is shown that the major energy loss channels for ion and electron are charge-exchange loss and radiative power loss of the radiator gas, respectively. These outcomes indicate that Xe injection in the plasma edge region is effective for reducing plasma energy and generating detached plasma in linear device GAMMA 10/PDX.

Stellar and laboratory XUV/EUV line ratios in Fe XVIII and Fe XIX

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

Traebert, E.; Beiersdorfer, P.; Clementson, J.

2012-05-25

A so-called XUV excess has been suspected with the relative fluxes of Fe XVIII and Fe XIX lines observed in the XUV and EUV ranges of the spectrum of the star Capella as observed by the Chandra spacecraft, even after correction for interstellar absorption. This excess becomes apparent in the comparison of the observations with simulations of stellar spectra obtained using collisional-radiative models that employ, for example, the Atomic Plasma Emission Code (APEC) or the Flexible Atomic Code (FAC). We have addressed this problem by laboratory studies using the Livermore electron beam ion trap (EBIT).

Electron-Impact Excitation Cross Sections for Modeling Non-Equilibrium Gas

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Liu, Yen; Panesi, Marco; Munafo, Alessandro; Wray, Alan; Carbon, Duane F.

2015-01-01

In order to provide a database for modeling hypersonic entry in a partially ionized gas under non-equilibrium, the electron-impact excitation cross sections of atoms have been calculated using perturbation theory. The energy levels covered in the calculation are retrieved from the level list in the HyperRad code. The downstream flow-field is determined by solving a set of continuity equations for each component. The individual structure of each energy level is included. These equations are then complemented by the Euler system of equations. Finally, the radiation field is modeled by solving the radiative transfer equation.

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.

PubMed

Moal, Iain H; Barradas-Bautista, Didier; Jiménez-García, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A; Fernández-Recio, Juan

2017-06-15

In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. IRaPPA has been implemented in the SwarmDock server ( http://bmm.crick.ac.uk/∼SwarmDock/ ), pyDock server ( http://life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http://zdock.umassmed.edu/ ), with code available on request. moal@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Pnma-BN: Another Boron Nitride Polymorph with Interesting Physical Properties

PubMed Central

Ma, Zhenyang; Han, Zheng; Liu, Xuhong; Yu, Xinhai; Wang, Dayun; Tian, Yi

2016-01-01

Structural, mechanical, electronic properties, and stability of boron nitride (BN) in Pnma structure were studied using first-principles calculations by Cambridge Serial Total Energy Package (CASTEP) plane-wave code, and the calculations were performed with the local density approximation and generalized gradient approximation in the form of Perdew–Burke–Ernzerhof. This BN, called Pnma-BN, contains four boron atoms and four nitrogen atoms buckled through sp3-hybridized bonds in an orthorhombic symmetry unit cell with Space group of Pnma. Pnma-BN is energetically stable, mechanically stable, and dynamically stable at ambient pressure and high pressure. The calculated Pugh ratio and Poisson’s ratio revealed that Pnma-BN is brittle, and Pnma-BN is found to turn brittle to ductile (~94 GPa) in this pressure range. It shows a higher mechanical anisotropy in Poisson’s ratio, shear modulus, Young’s modulus, and the universal elastic anisotropy index AU. Band structure calculations indicate that Pnma-BN is an insulator with indirect band gap of 7.18 eV. The most extraordinary thing is that the band gap increases first and then decreases with the increase of pressure from 0 to 60 GPa, and from 60 to 100 GPa, the band gap increases first and then decreases again. PMID:28336837

In Situ Three-Dimensional Reciprocal-Space Mapping of Diffuse Scattering Intensity Distribution and Data Analysis for Precursor Phenomenon in Shape-Memory Alloy

NASA Astrophysics Data System (ADS)

Cheng, Tian-Le; Ma, Fengde D.; Zhou, Jie E.; Jennings, Guy; Ren, Yang; Jin, Yongmei M.; Wang, Yu U.

2012-01-01

Diffuse scattering contains rich information on various structural disorders, thus providing a useful means to study the nanoscale structural deviations from the average crystal structures determined by Bragg peak analysis. Extraction of maximal information from diffuse scattering requires concerted efforts in high-quality three-dimensional (3D) data measurement, quantitative data analysis and visualization, theoretical interpretation, and computer simulations. Such an endeavor is undertaken to study the correlated dynamic atomic position fluctuations caused by thermal vibrations (phonons) in precursor state of shape-memory alloys. High-quality 3D diffuse scattering intensity data around representative Bragg peaks are collected by using in situ high-energy synchrotron x-ray diffraction and two-dimensional digital x-ray detector (image plate). Computational algorithms and codes are developed to construct the 3D reciprocal-space map of diffuse scattering intensity distribution from the measured data, which are further visualized and quantitatively analyzed to reveal in situ physical behaviors. Diffuse scattering intensity distribution is explicitly formulated in terms of atomic position fluctuations to interpret the experimental observations and identify the most relevant physical mechanisms, which help set up reduced structural models with minimal parameters to be efficiently determined by computer simulations. Such combined procedures are demonstrated by a study of phonon softening phenomenon in precursor state and premartensitic transformation of Ni-Mn-Ga shape-memory alloy.

FAC: Flexible Atomic Code

NASA Astrophysics Data System (ADS)

Gu, Ming Feng

2018-02-01

FAC calculates various atomic radiative and collisional processes, including radiative transition rates, collisional excitation and ionization by electron impact, energy levels, photoionization, and autoionization, and their inverse processes radiative recombination and dielectronic capture. The package also includes a collisional radiative model to construct synthetic spectra for plasmas under different physical conditions.

Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials

DTIC Science & Technology

2007-08-01

code) 2007 Reprint Aug 2006-Aug 2007 Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials W911NF-04-1-0178 sub 2781-USC-DOA...Priya Vashishta 213 821 2663 Reset Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials Priya Vashishta,∗ Rajiv K. Kalia...function of the particle velocity that drives the shock [18]. The MD and experimental data agree very well. Furthermore, the simulation shows a sudden

Coupled-cluster based R-matrix codes (CCRM): Recent developments

NASA Astrophysics Data System (ADS)

Sur, Chiranjib; Pradhan, Anil K.

2008-05-01

We report the ongoing development of the new coupled-cluster R-matrix codes (CCRM) for treating electron-ion scattering and radiative processes within the framework of the relativistic coupled-cluster method (RCC), interfaced with the standard R-matrix methodology. The RCC method is size consistent and in principle equivalent to an all-order many-body perturbation theory. The RCC method is one of the most accurate many-body theories, and has been applied for several systems. This project should enable the study of electron-interactions with heavy atoms/ions, utilizing not only high speed computing platforms but also improved theoretical description of the relativistic and correlation effects for the target atoms/ions as treated extensively within the RCC method. Here we present a comprehensive outline of the newly developed theoretical method and a schematic representation of the new suite of CCRM codes. We begin with the flowchart and description of various stages involved in this development. We retain the notations and nomenclature of different stages as analogous to the standard R-matrix codes.

Continuum Absorption Coefficient of Atoms and Ions

NASA Technical Reports Server (NTRS)

Armaly, B. F.

1979-01-01

The rate of heat transfer to the heat shield of a Jupiter probe has been estimated to be one order of magnitude higher than any previously experienced in an outer space exploration program. More than one-third of this heat load is due to an emission of continuum radiation from atoms and ions. The existing computer code for calculating the continuum contribution to the total load utilizes a modified version of Biberman's approximate method. The continuum radiation absorption cross sections of a C - H - O - N ablation system were examined in detail. The present computer code was evaluated and updated by being compared with available exact and approximate calculations and correlations of experimental data. A detailed calculation procedure, which can be applied to other atomic species, is presented. The approximate correlations can be made to agree with the available exact and experimental data.

Assessment of radiological protection systems among diagnostic radiology facilities in North East India.

PubMed

Singh, Thokchom Dewan; Jayaraman, T; Arunkumar Sharma, B

2017-03-01

This study aims to assess the adequacy level of radiological protection systems available in the diagnostic radiology facilities located in three capital cities of North East (NE) India. It further attempts to understand, using a multi-disciplinary approach, how the safety codes/standards in diagnostic radiology framed by the Atomic Energy Regulatory Board (AERB) and the International Atomic Energy Agency (IAEA) to achieve adequate radiological protection in facilities, have been perceived, conceptualized, and applied accordingly in these facilities. About 30 diagnostic radiology facilities were randomly selected from three capitals of states in NE India; namely Imphal (Manipur), Shillong (Meghalaya) and Guwahati (Assam). A semi-structured questionnaire developed based on a multi-disciplinary approach was used for this study. It was observed that radiological practices undertaken in these facilities were not exactly in line with safety codes/standards in diagnostic radiology of the AERB and the IAEA. About 50% of the facilities had registered/licensed x-ray equipment with the AERB. More than 80% of the workers did not use radiation protective devices, although these devices were available in the facilities. About 85% of facilities had no institutional risk management system. About 70% of the facilities did not carry out periodic quality assurance testing of their x-ray equipment or surveys of radiation leakage around the x-ray room, and did not display radiation safety indicators in the x-ray rooms. Workers in these facilities exhibited low risk perception about the risks associated with these practices. The majority of diagnostic radiology facilities in NE India did not comply with the radiological safety codes/standards framed by the AERB and IAEA. The study found inadequate levels of radiological protection systems in the majority of facilities. This study suggests a need to establish firm measures that comply with the radiological safety codes/standards of the AERB and IAEA to protect patients, workers and the public of this region.

Measuring the ionization balance of gold in a low-density plasma of importance to ICF

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

May, M; Beiersdorfer, P; Schneider, M

Charge state distributions (CSDs) have been determined in low density ({approx}10 {sup 12} cm{sup -3}) gold plasmas having either a monoenergetic beam (E{sub Beam} = 2.66, 3.53 and 4.54 keV) or experimentally simulated thermal electron distributions (T{sub e} = 2.0, 2.5 and 3.0 keV). These plasmas were created in the Livermore electron beam ion traps EBIT-I and EBIT-II. Line emission and radiative recombination features of Ni to Kr-like gold ions were recorded in the x-ray region with a crystal spectrometer and a photometrically calibrated microcalorimeter. The CSDs in the experimentally simulated thermal plasmas were inferred by fitting the observed 4f{yields}3dmore » and 5f{yields}3d lines with synthetic spectra from the Hebrew University Lawrence Livermore Atomic Code (HULLAC). Additionally, the CSDs in the beam plasmas were inferred both from fitting the line emission and fitting the radiative recombination emission to calculations from the General Relativistic Atomic Structure Program (GRASP). Despite the relatively simple atomic physics in the low density plasma, differences existed between the experimental CSDs and the simulations from several available codes (e.g. RIGEL). Our experimental CSD relied upon accurate electron impact cross sections provided by HULLAC. To determine their reliability, we have experimentally determined the cross sections for several of the n=3{yields}4 and n=3{yields}5 excitations in Ni to Ga-like Au and compared them to distorted wave calculations. Recent Au spectra recorded during experiments at the HELEN laser facility are presented and compared with those from EBIT-I and EBIT-II.« less

Measuring the Ionization Balance of Gold in a Low-Density Plasma of Importance to ICF

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

May, M.J.; Beiersdorfer, P.; Schneider, M.

Charge state distributions (CSDs) have been determined in low density ({approx_equal}1012 cm-3) gold plasmas having either a monoenergetic beam (EBeam = 2.66, 3.53 and 4.54 keV) or experimentally simulated thermal electron distributions (Te = 2.0, 2.5 and 3.0 keV). These plasmas were created in the Livermore electron beam ion traps EBIT-I and EBIT-II. Line emission and radiative recombination features of Ni to Kr-like gold ions were recorded in the x-ray region with a crystal spectrometer and a photometrically calibrated microcalorimeter. The CSDs in the experimentally simulated thermal plasmas were inferred by fitting the observed 4f{yields}3d and 5f{yields}3d lines with syntheticmore » spectra from the Hebrew University Lawrence Livermore Atomic Code (HULLAC). Additionally, the CSDs in the beam plasmas were inferred both from fitting the line emission and fitting the radiative recombination emission to calculations from the General Relativistic Atomic Structure Program (GRASP). Despite the relatively simple atomic physics in the low density plasma, differences existed between the experimental CSDs and the simulations from several available codes (e.g. RIGEL). Our experimental CSD relied upon accurate electron impact cross sections provided by HULLAC. To determine their reliability, we have experimentally determined the cross sections for several of the n=3{yields}4 and n=3{yields}5 excitations in Ni to Ga-like Au and compared them to distorted wave calculations. Recent Au spectra recorded during experiments at the HELEN laser facility are presented and compared with those from EBIT-I and EB0011IT-.« less

Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

NASA Astrophysics Data System (ADS)

Sterling, Nicholas C.; Kerlin, Austin B.

2016-01-01

We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

Global Organization of a Positive-strand RNA Virus Genome

PubMed Central

Wu, Baodong; Grigull, Jörg; Ore, Moriam O.; Morin, Sylvie; White, K. Andrew

2013-01-01

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2′-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context. PMID:23717202

The PSML format and library for norm-conserving pseudopotential data curation and interoperability

NASA Astrophysics Data System (ADS)

García, Alberto; Verstraete, Matthieu J.; Pouillon, Yann; Junquera, Javier

2018-06-01

Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability.

Affinity comparison of different THCA synthase to CBGA using modeling computational approaches.

PubMed

Alaoui, Moulay Abdelaziz El; Ibrahimi, Azeddine; Semlali, Oussama; Tarhda, Zineb; Marouane, Melloul; Najwa, Alaoui; Soulaymani, Abdelmajid; Fahime, Elmostafa El

2014-01-01

The Δ(9-)Tetrahydrocannabinol (THCA) is the primary psychoactive compound of Cannabis Sativa. It is produced by Δ(1-) Tetrahydrocannabinolic acid synthase (THCA) which catalyzes the oxidative cyclization of cannabigerolic acid (CBGA) the precursor of the THCA. In this study, we were interested by the three dimensional structure of THCA synthase protein. Generation of models were done by MODELLER v9.11 and homology modeling with Δ1-tetrahydrocannabinolic acid (THCA) synthase X ray structure (PDB code 3VTE) on the basis of sequences retrieved from GenBank. Procheck, Errat, and Verify 3D tools were used to verify the reliability of the six 3D models obtained, the overall quality factor and the Prosa Z-score were also used to check the quality of the six modeled proteins. The RMSDs for C-alpha atoms, main-chain atoms, side-chain atoms and all atoms between the modeled structures and the corresponding template ranged between 0.290 Å-1.252 Å, reflecting the good quality of the obtained models. Our study of the CBGA-THCA synthase docking demonstrated that the active site pocket was successfully recognized using computational approach. The interaction energy of CBGA computed in 'fiber types' proteins ranged between -4.1 95 kcal/mol and -5.95 kcal/mol whereas in the 'drug type' was about -7.02 kcal/mol to -7.16 kcal/mol, which maybe indicate the important role played by the interaction energy of CBGA in the determination of the THCA level in Cannabis Sativa L. varieties. Finally, we have proposed an experimental design in order to explore the binding energy source of ligand-enzyme in Cannabis Sativa and the production level of the THCA in the absence of any information regarding the correlation between the enzyme affinity and THCA level production. This report opens the doors to more studies predicting the binding site pocket with accuracy from the perspective of the protein affinity and THCA level produced in Cannabis Sativa.

Improved Simulations of Astrophysical Plasmas: Computation of New Atomic Data

NASA Technical Reports Server (NTRS)

Gorczyca, Thomas W.; Korista, Kirk T.

2005-01-01

Our research program is designed to carry out state-of-the-art atomic physics calculations crucial to advancing our understanding of fundamental astrophysical problems. We redress the present inadequacies in the atomic data base along two important areas: dielectronic recombination and inner-shell photoionization and multiple electron ejection/Auger fluorescence therefrom. All of these data are disseminated to the astrophysical community in the proper format for implementation in spectral simulation code.

Models for Amorphous Calcium Carbonate

NASA Astrophysics Data System (ADS)

Sinha, Sourabh

Many species e.g. sea urchin form amorphous calcium carbonate (ACC) precursor phases that subsequently transform into crystalline CaCO3. It is certainly possible that the biogenic ACC might have more than 10 wt% Mg and ˜3 wt% of water. The structure of ACC and the mechanisms by which it transforms to crystalline phase are still poorly understood. In this dissertation our goal is to determine an atomic structure model that is consistent with diffraction and IR measurements of ACC. For this purpose a calcite supercell with 24 formula units, containing 120 atoms, was constructed. Various configurations with substitution of Ca by 6 Mg ions (6 wt.%) and insertion of 3-5 H 2O molecules (2.25-3.75 wt.%) in the interstitial positions of the supercell, were relaxed using a robust density function code VASP. The most noticeable effects were the tilts of CO3 groups and the distortion of Ca sub-lattice, especially in the hydrated case. The distributions of Ca-Ca nearest neighbor distance and CO3 tilts were extracted from various configurations. The same methods were also applied to aragonite. Sampling from the calculated distortion distributions, we built models for amorphous calcite/aragonite of size ˜ 1700 nm3 based on a multi-scale modeling scheme. We used these models to generate diffraction patterns and profiles with our diffraction code. We found that the induced distortions were not enough to generate a diffraction profile typical of an amorphous material. We then studied the diffraction profiles from several nano-crystallites as recent studies suggest that ACC might be a random array of nano-cryatallites. It was found that the generated diffraction profile from a nano-crystallite of size ˜ 2 nm3 is similar to that from the ACC.

Aminotryptophan-containing barstar: structure--function tradeoff in protein design and engineering with an expanded genetic code.

PubMed

Rubini, Marina; Lepthien, Sandra; Golbik, Ralph; Budisa, Nediljko

2006-07-01

The indole ring of the canonical amino acid tryptophan (Trp) possesses distinguished features, such as sterical bulk, hydrophobicity and the nitrogen atom which is capable of acting as a hydrogen bond donor. The introduction of an amino group into the indole moiety of Trp yields the structural analogs 4-aminotryptophan ((4-NH(2))Trp) and 5-aminotryptophan ((5-NH(2))Trp). Their hydrophobicity and spectral properties are substantially different when compared to those of Trp. They resemble the purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. The Trp --> aminotryptophan substitution in proteins during ribosomal translation is expected to result in related protein variants that acquire these features. These expectations have been fulfilled by incorporating (4-NH(2))Trp and (5-NH(2))Trp into barstar, an intracellular inhibitor of the ribonuclease barnase from Bacillus amyloliquefaciens. The crystal structure of (4-NH(2))Trp-barstar is similar to that of the parent protein, whereas its spectral and thermodynamic behavior is found to be remarkably different. The T(m) value of (4-NH(2))Trp- and (5-NH(2))Trp-barstar is lowered by about 20 degrees Celsius, and they exhibit a strongly reduced unfolding cooperativity and substantial loss of free energy in folding. Furthermore, folding kinetic study of (4-NH(2))Trp-barstar revealed that the denatured state is even preferred over native one. The combination of structural and thermodynamic analyses clearly shows how structures of substituted barstar display a typical structure-function tradeoff: the acquirement of unique pH-sensitive charge transfer as a novel function is achieved at the expense of protein stability. These findings provide a new insight into the evolution of the amino acid repertoire of the universal genetic code and highlight possible problems regarding protein engineering and design by using an expanded genetic code.

Method for large-scale fabrication of atomic-scale structures on material surfaces using surface vacancies

DOEpatents

Lim, Chong Wee; Ohmori, Kenji; Petrov, Ivan Georgiev; Greene, Joseph E.

2004-07-13

A method for forming atomic-scale structures on a surface of a substrate on a large-scale includes creating a predetermined amount of surface vacancies on the surface of the substrate by removing an amount of atoms on the surface of the material corresponding to the predetermined amount of the surface vacancies. Once the surface vacancies have been created, atoms of a desired structure material are deposited on the surface of the substrate to enable the surface vacancies and the atoms of the structure material to interact. The interaction causes the atoms of the structure material to form the atomic-scale structures.

Atomic Data and Spectral Line Intensities for NI XVII

NASA Technical Reports Server (NTRS)

Bhatia, A. K.; Landi, E.

2011-01-01

Electron impact collision strengths, energy levels, oscillator strengths, and spontaneous radiative decay rates are calculated for Ni XVII. We include in the calculations the 23 lowest configurations, corresponding to 159 fine-structure levels: 3l3l', 3l4l0'' , and 3s5l0''' , with l,l' = s,p,d, l'' = s,p,d, f, and l''' = s,p,d. Collision strengths are calculated at five incident energies for all transitions at varying energies above the threshold of each transition. One additional energy, very close to the threshold of each transition, has also been included. Calculations have been carried out using the Flexible Atomic Code in the distorted wave approximation. Additional calculations have been performed with the University College London suite of codes for comparison. Excitation rate coefficients are calculated as a function of electron temperature by assuming a Maxwellian electron velocity distribution. Using the excitation rate coefficients and the radiative transition rates of the present work, statistical equilibrium equations for level populations are solved at electron densities covering the range of 10(exp 8) - 10(exp 14) / cubic cm and at an electron temperature of logT(sub e)e(K) = 6.5, corresponding to the maximum abundance of Ni XVII. Spectral line intensities are calculated, and their diagnostic relevance is discussed. This dataset will be made available in the next version of the CHIANTI database

Silicon nitride equation of state

NASA Astrophysics Data System (ADS)

Brown, Robert C.; Swaminathan, Pazhayannur K.

2017-01-01

This report presents the development of a global, multi-phase equation of state (EOS) for the ceramic silicon nitride (Si3N4).1 Structural forms include amorphous silicon nitride normally used as a thin film and three crystalline polymorphs. Crystalline phases include hexagonal α-Si3N4, hexagonal β-Si3N4, and the cubic spinel c-Si3N4. Decomposition at about 1900 °C results in a liquid silicon phase and gas phase products such as molecular nitrogen, atomic nitrogen, and atomic silicon. The silicon nitride EOS was developed using EOSPro which is a new and extended version of the PANDA II code. Both codes are valuable tools and have been used successfully for a variety of material classes. Both PANDA II and EOSPro can generate a tabular EOS that can be used in conjunction with hydrocodes. The paper describes the development efforts for the component solid phases and presents results obtained using the EOSPro phase transition model to investigate the solid-solid phase transitions in relation to the available shock data that have indicated a complex and slow time dependent phase change to the c-Si3N4 phase. Furthermore, the EOSPro mixture model is used to develop a model for the decomposition products; however, the need for a kinetic approach is suggested to combine with the single component solid models to simulate and further investigate the global phase coexistences.

Computational code in atomic and nuclear quantum optics: Advanced computing multiphoton resonance parameters for atoms in a strong laser field

NASA Astrophysics Data System (ADS)

Glushkov, A. V.; Gurskaya, M. Yu; Ignatenko, A. V.; Smirnov, A. V.; Serga, I. N.; Svinarenko, A. A.; Ternovsky, E. V.

2017-10-01

The consistent relativistic energy approach to the finite Fermi-systems (atoms and nuclei) in a strong realistic laser field is presented and applied to computing the multiphoton resonances parameters in some atoms and nuclei. The approach is based on the Gell-Mann and Low S-matrix formalism, multiphoton resonance lines moments technique and advanced Ivanov-Ivanova algorithm of calculating the Green’s function of the Dirac equation. The data for multiphoton resonance width and shift for the Cs atom and the 57Fe nucleus in dependence upon the laser intensity are listed.

Atomistic structures of nano-engineered SiC and radiation-induced amorphization resistance

DOE PAGES

Imada, Kenta; Ishimaru, Manabu; Sato, Kazuhisa; ...

2015-06-18

In this paper, nano-engineered 3C–SiC thin films, which possess columnar structures with high-density stacking faults and twins, were irradiated with 2 MeV Si ions at cryogenic and room temperatures. From cross-sectional transmission electron microscopy observations in combination with Monte Carlo simulations based on the Stopping and Range of Ions in Matter code, it was found that their amorphization resistance is six times greater than bulk crystalline SiC at room temperature. High-angle bright-field images taken by spherical aberration corrected scanning transmission electron microscopy revealed that the distortion of atomic configurations is localized near the stacking faults. Finally, the resultant strain fieldmore » probably contributes to the enhancement of radiation tolerance of this material.« less

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

Friebel, Daniel

In situ x-ray absorption spectroscopy (XAS) at the Pt L{sub 3} edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard x-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF8 code and complementary extended x-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at highmore » electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.« less

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

ShelXle: a Qt graphical user interface for SHELXL.

PubMed

Hübschle, Christian B; Sheldrick, George M; Dittrich, Birger

2011-12-01

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (F(o)) and difference density (F(o)-F(c)) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

An investigation into the role of metastable states on excited populations of weakly ionized argon plasmas, with applications for optical diagnostics

NASA Astrophysics Data System (ADS)

Arnold, Nicholas; Loch, Stuart; Ballance, Connor; Thomas, Ed

2017-10-01

Low temperature plasmas (Te < 10 eV) are ubiquitous in the medical, industrial, basic, and dusty plasma communities, and offer an opportunity for researchers to gain a better understanding of atomic processes in plasmas. Here, we report on a new atomic dataset for neutral and low charge states of argon, from which rate coefficients and cross-sections for the electron-impact excitation of neutral argon are determined. We benchmark by comparing with electron impact excitation cross-sections available in the literature, with very good agreement. We have used the Atomic Data and Analysis Structure (ADAS) code suite to calculate a level-resolved, generalized collisional-radiative (GCR) model for line emission in low temperature argon plasmas. By combining our theoretical model with experimental electron temperature, density, and spectral measurements from the Auburn Linear eXperiment for Instability Studies (ALEXIS), we have developed diagnostic techniques to measure metastable fraction, electron temperature, and electron density. In the future we hope to refine our methods, and extend our model to plasmas other than ALEXIS. Supported by the U.S. Department of Energy. Grant Number: DE-FG02-00ER54476.

Large-scale quantum transport calculations for electronic devices with over ten thousand atoms

NASA Astrophysics Data System (ADS)

Lu, Wenchang; Lu, Yan; Xiao, Zhongcan; Hodak, Miro; Briggs, Emil; Bernholc, Jerry

The non-equilibrium Green's function method (NEGF) has been implemented in our massively parallel DFT software, the real space multigrid (RMG) code suite. Our implementation employs multi-level parallelization strategies and fully utilizes both multi-core CPUs and GPU accelerators. Since the cost of the calculations increases dramatically with the number of orbitals, an optimal basis set is crucial for including a large number of atoms in the ``active device'' part of the simulations. In our implementation, the localized orbitals are separately optimized for each principal layer of the device region, in order to obtain an accurate and optimal basis set. As a large example, we calculated the transmission characteristics of a Si nanowire p-n junction. The nanowire is along (110) direction in order to minimize the number dangling bonds that are saturated by H atoms. Its diameter is 3 nm. The length of 24 nm is necessary because of the long-range screening length in Si. Our calculations clearly show the I-V characteristics of a diode, i.e., the current increases exponentially with forward bias and is near zero with backward bias. Other examples will also be presented, including three-terminal transistors and large sensor structures.

Inelastic transport theory from first principles: Methodology and application to nanoscale devices

NASA Astrophysics Data System (ADS)

Frederiksen, Thomas; Paulsson, Magnus; Brandbyge, Mads; Jauho, Antti-Pekka

2007-05-01

We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TRANSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green’s function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in Frederiksen [Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.

Molybdoenzyme That Catalyzes the Anaerobic Hydroxylation of a Tertiary Carbon Atom in the Side Chain of Cholesterol*

PubMed Central

Dermer, Juri; Fuchs, Georg

2012-01-01

Cholesterol is a ubiquitous hydrocarbon compound that can serve as substrate for microbial growth. This steroid and related cyclic compounds are recalcitrant due to their low solubility in water, complex ring structure, the presence of quaternary carbon atoms, and the low number of functional groups. Aerobic metabolism therefore makes use of reactive molecular oxygen as co-substrate of oxygenases to hydroxylate and cleave the sterane ring system. Consequently, anaerobic metabolism must substitute oxygenase-catalyzed steps by O2-independent hydroxylases. Here we show that one of the initial reactions of anaerobic cholesterol metabolism in the β-proteobacterium Sterolibacterium denitrificans is catalyzed by an unprecedented enzyme that hydroxylates the tertiary C25 atom of the side chain without molecular oxygen forming a tertiary alcohol. This steroid C25 dehydrogenase belongs to the dimethyl sulfoxide dehydrogenase molybdoenzyme family, the closest relative being ethylbenzene dehydrogenase. It is a heterotrimer, which is probably located at the periplasmic side of the membrane and contains one molybdenum cofactor, five [Fe-S] clusters, and one heme b. The draft genome of the organism contains several genes coding for related enzymes that probably replace oxygenases in steroid metabolism. PMID:22942275

Atomic data and line intensities for the S V ion

NASA Astrophysics Data System (ADS)

Iorga, C.; Stancalie, V.

2017-05-01

The energy levels, oscillator strengths, spontaneous radiative decay rates, lifetimes and electron impact collision strengths have been obtained for the [ Ne ] 3s nl, [ Ne ] 3p nl, [ Ne ] 3d nl configurations belonging to S V ion, with n ≤ 7 and l ≤ 4, resulting in 567 fine-structure levels. The calculations have been performed within the fully relativistic Flexible Atomic Code (FAC, Gu, 2008) framework and the distorted wave approximation. To attain the desired accuracy for the levels energy, the valence-valence and valence-core correlations have been taken care of by including 96 configuration state functions (CSFs) in the model, reaching a total of 3147 fine-structure levels. Two separate calculations have been performed with the local central potential computed for two different average configurations. A third calculation is also performed without the addition of the core-excited states in the atomic model for completeness. The effects of slightly different mean configurations and valence-core correlations on the energy levels and decay rates are investigated. The collision data have been computed employing the relativistic distorted-wave method along with the atomic model containing the 96 CSFs and corresponding to the ground state mean configuration. The collision strengths corresponding to excitation from the first four fine-structure levels are given for five energy values of the scattered electron 2.65, 6.18, 11.02, 17.36, 25.43 Rydberg, plus an additional variable small energy value near the threshold. A collisional-radiative model has been employed to solve the rate equations for the populations of the 567 fine-structure levels, for a temperature of LogTE(K) = 5.2 corresponding to the maximum abundance of S V, and at densities 106-1016cm-3, assuming a Maxwellian electron energy distribution function and black body radiation of temperature 6000 K and dilution factor 0.35 for the photon distribution function. The main processes responsible for the level population variations are the electron-impact collisional excitation and the radiative decay along with their inverse processes. As a result, the level populations along with the spectral high-line intensity ratios are provided.

Structural, electronic and optical properties of CO adsorbed on the defective anatase TiO2 (101) surface; a DFT study

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hassan, Muhammad

2017-08-01

This paper illustrates the study of stable structural, electronic and optical properties of carbon mono oxide (CO) molecule adsorbed on pure anatase TiO2 (101) surface and CO molecule adsorbed on defective anatase TiO2 (101) surface containing oxygen (O) atom subsurface vacancy using first-principles study calculations based on density functional theory (DFT) method. A foreign molecule CO was added in the interstitial space of anatase TiO2 (101) surface. It was observed that, adsorption of CO molecule is not favorable on pure anatase TiO2 (101) surface, however adsorption process is improved when subsurface contains O atom vacancy defect. In case of anatase TiO2 (101) surface containing subsurface vacancy, adsorption process is exothermic, resulting in stable structures. The adsorption energies calculated for CO molecules adsorbed at O2c site, at defect site and at Ti5c site of anatase surface containing subsurface O vacancy are 0.16 eV (at O2c), 0.32 eV (at defect site) and 0.43 eV (at Ti5c) site. DOS and PDOS plots are calculated for all the structures. Results indicated that CO molecule adsorption introduces surface states at the Fermi energy level (EF) as shown in partial density of states (PDOS) plots. The dielectric matrix and absorption coefficient (α) for defective anatase TiO2 (101) surface, CO adsorbed at O2c site, at defect site and at Ti5C site of anatase TiO2 (101) surface containing O atom subsurface vacancy has been calculated within the random phase approximation (RPA) using VASP (Vienna ab-initio simulation package) code. It was observed that upon CO adsorption at defective anatase surface, real and imaginary dielectric function peaks were shifted towards lower energy level and a small absorption peak was observed at 1.1 eV energy level which is not present in case of defective anatase (101) surface. CO adsorption produces a red shift in the absorption spectrum of anatase TiO2 (101) surface containing subsurface O atom vacancy.

MolProbity: More and better reference data for improved all-atom structure validation.

PubMed

Williams, Christopher J; Headd, Jeffrey J; Moriarty, Nigel W; Prisant, Michael G; Videau, Lizbeth L; Deis, Lindsay N; Verma, Vishal; Keedy, Daniel A; Hintze, Bradley J; Chen, Vincent B; Jain, Swati; Lewis, Steven M; Arendall, W Bryan; Snoeyink, Jack; Adams, Paul D; Lovell, Simon C; Richardson, Jane S; Richardson, David C

2018-01-01

This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore. © 2017 The Protein Society.

Effect of the interfacial O and Mg vacancies on electronic structure and transport properties of the FeRh/MgO/FeRh (0 0 1) magnetic tunnel junction: DFT calculations

NASA Astrophysics Data System (ADS)

Sakhraoui, T.; Said, M.

2017-12-01

The electronic, magnetic and transport properties of oxygen or magnesium vacancies at the FeRh/MgO/FeRh (0 0 1) magnetic tunnel junction are studied within first principles. Configurations with one O or Mg vacancy per C(2 × 2) surface unit cell, which is located in the MgO interfacial layers, are investigated. We observed that the O and Mg vacancies defect have a very little influence on the magnetic state of the spacer. Very interestingly, the Fe atoms exhibit an enhanced magnetic moment in the case of Mg-vacancy, this latter was found to decrease in the case of O-vacancy. The variations in the spin polarization and magnetic moment values for Fe and Rh atoms at the interface were found to be larger in presence of Mg vacancy. An analysis of the charge densities of our systems was also performed; large variations in the Mg-vacancy system were observed. This affects more the t2g states of the interfacial Fe atom. Moreover, we present an ab initio calculated transmission and I-V characteristics for FeRh/MgO/FeRh (0 0 1) magnetic tunnel junction and we compare results to those of O and Mg-vacancy at the interface using the TRANSIESTA code, which combines the DFT electronic structure calculations with the non-equilibrium Green function formalism (NEGF) for transport properties. The results show that the zero-bias minority spin transmission is much larger than the majority spin transmission for all structures. In all systems and for all magnetic configurations, minority spin currents are higher than majority spin ones, this means that transport properties are, mainly, determined by minority spin channel.

A modified Stillinger-Weber potential for TlBr and its polymorphic extension

DOE PAGES

Zhou, Xiaowang; Foster, Michael E.; Jones, Reese E.; ...

2015-04-30

TlBr is promising for g- and x- radiation detection, but suffers from rapid performance degradation under the operating external electric fields. To enable molecular dynamics (MD) studies of this degradation, we have developed a Stillinger-Weber type of TlBr interatomic potential. During this process, we have also addressed two problems of wider interests. First, the conventional Stillinger-Weber potential format is only applicable for tetrahedral structures (e.g., diamond-cubic, zinc-blende, or wurtzite). Here we have modified the analytical functions of the Stillinger-Weber potential so that it can now be used for other crystal structures. Second, past modifications of interatomic potentials cannot always bemore » applied by a broad community because any new analytical functions of the potential would require corresponding changes in the molecular dynamics codes. Here we have developed a polymorphic potential model that simultaneously incorporates Stillinger-Weber, Tersoff, embedded-atom method, and any variations (i.e., modified functions) of these potentials. As a result, we have implemented this polymorphic model in MD code LAMMPS, and demonstrated that our TlBr potential enables stable MD simulations under external electric fields.« less

Track structure: time evolution from physics to chemistry.

PubMed

Dingfelder, M

2006-01-01

This review discusses interaction cross sections of charged particles (electrons, protons, light ions) with atoms and molecules. The focus is on biological relevant targets like liquid water which serves as a substitute of soft tissue in most Monte Carlo codes. The spatial distribution of energy deposition patterns by different radiation qualities and their importance to the time evolution from the physical to the chemical stage or radiation response is discussed. The determination of inelastic interaction cross sections for charged particles in condensed matter is discussed within the relativistic plane-wave Born approximation and semi-empirical models. The dielectric-response-function of liquid water is discussed.

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.

PubMed

Maisuradze, Gia G; Senet, Patrick; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A

2010-04-08

Coarse-grained molecular dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 residues can be obtained in days. A straightforward application of canonical UNRES/MD simulations, demonstrated with the example of the N-terminal part of the B-domain of staphylococcal protein A (PDB code: 1BDD, a three-alpha-helix bundle), discerns the folding mechanism and determines kinetic parameters by parallel simulations of several hundred or more trajectories. Use of generalized-ensemble techniques, of which the multiplexed replica exchange method proved to be the most effective, enables us to compute thermodynamics of folding and carry out fully physics-based prediction of protein structure, in which the predicted structure is determined as a mean over the most populated ensemble below the folding-transition temperature. By using principal component analysis of the UNRES folding trajectories of the formin-binding protein WW domain (PDB code: 1E0L; a three-stranded antiparallel beta-sheet) and 1BDD, we identified representative structures along the folding pathways and demonstrated that only a few (low-indexed) principal components can capture the main structural features of a protein-folding trajectory; the potentials of mean force calculated along these essential modes exhibit multiple minima, as opposed to those along the remaining modes that are unimodal. In addition, a comparison between the structures that are representative of the minima in the free-energy profile along the essential collective coordinates of protein folding (computed by principal component analysis) and the free-energy profile projected along the virtual-bond dihedral angles gamma of the backbone revealed the key residues involved in the transitions between the different basins of the folding free-energy profile, in agreement with existing experimental data for 1E0L .

Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code

NASA Astrophysics Data System (ADS)

Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; Manchanda, R.; Banerjee, S.; Ramaiya, N.; Sharma, Deepti; Srinivasan, R.; Stotler, D. P.; Aditya Team

2017-08-01

Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated and matched with the experimental one. The dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7-40 eV).

Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code

DOE PAGES

Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; ...

2017-06-09

Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated which was matched with the experimental one. Themore » dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~ 2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7 to 40 eV).« less

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

NASA Technical Reports Server (NTRS)

Kallman, Tim

2006-01-01

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn 011 many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

NASA Technical Reports Server (NTRS)

Kallman, Tim

2006-01-01

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Scalable real space pseudopotential density functional codes for materials in the exascale regime

NASA Astrophysics Data System (ADS)

Lena, Charles; Chelikowsky, James; Schofield, Grady; Biller, Ariel; Kronik, Leeor; Saad, Yousef; Deslippe, Jack

Real-space pseudopotential density functional theory has proven to be an efficient method for computing the properties of matter in many different states and geometries, including liquids, wires, slabs, and clusters with and without spin polarization. Fully self-consistent solutions using this approach have been routinely obtained for systems with thousands of atoms. Yet, there are many systems of notable larger sizes where quantum mechanical accuracy is desired, but scalability proves to be a hindrance. Such systems include large biological molecules, complex nanostructures, or mismatched interfaces. We will present an overview of our new massively parallel algorithms, which offer improved scalability in preparation for exascale supercomputing. We will illustrate these algorithms by considering the electronic structure of a Si nanocrystal exceeding 104 atoms. Support provided by the SciDAC program, Department of Energy, Office of Science, Advanced Scientific Computing Research and Basic Energy Sciences. Grant Numbers DE-SC0008877 (Austin) and DE-FG02-12ER4 (Berkeley).

The ab initio Calculation of Electric Field Gradient at the Site of P Impurity in α-Al3O2

NASA Astrophysics Data System (ADS)

Zhang, Qiao-Li; Yuan, Da-Qing; Zhang, Huan-Qiao; Fan, Ping; Zuo, Yi; Zheng, Yong-Nan; Masuta, K.; Fukuda, M.; Mihara, M.; Minamisono, T.; Kitagawa, A.; Zhu, Sheng-Yun

2012-09-01

An ab initio calculation of the electric-field gradient (EFG) at the site of a phosphorous impurity substituting an Al atom in α-Al2O3 is carried out using the WIEN2k code with the full-potential linearized augmented plane wave plus local orbital method (LAPW+lo) in the frame of density functional theory. The atomic lattice relaxations caused by the implanted impurities were calculated for two different charged states to well describe the electronic structure of the doped system. The EFG at the site of the phosphorous impurity in the charged supercell calculated with the exchange-correlation potential of the Wu-Cohen generalized gradient approximation (WC-GGA) is 0.573 × 1021 V/m2. Then, the nuclear quadrupole moment of the I = 3 state in 28P is deduced to be 137 mb from the quadrupole interaction frequency of 190 kHz measured recently by the β-NQR method.

{sup 45}Sc Solid State NMR studies of the silicides ScTSi (T=Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt)

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

Harmening, Thomas; Eckert, Hellmut, E-mail: eckerth@uni-muenster.de; Fehse, Constanze M.

The silicides ScTSi (T=Fe, Co, Ni, Cu, Ru, Rh, Pd, Ir, Pt) were synthesized by arc-melting and characterized by X-ray powder diffraction. The structures of ScCoSi, ScRuSi, ScPdSi, and ScIrSi were refined from single crystal diffractometer data. These silicides crystallize with the TiNiSi type, space group Pnma. No systematic influences of the {sup 45}Sc isotropic magnetic shift and nuclear electric quadrupolar coupling parameters on various structural distortion parameters calculated from the crystal structure data can be detected. {sup 45}Sc MAS-NMR data suggest systematic trends in the local electronic structure probed by the scandium atoms: both the electric field gradients andmore » the isotropic magnetic shifts relative to a 0.2 M aqueous Sc(NO{sub 3}){sub 3} solution decrease with increasing valence electron concentration and within each T group the isotropic magnetic shift decreases monotonically with increasing atomic number. The {sup 45}Sc nuclear electric quadrupolar coupling constants are generally well reproduced by quantum mechanical electric field gradient calculations using the WIEN2k code. Highlights: Black-Right-Pointing-Pointer Arc-melting synthesis of silicides ScTSi. Black-Right-Pointing-Pointer Single crystal X-ray data of ScCoSi, ScRuSi, ScPdSi, and ScIrSi. Black-Right-Pointing-Pointer {sup 45}Sc solid state NMR of silicides ScTSi.« less

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

Trevisanutto, Paolo E.; Vignale, Giovanni, E-mail: vignaleg@missouri.edu

Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is “native” to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basicmore » tools of ab initio electronic structure theory — density functional theory, GW approximation and Bethe-Salpeter equation — are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.« less

Stretching of short monatomic gold chains-some model calculations

NASA Astrophysics Data System (ADS)

Sumali, Priyanka, Verma, Veena; Dharamvir, Keya

2012-06-01

The Mechanical properties of zig-zag monatomic gold chains containing 5 and 7 atoms were studied using the Siesta Code (SC), which works within the framework of DFT formalism and Gupta Potential (GP), which is an effective atom-atom potential. The zig-zag chains were stretched by keeping the end atoms fixed while rest of the atoms were relaxed till minimum energy is obtained. Energy, Force and Young's Modulus found using GP and SC were plotted as functions of total length. It is found that the breaking force in case of GP is of order of 1.6nN while for SIESTA is of the order of 2.9nN for both the chains.

RNA Thermodynamic Structural Entropy

PubMed Central

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs. PMID:26555444

RNA Thermodynamic Structural Entropy.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.

Low-energy Scattering of Positronium by Atoms

NASA Technical Reports Server (NTRS)

Ray, Hasi

2007-01-01

The survey reports theoretical studies involving positronium (Ps) - atom scattering. Investigations carried out in last few decades have been briefly reviewed in this article. A brief description of close-coupling approximation (CCA), the first-Born approximation (FBA) and the Born-Oppenheimer approximation (BOA) for Ps-Atom systems are made. The CCA codes of Ray et a1 [1-6] are reinvestigated using very fine mesh-points to search for resonances. The article advocates the need for an extended basis set & a systematic study using CCAs.

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; ...

2016-08-31

Researcher feedback has indicated that in Urzhumtsevet al.[(2015)Acta Cryst.D71, 1668–1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. Lastly, these issues are addressed in this article.

Index to the Understanding the Atom Series.

ERIC Educational Resources Information Center

Atomic Energy Commission, Oak Ridge, TN. Div. of Technical Information.

The topics covered by 47 booklets in the series are indexed. Page references are not given, but the booklet covering each topic is indicated by a code explained in the first two pages of the index. A brief account of the educational services program of the Atomic Energy Commission describing the booklets, films, and other services provided for…

Related Structure Characters and Stability of Structural Defects in a Metallic Glass

PubMed Central

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-01-01

Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr50Cu50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs. When two atoms have the same coordination number, the atom with larger five-fold symmetry has less QNAs. The number of QNAs around an atom changes rather frequently and the change of QNAs might be correlated with the fast relaxation metallic glasses. PMID:29565298

Diagnosing Students’ conception on atomic structure using open ended questions

NASA Astrophysics Data System (ADS)

Fitriza, Z.; Gazali, F.

2018-05-01

This study aims to diagnose students’ conception on atomic structure concepts using open ended questions. For this reason, a 7 items of assay test was administered to 135 senior high school students from different schools in West Sumatera. The data were collected using a an open ended test which is covering the concept used in the topic Atomic Structure. The open ended test of students’ conceptual was developed to identify the alternative conceptions that student might have regarding the concepts in Atomic Structure, to measure the level of students’ conceptions, and the way of students’ thinking concerning the concepts. The results showed that students find difficulties about some concepts of Atomic structure such as atom, atomic model, electron configuration, period and group.The result of this study illuminated the concepts to be underlined in developing teaching and learning approach concerning the topic of Atomic Structure.

Time-resolved x-ray spectra from laser-generated high-density plasmas

NASA Astrophysics Data System (ADS)

Andiel, U.; Eidmann, Klaus; Witte, Klaus-Juergen

2001-04-01

We focused frequency doubled ultra short laser pulses on solid C, F, Na and Al targets, K-shell emission was systematically investigated by time resolved spectroscopy using a sub-ps streak camera. A large number of laser shots can be accumulated when triggering the camera with an Auston switch system at very high temporal precision. The system provides an outstanding time resolution of 1.7ps accumulating thousands of laser shots. The time duration of the He-(alpha) K-shell resonance lines was observed in the range of (2-4)ps and shows a decrease with the atomic number. The experimental results are well reproduced by hydro code simulations post processed with an atomic kinetics code.

Cooperative and competitive concurrency in scientific computing. A full open-source upgrade of the program for dynamical calculations of RHEED intensity oscillations

NASA Astrophysics Data System (ADS)

Daniluk, Andrzej

2011-06-01

A computational model is a computer program, which attempts to simulate an abstract model of a particular system. Computational models use enormous calculations and often require supercomputer speed. As personal computers are becoming more and more powerful, more laboratory experiments can be converted into computer models that can be interactively examined by scientists and students without the risk and cost of the actual experiments. The future of programming is concurrent programming. The threaded programming model provides application programmers with a useful abstraction of concurrent execution of multiple tasks. The objective of this release is to address the design of architecture for scientific application, which may execute as multiple threads execution, as well as implementations of the related shared data structures. New version program summaryProgram title: GrowthCP Catalogue identifier: ADVL_v4_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVL_v4_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 32 269 No. of bytes in distributed program, including test data, etc.: 8 234 229 Distribution format: tar.gz Programming language: Free Object Pascal Computer: multi-core x64-based PC Operating system: Windows XP, Vista, 7 Has the code been vectorised or parallelized?: No RAM: More than 1 GB. The program requires a 32-bit or 64-bit processor to run the generated code. Memory is addressed using 32-bit (on 32-bit processors) or 64-bit (on 64-bit processors with 64-bit addressing) pointers. The amount of addressed memory is limited only by the available amount of virtual memory. Supplementary material: The figures mentioned in the "Summary of revisions" section can be obtained here. Classification: 4.3, 7.2, 6.2, 8, 14 External routines: Lazarus [1] Catalogue identifier of previous version: ADVL_v3_0 Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 709 Does the new version supersede the previous version?: Yes Nature of problem: Reflection high-energy electron diffraction (RHEED) is an important in-situ analysis technique, which is capable of giving quantitative information about the growth process of thin layers and its control. It can be used to calibrate growth rate, analyze surface morphology, calibrate surface temperature, monitor the arrangement of the surface atoms, and provide information about growth kinetics. Such control allows the development of structures where the electrons can be confined in space, giving quantum wells or even quantum dots. In order to determine the atomic positions of atoms in the first few layers, the RHEED intensity must be measured as a function of the scattering angles and then compared with dynamic calculations. The objective of this release is to address the design of architecture for application that simulates the rocking curves RHEED intensities during hetero-epitaxial growth process of thin films. Solution method: The GrowthCP is a complex numerical model that uses multiple threads for simulation of epitaxial growth of thin layers. This model consists of two transactional parts. The first part is a mathematical model being based on the Runge-Kutta method with adaptive step-size control. The second part represents first-principles of the one-dimensional RHEED computational model. This model is based on solving a one-dimensional Schrödinger equation. Several problems can arise when applications contain a mixture of data access code, numerical code, and presentation code. Such applications are difficult to maintain, because interdependencies between all the components cause strong ripple effects whenever a change is made anywhere. Adding new data views often requires reimplementing a numerical code, which then requires maintenance in multiple places. In order to solve problems of this type, the computational and threading layers of the project have been implemented in the form of one design pattern as a part of Model-View-Controller architecture. Reasons for new version: Responding to the users' feedback the Growth09 project has been upgraded to a standard that allows the carrying out of sample computations of the RHEED intensities for a disordered surface for a wide range of single- and epitaxial hetero-structures. The design pattern on which the project is based has also been improved. It is shown that this model can be effectively used for multithreaded growth simulations of thin epitaxial layers and corresponding RHEED intensities for a wide range of single- and hetero-structures. Responding to the users' feedback the present release has been implemented using a well-documented free compiler [1] not requiring the special configuration and installation additional libraries. Summary of revisions: The logical structure of the Growth09 program has been modified according to the scheme showed in Fig. 1. The class diagram in Fig. 1 is a static view of the main platform-specific elements of the GrowthCP architecture. Fig. 2 provides a dynamic view by showing the creation and destruction simplistic sequence diagram for the process. The program requires the user to provide the appropriate parameters in the form of a knowledge base for the crystal structures under investigation. These parameters are loaded from the parameters. ini files at run-time. Instructions to prepare the .ini files can be found in the new distribution. The program enables carrying out different growth models and one-dimensional dynamical RHEED calculations for the fcc lattice with basis of three-atoms, fcc lattice with basis of two-atoms, fcc lattice with single atom basis, Zinc-Blende, Sodium Chloride, and Wurtzite crystalline structures and hetero-structures, but yet the Fourier component of the scattering potential in the TRHEEDCalculations.crystPotUgXXX() procedure can be modified and implemented according to users' specific application requirements. The Fourier component of the scattering potential of the whole crystalline hetero-structures can be determined as a sum of contributions coming from all thin slices of individual atomic layers. To carry out one-dimensional calculations of the scattering potentials, the program uses properly constructed self-consistent procedures. Each component of the system shown in Figs. 1 and 2 is fully extendable and can easily be adapted to new changeable requirements. Two essential logical elements of the system, i.e. TGrowthTransaction and TRHEEDCalculations classes, were designed and implemented in this way for them to pass the information to themselves without the need to use the data-exchange files given. In consequence each of them can be independently modified and/or extended. Implementing other types of differential equations and the different algorithm for solving them in the TGrowthTransaction class does not require another implementation of the TRHEEDCalculations class. Similarly, implementing other forms of scattering potential and different algorithm for RHEED calculation stays without the influence on the TGrowthTransaction class construction. Unusual features: The program is distributed in the form of main project GrowthCP.lpr, with associated files, and should be compiled using Lazarus IDE. The program should be compiled with English/USA regional and language options. Running time: The typical running time is machine and user-parameters dependent. References: http://sourceforge.net/projects/lazarus/files/.

The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

PubMed

Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

2015-06-01

Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

In situ X-ray probing reveals fingerprints of surface platinum oxide.

PubMed

Friebel, Daniel; Miller, Daniel J; O'Grady, Christopher P; Anniyev, Toyli; Bargar, John; Bergmann, Uwe; Ogasawara, Hirohito; Wikfeldt, Kjartan Thor; Pettersson, Lars G M; Nilsson, Anders

2011-01-07

In situ X-ray absorption spectroscopy (XAS) at the Pt L(3) edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard X-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF code and complementary extended X-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling

PubMed Central

MacDonald, James T.; Kelley, Lawrence A.; Freemont, Paul S.

2013-01-01

Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http://www.sbg.bio.ic.ac.uk/phyre2/PD2/. PMID:23824634

Simulated GOLD Observations of Atmospheric Waves

NASA Astrophysics Data System (ADS)

Correira, J.; Evans, J. S.; Lumpe, J. D.; Rusch, D. W.; Chandran, A.; Eastes, R.; Codrescu, M.

2016-12-01

The Global-scale Observations of the Limb and Disk (GOLD) mission will measure structures in the Earth's airglow layer due to dynamical forcing by vertically and horizontally propagating waves. These measurements focus on global-scale structures, including compositional and temperature responses resulting from dynamical forcing. Daytime observations of far-UV emissions by GOLD will be used to generate two-dimensional maps of the ratio of atomic oxygen and molecular nitrogen column densities (ΣO/N2 ) as well as neutral temperature that provide signatures of large-scale spatial structure. In this presentation, we use simulations to demonstrate GOLD's capability to deduce periodicities and spatial dimensions of large-scale waves from the spatial and temporal evolution observed in composition and temperature maps. Our simulations include sophisticated forward modeling of the upper atmospheric airglow that properly accounts for anisotropy in neutral and ion composition, temperature, and solar illumination. Neutral densities and temperatures used in the simulations are obtained from global circulation and climatology models that have been perturbed by propagating waves with a range of amplitudes, periods, and sources of excitation. Modeling of airglow emission and predictions of ΣO/N2 and neutral temperatures are performed with the Atmospheric Ultraviolet Radiance Integrated Code (AURIC) and associated derived product algorithms. Predicted structure in ΣO/N2 and neutral temperature due to dynamical forcing by propagating waves is compared to existing observations. Realistic GOLD Level 2 data products are generated from simulated airglow emission using algorithm code that will be implemented operationally at the GOLD Science Data Center.

A predictive structural model for bulk metallic glasses

PubMed Central

Laws, K. J.; Miracle, D. B.; Ferry, M.

2015-01-01

Great progress has been made in understanding the atomic structure of metallic glasses, but there is still no clear connection between atomic structure and glass-forming ability. Here we give new insights into perhaps the most important question in the field of amorphous metals: how can glass-forming ability be predicted from atomic structure? We give a new approach to modelling metallic glass atomic structures by solving three long-standing problems: we discover a new family of structural defects that discourage glass formation; we impose efficient local packing around all atoms simultaneously; and we enforce structural self-consistency. Fewer than a dozen binary structures satisfy these constraints, but extra degrees of freedom in structures with three or more different atom sizes significantly expand the number of relatively stable, ‘bulk' metallic glasses. The present work gives a new approach towards achieving the long-sought goal of a predictive capability for bulk metallic glasses. PMID:26370667

Shock Wave Propagation in Cementitious Materials at Micro/Meso Scales

NASA Astrophysics Data System (ADS)

Rajendran, Arunachalam

2015-06-01

The mechanical and constitutive response of materials like cement, and bio materials like fish scale and abalone shell is very complex due to heterogeneities that are inherently present in the nano and microstructures. The intrinsic constitutive behaviors are driven by the chemical composition and the molecular, micro, and meso structures. Therefore, it becomes important to identify the material genome as the building block for the material. For instance, in cementitious materials, the genome of C-S-H phase (the glue or the paste) that holds the various clinkers, such as the dicalcium silicate, tricalcium silicate, calcium ferroaluminates, and others is extremely complex. Often mechanical behaviors of C-S-H type materials are influenced by the chemistry and the structures at all nano to micro length scales. By explicitly modeling the molecular structures using appropriate potentials, it is then possible to compute the elastic tensor from molecular dynamics simulations using all atom method. The elastic tensors for the C-S-H gel and other clinkers are determined using the software suite ``Accelrys Materials Studio.'' A strain rate dependent, fracture mechanics based tensile damage model has been incorporated into ABAQUS finite element code to model spall evolution in the heterogeneous cementitious material with all constituents explicitly modeled through one micron element resolution. This paper presents results from nano/micro/meso scale analyses of shock wave propagation in a heterogeneous cementitious material using both molecular dynamic and finite element codes.

Algorithms and physical parameters involved in the calculation of model stellar atmospheres

NASA Astrophysics Data System (ADS)

Merlo, D. C.

This contribution summarizes the Doctoral Thesis presented at Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba for the degree of PhD in Astronomy. We analyze some algorithms and physical parameters involved in the calculation of model stellar atmospheres, such as atomic partition functions, functional relations connecting gaseous and electronic pressure, molecular formation, temperature distribution, chemical compositions, Gaunt factors, atomic cross-sections and scattering sources, as well as computational codes for calculating models. Special attention is paid to the integration of hydrostatic equation. We compare our results with those obtained by other authors, finding reasonable agreement. We make efforts on the implementation of methods that modify the originally adopted temperature distribution in the atmosphere, in order to obtain constant energy flux throughout. We find limitations and we correct numerical instabilities. We integrate the transfer equation solving directly the integral equation involving the source function. As a by-product, we calculate updated atomic partition functions of the light elements. Also, we discuss and enumerate carefully selected formulae for the monochromatic absorption and dispersion of some atomic and molecular species. Finally, we obtain a flexible code to calculate model stellar atmospheres.

Liquid rocket combustor computer code development

NASA Technical Reports Server (NTRS)

Liang, P. Y.

1985-01-01

The Advanced Rocket Injector/Combustor Code (ARICC) that has been developed to model the complete chemical/fluid/thermal processes occurring inside rocket combustion chambers are highlighted. The code, derived from the CONCHAS-SPRAY code originally developed at Los Alamos National Laboratory incorporates powerful features such as the ability to model complex injector combustion chamber geometries, Lagrangian tracking of droplets, full chemical equilibrium and kinetic reactions for multiple species, a fractional volume of fluid (VOF) description of liquid jet injection in addition to the gaseous phase fluid dynamics, and turbulent mass, energy, and momentum transport. Atomization and droplet dynamic models from earlier generation codes are transplated into the present code. Currently, ARICC is specialized for liquid oxygen/hydrogen propellants, although other fuel/oxidizer pairs can be easily substituted.

A Model for Atomic and Molecular Interstellar Gas: The Meudon PDR Code

NASA Astrophysics Data System (ADS)

Le Petit, Franck; Nehmé, Cyrine; Le Bourlot, Jacques; Roueff, Evelyne

2006-06-01

We present the revised ``Meudon'' model of photon-dominated region (PDR) code, available on the Web under the GNU Public License. General organization of the code is described down to a level that should allow most observers to use it as an interpretation tool with minimal help from our part. Two grids of models, one for low-excitation diffuse clouds and one for dense highly illuminated clouds, are discussed, and some new results on PDR modelization highlighted.

PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser-atom interactions

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

2017-01-01

We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser-atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good parallel scaling on modern supercomputers. We give simple applications for the hydrogen atom using the benchmark problems coming from the references and obtain repeatable results. The extensions to other laser-atom systems are straightforward with minimal modifications of the source code.

Holographic Reconstruction of Photoelectron Diffraction and Its Circular Dichroism for Local Structure Probing

NASA Astrophysics Data System (ADS)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

The local atomic structure around a specific element atom can be recorded as a photoelectron diffraction pattern. Forward focusing peaks and diffraction rings around them indicate the directions and distances from the photoelectron emitting atom to the surrounding atoms. The state-of-the-art holography reconstruction algorithm enables us to image the local atomic arrangement around the excited atom in a real space. By using circularly polarized light as an excitation source, the angular momentum transfer from the light to the photoelectron induces parallax shifts in these diffraction patterns. As a result, stereographic images of atomic arrangements are obtained. These diffraction patterns can be used as atomic-site-resolved probes for local electronic structure investigation in combination with spectroscopy techniques. Direct three-dimensional atomic structure visualization and site-specific electronic property analysis methods are reviewed. Furthermore, circular dichroism was also found in valence photoelectron and Auger electron diffraction patterns. The investigation of these new phenomena provides hints for the development of new techniques for local structure probing.

Proposed software system for atomic-structure calculation

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

Fischer, C.F.

1981-07-01

Atomic structure calculations are understood well enough that, at a routine level, an atomic structure software package can be developed. At the Atomic Physics Conference in Riga, 1978 L.V. Chernysheva and M.Y. Amusia of Leningrad University, presented a paper on Software for Atomic Calculations. Their system, called ATOM is based on the Hartree-Fock approximation and correlation is included within the framework of RPAE. Energy level calculations, transition probabilities, photo-ionization cross-sections, electron scattering cross-sections are some of the physical properties that can be evaluated by their system. The MCHF method, together with CI techniques and the Breit-Pauli approximation also provides amore » sound theoretical basis for atomic structure calculations.« less

A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation

PubMed Central

Sattelle, Benedict M.; Shakeri, Javad; Roberts, Ian S.; Almond, Andrew

2010-01-01

The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-strucutre at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without 15N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the β(1→3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the β(1→3) ψ dihedral (as previously predicted by simulation), while the β(1→4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties. PMID:20022001

Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

NASA Astrophysics Data System (ADS)

Huhn, William; Blum, Volker

2015-03-01

Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

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

Pagola, Silvina; Polymeros, Alekos; Kourkoumelis, Nikolaos

2017-02-01

The direct-space methods softwarePowder Structure Solution Program(PSSP) [Pagola & Stephens (2010).J. Appl. Cryst.43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs.WinPSSPis a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinatesmore » into the Rietveld analysis softwareGSAS. WinPSSPperformance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.« less

PyNeb: a new tool for analyzing emission lines. I. Code description and validation of results

NASA Astrophysics Data System (ADS)

Luridiana, V.; Morisset, C.; Shaw, R. A.

2015-01-01

Analysis of emission lines in gaseous nebulae yields direct measures of physical conditions and chemical abundances and is the cornerstone of nebular astrophysics. Although the physical problem is conceptually simple, its practical complexity can be overwhelming since the amount of data to be analyzed steadily increases; furthermore, results depend crucially on the input atomic data, whose determination also improves each year. To address these challenges we created PyNeb, an innovative code for analyzing emission lines. PyNeb computes physical conditions and ionic and elemental abundances and produces both theoretical and observational diagnostic plots. It is designed to be portable, modular, and largely customizable in aspects such as the atomic data used, the format of the observational data to be analyzed, and the graphical output. It gives full access to the intermediate quantities of the calculation, making it possible to write scripts tailored to the specific type of analysis one wants to carry out. In the case of collisionally excited lines, PyNeb works by solving the equilibrium equations for an n-level atom; in the case of recombination lines, it works by interpolation in emissivity tables. The code offers a choice of extinction laws and ionization correction factors, which can be complemented by user-provided recipes. It is entirely written in the python programming language and uses standard python libraries. It is fully vectorized, making it apt for analyzing huge amounts of data. The code is stable and has been benchmarked against IRAF/NEBULAR. It is public, fully documented, and has already been satisfactorily used in a number of published papers.

MC3, Version 1

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

Cawkwell, Marc Jon

2016-09-09

The MC3 code is used to perform Monte Carlo simulations in the isothermal-isobaric ensemble (constant number of particles, temperature, and pressure) on molecular crystals. The molecules within the periodic simulation cell are treated as rigid bodies, alleviating the requirement for a complex interatomic potential. Intermolecular interactions are described using generic, atom-centered pair potentials whose parameterization is taken from the literature [D. E. Williams, J. Comput. Chem., 22, 1154 (2001)] and electrostatic interactions arising from atom-centered, fixed, point partial charges. The primary uses of the MC3 code are the computation of i) the temperature and pressure dependence of lattice parameters andmore » thermal expansion coefficients, ii) tensors of elastic constants and compliances via the Parrinello and Rahman’s fluctuation formula [M. Parrinello and A. Rahman, J. Chem. Phys., 76, 2662 (1982)], and iii) the investigation of polymorphic phase transformations. The MC3 code is written in Fortran90 and requires LAPACK and BLAS linear algebra libraries to be linked during compilation. Computationally expensive loops are accelerated using OpenMP.« less

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

Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.

Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated which was matched with the experimental one. Themore » dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~ 2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7 to 40 eV).« less

Handling of Atomic Data

NASA Astrophysics Data System (ADS)

Rauch, T.; Deetjen, J. L.

2003-01-01

State-of-the-art NLTE model atmosphere codes have arrived at a high level of ``numerical'' sophistication and are an adequate tool to analyze the available high-quality spectra from the infrared to the X-ray wavelength range. The computational capacities allow the calculation which include all elements from hydrogen up to the iron group and the lack of reliable atomic data has become a crucial problem for further progress. We summarize briefly the available sources of atomic data and how these are implemented in the Tübingen Model Atmosphere Package (TMAP).

Atomization and Mixing Study

NASA Technical Reports Server (NTRS)

Ferrenberg, A.; Hunt, K.; Duesberg, J.

1985-01-01

The primary objective was the obtainment of atomization and mixing performance data for a variety of typical liquid oxygen/hydrocarbon injector element designs. Such data are required to establish injector design criteria and to provide critical inputs to liquid rocket engine combustor performance and stability analysis, and computational codes and methods. Deficiencies and problems with the atomization test equipment were identified, and action initiated to resolve them. Test results of the gas/liquid mixing tests indicated that an assessment of test methods was required. A series of 71 liquid/liquid tests were performed.

Observing heliospheric neutral atoms at 1 AU

NASA Astrophysics Data System (ADS)

Heerikhuisen, Jacob; Pogorelov, Nikolai; Florinski, Vladimir; Zank, Gary

2006-09-01

Although in situ observations of distant heliospheric plasma by the Voyagers has proven to be extremely enlightening, such point observations need to be complemented with global measurements taken remotely to obtain a complete picture of the heliosphere and local interstellar environment. Neutral atoms, with their contempt for magnetic fields, provide useful probes of the plasma that generated them. However, there will be a number of ambiguities in neutral atom readings that require a deeper understanding of the plasma processes generating neutral atoms, as well as the loss mechanisms on their flight to the observation point. We introduce a procedure for generating all-sky maps of energetic H-atoms, calculated directly in our Monte-Carlo neutral atom code. Results obtained for a self-consistent axisymmetric MHD-Boltzmann calculation, as well as several non-selfconsistent 3D sky maps, will be presented.

Magnetism of CrO overlayers on Fe(001)bcc surface: first principles calculations

NASA Astrophysics Data System (ADS)

Félix-Medina, Raúl Enrique; Leyva-Lucero, Manuel Andrés; Meza-Aguilar, Salvador; Demangeat, Claude

2018-04-01

Riva et al. [Surf. Sci. 621, 55 (2014)] as well as Calloni et al. [J. Phys.: Condens. Matter 26, 445001 (2014)] have studied the oxydation of Cr films deposited on Fe(001)bcc through low-energy electron diffraction, Auger electron spectroscopy and scanning tunneling microscopy. In the present work we perform a density functional approach within Quantum Expresso code in order to study structural and magnetic properties of CrO overlayers on Fe(001)bcc. The calculations are performed using DFT+U. The investigated systems include O/Cr/Fe(001)bcc, Cr/O/Fe(001)bcc, Cr0.25O0.75/Fe(001)bcc, as well as the O coverage Ox/Cr/Fe(001)bcc (x = 0.25; 0.50). We have found that the ordered CrO overlayer presents an antiferromagnetic coupling between Cr and Fe atoms. The O atoms are located closer to the Fe atoms of the surface than the Cr atoms. The ground state of the systems O/Cr/Fe(001)bcc and Cr/O/Fe(001)bcc corresponds to the O/Cr/Fe(001)bcc system with a magnetic coupling c(2 × 2). The effect of the O monolayer on Cr/Fe(001)bcc changes the ground state from p(1 × 1) ↓ to c(2 × 2) and produces an enhancement of the magnetic moments. The Ox overlayer on Cr/Fe(001)bcc produces an enhancement of the Cr magnetic moments.

VizieR Online Data Catalog: Energy levels & transition rates for F-like ions (Si+, 2016)

NASA Astrophysics Data System (ADS)

Si, R.; Li, S.; Guo, X. L.; Chen, Z. B.; Brage, T.; Jonsson, P.; Wang, K.; Yan, J.; Chen, C. Y.; Zou, Y. M.

2017-01-01

For the multiconfiguration Dirac-Hartree-Fock (MCDHF) calculation we use the latest version of the GRASP2K code (Jonsson+ 2013CoPhC.184.2197J), while the many-body perturbation theory (MBPT) calculation is performed using the Flexible Atomic Code (FAC; Gu 2008CaJPh..86..675G). (2 data files).

The argon nuclear quadrupole moments

NASA Astrophysics Data System (ADS)

Sundholm, Dage; Pyykkö, Pekka

2018-07-01

New standard values -116(2) mb and 76(3) mb are suggested for the nuclear quadrupole moments (Q) of the 39Ar and 37Ar nuclei, respectively. The Q values were obtained by combining optical measurements of the quadrupole coupling constant (B or eqQ/h) of the 3s23p54s[3/2]2 (3Po) and 3s23p54p[5/2]3 (3De) states of argon with large scale numerical complete active space self-consistent field and restricted active space self-consistent field calculations of the electric field gradient at the nucleus (q) using the LUCAS code, which is a finite-element based multiconfiguration Hartree-Fock program for atomic structure calculations.

Dopant distributions in n-MOSFET structure observed by atom probe tomography.

PubMed

Inoue, K; Yano, F; Nishida, A; Takamizawa, H; Tsunomura, T; Nagai, Y; Hasegawa, M

2009-11-01

The dopant distributions in an n-type metal-oxide-semiconductor field effect transistor (MOSFET) structure were analyzed by atom probe tomography. The dopant distributions of As, P, and B atoms in a MOSFET structure (gate, gate oxide, channel, source/drain extension, and halo) were obtained. P atoms were segregated at the interface between the poly-Si gate and the gate oxide, and on the grain boundaries of the poly-Si gate, which had an elongated grain structure along the gate height direction. The concentration of B atoms was enriched near the edge of the source/drain extension where the As atoms were implanted.

Atomistic Method Applied to Computational Modeling of Surface Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo H.; Abel, Phillip B.

2000-01-01

The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of the energetics, consists of a small number of simple PCbased computer codes that deal with the different aspects of surface alloy formation. Two analysis modes are available within this package. The first mode provides an atom-by-atom description of real and virtual stages 1. during the process of surface alloying, based on the construction of catalogues of configurations where each configuration describes one possible atomic distribution. BFS analysis of this catalogue provides information on accessible states, possible ordering patterns, and details of island formation or film growth. More importantly, it provides insight into the evolution of the system. Software developed by the Computational Materials Group allows for the study of an arbitrary number of elements forming surface alloys, including an arbitrary number of surface atomic layers. The second mode involves large-scale temperature-dependent computer 2. simulations that use the BFS method for the energetics and provide information on the dynamic processes during surface alloying. These simulations require the implementation of Monte-Carlo-based codes with high efficiency within current workstation environments. This methodology capitalizes on the advantages of the BFS method: there are no restrictions on the number or type of elements or on the type of crystallographic structure considered. This removes any restrictions in the definition of the configuration catalogues used in the analytical calculations, thus allowing for the study of arbitrary ordering patterns, ultimately leading to the actual surface alloy structure. Moreover, the Monte Carlo numerical technique used for the large-scale simulations allows for a detailed visualization of the simulated process, the main advantage of this type of analysis being the ability to understand the underlying features that drive these processes. Because of the simplicity of the BFS method for e energetics used in these calculations, a detailed atom-by-atom analysis can be performed at any point in the simulation, providing necessary insight on the details of the process. The main objective of this research program is to develop a tool to guide experimenters in understanding and interpreting often unexpected results in alloy formation experiments. By reducing the computational effort without losing physical accuracy, we expect that powerful simulation tools will be developed in the immediate future, which will allow material scientists to easily visualize and analyze processes at a level not achievable experimentally.

First-principles study of structure, electronic properties and stability of tungsten adsorption on TiC(111) surface with disordered vacancies

NASA Astrophysics Data System (ADS)

Ilyasov, Victor V.; Pham, Khang D.; Zhdanova, Tatiana P.; Phuc, Huynh V.; Hieu, Nguyen N.; Nguyen, Chuong V.

2017-12-01

In this paper, we systematically investigate the atomic structure, electronic and thermodynamic properties of adsorbed W atoms on the polar Ti-terminated TixCy (111) surface with different configurations of adsorptions using first principle calculations. The bond length, adsorption energy, and formation energy for different reconstructions of the atomic structure of the W/TixCy (111) systems were established. The effect of the tungsten coverage on the electronic structure and the adsorption mechanism of tungsten atom on the TixCy (111) are also investigated. We also suggest the possible mechanisms of W nucleation on the TixCy (111) surface. The effective charges on W atoms and nearest-neighbor atoms in the examined reconstructions were identified. Additionally, we have established the charge transfer from titanium atom to tungsten and carbon atoms which determine by the reconstruction of the local atomic and electronic structures. Our calculations showed that the charge transfer correlates with the electronegativity of tungsten and nearest-neighbor atoms. We also determined the effective charge per atom of titanium, carbon atoms, and neighboring adsorbed tungsten atom in different binding configurations. We found that, with reduction of the lattice symmetry associated with titanium and carbon vacancies, the adsorption energy increases by 1.2 times in the binding site A of W/TixCy systems.

Ignition and combustion characteristics of metallized propellants, phase 2

NASA Technical Reports Server (NTRS)

Mueller, D. C.; Turns, S. R.

1994-01-01

Experimental and analytical investigations focusing on aluminum/hydrocarbon gel droplet secondary atomization and its effects on gel-fueled rocket engine performance are being conducted. A single laser sheet sizing/velocimetry diagnostic technique, which should eliminate sizing bias in the data collection process, has been designed and constructed to overcome limitations of the two-color forward-scatter technique used in previous work. Calibration of this system is in progress and the data acquisition/validation code is being written. Narrow-band measurements of radiant emission, discussed in previous reports, will be used to determine if aluminum ignition has occurred in a gel droplet. A one-dimensional model of a gel-fueled rocket combustion chamber, described in earlier reports, has been exercised in conjunction with a two-dimensional, two-phase nozzle code to predict the performance of an aluminum/hydrocarbon fueled engine. Estimated secondary atomization effects on propellant burnout distance, condensed particle radiation losses to the chamber walls, and nozzle two phase flow losses are also investigated. Calculations indicate that only modest secondary atomization is required to significantly reduce propellant burnout distances, aluminum oxide residual size, and radiation heat losses. Radiation losses equal to approximately 2-13 percent of the energy released during combustion were estimated, depending on secondary atomization intensity. A two-dimensional, two-phase nozzle code was employed to estimate radiation and nozzle two phase flow effects on overall engine performance. Radiation losses yielded a one percent decrease in engine Isp. Results also indicate that secondary atomization may have less effect on two-phase losses than it does on propellant burnout distance and no effect if oxide particle coagulation and shear induced droplet breakup govern oxide particle size. Engine Isp was found to decrease from 337.4 to 293.7 seconds as gel aluminum mass loading was varied from 0-70 wt percent. Engine Isp efficiencies, accounting for radiation and two phase flow effects, on the order of 0.946 were calculated for a 60 wt percent gel, assuming a fragmentation ratio of five.

Structure and Properties of Sn2Se3, a mixed valent tin selenium compound

NASA Astrophysics Data System (ADS)

Xing, Guangzong; Li, Yuwei; Fan, Xiaofeng; Zhang, Lijun; Singh, David

Sn2Se3 is a possibly expected phase based on analogy with Sn2S3 but it has never been reported. It is of interest due to reported phase change memories using this composition using transitions between an amorphous phase and an unknown crystalline phase. We identify the crystal structure Sn2Se3 and report its properties at ambient pressure based on the ab initio evolutionary methodology for crystal structure prediction implemented in the Calypso code. We find a structure based on Sn-Se ribbons with clear Sn(II)and Sn(IV)sites similar to the structure of Sn2S3. Compared with the known phase SnSe (Pnma) +SnSe2 (P-3m1), the energy is only 2.3meV/atom higher. The electronic structure of this phase shows mixed valent tins Sn2+ and Sn4+ in this compound. A small band gap of 0.023 eV is obtained from the band structure consistent with the small resistance reported by Kyung-Min Chung et al. Work at the University of Missouri is supported by DOE through the S3TEC EFRC.

An intrinsic representation of atomic structure: From clusters to periodic systems

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-01

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

An intrinsic representation of atomic structure: From clusters to periodic systems.

PubMed

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-14

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

Theoretical predictions of a bucky-diamond SiC cluster.

PubMed

Yu, Ming; Jayanthi, C S; Wu, S Y

2012-06-15

A study of structural relaxations of Si(n)C(m) clusters corresponding to different compositions, different relative arrangements of Si/C atoms, and different types of initial structure, reveals that the Si(n)C(m) bucky-diamond structure can be obtained for an initial network structure constructed from a truncated bulk 3C-SiC for a magic composition corresponding to n = 68 and m = 79. This study was performed using a semi-empirical Hamiltonian (SCED-LCAO) since it allowed an extensive search of different types of initial structures. However, the bucky-diamond structure predicted by this method was also confirmed by a more accurate density functional theory (DFT) based method. The bucky-diamond structure exhibited by a SiC-based system represents an interesting paradigm where a Si atom can form three-coordinated as well as four-coordinated networks with carbon atoms and vice versa and with both types of network co-existing in the same structure. Specifically, the bucky-diamond structure of the Si(68)C(79) cluster consists of a 35-atom diamond-like inner core (four-atom coordinations) suspended inside a 112-atom fullerene-like shell (three-atom coordinations).

Highly Efficient Parallel Multigrid Solver For Large-Scale Simulation of Grain Growth Using the Structural Phase Field Crystal Model

NASA Astrophysics Data System (ADS)

Guan, Zhen; Pekurovsky, Dmitry; Luce, Jason; Thornton, Katsuyo; Lowengrub, John

The structural phase field crystal (XPFC) model can be used to model grain growth in polycrystalline materials at diffusive time-scales while maintaining atomic scale resolution. However, the governing equation of the XPFC model is an integral-partial-differential-equation (IPDE), which poses challenges in implementation onto high performance computing (HPC) platforms. In collaboration with the XSEDE Extended Collaborative Support Service, we developed a distributed memory HPC solver for the XPFC model, which combines parallel multigrid and P3DFFT. The performance benchmarking on the Stampede supercomputer indicates near linear strong and weak scaling for both multigrid and transfer time between multigrid and FFT modules up to 1024 cores. Scalability of the FFT module begins to decline at 128 cores, but it is sufficient for the type of problem we will be examining. We have demonstrated simulations using 1024 cores, and we expect to achieve 4096 cores and beyond. Ongoing work involves optimization of MPI/OpenMP-based codes for the Intel KNL Many-Core Architecture. This optimizes the code for coming pre-exascale systems, in particular many-core systems such as Stampede 2.0 and Cori 2 at NERSC, without sacrificing efficiency on other general HPC systems.

Study of premixing phase of steam explosion with JASMINE code in ALPHA program

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

Moriyama, Kiyofumi; Yamano, Norihiro; Maruyama, Yu

Premixing phase of steam explosion has been studied in ALPHA Program at Japan Atomic Energy Research Institute (JAERI). An analytical model to simulate the premixing phase, JASMINE (JAERI Simulator for Multiphase Interaction and Explosion), has been developed based on a multi-dimensional multi-phase thermal hydraulics code MISTRAL (by Fuji Research Institute Co.). The original code was extended to simulate the physics in the premixing phenomena. The first stage of the code validation was performed by analyzing two mixing experiments with solid particles and water: the isothermal experiment by Gilbertson et al. (1992) and the hot particle experiment by Angelini et al.more » (1993) (MAGICO). The code predicted reasonably well the experiments. Effectiveness of the TVD scheme employed in the code was also demonstrated.« less

Direct Determination of Atomic Structure and Magnetic Coupling of Magnetite Twin Boundaries.

PubMed

Chen, Chunlin; Li, Hongping; Seki, Takehito; Yin, Deqiang; Sanchez-Santolino, Gabriel; Inoue, Kazutoshi; Shibata, Naoya; Ikuhara, Yuichi

2018-03-27

Clarifying how the atomic structure of interfaces/boundaries in materials affects the magnetic coupling nature across them is of significant academic value and will facilitate the development of state-of-the-art magnetic devices. Here, by combining atomic-resolution transmission electron microscopy, atomistic spin-polarized first-principles calculations, and differential phase contrast imaging, we conduct a systematic investigation of the atomic and electronic structures of individual Fe 3 O 4 twin boundaries (TBs) and determine their concomitant magnetic couplings. We demonstrate that the magnetic coupling across the Fe 3 O 4 TBs can be either antiferromagnetic or ferromagnetic, which directly depends on the TB atomic core structures and resultant electronic structures within a few atomic layers. Revealing the one-to-one correspondence between local atomic structures and magnetic properties of individual grain boundaries will shed light on in-depth understanding of many interesting magnetic behaviors of widely used polycrystalline magnetic materials, which will surely promote the development of advanced magnetic materials and devices.

Neutron displacement cross-sections for tantalum and tungsten at energies up to 1 GeV

NASA Astrophysics Data System (ADS)

Broeders, C. H. M.; Konobeyev, A. Yu.; Villagrasa, C.

2005-06-01

The neutron displacement cross-section has been evaluated for tantalum and tungsten at energies from 10 -5 eV up to 1 GeV. The nuclear optical model, the intranuclear cascade model combined with the pre-equilibrium and evaporation models were used for the calculations. The number of defects produced by recoil atoms nuclei in materials was calculated by the Norgett, Robinson, Torrens model and by the approach combining calculations using the binary collision approximation model and the results of the molecular dynamics simulation. The numerical calculations were done using the NJOY code, the ECIS96 code, the MCNPX code and the IOTA code.

Lithium doping and vacancy effects on the structural, electronic and magnetic properties of hexagonal boron nitride sheet: A first-principles calculation

NASA Astrophysics Data System (ADS)

Fartab, Dorsa S.; Kordbacheh, Amirhossein Ahmadkhan

2018-06-01

The first-principles calculations based on spin-polarized density functional theory is carried out to investigate the structural, electronic and magnetic properties of a hexagonal boron nitride sheet (h-BNS) doped by one or two lithium atom(s). Moreover, a vacancy in the neighborhood of one Li-substituted atom is introduced into the system. All optimized structures indicate significant local deformations with Li atom(s) protruded to the exterior of the sheet. The defects considered at N site are energetically more favorable than their counterpart structures at B site. The spin-polarized impurity states appear within the bandgap region of the pristine h-BNS, which lead to a spontaneous magnetization with the largest magnetic moments of about 2 μB in where a single or two B atom(s) are replaced by Li atom(s). Furthermore, the Li substitution for a single B atom increases the density of holes compared to that of electrons forming a p-type semiconductor. More interestingly, the structure in which two Li are substituted two neighboring B atoms appears to show desired half-metallic behavior that may be applicable in spintronic. The results provide a way to enhance the conductivity and magnetism of the pristine h-BNS for potential applications in BN-based nanoscale devices.

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Understanding Atomic Structure: Is There a More Direct and Compelling Connection between Atomic Line Spectra and the Quantization of an Atom's Energy?

ERIC Educational Resources Information Center

Rittenhouse, Robert C.

2015-01-01

The "atoms first" philosophy, adopted by a growing number of General Chemistry textbook authors, places greater emphasis on atomic structure as a key to a deeper understanding of the field of chemistry. A pivotal concept needed to understand the behavior of atoms is the restriction of an atom's energy to specific allowed values. However,…

Stereospecificity of {beta}-O-4 lignin oligomers

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

Faulon, J.L.; Pohl, P.I.

1995-12-01

Lignin, a complex macromolecule of vascular plants is a cross-linked polymer of glyceryl methoxyphenol units. The major type of linkage between the monomers is the {beta}-O-4 bond. We have studied the conformations of {beta}-O-4 lignin oligomers in a vacuum, and in the presence of water, cations, and cellulosic materials. There are several stereoisomers of {beta}-O-4 lignin oligomers because lignin monomers contain chiral atoms. We have constructed the stereoisomers using a stochastic chemical structure generator (the SIGNATURE program). The potential energies of the resulting structures were calculated using several force fields (MM2, DREIDING, CVFF), and several semiempirical codes (AM1, PM3). Themore » conformational space of the stereoisomers were investigated using Monte Carlo and simulated annealing modeling techniques. It was observed that the lowest energies were obtained for the stereospecific all-three and all-erythro isomers independently of the degree of polymerization.« less

Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2017-10-26

We investigate the influence of various solvent models on the structural stability and protein-water interface of three ubiquitin complexes (PDB access codes: 1Q0W , 2MBB , 2G3Q ) modeled using the Amber99sb force field (FF) and two different point charge distributions. A previously developed reduced point charge model (RPCM), wherein each amino acid residue is described by a limited number of point charges, is tested and compared to its all-atom (AA) version. The complexes are solvated in TIP4P-Ew or TIP3P type water molecules, involving either the scaling of the Lennard-Jones protein-O water interaction parameters, or the coarse-grain (CG) SIRAH water description. The best agreements between the RPCM and AA models were obtained for structural, protein-water, and ligand-ubiquitin properties when using the TIP4P-Ew water FF with a scaling factor γ of 0.7. At the RPCM level, a decrease in γ, or the inclusion of SIRAH particles, allows weakening of the protein-water interactions. It results in a slight collapse of the protein structure and a less compact hydration shell and, thus, in a decrease in the number of protein-water and water-water H-bonds. The dynamics of the surface protein atoms and of the water shell molecules are also slightly refrained, which allow the generation of stable RPCM trajectories.

Benchmarking atomic physics models for magnetically confined fusion plasma physics experiments

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

May, M.J.; Finkenthal, M.; Soukhanovskii, V.

In present magnetically confined fusion devices, high and intermediate {ital Z} impurities are either puffed into the plasma for divertor radiative cooling experiments or are sputtered from the high {ital Z} plasma facing armor. The beneficial cooling of the edge as well as the detrimental radiative losses from the core of these impurities can be properly understood only if the atomic physics used in the modeling of the cooling curves is very accurate. To this end, a comprehensive experimental and theoretical analysis of some relevant impurities is undertaken. Gases (Ne, Ar, Kr, and Xe) are puffed and nongases are introducedmore » through laser ablation into the FTU tokamak plasma. The charge state distributions and total density of these impurities are determined from spatial scans of several photometrically calibrated vacuum ultraviolet and x-ray spectrographs (3{endash}1600 {Angstrom}), the multiple ionization state transport code transport code (MIST) and a collisional radiative model. The radiative power losses are measured with bolometery, and the emissivity profiles were measured by a visible bremsstrahlung array. The ionization balance, excitation physics, and the radiative cooling curves are computed from the Hebrew University Lawrence Livermore atomic code (HULLAC) and are benchmarked by these experiments. (Supported by U.S. DOE Grant No. DE-FG02-86ER53214 at JHU and Contract No. W-7405-ENG-48 at LLNL.) {copyright} {ital 1999 American Institute of Physics.}« less

77 FR 42483 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

... creating artificial nanoscale structures on an atom-by- atom basis using nascent atom manipulation techniques. The instrument will be used to investigate the amount of force required to move one atom on a materials surface while simultaneously measuring local electronic structural changes during atom movement...

An analytical benchmark and a Mathematica program for MD codes: Testing LAMMPS on the 2nd generation Brenner potential

NASA Astrophysics Data System (ADS)

Favata, Antonino; Micheletti, Andrea; Ryu, Seunghwa; Pugno, Nicola M.

2016-10-01

An analytical benchmark and a simple consistent Mathematica program are proposed for graphene and carbon nanotubes, that may serve to test any molecular dynamics code implemented with REBO potentials. By exploiting the benchmark, we checked results produced by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) when adopting the second generation Brenner potential, we made evident that this code in its current implementation produces results which are offset from those of the benchmark by a significant amount, and provide evidence of the reason.

Science & Technology Review November 2007

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

Chinn, D J

2007-10-16

This month's issue has the following articles: (1) Simulating the Electromagnetic World--Commentary by Steven R. Patterson; (2) A Code to Model Electromagnetic Phenomena--EMSolve, a Livermore supercomputer code that simulates electromagnetic fields, is helping advance a wide range of research efforts; (3) Characterizing Virulent Pathogens--Livermore researchers are developing multiplexed assays for rapid detection of pathogens; (4) Imaging at the Atomic Level--A powerful new electron microscope at the Laboratory is resolving materials at the atomic level for the first time; (5) Scientists without Borders--Livermore scientists lend their expertise on peaceful nuclear applications to their counterparts in other countries; and (6) Probing Deepmore » into the Nucleus--Edward Teller's contributions to the fast-growing fields of nuclear and particle physics were part of a physics golden age.« less

PREFACE: Proceedings of the First International Workshop on the Theoretical Calculation of ELNES and XANES (TEX2008) (Nagoya, Japan, 2-4 July 2008) Proceedings of the First International Workshop on the Theoretical Calculation of ELNES and XANES (TEX2008) (Nagoya, Japan, 2-4 July 2008)

NASA Astrophysics Data System (ADS)

Tanaka, Isao; Mizoguchi, Teruyasu; Yamamoto, Tomoyuki

2009-03-01

Both electron energy loss near edge structure (ELNES) spectroscopy and x-ray absorption near edge structure (XANES) spectroscopy provide information on the local structural and chemical environments of selected elements of interest. Recent technological progress in scanning transmission electron microscopy has enabled ELNES measurements with atomic column spatial resolution. Very dilute concentrations (nanograms per milliliter or ppb level) of dopants can be observed using third-generation synchrotron facilities when x-ray fluorescence is measured with highly efficient detectors. With such technical developments, ELNES and XANES have become established as essential tools in a large number of fields of natural science, including condensed matter physics, chemistry, mineralogy and materials science. In addition to these developments in experimental methodology, notable progress in reproducing spectra using theoretical methods has recently been made. Using first-principles methods, one can analyze and interpret spectra without reference to experiment. This is quite important since we are often interested in the analysis of exotic materials or specific atoms located at lattice discontinuities such as surfaces and interfaces, where appropriate experimental data are difficult to obtain. Using the structures predicted by reliable first-principles calculations, one can calculate theoretical ELNES and XANES spectra without too much difficulty even in such cases. Despite the fact that ELNES and XANES probe the same phenomenon—essentially the electric dipole transition from a core orbital to an unoccupied band—there have not been many opportunities for researchers in the two areas to meet and discuss. Theoretical calculations of ELNES spectra have been mainly confined to the electron microscopy community. On the other hand, the theory of XANES has been developed principally by researchers in the x-ray community. Publications describing the methods have been written more-or-less independently by the two communities. The three-day workshop on the Theoretical Calculation of ELNES and XANES (TEX2008) was planned to help remedy this situation. It aimed to demonstrate capability of state-of-the-art theoretical techniques to explain and predict ELNES and XANES spectra, and to allow deep discussion between scientists in the two communities. It also provided an excellent opportunity to introduce experimentalists to the computational techniques available. Invited talks and poster presentations by leading scientists were given on the first day, which was followed by tutorial sessions for five computer programs on the second and third days. Excellent lectures were given by Peter Blaha (Vienna, Austria) on the WIEN2k code, Chris J Pickard (St Andrews, UK) on the CASTEP code, John J Rehr (Seattle, USA) on the FEFF8 code, Frank de Groot (Utrecht, The Netherlands) on the CTM4XAS code, and Hidekazu Ikeno (Kyoto, Japan) on the first-principles CI-multiplet code. Thanks to the enthusiastic participation of more than 100 scientists from around the world, the workshop was a complete success. The aim of this special issue in Journal of Physics: Condensed Matter is to share with the readers the most up-to-date knowledge presented at the workshop. We believe this will prove useful as a reference for researchers in many different fields, as well as an overview of the current status and future directions of theoretical calculations for ELNES and XANES. TEX2008 was a satellite meeting of the First International Symposium on Advanced Microscopy and Theoretical Calculations (AMTC1) (Nagoya, Japan, 29-30 June 2008), which was held in commemoration of the establishment of the Nanostuctures Research Laboratory (NSRL) at the Japan Fine Ceramics Center (JFCC) and as a daughter event of EXPO 2005, Aichi, Japan. A Grant-in-Aid for Scientific Research on Priority Areas 'Nano Materials Science for Atomic-Scale Modification' from the Ministry of Education, Culture, Sports and Technology (MEXT) and support from the Chubu Economic Federation for the workshop are gratefully acknowledged.

AtomDB Progress Report: Atomic data and new models for X-ray spectroscopy.

NASA Astrophysics Data System (ADS)

Smith, Randall K.; Foster, Adam; Brickhouse, Nancy S.; Stancil, Phillip C.; Cumbee, Renata; Mullen, Patrick Dean; AtomDB Team

2018-06-01

The AtomDB project collects atomic data from both theoretical and observational/experimental sources, providing both a convenient interface (http://www.atomdb.org/Webguide/webguide.php) as well as providing input to spectral models for many types of astrophysical X-ray plasmas. We have released several updates to AtomDB in response to the Hitomi data, including new data for the Fe K complex, and have expanded the range of models available in AtomDB to include the Kronos charge exchange models from Mullen at al. (2016, ApJS, 224, 2). Combined with the previous AtomDB charge exchange model (http://www.atomdb.org/CX/), these data enable a velocity-dependent model for X-ray and EUV charge exchange spectra. We also present a new Kappa-distribution spectral model, enabling plasmas with non-Maxwellian electron distributions to be modeled with AtomDB. Tools are provided within pyAtomDB to explore and exploit these new plasma models. This presentation will review these enhancements and describe plans for the new few years of database and code development in preparation for XARM, Athena, and (hopefully) Arcus.

Testing Photoionization Calculations Using Chandra X-ray Spectra

NASA Technical Reports Server (NTRS)

Kallman, Tim

2008-01-01

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

First principles study of the ground state properties of Si, Ga, and Ge doped Fe50Al50

NASA Astrophysics Data System (ADS)

Pérez, Carlos Ariel Samudio; dos Santos, Antonio Vanderlei

2018-06-01

The first principles calculation of the structural, electronic and associated properties of the Fe50Al50 alloy (B2 phase) doped by s-p elements (Im = Si, Ga, and Ge) are performed as a function of the atomic concentration on the basis of the Full Potential Linear Augmented Plane Wave (FP-LAPW) method as implemented in the WIEN2k code. The Al substitution by Im (Si and Ge) atoms (principally at a concentration of 6.25 at%) induces a pronounced redistribution of the electronic charge leading to a strong Fe-Im interaction with covalent bonding character. At the same time, decrease the lattice volume (V) while increase the bulk modulus (B). For the alloys containing Ga, the Fe-Ga interaction is also observed but the V and B of the alloy are very near to that of pure Fe-Al alloy. The magnetic moment and hyperfine parameters observed at the lattice sites of studied alloys also show variations, they increase or decrease in relation to that in Fe50Al50 according to the Im that substitutes Al.

First-principles calculations of electronic transport through graphene with realistic metallic leads

NASA Astrophysics Data System (ADS)

Barraza-Lopez, Salvador; Chou, M. Y.

2009-03-01

We present transmission characteristics for electrons through graphene with realistic metallic contacts. The methodology relies on an in-house version of the electronic transport SMEAGOL code [1], in which the memory required to allocate for the matrices of contact leads and the graphene sheet in the Green's function solver is distributed into more than one processor, for a given electron energy. We are able to accommodate for commensurate graphene-metal supercells which have the correct atomic structure (namely, stress caused by contracting/extending the metal contacts to match the periodicity of graphene is avoided). In addition, and despite of the large size of the leads, the electronic properties and transport are computed at the density-functional theory level [2] within a double-zeta plus polarization basis[3], ensuring the accuracy of the atomic forces in the system, as well as on the final transmission characteristics. [1] A. R. Rocha et al, PRB. 73, 085414 (2006); [2] J. M. Soler et al, J. Phys.: Condens. Matter 14, 2745-2779 (2002); [3] J. Junquera et al, PRB 64, 235111 (2001).

Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

PubMed Central

Sekhar, Ashok; Rumfeldt, Jessica AO; Broom, Helen R; Doyle, Colleen M; Bouvignies, Guillaume; Meiering, Elizabeth M; Kay, Lewis E

2015-01-01

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD12SH). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD12SH has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization. DOI: http://dx.doi.org/10.7554/eLife.07296.001 PMID:26099300

CH5M3D: an HTML5 program for creating 3D molecular structures.

PubMed

Earley, Clarke W

2013-11-18

While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/.

CH5M3D: an HTML5 program for creating 3D molecular structures

PubMed Central

2013-01-01

Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

ELSEPA—Dirac partial-wave calculation of elastic scattering of electrons and positrons by atoms, positive ions and molecules

NASA Astrophysics Data System (ADS)

Salvat, Francesc; Jablonski, Aleksander; Powell, Cedric J.

2005-01-01

The FORTRAN 77 code system ELSEPA for the calculation of elastic scattering of electrons and positrons by atoms, positive ions and molecules is presented. These codes perform relativistic (Dirac) partial-wave calculations for scattering by a local central interaction potential V(r). For atoms and ions, the static-field approximation is adopted, with the potential set equal to the electrostatic interaction energy between the projectile and the target, plus an approximate local exchange interaction when the projectile is an electron. For projectiles with kinetic energies up to 10 keV, the potential may optionally include a semiempirical correlation-polarization potential to describe the effect of the target charge polarizability. Also, for projectiles with energies less than 1 MeV, an imaginary absorptive potential can be introduced to account for the depletion of the projectile wave function caused by open inelastic channels. Molecular cross sections are calculated by means of a single-scattering independent-atom approximation in which the electron density of a bound atom is approximated by that of the free neutral atom. Elastic scattering by individual atoms in solids is described by means of a muffin-tin model potential. Partial-wave calculations are feasible on modest personal computers for energies up to about 5 MeV. The ELSEPA code also implements approximate factorization methods that allow the fast calculation of elastic cross sections for much higher energies. The interaction model adopted in the calculations is defined by the user by combining the different options offered by the code. The nuclear charge distribution can be selected among four analytical models (point nucleus, uniformly charged sphere, Fermi's distribution and Helm's uniform-uniform distribution). The atomic electron density is handled in numerical form. The distribution package includes data files with electronic densities of neutral atoms of the elements hydrogen to lawrencium ( Z=1-103) obtained from multiconfiguration Dirac-Fock self-consistent calculations. For comparison purposes, three simple analytical approximations to the electron density of neutral atoms (corresponding to the Thomas-Fermi, the Thomas-Fermi-Dirac and the Dirac-Hartree-Fock-Slater models) are also included. For calculations of elastic scattering by ions, the electron density should be provided by the user. The exchange potential for electron scattering can be selected among three different analytical approximations (Thomas-Fermi, Furness-McCarthy, Riley-Truhlar). The offered options for the correlation-polarization potential are based on the empirical Buckingham potential. The imaginary absorption potential is calculated from the local-density approximation proposed by Salvat [Phys. Rev. A 68 (2003) 012708]. Program summaryTitle of program:ELSEPA Catalogue identifier: ADUS Program summary URL:http://cpc.cs.qub.ac.uk/cpc/summaries/ADUS Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland License provisions: none Computer for which the program is designed and others in which it is operable: Any computer with a FORTRAN 77 compiler Operating systems under which the program has been tested: Windows XP, Windows 2000, Debian GNU/Linux 3.0r0 (sarge) Compilers:Compaq Visual Fortran v6.5 (Windows); GNU FORTRAN, g77 (Windows and Linux) Programming language used: FORTRAN 77 No. of bits in a word: 32 Memory required to execute with typical data: 0.6 Mb No. of lines in distributed program, including test data, etc.:135 489 No. of bytes in distributed program, including test data, etc.: 1 280 006 Distribution format: tar.gz Keywords: Dirac partial-wave analysis, electron elastic scattering, positron elastic scattering, differential cross sections, momentum transfer cross sections, transport cross sections, scattering amplitudes, spin polarization, scattering by complex potentials, high-energy atomic screening functions Nature of the physical problem: The code calculates differential cross sections, total cross sections and transport cross sections for single elastic scattering of electrons and positrons by neutral atoms, positive ions and randomly oriented molecules. For projectiles with kinetic energies less than about 5 MeV, the programs can also compute scattering amplitudes and spin polarization functions. Method of solution: The effective interaction between the projectile and a target atom is represented by a local central potential that can optionally include an imaginary (absorptive) part to account approximately for the coupling with inelastic channels. For projectiles with kinetic energy less that about 5 MeV, the code performs a conventional relativistic Dirac partial-wave analysis. For higher kinetic energies, where the convergence of the partial-wave series is too slow, approximate factorization methods are used. Restrictions on the complexity of the program: The calculations are based on the static-field approximation. The optional correlation-polarization and inelastic absorption corrections are obtained from approximate, semiempirical models. Calculations for molecules are based on a single-scattering independent-atom approximation. To ensure accuracy of the results for scattering by ions, the electron density of the ion must be supplied by the user. Typical running time: on a 2.8 GHz Pentium 4, the calculation of elastic scattering by atoms and ions takes between a few seconds and about two minutes, depending on the atomic number of the target, the adopted potential model and the kinetic energy of the projectile. Unusual features of the program: The program calculates elastic cross sections for electrons and positrons with kinetic energies in a wide range, from a few tens of eV up to about 1 GeV. Calculations can be performed for neutral atoms of all elements, from hydrogen to lawrencium ( Z=1-103), ions and simple molecules. Commercial products are identified to specify the calculational procedures. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, the University of Barcelona or the Polish Academy of Sciences, nor does it imply that the products are necessarily the best available for the purpose.

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

PubMed Central

Alerstam, Erik; Lo, William Chun Yip; Han, Tianyi David; Rose, Jonathan; Andersson-Engels, Stefan; Lilge, Lothar

2010-01-01

A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml). PMID:21258498

Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Medley, S. S.; Liu, D.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

2016-02-01

A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a ‘beam-in-a-box’ model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.

Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

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

Medley, S. S.; Liu, D.; Gorelenkova, M. V.

2016-01-12

A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a 'beam-in-a-box' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components producemore » first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.« less

Structures of 38-atom gold-platinum nanoalloy clusters

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

Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atomsmore » are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.« less

Statistical study of defects caused by primary knock-on atoms in fcc Cu and bcc W using molecular dynamics

NASA Astrophysics Data System (ADS)

Warrier, M.; Bhardwaj, U.; Hemani, H.; Schneider, R.; Mutzke, A.; Valsakumar, M. C.

2015-12-01

We report on molecular Dynamics (MD) simulations carried out in fcc Cu and bcc W using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code to study (i) the statistical variations in the number of interstitials and vacancies produced by energetic primary knock-on atoms (PKA) (0.1-5 keV) directed in random directions and (ii) the in-cascade cluster size distributions. It is seen that around 60-80 random directions have to be explored for the average number of displaced atoms to become steady in the case of fcc Cu, whereas for bcc W around 50-60 random directions need to be explored. The number of Frenkel pairs produced in the MD simulations are compared with that from the Binary Collision Approximation Monte Carlo (BCA-MC) code SDTRIM-SP and the results from the NRT model. It is seen that a proper choice of the damage energy, i.e. the energy required to create a stable interstitial, is essential for the BCA-MC results to match the MD results. On the computational front it is seen that in-situ processing saves the need to input/output (I/O) atomic position data of several tera-bytes when exploring a large number of random directions and there is no difference in run-time because the extra run-time in processing data is offset by the time saved in I/O.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

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

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

Sparse Representation with Spatio-Temporal Online Dictionary Learning for Efficient Video Coding.

PubMed

Dai, Wenrui; Shen, Yangmei; Tang, Xin; Zou, Junni; Xiong, Hongkai; Chen, Chang Wen

2016-07-27

Classical dictionary learning methods for video coding suer from high computational complexity and interfered coding eciency by disregarding its underlying distribution. This paper proposes a spatio-temporal online dictionary learning (STOL) algorithm to speed up the convergence rate of dictionary learning with a guarantee of approximation error. The proposed algorithm incorporates stochastic gradient descents to form a dictionary of pairs of 3-D low-frequency and highfrequency spatio-temporal volumes. In each iteration of the learning process, it randomly selects one sample volume and updates the atoms of dictionary by minimizing the expected cost, rather than optimizes empirical cost over the complete training data like batch learning methods, e.g. K-SVD. Since the selected volumes are supposed to be i.i.d. samples from the underlying distribution, decomposition coecients attained from the trained dictionary are desirable for sparse representation. Theoretically, it is proved that the proposed STOL could achieve better approximation for sparse representation than K-SVD and maintain both structured sparsity and hierarchical sparsity. It is shown to outperform batch gradient descent methods (K-SVD) in the sense of convergence speed and computational complexity, and its upper bound for prediction error is asymptotically equal to the training error. With lower computational complexity, extensive experiments validate that the STOL based coding scheme achieves performance improvements than H.264/AVC or HEVC as well as existing super-resolution based methods in ratedistortion performance and visual quality.

Structures of small Pd Pt bimetallic clusters by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Cheng, Daojian; Huang, Shiping; Wang, Wenchuan

2006-11-01

Segregation phenomena of Pd-Pt bimetallic clusters with icosahedral and decahedral structures are investigated by using Monte Carlo method based on the second-moment approximation of the tight-binding (TB-SMA) potentials. The simulation results indicate that the Pd atoms generally lie on the surface of the smaller clusters. The three-shell onion-like structures are observed in 55-atom Pd-Pt bimetallic clusters, in which a single Pd atom is located in the center, and the Pt atoms are in the middle shell, while the Pd atoms are enriched on the surface. With the increase of Pd mole fraction in 55-atom Pd-Pt bimetallic clusters, the Pd atoms occupy the vertices of clusters first, then edge and center sites, and finally the interior shell. It is noticed that some decahedral structures can be transformed into the icosahedron-like structure at 300 and 500 K. Comparisons are made with previous experiments and theoretical studies of Pd-Pt bimetallic clusters.

CFD Simulation of Liquid Rocket Engine Injectors

NASA Technical Reports Server (NTRS)

Farmer, Richard; Cheng, Gary; Chen, Yen-Sen; Garcia, Roberto (Technical Monitor)

2001-01-01

Detailed design issues associated with liquid rocket engine injectors and combustion chamber operation require CFD methodology which simulates highly three-dimensional, turbulent, vaporizing, and combusting flows. The primary utility of such simulations involves predicting multi-dimensional effects caused by specific injector configurations. SECA, Inc. and Engineering Sciences, Inc. have been developing appropriate computational methodology for NASA/MSFC for the past decade. CFD tools and computers have improved dramatically during this time period; however, the physical submodels used in these analyses must still remain relatively simple in order to produce useful results. Simulations of clustered coaxial and impinger injector elements for hydrogen and hydrocarbon fuels, which account for real fluid properties, is the immediate goal of this research. The spray combustion codes are based on the FDNS CFD code' and are structured to represent homogeneous and heterogeneous spray combustion. The homogeneous spray model treats the flow as a continuum of multi-phase, multicomponent fluids which move without thermal or velocity lags between the phases. Two heterogeneous models were developed: (1) a volume-of-fluid (VOF) model which represents the liquid core of coaxial or impinger jets and their atomization and vaporization, and (2) a Blob model which represents the injected streams as a cloud of droplets the size of the injector orifice which subsequently exhibit particle interaction, vaporization, and combustion. All of these spray models are computationally intensive, but this is unavoidable to accurately account for the complex physics and combustion which is to be predicted, Work is currently in progress to parallelize these codes to improve their computational efficiency. These spray combustion codes were used to simulate the three test cases which are the subject of the 2nd International Workshop on-Rocket Combustion Modeling. Such test cases are considered by these investigators to be very valuable for code validation because combustion kinetics, turbulence models and atomization models based on low pressure experiments of hydrogen air combustion do not adequately verify analytical or CFD submodels which are necessary to simulate rocket engine combustion. We wish to emphasize that the simulations which we prepared for this meeting are meant to test the accuracy of the approximations used in our general purpose spray combustion models, rather than represent a definitive analysis of each of the experiments which were conducted. Our goal is to accurately predict local temperatures and mixture ratios in rocket engines; hence predicting individual experiments is used only for code validation. To replace the conventional JANNAF standard axisymmetric finite-rate (TDK) computer code 2 for performance prediction with CFD cases, such codes must posses two features. Firstly, they must be as easy to use and of comparable run times for conventional performance predictions. Secondly, they must provide more detailed predictions of the flowfields near the injector face. Specifically, they must accurately predict the convective mixing of injected liquid propellants in terms of the injector element configurations.

Solid-solution thermodynamics in Al-Li alloys

NASA Astrophysics Data System (ADS)

Alekseev, A. A.; Lukina, E. A.

2016-05-01

The relative equilibrium concentrations of lithium atoms distributed over different electron-structural states has been estimated. The possibility of the existence of various nonequilibrium electron-structural states of Li atoms in the solid solution in Al has been substantiated thermodynamically. Upon the decomposition of the supersaturated solid solution, the supersaturation on three electron-structural states of Li atoms that arises upon the quenching of the alloy can lead to the formation of lithium-containing phases in which the lithium atoms enter in one electron-structural state.

The Challenges of Plasma Modeling: Current Status and Future Plans

NASA Astrophysics Data System (ADS)

Foster, A. R.; Smith, R. K.; Brickhouse, N. S.; Kallman, T. R.; Witthoeft, M. C.

2010-12-01

Successfully modeling X-ray emission from astrophysical plasmas requires a wide range of atomic data to be rapidly accessible by modeling codes, enabling calculation of synthetic spectra for fitting with observations. Over many years the astrophysical databases have roughly kept pace with the advances in detector and spectrometer technology. We outline here the basic atomic processes contributing to the emission from different types of plasmas and briefly touch on the difference between the methods used to calculate this data. We then discuss in more detail the different issues addressed by atomic databases in regards to what data to store and how to make it accessible. Finally, the question of the effect of uncertainties in atomic data is explored, as a reminder to observers that atomic data is not known to infinite precision, and should not be treated as such.

Correlations between dynamics and atomic structures in Cu64.5Zr35.5 metallic glass

NASA Astrophysics Data System (ADS)

Wang, C. Z.; Zhang, Y.; Zhang, F.; Mendelev, M. I.; Kramer, M. J.; Ho, K. M.

2015-03-01

The atomic structure of Cu-Zr metallic glasses (MGs) has been widely accepted to be heterogeneous and dominated by icosahedral short range order (ISRO). However, the correlations between dynamics and atomic structures in Cu-Zr MGs remain an enigma. Using molecular dynamics (MD) simulations, we investigated the correlations between dynamics and atomic structures in Cu64.5Zr35.5 MG. The atomic structures are characterized using ISRO and the Bergman-type medium range order (BMRO). The simulation and analysis results show that the majority of the mobile atoms are not involved in ISRO or BMRO, indicating that the dynamical heterogeneity has a strong correlation to structural heterogeneity. Moreover, we found that the localized soft vibration modes below 1.0 THz are mostly concentrated on the mobile atoms. The diffusion was studied using the atomic trajectory collected in an extended time interval of 1.2 μs at 700 K in MD simulations. It was found that the long range diffusion in MGs is highly heterogeneous, which is confined to the liquid-like regions and strongly avoids the ISRO and the Bergman-type MRO. All These results clearly demonstrate strong correlations between dynamics (in terms of dynamical heterogeneity and diffusion) and atomic structures in Cu64.5Zr35.5 MGs. This work was supported by the U.S. Department of Energy, Basic Energy Sciences, Division of Materials Science and Engineering under the Contract No. DE-AC02-07CH11358.

Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.

PubMed

Ferreira, Diogo C; van der Linden, Marx G; de Oliveira, Leandro C; Onuchic, José N; de Araújo, Antônio F Pereira

2016-04-01

Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations. © 2016 Wiley Periodicals, Inc.

Functional Identification and Structure Determination of Two Novel Prolidases from cog1228 in the Amidohydrolase Superfamily

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

Xiang, Dao Feng; Patskovsky, Yury; Xu, Chengfu

2010-12-07

Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed, and purified to homogeneity. The two proteins, Sgx9260c (gi|44242006) and Sgx9260b (gi|44479596), were derived from environmental DNA samples originating from the Sargasso Sea. The catalytic function and substrate profiles for Sgx9260c and Sgx9260b were determined using a comprehensive library of dipeptides and N-acyl derivative of L-amino acids. Sgx9260c catalyzes the hydrolysis of Gly-L-Pro, L-Ala-L-Pro, and N-acyl derivatives of L-Pro. The best substrate identified to date is N-acetyl-L-Pro with a value of k{sub cat}/K{sub m} of 3 x 10{sup 5} M{sup -1} s{sup -1}. Sgx9260b catalyzes the hydrolysismore » of L-hydrophobic L-Pro dipeptides and N-acyl derivatives of L-Pro. The best substrate identified to date is N-propionyl-L-Pro with a value of k{sub cat}/K{sub m} of 1 x 10{sup 5} M{sup -1} s{sup -1}. Three-dimensional structures of both proteins were determined by X-ray diffraction methods (PDB codes 3MKV and 3FEQ). These proteins fold as distorted ({beta}/{alpha})8-barrels with two divalent cations in the active site. The structure of Sgx9260c was also determined as a complex with the N-methylphosphonate derivative of L-Pro (PDB code 3N2C). In this structure the phosphonate moiety bridges the binuclear metal center, and one oxygen atom interacts with His-140. The {alpha}-carboxylate of the inhibitor interacts with Tyr-231. The proline side chain occupies a small substrate binding cavity formed by residues contributed from the loop that follows {beta}-strand 7 within the ({beta}/{alpha})8-barrel. A total of 38 other proteins from cog1228 are predicted to have the same substrate profile based on conservation of the substrate binding residues. The structure of an evolutionarily related protein, Cc2672 from Caulobacter crecentus, was determined as a complex with the N-methylphosphonate derivative of L-arginine (PDB code 3MTW).« less

Classical And Quantum Rainbow Scattering From Surfaces

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

Winter, H.; Schueller, A.; Busch, M.

2011-06-01

The structure of clean and adsorbate covered surfaces as well as of ultrathin films can be investigated by grazing scattering of fast atoms. We present two recent experimental techniques which allow one to study the structure of ordered arrangements of surface atoms in detail. (1) Rainbow scattering under axial surface channeling conditions, and (2) fast atom diffraction. Our examples demonstrate the attractive features of grazing fast atom scattering as a powerful analytical tool in studies on the structure of surfaces. We will concentrate our discussion on the structure of ultrathin silica films on a Mo(112) surface and of adsorbed oxygenmore » atoms on a Fe(110) surface.« less

Nursing Classification Systems

PubMed Central

Henry, Suzanne Bakken; Mead, Charles N.

1997-01-01

Abstract Our premise is that from the perspective of maximum flexibility of data usage by computer-based record (CPR) systems, existing nursing classification systems are necessary, but not sufficient, for representing important aspects of “what nurses do.” In particular, we have focused our attention on those classification systems that represent nurses' clinical activities through the abstraction of activities into categories of nursing interventions. In this theoretical paper, we argue that taxonomic, combinatorial vocabularies capable of coding atomic-level nursing activities are required to effectively capture in a reproducible and reversible manner the clinical decisions and actions of nurses, and that, without such vocabularies and associated grammars, potentially important clinical process data is lost during the encoding process. Existing nursing intervention classification systems do not fulfill these criteria. As background to our argument, we first present an overview of the content, methods, and evaluation criteria used in previous studies whose focus has been to evaluate the effectiveness of existing coding and classification systems. Next, using the Ingenerf typology of taxonomic vocabularies, we categorize the formal type and structure of three existing nursing intervention classification systems—Nursing Interventions Classification, Omaha System, and Home Health Care Classification. Third, we use records from home care patients to show examples of lossy data transformation, the loss of potentially significant atomic data, resulting from encoding using each of the three systems. Last, we provide an example of the application of a formal representation methodology (conceptual graphs) which we believe could be used as a model to build the required combinatorial, taxonomic vocabulary for representing nursing interventions. PMID:9147341

Dielectronic and Trielectronic Recombination Rate Coefficients of Be-like Ar14+

NASA Astrophysics Data System (ADS)

Huang, Z. K.; Wen, W. Q.; Xu, X.; Mahmood, S.; Wang, S. X.; Wang, H. B.; Dou, L. J.; Khan, N.; Badnell, N. R.; Preval, S. P.; Schippers, S.; Xu, T. H.; Yang, Y.; Yao, K.; Xu, W. Q.; Chuai, X. Y.; Zhu, X. L.; Zhao, D. M.; Mao, L. J.; Ma, X. M.; Li, J.; Mao, R. S.; Yuan, Y. J.; Wu, B.; Sheng, L. N.; Yang, J. C.; Xu, H. S.; Zhu, L. F.; Ma, X.

2018-03-01

Electron–ion recombination of Be-like 40Ar14+ has been measured by employing the electron–ion merged-beams method at the cooler storage ring CSRm. The measured absolute recombination rate coefficients for collision energies from 0 to 60 eV are presented, covering all dielectronic recombination (DR) resonances associated with 2s 2 → 2s2p core transitions. In addition, strong trielectronic recombination (TR) resonances associated with 2s 2 → 2p 2 core transitions were observed. Both DR and TR processes lead to series of peaks in the measured recombination spectrum, which have been identified by the Rydberg formula. Theoretical calculations of recombination rate coefficients were performed using the state-of-the-art multi-configuration Breit–Pauli atomic structure code AUTOSTRUCTURE to compare with the experimental results. The plasma rate coefficients for DR+TR of Ar14+ were deduced from the measured electron–ion recombination rate coefficients in the temperature range from 103 to 107 K, and compared with calculated data from the literature. The experimentally derived plasma rate coefficients are 60% larger and 30% lower than the previously recommended atomic data for the temperature ranges of photoionized plasmas and collisionally ionized plasmas, respectively. However, good agreement was found between experimental results and the calculations by Gu and Colgan et al. The plasma rate coefficients deduced from experiment and calculated by the current AUTOSTRUCTURE code show agreement that is better than 30% from 104 to 107 K. The present results constitute a set of benchmark data for use in astrophysical modeling.

Thermal-hydraulic interfacing code modules for CANDU reactors

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

Liu, W.S.; Gold, M.; Sills, H.

1997-07-01

The approach for CANDU reactor safety analysis in Ontario Hydro Nuclear (OHN) and Atomic Energy of Canada Limited (AECL) is presented. Reflecting the unique characteristics of CANDU reactors, the procedure of coupling the thermal-hydraulics, reactor physics and fuel channel/element codes in the safety analysis is described. The experience generated in the Canadian nuclear industry may be useful to other types of reactors in the areas of reactor safety analysis.

NASA Radiation Protection Research for Exploration Missions

NASA Technical Reports Server (NTRS)

Wilson, John W.; Cucinotta, Francis A.; Tripathi, Ram K.; Heinbockel, John H.; Tweed, John; Mertens, Christopher J.; Walker, Steve A.; Blattnig, Steven R.; Zeitlin, Cary J.

2006-01-01

The HZETRN code was used in recent trade studies for renewed lunar exploration and currently used in engineering development of the next generation of space vehicles, habitats, and EVA equipment. A new version of the HZETRN code capable of simulating high charge and energy (HZE) ions, light-ions and neutrons with either laboratory or space boundary conditions with enhanced neutron and light-ion propagation is under development. Atomic and nuclear model requirements to support that development will be discussed. Such engineering design codes require establishing validation processes using laboratory ion beams and space flight measurements in realistic geometries. We discuss limitations of code validation due to the currently available data and recommend priorities for new data sets.

A Variational Monte Carlo Approach to Atomic Structure

ERIC Educational Resources Information Center

Davis, Stephen L.

2007-01-01

The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.

Adhesion and Atomic Structures of Gold on Ceria Nanostructures:The Role of Surface Structure and Oxidation State of Ceria Supports

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

Lin, Yuyuan; Wu, Zili; Wen, Jianguo

2015-01-01

Recent advances in heterogeneous catalysis have demonstrated that oxides supports with the same material but different shapes can result in metal catalysts with distinct catalytic properties. The shape-dependent catalysis was not well-understood owing to the lack of direct visualization of the atomic structures at metal-oxide interface. Herein, we utilized aberration-corrected electron microscopy and revealed the atomic structures of gold particles deposited on ceria nanocubes and nanorods with {100} or {111} facets exposed. For the ceria nanocube support, gold nanoparticles have extended atom layers at the metal-support interface. In contrast, regular gold nanoparticles and rafts are present on the ceria nanorodmore » support. After hours of water gas shift reaction, the extended gold atom layers and rafts vanish, which is associated with the decrease of the catalytic activities. By understanding the atomic structures of the support surfaces, metal-support interfaces, and morphologies of the gold particles, a direct structure-property relationship is established.« less

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

Development of a New System for Transport Simulation and Analysis at General Atomics

NASA Astrophysics Data System (ADS)

St. John, H. E.; Peng, Q.; Freeman, J.; Crotinger, J.

1997-11-01

General Atomics has begun a long term program to improve all aspects of experimental data analysis related to DIII--D. The object is to make local and visiting physicists as productive as possible, with only a small investment in training, by developing intuitive, sophisticated interfaces to existing and newly created computer programs. Here we describe our initial work and results of a pilot project in this program. The pilot project is a collaboratory effort between LLNL and GA which will ultimately result in the merger of Corsica and ONETWO (and selected modules from other codes) into a new advanced transport code system. The initial goal is to produce a graphical user interface to the transport code ONETWO which will couple to a programmable (steerable) front end designed for the transport system. This will be an object oriented scheme written primarily in python. The programmable application will integrate existing C, C^++, and Fortran methods in a single computational paradigm. Its most important feature is the use of plug in physics modules which will allow a high degree of customization.

SOLAR OPACITY CALCULATIONS USING THE SUPER-TRANSITION-ARRAY METHOD

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

Krief, M.; Feigel, A.; Gazit, D., E-mail: menahem.krief@mail.huji.ac.il

A new opacity model has been developed based on the Super-Transition-Array (STA) method for the calculation of monochromatic opacities of plasmas in local thermodynamic equilibrium. The atomic code, named STAR (STA-Revised), is described and used to calculate spectral opacities for a solar model implementing the recent AGSS09 composition. Calculations are carried out throughout the solar radiative zone. The relative contributions of different chemical elements and atomic processes to the total Rosseland mean opacity are analyzed in detail. Monochromatic opacities and charge-state distributions are compared with the widely used Opacity Project (OP) code, for several elements near the radiation–convection interface. STARmore » Rosseland opacities for the solar mixture show a very good agreement with OP and the OPAL opacity code throughout the radiation zone. Finally, an explicit STA calculation was performed of the full AGSS09 photospheric mixture, including all heavy metals. It was shown that, due to their extremely low abundance, and despite being very good photon absorbers, the heavy elements do not affect the Rosseland opacity.« less

molgw 1: Many-body perturbation theory software for atoms, molecules, and clusters

DOE PAGES

Bruneval, Fabien; Rangel, Tonatiuh; Hamed, Samia M.; ...

2016-07-12

Here, we summarize the MOLGW code that implements density-functional theory and many-body perturbation theory in a Gaussian basis set. The code is dedicated to the calculation of the many-body self-energy within the GW approximation and the solution of the Bethe–Salpeter equation. These two types of calculations allow the user to evaluate physical quantities that can be compared to spectroscopic experiments. Quasiparticle energies, obtained through the calculation of the GW self-energy, can be compared to photoemission or transport experiments, and neutral excitation energies and oscillator strengths, obtained via solution of the Bethe–Salpeter equation, are measurable by optical absorption. The implementation choicesmore » outlined here have aimed at the accuracy and robustness of calculated quantities with respect to measurements. Furthermore, the algorithms implemented in MOLGW allow users to consider molecules or clusters containing up to 100 atoms with rather accurate basis sets, and to choose whether or not to apply the resolution-of-the-identity approximation. Finally, we demonstrate the parallelization efficacy of the MOLGW code over several hundreds of processors.« less

Significance of structural changes in proteins: expected errors in refined protein structures.

PubMed Central

Stroud, R. M.; Fauman, E. B.

1995-01-01

A quantitative expression key to evaluating significant structural differences or induced shifts between any two protein structures is derived. Because crystallography leads to reports of a single (or sometimes dual) position for each atom, the significance of any structural change based on comparison of two structures depends critically on knowing the expected precision of each median atomic position reported, and on extracting it for each atom, from the information provided in the Protein Data Bank and in the publication. The differences between structures of protein molecules that should be identical, and that are normally distributed, indicating that they are not affected by crystal contacts, were analyzed with respect to many potential indicators of structure precision, so as to extract, essentially by "machine learning" principles, a generally applicable expression involving the highest correlates. Eighteen refined crystal structures from the Protein Data Bank, in which there are multiple molecules in the crystallographic asymmetric unit, were selected and compared. The thermal B factor, the connectivity of the atom, and the ratio of the number of reflections to the number of atoms used in refinement correlate best with the magnitude of the positional differences between regions of the structures that otherwise would be expected to be the same. These results are embodied in a six-parameter equation that can be applied to any crystallographically refined structure to estimate the expected uncertainty in position of each atom. Structure change in a macromolecule can thus be referenced to the expected uncertainty in atomic position as reflected in the variance between otherwise identical structures with the observed values of correlated parameters. PMID:8563637

Monte Carlo modelling the dosimetric effects of electrode material on diamond detectors.

PubMed

Baluti, Florentina; Deloar, Hossain M; Lansley, Stuart P; Meyer, Juergen

2015-03-01

Diamond detectors for radiation dosimetry were modelled using the EGSnrc Monte Carlo code to investigate the influence of electrode material and detector orientation on the absorbed dose. The small dimensions of the electrode/diamond/electrode detector structure required very thin voxels and the use of non-standard DOSXYZnrc Monte Carlo model parameters. The interface phenomena was investigated by simulating a 6 MV beam and detectors with different electrode materials, namely Al, Ag, Cu and Au, with thickens of 0.1 µm for the electrodes and 0.1 mm for the diamond, in both perpendicular and parallel detector orientation with regards to the incident beam. The smallest perturbations were observed for the parallel detector orientation and Al electrodes (Z = 13). In summary, EGSnrc Monte Carlo code is well suited for modelling small detector geometries. The Monte Carlo model developed is a useful tool to investigate the dosimetric effects caused by different electrode materials. To minimise perturbations cause by the detector electrodes, it is recommended that the electrodes should be made from a low-atomic number material and placed parallel to the beam direction.

An atomistic model for cross-linked HNBR elastomers used in seals

NASA Astrophysics Data System (ADS)

Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

2015-03-01

Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

Thermally induced distortion of a high-average-power laser system by an optical transport system

NASA Astrophysics Data System (ADS)

Chow, Robert; Ault, Linda E.; Taylor, John R.; Jedlovec, Don

1999-11-01

The atomic vapor laser isotope separation process uses high- average power lasers that have the commercial potential to enrich uranium for the electric power utilities. The transport of the laser beam through the laser system to the separation chambers requires high performance optical components, most of which have either fused silica or Zerodur as the substrate material. One of the requirements of the optical components is to preserve the wavefront quality of the laser beam that propagate over long distances. Full aperture tests with the high power process lasers and finite element analysis (FEA) have been performed on the transport optics. The wavefront distortions of the various sections of the transport path were measured with diagnostic Hartmann sensor packages. The FEA results were derived from an in-house thermal-structural- optical code which is linked to the commercially available CodeV program. In comparing the measured and predicted results, the bulk absorptance of fused silica was estimated to about 50 ppm/cm in the visible wavelength regime. Wavefront distortions will be reported on optics made from fused silica and Zerodur substrate materials.

LSPRAY-IV: A Lagrangian Spray Module

NASA Technical Reports Server (NTRS)

Raju, M. S.

2012-01-01

LSPRAY-IV is a Lagrangian spray solver developed for application with parallel computing and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and/or Monte Carlo Probability Density Function (PDF) solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type for the gas flow grid representation. It is mainly designed to predict the flow, thermal and transport properties of a rapidly vaporizing spray. Some important research areas covered as a part of the code development are: (1) the extension of combined CFD/scalar-Monte- Carlo-PDF method to spray modeling, (2) the multi-component liquid spray modeling, and (3) the assessment of various atomization models used in spray calculations. The current version contains the extension to the modeling of superheated sprays. The manual provides the user with an understanding of various models involved in the spray formulation, its code structure and solution algorithm, and various other issues related to parallelization and its coupling with other solvers.

Generation of bright attosecond x-ray pulse trains via Thomson scattering from laser-plasma accelerators.

PubMed

Luo, W; Yu, T P; Chen, M; Song, Y M; Zhu, Z C; Ma, Y Y; Zhuo, H B

2014-12-29

Generation of attosecond x-ray pulse attracts more and more attention within the advanced light source user community due to its potentially wide applications. Here we propose an all-optical scheme to generate bright, attosecond hard x-ray pulse trains by Thomson backscattering of similarly structured electron beams produced in a vacuum channel by a tightly focused laser pulse. Design parameters for a proof-of-concept experiment are presented and demonstrated by using a particle-in-cell code and a four-dimensional laser-Compton scattering simulation code to model both the laser-based electron acceleration and Thomson scattering processes. Trains of 200 attosecond duration hard x-ray pulses holding stable longitudinal spacing with photon energies approaching 50 keV and maximum achievable peak brightness up to 10²⁰ photons/s/mm²/mrad²/0.1%BW for each micro-bunch are observed. The suggested physical scheme for attosecond x-ray pulse trains generation may directly access the fastest time scales relevant to electron dynamics in atoms, molecules and materials.

Investigation of the impact of high liquid viscosity on jet atomization in crossflow via high-fidelity simulations

NASA Astrophysics Data System (ADS)

Li, Xiaoyi; Gao, Hui; Soteriou, Marios C.

2017-08-01

Atomization of extremely high viscosity liquid can be of interest for many applications in aerospace, automotive, pharmaceutical, and food industries. While detailed atomization measurements usually face grand challenges, high-fidelity numerical simulations offer the advantage to comprehensively explore the atomization details. In this work, a previously validated high-fidelity first-principle simulation code HiMIST is utilized to simulate high-viscosity liquid jet atomization in crossflow. The code is used to perform a parametric study of the atomization process in a wide range of Ohnesorge numbers (Oh = 0.004-2) and Weber numbers (We = 10-160). Direct comparisons between the present study and previously published low-viscosity jet in crossflow results are performed. The effects of viscous damping and slowing on jet penetration, liquid surface instabilities, ligament formation/breakup, and subsequent droplet formation are investigated. Complex variations in near-field and far-field jet penetrations with increasing Oh at different We are observed and linked with the underlying jet deformation and breakup physics. Transition in breakup regimes and increase in droplet size with increasing Oh are observed, mostly consistent with the literature reports. The detailed simulations elucidate a distinctive edge-ligament-breakup dominated process with long surviving ligaments for the higher Oh cases, as opposed to a two-stage edge-stripping/column-fracture process for the lower Oh counterparts. The trend of decreasing column deflection with increasing We is reversed as Oh increases. A predominantly unimodal droplet size distribution is predicted at higher Oh, in contrast to the bimodal distribution at lower Oh. It has been found that both Rayleigh-Taylor and Kelvin-Helmholtz linear stability theories cannot be easily applied to interpret the distinct edge breakup process and further study of the underlying physics is needed.

Size and habit evolution of PETN crystals - a lattice Monte Carlo study

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

Zepeda-Ruiz, L A; Maiti, A; Gee, R

2006-02-28

Starting from an accurate inter-atomic potential we develop a simple scheme of generating an ''on-lattice'' molecular potential of short range, which is then incorporated into a lattice Monte Carlo code for simulating size and shape evolution of nanocrystallites. As a specific example, we test such a procedure on the morphological evolution of a molecular crystal of interest to us, e.g., Pentaerythritol Tetranitrate, or PETN, and obtain realistic facetted structures in excellent agreement with experimental morphologies. We investigate several interesting effects including, the evolution of the initial shape of a ''seed'' to an equilibrium configuration, and the variation of growth morphologymore » as a function of the rate of particle addition relative to diffusion.« less

First principles calculation of the structural, electronic, and magnetic properties of Au-Pd atomic chains

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

Dave, Mudra R., E-mail: mdave-phy@yahoo.co.in; Sharma, A. C.

2015-06-24

The structural, electronic and magnetic properties of free standing Au-Pd bimetallic atomic chain is studied using ab-initio method. It is found that electronic and magnetic properties of chains depend on position of atoms and number of atoms. Spin polarization factor for different atomic configuration of atomic chain is calculated predicting a half metallic behavior. It suggests a total spin polarised transport in these chains.

High performance computing in biology: multimillion atom simulations of nanoscale systems

PubMed Central

Sanbonmatsu, K. Y.; Tung, C.-S.

2007-01-01

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

Statistical inference of protein structural alignments using information and compression.

PubMed

Collier, James H; Allison, Lloyd; Lesk, Arthur M; Stuckey, Peter J; Garcia de la Banda, Maria; Konagurthu, Arun S

2017-04-01

Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . arun.konagurthu@monash.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

ERIC Educational Resources Information Center

Cipolla, Laura; Ferrari, Lia A.

2016-01-01

A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

Modeling of radiative properties of Sn plasmas for extreme-ultraviolet source

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

Sasaki, Akira; Sunahara, Atsushi; Furukawa, Hiroyuki

Atomic processes in Sn plasmas are investigated for application to extreme-ultraviolet (EUV) light sources used in microlithography. We develop a full collisional radiative (CR) model of Sn plasmas based on calculated atomic data using Hebrew University Lawrence Livermore Atomic Code (HULLAC). Resonance and satellite lines from singly and multiply excited states of Sn ions, which contribute significantly to the EUV emission, are identified and included in the model through a systematic investigation of their effect on the emission spectra. The wavelengths of the 4d-4f+4p-4d transitions of Sn{sup 5+} to Sn{sup 13+} are investigated, because of their importance for determining themore » conversion efficiency of the EUV source, in conjunction with the effect of configuration interaction in the calculation of atomic structure. Calculated emission spectra are compared with those of charge exchange spectroscopy and of laser produced plasma EUV sources. The comparison is also carried out for the opacity of a radiatively heated Sn sample. A reasonable agreement is obtained between calculated and experimental EUV emission spectra observed under the typical condition of EUV sources with the ion density and ionization temperature of the plasma around 10{sup 18} cm{sup -3} and 20 eV, respectively, by applying a wavelength correction to the resonance and satellite lines. Finally, the spectral emissivity and opacity of Sn plasmas are calculated as a function of electron temperature and ion density. The results are useful for radiation hydrodynamics simulations for the optimization of EUV sources.« less

Molecular Building Block-Based Electronic Charges for High-Throughput Screening of Metal-Organic Frameworks for Adsorption Applications.

PubMed

Argueta, Edwin; Shaji, Jeena; Gopalan, Arun; Liao, Peilin; Snurr, Randall Q; Gómez-Gualdrón, Diego A

2018-01-09

Metal-organic frameworks (MOFs) are porous crystalline materials with attractive properties for gas separation and storage. Their remarkable tunability makes it possible to create millions of MOF variations but creates the need for fast material screening to identify promising structures. Computational high-throughput screening (HTS) is a possible solution, but its usefulness is tied to accurate predictions of MOF adsorption properties. Accurate adsorption simulations often require an accurate description of electrostatic interactions, which depend on the electronic charges of the MOF atoms. HTS-compatible methods to assign charges to MOF atoms need to accurately reproduce electrostatic potentials (ESPs) and be computationally affordable, but current methods present an unsatisfactory trade-off between computational cost and accuracy. We illustrate a method to assign charges to MOF atoms based on ab initio calculations on MOF molecular building blocks. A library of building blocks with built-in charges is thus created and used by an automated MOF construction code to create hundreds of MOFs with charges "inherited" from the constituent building blocks. The molecular building block-based (MBBB) charges are similar to REPEAT charges-which are charges that reproduce ESPs obtained from ab initio calculations on crystallographic unit cells of nanoporous crystals-and thus similar predictions of adsorption loadings, heats of adsorption, and Henry's constants are obtained with either method. The presented results indicate that the MBBB method to assign charges to MOF atoms is suitable for use in computational high-throughput screening of MOFs for applications that involve adsorption of molecules such as carbon dioxide.

Measurement of neutron spectra in the AWE workplace using a Bonner sphere spectrometer.

PubMed

Danyluk, Peter

2010-12-01

A Bonner sphere spectrometer has been used to measure the neutron spectra in eight different workplace areas at AWE (Atomic Weapons Establishment). The spectra were analysed by the National Physical Laboratory using their principal unfolding code STAY'SL and the results were also analysed by AWE using a bespoke parametrised unfolding code. The bespoke code was designed specifically for the AWE workplace and is very simple to use. Both codes gave results, in good agreement. It was found that the measured fluence rate varied from 2 to 70 neutrons cm⁻² s⁻¹ (± 10%) and the ambient dose equivalent H*(10) varied from 0.5 to 57 µSv h⁻¹ (± 20%). A detailed description of the development and use of the bespoke code is presented.

Structural and magnetic properties of FeGen-/0 (n = 3-12) clusters: Mass-selected anion photoelectron spectroscopy and density functional theory calculations

NASA Astrophysics Data System (ADS)

Deng, Xiao-Jiao; Kong, Xiang-Yu; Liang, Xiaoqing; Yang, Bin; Xu, Hong-Guang; Xu, Xi-Ling; Feng, Gang; Zheng, Wei-Jun

2017-12-01

The structural, electronic, and magnetic properties of FeGen-/0 (n = 3-12) clusters were investigated by using anion photoelectron spectroscopy in combination with density functional theory calculations. For both anionic and neutral FeGen (n = 3-12) clusters with n ≤ 7, the dominant structures are exohedral. The FeGe8-/0 clusters have half-encapsulated boat-shaped structures, and the opening of the boat-shaped structure is gradually covered by the additional Ge atoms to form Gen cage from n = 9 to 11. The structures of FeGe10-/0 can be viewed as two Ge atoms symmetrically capping the opening of the boat-shaped structure of FeGe8, and those of FeGe12-/0 are distorted hexagonal prisms with the Fe atom at the center. Natural population analysis shows that there is an electron transfer from the Ge atoms to the Fe atom at n = 8-12. The total magnetic moment of FeGen-/0 and local magnetic moment of the Fe atom have not been quenched.

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Revision of the Li13Si4 structure.

PubMed

Zeilinger, Michael; Fässler, Thomas F

2013-11-06

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li-Si system is the phase Li13Si4 (trideca-lithium tetra-silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10-13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si-Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si-Si dumbbells at z = 0.5.

Finite size effect on hydrogen bond cooperativity in (Ala)n polypeptides: A DFT study using numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Ireta, Joel; Scheffler, Matthias

2007-03-01

An accurate representation of the energetic contribution Ehb of hydrogen bonds to structure formation is paramount to understand the secondary structure stability of proteins, both qualitatively and quantitatively. However, Ehb depends strongly on its environment, and even on the surrounding peptide conformation itself. For instance, a short α-helical polypeptide (Ala)4 can not be stabilized by its single hydrogen bond, whereas an infinite α-helical chain (Ala)∞ is clearly energetically stable over a fully extended conformation. We here use all-electron density functional calculations in the PBE generalized gradient approximation by a recently developed, computationally efficient numeric atom-centered orbital based code^1 to investigate this H-bond cooperativity that is intrinsic to Alanine-based polypeptides (Ala)n (n=1-20,∞). We compare finite and infinite prototypical helical conformations (α, π, 310) on equal footing, with both neutral and ionic termination for finite (Ala)n peptides. Moderately sized NAO basis sets allow to capture Ehb with meV accuracy, revealing a clear jump in Ehb (cooperativity) when two H-bonds first appear in line, followed by slower and more continuous increase of Ehb towards n->∞. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Name that compound: The numbers game for CFCs, HFCs, HCFCs, and Halons

DOE Data Explorer

Blasing, T. J.; Jones, Sonja

2012-02-01

Chlorofluorocarbons (CFCs) contain Carbon and some combination of Fluorine and Chlorine atoms. Hydrofluorocarbons (HFCs) contain Hydrogen, Fluorine, and Carbon (no chlorine). Hydrochlorofluorocarbons (HCFCs) contain Hydrogen, Chlorine, Fluorine, and Carbon atoms. Hydrobromofluorocarbons (HBFCs) contain Hydrogen, Bromine, Fluorine, and Carbon atoms. Perfluorocarbons contain Fluorine, Carbon, and Bromine atoms, and some contain Chlorine and/or Hydrogen atoms. These compounds are often designated by a combination of letters and numbers (e.g., CFC-11, HCFC-142b). In the latter example, the lower-case b refers to an isomer, which has no relationship to the chemical formula (C2H3F2Cl), but designates a particular structural arrangement of the atoms included. For example, HCFC-142b identifies the isomer in which all three hydrogen atoms are attached to the same carbon atom, and the structural formula is written as CH3CF2Cl. By contrast, HCFC-142 (without the b) refers to an arrangement in which one carbon atom is attached to two hydrogen atoms and one chlorine atom, while the other carbon atom is attached to the third hydrogen atom and two fluorine atoms. Hence, it has a different structural formula (CH2ClCHF2).

Simulation of decay processes and radiation transport times in radioactivity measurements

NASA Astrophysics Data System (ADS)

García-Toraño, E.; Peyres, V.; Bé, M.-M.; Dulieu, C.; Lépy, M.-C.; Salvat, F.

2017-04-01

The Fortran subroutine package PENNUC, which simulates random decay pathways of radioactive nuclides, is described. The decay scheme of the active nuclide is obtained from the NUCLEIDE database, whose web application has been complemented with the option of exporting nuclear decay data (possible nuclear transitions, branching ratios, type and energy of emitted particles) in a format that is readable by the simulation subroutines. In the case of beta emitters, the initial energy of the electron or positron is sampled from the theoretical Fermi spectrum. De-excitation of the atomic electron cloud following electron capture and internal conversion is described using transition probabilities from the LLNL Evaluated Atomic Data Library and empirical or calculated energies of released X rays and Auger electrons. The time evolution of radiation showers is determined by considering the lifetimes of nuclear and atomic levels, as well as radiation propagation times. Although PENNUC is designed to operate independently, here it is used in conjunction with the electron-photon transport code PENELOPE, and both together allow the simulation of experiments with radioactive sources in complex material structures consisting of homogeneous bodies limited by quadric surfaces. The reliability of these simulation tools is demonstrated through comparisons of simulated and measured energy spectra from radionuclides with complex multi-gamma spectra, nuclides with metastable levels in their decay pathways, nuclides with two daughters, and beta plus emitters.

Accurate atomic data for xenon: energy levels, oscillator strengths, and electron collision cross sections

NASA Astrophysics Data System (ADS)

Bartschat, Klaus; Zatsarinny, Oleg

2009-10-01

We have applied our recently developed fully relativistic Dirac B-spline R-matrix (DBSR) code [1] to calculate the atomic structure (energy levels and oscillator strengths) as well as electron scattering from xenon atoms. Results from a 31-state close-coupling model for the excitation function of the metastable (5p^5 6s) J=0,2 states show excellent agreement with experiment [2], thereby presenting a significant improvement over the most sophisticated previous Breit-Pauli calculations [3,4]. The same model is currently being used to calculate electron-impact excitation from the metastable J=2 state. The results will be compared with recent experimental data [5] and predictions from other theoretical models [6,7]. Our dataset is an excellent basis for modeling plasma discharges containing xenon.[0pt] [1] O. Zatsarinny and K. Bartschat, Phys. Rev. A 77 (2008) 062701.[0pt] [2] S. J. Buckman et al., J. Phys. B 16 (1983) 4219.[0pt] [3] A. N. Grum-Grzhimailo and K. Bartschat, J. Phys. B 35 (2002) 3479.[0pt] [4] M. Allan et al., Phys. Rev. A 74 (2006) 030701(R).[0pt] [5] R. O. Jung et al., Phys. Rev. A 72 (2005) 022723.[0pt] [6] R. Srivastava et al., Phys. Rev. A 74 (2006) 012715.[0pt] [7] J. Jiang et al., J. Phys. B 41 (2008) 245204.

Unique atom hyper-kagome order in Na4Ir3O8 and in low-symmetry spinel modifications.

PubMed

Talanov, V M; Shirokov, V B; Talanov, M V

2015-05-01

Group-theoretical and thermodynamic methods of the Landau theory of phase transitions are used to investigate the hyper-kagome atomic order in structures of ordered spinels and a spinel-like Na4Ir3O8 crystal. The formation of an atom hyper-kagome sublattice in Na4Ir3O8 is described theoretically on the basis of the archetype (hypothetical parent structure/phase) concept. The archetype structure of Na4Ir3O8 has a spinel-like structure (space group Fd\\bar 3m) and composition [Na1/2Ir3/2](16d)[Na3/2](16c)O(32e)4. The critical order parameter which induces hypothetical phase transition has been stated. It is shown that the derived structure of Na4Ir3O8 is formed as a result of the displacements of Na, Ir and O atoms, and ordering of Na, Ir and O atoms, ordering dxy, dxz, dyz orbitals as well. Ordering of all atoms takes place according to the type 1:3. Ir and Na atoms form an intriguing atom order: a network of corner-shared Ir triangles called a hyper-kagome lattice. The Ir atoms form nanoclusters which are named decagons. The existence of hyper-kagome lattices in six types of ordered spinel structures is predicted theoretically. The structure mechanisms of the formation of the predicted hyper-kagome atom order in some ordered spinel phases are established. For a number of cases typical diagrams of possible crystal phase states are built in the framework of the Landau theory of phase transitions. Thermodynamical conditions of hyper-kagome order formation are discussed by means of these diagrams. The proposed theory is in accordance with experimental data.

Structure and properties of fullerene molecular crystals with linear-scaling van der Waals density functional theory

NASA Astrophysics Data System (ADS)

Mostofi, Arash; Andrinopoulos, Lampros; Hine, Nicholas

2014-03-01

Fullerene molecular crystals are of technological promise for their use in heterojunction photovoltaic cells. An improved theoretical understanding of their structure and properties would be a step towards the rational design of new devices. Simulations based on density-functional theory (DFT) are invaluable for developing such insight, but standard semi-local functionals do not capture the important inter-molecular van der Waals (vdW) interactions in fullerene crystals. Furthermore the computational cost associated with the large unit cells needed are at the limit or beyond the capabilities of traditional DFT methods. In this work we overcome these limitations by using our implementation of a number of vdW-DFs in the ONETEP linear-scaling DFT code to study the structural properties of C60 molecular crystals. Powder neutron diffraction shows that the low-temperature Pa-3 phase is orientationally ordered with individual C60 units rotated around the [111] direction. We fully explore the energy landscape associated with the rotation angle and find two stable structures that are energetically very close, one of which corresponds to the experimentally observed structure. We further consider the effect of orientational disorder in very large supercells of thousands of atoms.

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

PubMed

Jain, Swati; Schlick, Tamar

2017-11-24

Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles.

PubMed

Snyder, David A; Montelione, Gaetano T

2005-06-01

An important open question in the field of NMR-based biomolecular structure determination is how best to characterize the precision of the resulting ensemble of structures. Typically, the RMSD, as minimized in superimposing the ensemble of structures, is the preferred measure of precision. However, the presence of poorly determined atomic coordinates and multiple "RMSD-stable domains"--locally well-defined regions that are not aligned in global superimpositions--complicate RMSD calculations. In this paper, we present a method, based on a novel, structurally defined order parameter, for identifying a set of core atoms to use in determining superimpositions for RMSD calculations. In addition we present a method for deciding whether to partition that core atom set into "RMSD-stable domains" and, if so, how to determine partitioning of the core atom set. We demonstrate our algorithm and its application in calculating statistically sound RMSD values by applying it to a set of NMR-derived structural ensembles, superimposing each RMSD-stable domain (or the entire core atom set, where appropriate) found in each protein structure under consideration. A parameter calculated by our algorithm using a novel, kurtosis-based criterion, the epsilon-value, is a measure of precision of the superimposition that complements the RMSD. In addition, we compare our algorithm with previously described algorithms for determining core atom sets. The methods presented in this paper for biomolecular structure superimposition are quite general, and have application in many areas of structural bioinformatics and structural biology.

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

Extreme ultraviolet emission spectra of Gd and Tb ions

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

Kilbane, D.; O'Sullivan, G.

2010-11-15

Theoretical extreme ultraviolet emission spectra of gadolinium and terbium ions calculated with the Cowan suite of codes and the flexible atomic code (FAC) relativistic code are presented. 4d-4f and 4p-4d transitions give rise to unresolved transition arrays in a range of ions. The effects of configuration interaction are investigated for transitions between singly excited configurations. Optimization of emission at 6.775 nm and 6.515 nm is achieved for Gd and Tb ions, respectively, by consideration of plasma effects. The resulting synthetic spectra are compared with experimental spectra recorded using the laser produced plasma technique.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

NASA Astrophysics Data System (ADS)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Density functional theory calculations establish the experimental evidence of the DX center atomic structure in CdTe.

PubMed

Lany, Stephan; Wolf, Herbert; Wichert, Thomas

2004-06-04

The In DX center and the DX-like configuration of the Cd host atom in CdTe are investigated using density functional theory. The simultaneous calculation of the atomic structure and the electric field gradient (EFG) allows one to correlate the theoretically predicted structure of the DX center with an experimental observable, namely, the EFG obtained from radioactive 111In/111Cd probe atoms in In doped CdTe. In this way, the experimental identification of the DX center structure is established.

Exploring the atomic structure of 1.8nm monolayer-protected gold clusters with aberration-corrected STEM.

PubMed

Liu, Jian; Jian, Nan; Ornelas, Isabel; Pattison, Alexander J; Lahtinen, Tanja; Salorinne, Kirsi; Häkkinen, Hannu; Palmer, Richard E

2017-05-01

Monolayer-protected (MP) Au clusters present attractive quantum systems with a range of potential applications e.g. in catalysis. Knowledge of the atomic structure is needed to obtain a full understanding of their intriguing physical and chemical properties. Here we employed aberration-corrected scanning transmission electron microscopy (ac-STEM), combined with multislice simulations, to make a round-robin investigation of the atomic structure of chemically synthesised clusters with nominal composition Au 144 (SCH 2 CH 2 Ph) 60 provided by two different research groups. The MP Au clusters were "weighed" by the atom counting method, based on their integrated intensities in the high angle annular dark field (HAADF) regime and calibrated exponent of the Z dependence. For atomic structure analysis, we compared experimental images of hundreds of clusters, with atomic resolution, against a variety of structural models. Across the size range 123-151 atoms, only 3% of clusters matched the theoretically predicted Au 144 (SR) 60 structure, while a large proportion of the clusters were amorphous (i.e. did not match any model structure). However, a distinct ring-dot feature, characteristic of local icosahedral symmetry, was observed in about 20% of the clusters. Copyright © 2017. Published by Elsevier B.V.

‘Pd20Sn13’ revisited: crystal structure of Pd6.69Sn4.31

PubMed Central

Klein, Wilhelm; Jin, Hanpeng; Hlukhyy, Viktor; Fässler, Thomas F.

2015-01-01

The crystal structure of the title compound was previously reported with composition ‘Pd20Sn13’ [Sarah et al. (1981 ▸). Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3):0.62 (3). One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b). PMID:26279872

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the stem

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

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted directly without the need for preconceived atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementarymore » chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25{degree} symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}.« less

Effect of MultiSubstitution on the Thermoelectric Performance of the Ca11-xYbxSb10-yGez (0 ≤ x ≤ 9; 0 ≤ y ≤ 3; 0 ≤ z ≤ 3) System: Experimental and Theoretical Studies.

PubMed

Nam, Gnu; Choi, Woongjin; Lee, Junsu; Lim, Seong-Ji; Jo, Hongil; Ok, Kang Min; Ahn, Kyunghan; You, Tae-Soo

2017-06-19

The Zintl phase solid-solution Ca 11-x Yb x Sb 10-y Ge z (0 ≤ x ≤ 9; 0 ≤ y ≤ 3; 0 ≤ z ≤ 3) system with the cationic/anionic multisubstitution has been synthesized by molten Sn metal flux and arc-melting methods. The crystal structure of the nine title compounds were characterized by both powder and single-crystal X-ray diffractions and adopted the Ho 11 Ge 10 -type structure with the tetragonal space group I4/mmm (Z = 4, Pearson Code tI84). The overall isotypic structure of the nine title compounds can be illustrated as an assembly of three different types of cationic polyhedra sharing faces with their neighboring polyhedra and the three-dimensional cage-shaped anionic frameworks consisting of the dumbbell-shaped Sb 2 units and the square-shaped Sb 4 or (Sb/Ge) 4 units. During the multisubstitution trials, interestingly, we observed a metal-to-semiconductor transition as the Ca and Ge contents increased in the title system from Yb 11 Sb 10 to Ca 9 Yb 2 Sb 7 Ge 3 (nominal compositions) on the basis of a series of thermoelectric property measurements. This phenomenon can be elucidated by the suppression of a bipolar conduction of holes and electrons via an extra hole-carrier doping. The tight-binding linear muffin-tin orbital calculations using four hypothetical structural models nicely proved that the size of a pseudogap and the magnitude of the density of states at the Fermi level are significantly influenced by substituting elements as well as their atomic sites in a unit cell. The observed particular cationic/anionic site preferences, the historically known abnormalities of atomic displacement parameters, and the occupation deficiencies of particular atomic sites are further rationalized by the QVAL value criterion on the basis of the theoretical calculations. The results of SEM, EDS, and TGA analyses are also provided.

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

PubMed Central

Najmanovich, Rafael

2013-01-01

IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity) and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder. PMID:24555058

Spatial organization of cellulose microfibrils and matrix polysaccharides in primary plant cell walls as imaged by multichannel atomic force microscopy.

PubMed

Zhang, Tian; Zheng, Yunzhen; Cosgrove, Daniel J

2016-01-01

We used atomic force microscopy (AFM), complemented with electron microscopy, to characterize the nanoscale and mesoscale structure of the outer (periclinal) cell wall of onion scale epidermis - a model system for relating wall structure to cell wall mechanics. The epidermal wall contains ~100 lamellae, each ~40 nm thick, containing 3.5-nm wide cellulose microfibrils oriented in a common direction within a lamella but varying by ~30 to 90° between adjacent lamellae. The wall thus has a crossed polylamellate, not helicoidal, wall structure. Montages of high-resolution AFM images of the newly deposited wall surface showed that single microfibrils merge into and out of short regions of microfibril bundles, thereby forming a reticulated network. Microfibril direction within a lamella did not change gradually or abruptly across the whole face of the cell, indicating continuity of the lamella across the outer wall. A layer of pectin at the wall surface obscured the underlying cellulose microfibrils when imaged by FESEM, but not by AFM. The AFM thus preferentially detects cellulose microfibrils by probing through the soft matrix in these hydrated walls. AFM-based nanomechanical maps revealed significant heterogeneity in cell wall stiffness and adhesiveness at the nm scale. By color coding and merging these maps, the spatial distribution of soft and rigid matrix polymers could be visualized in the context of the stiffer microfibrils. Without chemical extraction and dehydration, our results provide multiscale structural details of the primary cell wall in its near-native state, with implications for microfibrils motions in different lamellae during uniaxial and biaxial extensions. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Local Structures of High-Entropy Alloys (HEAs) on Atomic Scales: An Overview

DOE PAGES

Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; ...

2015-08-29

The high-entropy alloys (HEAs), containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on atomic level are essential to understand the mechanical behaviors and related mechanisms. In this paper, the local structure and stress on the atomic level are reviewed by the pair-distribution function (PDF) of neutron-diffraction data, ab-initio-molecular-dynamics (AIMD) simulations, and atomic-probe microscopy (APT).

Proton irradiation on materials

NASA Technical Reports Server (NTRS)

Chang, C. Ken

1993-01-01

A computer code is developed by utilizing a radiation transport code developed at NASA Langley Research Center to study the proton radiation effects on materials which have potential application in NASA's future space missions. The code covers the proton energy from 0.01 Mev to 100 Gev and is sufficient for energetic protons encountered in both low earth and geosynchronous orbits. With some modification, the code can be extended for particles heavier than proton as the radiation source. The code is capable of calculating the range, stopping power, exit energy, energy deposition coefficients, dose, and cumulative dose along the path of the proton in a target material. The target material can be any combination of the elements with atomic number ranging from 1 to 92, or any compound with known chemical composition. The generated cross section for a material is stored and is reused in future to save computer time. This information can be utilized to calculate the proton dose a material would receive in an orbit when the radiation environment is known. It can also be used to determine, in the laboratory, the parameters such as beam current of proton and irradiation time to attain the desired dosage for accelerated ground testing of any material. It is hoped that the present work be extended to include polymeric and composite materials which are prime candidates for use as coating, electronic components, and structure building. It is also desirable to determine, for ground testing these materials, the laboratory parameters in order to simulate the dose they would receive in space environments. A sample print-out for water subject to 1.5 Mev proton is included as a reference.

Atomic and electronic structure of Pd40Ni40P20 bulk metallic glass from ab initio simulations

NASA Astrophysics Data System (ADS)

Kumar, Vijay; Fujita, T.; Konno, K.; Matsuura, M.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

2011-10-01

The atomic structure of Pd40Ni40P20 bulk metallic glass has been simulated using an ab initio molecular dynamics method with projector-augmented wave pseudopotentials for electron-ion interaction and generalized gradient approximation for exchange-correlation energy. The calculated extended x-ray absorption fine structure (EXAFS) spectra of Pd-K and Ni-K edges, the mass density, and the electronic structure agree remarkably well with the available experimental data and the EXAFS spectra measured at the SPring-8 synchrotron radiation facility. Our results show that the atomic structure can be described in terms of P-centered polyhedra. There are no two P atoms that are nearest neighbors at this composition, and this could be a reason for the observed optimal P concentration of about 20 at.%. The neighboring polyhedra share metal (M) atoms and form a polar covalently bonded random network of P-M-P favoring certain angles. The remaining M atoms act as metallic glue with a tendency of nanoscale clustering of Pd-Pd and Ni-Ni atoms.

How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation

NASA Astrophysics Data System (ADS)

Giorgino, Toni

2018-07-01

The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented in a C++ framework; however, developing new CVs is still time consuming due to the need to provide code for the analytical derivatives of all functions with respect to atomic coordinates. We present two solutions to this problem, namely (a) symbolic differentiation and code generation, and (b) automatic code differentiation, in both cases leveraging open-source libraries (SymPy and Stan Math, respectively). The two approaches are demonstrated and discussed in detail implementing a realistic example CV, the local radius of curvature of a polymer. Users may use the code as a template to streamline the implementation of their own CVs using high-level constructs and automatic gradient computation.

PubChem atom environments.

PubMed

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased. The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log-log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.

Spin-polarized structural, elastic, electronic and magnetic properties of half-metallic ferromagnetism in V-doped ZnSe

NASA Astrophysics Data System (ADS)

Monir, M. El Amine.; Baltache, H.; Murtaza, G.; Khenata, R.; Ahmed, Waleed K.; Bouhemadou, A.; Omran, S. Bin; Seddik, T.

2015-01-01

Based on first principles spin-polarized density functional theory, the structural, elastic electronic and magnetic properties of Zn1-xVxSe (for x=0.25, 0.50, 0.75) in zinc blende structure have been studied. The investigation was done using the full-potential augmented plane wave method as implemented in WIEN2k code. The exchange-correlation potential was treated with the generalized gradient approximation PBE-GGA for the structural and elastic properties. Moreover, the PBE-GGA+U approximation (where U is the Hubbard correlation terms) is employed to treat the "d" electrons properly. A comparative study between the band structures, electronic structures, total and partial densities of states and local moments calculated within both GGA and GGA+U schemes is presented. The analysis of spin-polarized band structure and density of states shows the half-metallic ferromagnetic character and are also used to determine s(p)-d exchange constants N0α (conduction band) and N0β (valence band) due to Se(4p)-V(3d) hybridization. It has been clearly evidence that the magnetic moment of V is reduced from its free space change value of 3 μB and the minor atomic magnetic moment on Zn and Se are generated.

On the relationship between residue structural environment and sequence conservation in proteins.

PubMed

Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

2017-09-01

Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

Resonance of an unshared electron pair between two atoms connected by a single bond

PubMed Central

Pauling, Linus

1983-01-01

The reported structure of the dimer of a compound of bicovalent tin indicates that the tin-tin bond is of a new type. It can be described as involving resonance between two structures in which there is transfer of an electron pair from one tin atom to the other. The tin atoms are connected by a single covalent bond (each also forms two covalent bonds with carbon atoms), and an unshared electron pair resonates between the fourth sp3 orbitals of the two atoms. Similar structures probably occur in digermene and distannene. PMID:16593329

Orbital dependent functionals: An atom projector augmented wave method implementation

NASA Astrophysics Data System (ADS)

Xu, Xiao

This thesis explores the formulation and numerical implementation of orbital dependent exchange-correlation functionals within electronic structure calculations. These orbital-dependent exchange-correlation functionals have recently received renewed attention as a means to improve the physical representation of electron interactions within electronic structure calculations. In particular, electron self-interaction terms can be avoided. In this thesis, an orbital-dependent functional is considered in the context of Hartree-Fock (HF) theory as well as the Optimized Effective Potential (OEP) method and the approximate OEP method developed by Krieger, Li, and Iafrate, known as the KLI approximation. In this thesis, the Fock exchange term is used as a simple well-defined example of an orbital-dependent functional. The Projected Augmented Wave (PAW) method developed by P. E. Blochl has proven to be accurate and efficient for electronic structure calculations for local and semi-local functions because of its accurate evaluation of interaction integrals by controlling multiple moments. We have extended the PAW method to treat orbital-dependent functionals in Hartree-Fock theory and the Optimized Effective Potential method, particularly in the KLI approximation. In the course of study we develop a frozen-core orbital approximation that accurately treats the core electron contributions for above three methods. The main part of the thesis focuses on the treatment of spherical atoms. We have investigated the behavior of PAW-Hartree Fock and PAW-KLI basis, projector, and pseudopotential functions for several elements throughout the periodic table. We have also extended the formalism to the treatment of solids in a plane wave basis and implemented PWPAW-KLI code, which will appear in future publications.

The Influence of the Solar Coronal Radiation on Coronal Plasma Structures, I: Determination of the Incident Coronal Radiation

NASA Astrophysics Data System (ADS)

Brown, Gerrard M.; Labrosse, Nicolas

2018-02-01

Coronal structures receive radiation not only from the solar disc, but also from the corona. This height-dependent incident radiation plays a crucial role in the excitation and the ionisation of the illuminated plasma. The aim of this article is to present a method for computing the detailed incident radiation coming from the solar corona, which is perceived at a point located at an arbitrary height. The coronal radiation is calculated by integrating the radiation received at a point in the corona over all of the corona visible from this point. The emission from the corona at all wavelengths of interest is computed using atomic data provided by CHIANTI. We obtain the spectrum illuminating points located at varying heights in the corona at wavelengths between 100 and 912 Å when photons can ionise H or He atoms and ions in their ground states. As expected, individual spectral lines will contribute most at the height within the corona where the local temperature is closest to their formation temperature. As there are many spectral lines produced by many ions, the coronal intensity cannot be assumed to vary in the same way at all wavelengths and so must be calculated for each separate height that is to be considered. This code can be used to compute the spectrum from the corona illuminating a point at any given height above the solar surface. This brings a necessary improvement to models where an accurate determination of the excitation and ionisation states of coronal plasma structures is crucial.

Investigation of structural and multiferroic properties of three phases of BiFeO3 using modified Becke Johnson potential technique

NASA Astrophysics Data System (ADS)

Sagar, Elle; Mahesh, R.; Pavan Kumar, N.; Venugopal Reddy, P.

2017-11-01

Electronic band structure, ferroelectric and ferromagnetic properties of Cubic, Tetragonal and Rhombohedral (hexagonal axis) phases of multiferroic BiFeO3 compound has been investigated using first-principles calculations under the generalized gradient (GGA) and TB-mBJ semi local (Tran-Blaha modified Becke-Johnson) potential approximations using WIEN2k code. For this purpose, the total energies were calculated as a function of reduced volumes and the data were fitted to Brich Murnaghan equation. The estimated ground state parameters are found to be comparable with those of experimental ones. The semiconducting behavior of the material was obtained using TB-mBJ method in the spin polarized mode. Analysis of the density of states indicates that the valence band consists of Fe-d and O-p states, while the conduction band is composed of Fe-d and Bi-p states. The analysis of electron localization function shows that stereochemically active lone-pair electrons are present at Bi sites of Rhombohedral and Tetragonal phases and are responsible for the displacements of Bi atoms from the centro-symmetric to the non-centrosymmetric structure leading to the exhibition of ferroelectricity. Further, it has been concluded that the "lone pair" may have been formed due to the hybridization of 6s and 6p atomic orbitals with 6s2 electrons filling one of the resulting orbitals in Bi. The Polarization and the magnetic properties including susceptibility were obtained. The calculated magnetic moments at the iron sites are not integer values, since Fe electrons have a hybridization interaction with the neighboring O ions.

Nano Electronics on Atomically Controlled van der Waals Quantum Heterostructures

DTIC Science & Technology

2015-03-30

for the structural of the atomically sharp interface between hBN and Bi2Te3. Finally, we have developed unprecedentedly clean graphene supercoductor...crystals by MBE method. We also use transmission electron microscopy (TEM) analysis for the structural of the atomically sharp interface between hBN and...by MBE method. We also use transmission electron microscopy (TEM) analysis for the structural of the atomically sharp interface between hBN and Bi2Te3

First-principles study on silicon atom doped monolayer graphene

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hussain, Nayyar

2018-01-01

This paper illustrates the structural, electronic and optical properties of individual silicon (Si) atom-doped single layer graphene using density functional theory method. Si atom forms tight bonding with graphene layer. The effect of doping has been investigated by varying the concentration of Si atoms from 3.125% to 9.37% (i.e. From one to three Si atoms in 4 × 4 pure graphene supercell containing 32 carbon atoms), respectively. Electronic structure, partial density of states (PDOS) and optical properties of pure and Si atom-doped graphene sheet were calculated using VASP (Vienna ab-initio Simulation Package). The calculated results for pure graphene sheet were then compared with Si atom doped graphene. It is revealed that upon Si doping in graphene, a finite band gap appears at the high symmetric K-point, thereby making graphene a direct band gap semiconductor. Moreover, the band gap value is directly proportional to the concentration of impurity Si atoms present in graphene lattice. Upon analyzing the optical properties of Si atom-doped graphene structures, it is found that, there is significant change in the refractive index of the graphene after Si atom substitution in graphene. In addition, the overall absorption spectrum of graphene is decreased after Si atom doping. Although a significant red shift in absorption is found to occur towards visible range of radiation when Si atom is substituted in its lattice. The reflectivity of graphene improves in low energy region after Si atom substitution in graphene. These results can be useful for tuning the electronic structure and to manipulate the optical properties of graphene layer in the visible region.

Photoneutron Reaction Data for Nuclear Physics and Astrophysics

NASA Astrophysics Data System (ADS)

Utsunomiya, Hiroaki; Renstrøm, Therese; Tveten, Gry Merete; Gheorghe, Ioana; Filipescu, Dan Mihai; Belyshev, Sergey; Stopani, Konstantin; Wang, Hongwei; Fan, Gongtao; Lui, Yiu-Wing; Symochko, Dmytro; Goriely, Stephane; Larsen, Ann-Cecilie; Siem, Sunniva; Varlamov, Vladimir; Ishkhanov, Boris; Glodariu, Tudor; Krzysiek, Mateusz; Takenaka, Daiki; Ari-izumi, Takashi; Amano, Sho; Miyamoto, Shuji

2018-05-01

We discuss the role of photoneutron reaction data in nuclear physics and astrophysics in conjunction with the Coordinated Research Project of the International Atomic Energy Agency with the code F41032 (IAEA-CRP F41032).

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

PubMed Central

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster.

PubMed

Vergara, Sandra; Lukes, Dylan A; Martynowycz, Michael W; Santiago, Ulises; Plascencia-Villa, Germán; Weiss, Simon C; de la Cruz, M Jason; Black, David M; Alvarez, Marcos M; López-Lozano, Xochitl; Barnes, Christopher O; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L; Gonen, Tamir; Yacaman, Miguel Jose; Calero, Guillermo

2017-11-16

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au 146 (p-MBA) 57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C 2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au 146 (p-MBA) 57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster

PubMed Central

Vergara, Sandra; Lukes, Dylan A.; Martynowycz, Michael W.; Santiago, Ulises; Plascencia-Villa, German; Weiss, Simon C.; de la Cruz, M. Jason; Black, David M.; Alvarez, Marcos M.; Lopez-Lozano, Xochitl; Barnes, Christopher O.; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L.; Gonen, Tamir; Jose-Yacaman, Miguel; Calero, Guillermo

2018-01-01

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault. PMID:29072840

Semantic Interoperability for Computational Mineralogy: Experiences of the eMinerals Consortium

NASA Astrophysics Data System (ADS)

Walker, A. M.; White, T. O.; Dove, M. T.; Bruin, R. P.; Couch, P. A.; Tyer, R. P.

2006-12-01

The use of atomic scale computer simulation of minerals to obtain information for geophysics and environmental science has grown enormously over the past couple of decades. It is now routine to probe mineral behavior in the Earth's deep interior and in the surface environment by borrowing methods and simulation codes from computational chemistry and physics. It is becoming increasingly important to use methods embodied in more than one of these codes to solve any single scientific problem. However, scientific codes are rarely designed for easy interoperability and data exchange; data formats are often code-specific, poorly documented and fragile, liable to frequent change between software versions, and even compiler versions. This means that the scientist's simple desire to use the methodological approaches offered by multiple codes is frustrated, and even the sharing of data between collaborators becomes fraught with difficulties. The eMinerals consortium was formed in the early stages of the UK eScience program with the aim of developing the tools needed to apply atomic scale simulation to environmental problems in a grid-enabled world, and to harness the computational power offered by grid technologies to address some outstanding mineralogical problems. One example of the kind of problem we can tackle is the origin of the compressibility anomaly in silica glass. By passing data directly between simulation and analysis tools we were able to probe this effect in more detail than has previously been possible and have shown how the anomaly is related to the details of the amorphous structure. In order to approach this kind of problem we have constructed a mini-grid, a small scale and extensible combined compute- and data-grid that allows the execution of many calculations in parallel, and the transparent storage of semantically-rich marked-up result data. Importantly, we automatically capture multiple kinds of metadata and key results from each calculation. We believe that the lessons learned and tools developed will be useful in many areas of science beyond the computational mineralogy. Key tools that will be described include: a pure Fortran XML library (FoX) that presents XPath, SAX and DOM interfaces as well as permitting the easy production of valid XML from legacy Fortran programs; a job submission framework that automatically schedules calculations to remote grid resources, handles data staging and metadata capture; and a tool (AgentX) that map concepts from an ontology onto locations in documents of various formats that we use to enable data exchange.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures.

PubMed

Zhang, S; Nordlund, K; Djurabekova, F; Zhang, Y; Velisa, G; Wang, T S

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Molecules Without Atoms

NASA Astrophysics Data System (ADS)

Ruth, Anthony; Collins, Laura; Gomes, Kenjiro; Janko, Boldizsar

We present a real-space representation of molecules which results in the normal bonding rules and electronic structure of chemistry without atom-centered coulomb potentials. Using a simple mapping, we can generate atomless molecules from the structure of real molecules. Additionally, molecules without atoms show similar covalent bonding energies and transfer of charge in ionic bonds as real molecules. The atomless molecules contain only the valence and conduction electronic structure of the real molecule. Using the framework of the Atoms in Molecules (AIM) theory of Bader, we prove that the topological features of the valence charge distribution of molecules without atoms are identical to that of real molecules. In particular, the charge basins of atomless molecules show identical location and quantities of representative charge. We compare the accuracy, computational cost, and intuition gained from electronic structure calculations of molecules without atoms with the use of pseudopotentials to represent atomic cores in density functional theory. A. R. acknowledges support from a NASA Space Technology Research Fellowship.

An atomic finite element model for biodegradable polymers. Part 1. Formulation of the finite elements.

PubMed

Gleadall, Andrew; Pan, Jingzhe; Ding, Lifeng; Kruft, Marc-Anton; Curcó, David

2015-11-01

Molecular dynamics (MD) simulations are widely used to analyse materials at the atomic scale. However, MD has high computational demands, which may inhibit its use for simulations of structures involving large numbers of atoms such as amorphous polymer structures. An atomic-scale finite element method (AFEM) is presented in this study with significantly lower computational demands than MD. Due to the reduced computational demands, AFEM is suitable for the analysis of Young's modulus of amorphous polymer structures. This is of particular interest when studying the degradation of bioresorbable polymers, which is the topic of an accompanying paper. AFEM is derived from the inter-atomic potential energy functions of an MD force field. The nonlinear MD functions were adapted to enable static linear analysis. Finite element formulations were derived to represent interatomic potential energy functions between two, three and four atoms. Validation of the AFEM was conducted through its application to atomic structures for crystalline and amorphous poly(lactide). Copyright © 2015 Elsevier Ltd. All rights reserved.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

NASA Astrophysics Data System (ADS)

Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Revision of the Li13Si4 structure

PubMed Central

Zeilinger, Michael; Fässler, Thomas F.

2013-01-01

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li–Si system is the phase Li13Si4 (trideca­lithium tetra­silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10–13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si–Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si–Si dumbbells at z = 0.5. PMID:24454148

Population kinetics on K alpha lines of partially ionized Cl atoms.

PubMed

Kawamura, Tohru; Nishimura, Hiroaki; Koike, Fumihiro; Ochi, Yoshihiro; Matsui, Ryoji; Miao, Wen Yong; Okihara, Shinichiro; Sakabe, Shuji; Uschmann, Ingo; Förster, Eckhart; Mima, Kunioki

2002-07-01

A population kinetics code was developed to analyze K alpha emission from partially ionized chlorine atoms in hydrocarbon plasmas. Atomic processes are solved under collisional-radiative equilibrium for two-temperature plasmas. It is shown that the fast electrons dominantly contribute to ionize the K-shell bound electrons (i.e., inner-shell ionization) and the cold electrons to the outer-shell bound ones. Ratios of K alpha lines of partially ionized atoms are presented as a function of cold-electron temperature. The model was validated by observation of the K alpha lines from a chlorinated plastic target irradiated with 1 TW Ti:sapphire laser pulses at 1.5 x 10(17) W/cm(2), inferring a plasma temperature of about 100 eV on the target surface.

Doping Scheme in Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Toshishige, Yamada

1997-01-01

Due to the dramatic reduction in MOS size, there appear many unwanted effects. In these small devices, the number of dopant atoms in the channel is not macroscopic and electrons may suffer significantly different scattering from device to device since the spatial distribution of dopant atoms is no longer regarded as continuous. This prohibits integration, while it is impossible to control such dopant positions within atomic scale. A fundamental solution is to create electronics with simple but atomically precise structures, which could be fabricated with recent atom manipulation technology. All the constituent atoms are placed as planned, and then the device characteristics are deviation-free, which is mandatory for integration. Atomic chain electronics belongs to this category. Foreign atom chains or arrays form devices, and they are placed on the atomically flat substrate surface. We can design the band structure and the resultant Fermi energy of these structures by manipulating the lattice constant. Using the tight-binding theory with universal parameters, it has been predicted that isolated Si chains and arrays are metallic, Mg chains are insulating, and Mg arrays have metallic and insulating phases [1]. The transport properties along a metallic chain have been studied, emphasizing the role of the contact to electrodes [2]. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along die chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of pant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Influence of spray nozzle shape upon atomization process

NASA Astrophysics Data System (ADS)

Beniuga, Marius; Mihai, Ioan

2016-12-01

The atomization process is affected by a number of operating parameters (pressure, viscosity, temperature, etc.) [1-6] and the adopted constructive solution. In this article are compared parameters of atomized liquid jet with two nozzles that have different lifespan, one being new and the other one out. The last statement shows that the second nozzle was monitored as time of operation on the one hand and on the other hand, two dimensional nozzles have been analyzed using laser profilometry. To compare the experimental parameters was carried an experimental stand to change the period and pulse width in injecting liquid through two nozzles. Atomized liquid jets were photographed and filmed quickly. Images obtained were analyzed using a Matlab code that allowed to determine a number of parameters that characterize an atomized jet. Knowing the conditions and operating parameters of atomized jet, will establish a new wastewater nozzle block of parameter values that can be implemented in controller that provides dosing of the liquid injected. Experimental measurements to observe the myriad forms of atomized droplets to a wide range of operating conditions, realized using the electronic control module.

Structural investigation of the (010) surface of the Al13 Fe4 catalyst.

PubMed

Ledieu, J; Gaudry, É; Loli, L N Serkovic; Villaseca, S Alarcón; de Weerd, M-C; Hahne, M; Gille, P; Grin, Y; Dubois, J-M; Fournée, V

2013-02-15

We have investigated the structure of the Al(13)Fe(4)(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as "glue" atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al(13)Fe(4) catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster et al., Nat. Mater. 11, 690 (2012)].

Distortion of Local Atomic Structures in Amorphous Ge-Sb-Te Phase Change Materials

NASA Astrophysics Data System (ADS)

Hirata, A.; Ichitsubo, T.; Guan, P. F.; Fujita, T.; Chen, M. W.

2018-05-01

The local atomic structures of amorphous Ge-Sb-Te phase-change materials have yet to be clarified and the rapid crystal-amorphous phase change resulting in distinct optical contrast is not well understood. We report the direct observation of local atomic structures in amorphous Ge2Sb2Te5 using "local" reverse Monte Carlo modeling dedicated to an angstrom-beam electron diffraction analysis. The results corroborated the existence of local structures with rocksalt crystal-like topology that were greatly distorted compared to the crystal symmetry. This distortion resulted in the breaking of ideal octahedral atomic environments, thereby forming local disordered structures that basically satisfied the overall amorphous structure factor. The crystal-like distorted octahedral structures could be the main building blocks in the formation of the overall amorphous structure of Ge-Sb-Te.

Atomic level structural modulation during the structural relaxation and its effect on magnetic properties of Fe81Si4B10P4Cu1 nanocrystalline alloy

NASA Astrophysics Data System (ADS)

Cao, C. C.; Zhu, L.; Meng, Y.; Zhai, X. B.; Wang, Y. G.

2018-06-01

The evolution of local structure and defects in the Fe81Si4B10P4Cu1 amorphous alloy during the structural relaxation has been investigated by Mössbauer spectroscopy, positron annihilation lifetime spectroscopy and transmission electron microscopy to explore their effects on magnetic properties of the nanocrystalline. The atomic rearrangements at the early stage of the structural relaxation cause the density increase of the amorphous matrix, but the subsequent atomic rearrangements contribute to the transformation of Fe3B-like atomic arrangements to FeB-like ones with the temperature increasing. As the structural relaxation processes, the released Fe atoms both from Fe3B- and Fe3P-like atomic arrangements result in the formation of new Fe clusters and the increase of Fe-Fe coordination number in the existing Fe clusters and the nucleation sites for α-Fe gradually increase, both of which promote the crystallization. However, the homogeneity of amorphous matrix will be finally destroyed under excessive relaxation temperature, which coarsens nanograins during the crystallization instead. Therefore, soft magnetic properties of the Fe81Si4B10P4Cu1 nanocrystalline alloy can be improved by pre-annealing the amorphous precursor at an appropriate temperature due to the atomic level structural optimization.

Structure determination in 55-atom Li-Na and Na-K nanoalloys.

PubMed

Aguado, Andrés; López, José M

2010-09-07

The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

Robust procedure for creating and characterizing the atomic structure of scanning tunneling microscope tips.

PubMed

Tewari, Sumit; Bastiaans, Koen M; Allan, Milan P; van Ruitenbeek, Jan M

2017-01-01

Scanning tunneling microscopes (STM) are used extensively for studying and manipulating matter at the atomic scale. In spite of the critical role of the STM tip, procedures for controlling the atomic-scale shape of STM tips have not been rigorously justified. Here, we present a method for preparing tips in situ while ensuring the crystalline structure and a reproducibly prepared tip structure up to the second atomic layer. We demonstrate a controlled evolution of such tips starting from undefined tip shapes.

A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

NASA Technical Reports Server (NTRS)

Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

2015-01-01

Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

Formation and structural phase transition in Co atomic chains on a Cu(775) surface

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

Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.

The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomicmore » spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.« less

A computer model for liquid jet atomization in rocket thrust chambers

NASA Astrophysics Data System (ADS)

Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Yang, H. Q.; Ibrahim, E.; Chuech, S.; Przekwas, A. J.

1991-12-01

The process of atomization has been used as an efficient means of burning liquid fuels in rocket engines, gas turbine engines, internal combustion engines, and industrial furnaces. Despite its widespread application, this complex hydrodynamic phenomenon has not been well understood, and predictive models for this process are still in their infancy. The difficulty in simulating the atomization process arises from the relatively large number of parameters that influence it, including the details of the injector geometry, liquid and gas turbulence, and the operating conditions. In this study, numerical models are developed from first principles, to quantify factors influencing atomization. For example, the surface wave dynamics theory is used for modeling the primary atomization and the droplet energy conservation principle is applied for modeling the secondary atomization. The use of empirical correlations has been minimized by shifting the analyses to fundamental levels. During applications of these models, parametric studies are performed to understand and correlate the influence of relevant parameters on the atomization process. The predictions of these models are compared with existing experimental data. The main tasks of this study were the following: development of a primary atomization model; development of a secondary atomization model; development of a model for impinging jets; development of a model for swirling jets; and coupling of the primary atomization model with a CFD code.

Student perception and conceptual development as represented by student mental models of atomic structure

NASA Astrophysics Data System (ADS)

Park, Eun Jung

The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

Atomic Structure. Independent Learning Project for Advanced Chemistry (ILPAC). Unit S2.

ERIC Educational Resources Information Center

Inner London Education Authority (England).

This unit on atomic structure is one of 10 first year units produced by the Independent Learning Project for Advanced Chemistry (ILPAC). The unit consists of two levels. Level one focuses on the atomic nucleus. Level two focuses on the arrangement of extranuclear electrons, approaching atomic orbitals through both electron bombardment and spectra.…

Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch

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

Howe, John A.; Xiao, Li; Fischmann, Thierry O.

2016-08-02

Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil ismore » structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs.« less

Theoretical discovery of stable structures of group III-V monolayers: The materials for semiconductor devices

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

Suzuki, Tatsuo, E-mail: dr.tatsuosuzuki@gmail.com

Group III-V compounds are very important as the materials of semiconductor devices. Stable structures of the monolayers of group III-V binary compounds have been discovered by using first-principles calculations. The primitive unit cell of the discovered structures is a rectangle, which includes four group-III atoms and four group-V atoms. A group-III atom and its three nearest-neighbor group-V atoms are placed on the same plane; however, these connections are not the sp{sup 2} hybridization. The bond angles around the group-V atoms are less than the bond angle of sp{sup 3} hybridization. The discovered structure of GaP is an indirect transition semiconductor,more » while the discovered structures of GaAs, InP, and InAs are direct transition semiconductors. Therefore, the discovered structures of these compounds have the potential of the materials for semiconductor devices, for example, water splitting photocatalysts. The discovered structures may become the most stable structures of monolayers which consist of other materials.« less

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

NASA Astrophysics Data System (ADS)

Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari

2017-09-01

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

Spectral and Atomic Physics Analysis of Xenon L-Shell Emission From High Energy Laser Produced Plasmas

NASA Astrophysics Data System (ADS)

Thorn, Daniel; Kemp, G. E.; Widmann, K.; Benjamin, R. D.; May, M. J.; Colvin, J. D.; Barrios, M. A.; Fournier, K. B.; Liedahl, D.; Moore, A. S.; Blue, B. E.

2016-10-01

The spectrum of the L-shell (n =2) radiation in mid to high-Z ions is useful for probing plasma conditions in the multi-keV temperature range. Xenon in particular with its L-shell radiation centered around 4.5 keV is copiously produced from plasmas with electron temperatures in the 5-10 keV range. We report on a series of time-resolved L-shell Xe spectra measured with the NIF X-ray Spectrometer (NXS) in high-energy long-pulse (>10 ns) laser produced plasmas at the National Ignition Facility. The resolving power of the NXS is sufficiently high (E/ ∂E >100) in the 4-5 keV spectral band that the emission from different charge states is observed. An analysis of the time resolved L-shell spectrum of Xe is presented along with spectral modeling by detailed radiation transport and atomic physics from the SCRAM code and comparison with predictions from HYDRA a radiation-hydrodynamics code with inline atomic-physics from CRETIN. This work was performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

Update and evaluation of decay data for spent nuclear fuel analyses

NASA Astrophysics Data System (ADS)

Simeonov, Teodosi; Wemple, Charles

2017-09-01

Studsvik's approach to spent nuclear fuel analyses combines isotopic concentrations and multi-group cross-sections, calculated by the CASMO5 or HELIOS2 lattice transport codes, with core irradiation history data from the SIMULATE5 reactor core simulator and tabulated isotopic decay data. These data sources are used and processed by the code SNF to predict spent nuclear fuel characteristics. Recent advances in the generation procedure for the SNF decay data are presented. The SNF decay data includes basic data, such as decay constants, atomic masses and nuclide transmutation chains; radiation emission spectra for photons from radioactive decay, alpha-n reactions, bremsstrahlung, and spontaneous fission, electrons and alpha particles from radioactive decay, and neutrons from radioactive decay, spontaneous fission, and alpha-n reactions; decay heat production; and electro-atomic interaction data for bremsstrahlung production. These data are compiled from fundamental (ENDF, ENSDF, TENDL) and processed (ESTAR) sources for nearly 3700 nuclides. A rigorous evaluation procedure of internal consistency checks and comparisons to measurements and benchmarks, and code-to-code verifications is performed at the individual isotope level and using integral characteristics on a fuel assembly level (e.g., decay heat, radioactivity, neutron and gamma sources). Significant challenges are presented by the scope and complexity of the data processing, a dearth of relevant detailed measurements, and reliance on theoretical models for some data.

Progress in Visualizing Atomic Size Effects with DFT-Chemical Pressure Analysis: From Isolated Atoms to Trends in AB5 Intermetallics.

PubMed

Berns, Veronica M; Engelkemier, Joshua; Guo, Yiming; Kilduff, Brandon J; Fredrickson, Daniel C

2014-08-12

The notion of atomic size poses an important challenge to chemical theory: empirical evidence has long established that atoms have spatial requirements, which are summarized in tables of covalent, ionic, metallic, and van der Waals radii. Considerations based on these radii play a central role in the design and interpretation of experiments, but few methods are available to directly support arguments based on atomic size using electronic structure methods. Recently, we described an approach to elucidating atomic size effects using theoretical calculations: the DFT-Chemical Pressure analysis, which visualizes the local pressures arising in crystal structures from the interactions of atomic size and electronic effects. Using this approach, a variety of structural phenomena in intermetallic phases have already been understood in terms that provide guidance to new synthetic experiments. However, the applicability of the DFT-CP method to the broad range of the structures encountered in the solid state is limited by two issues: (1) the difficulty of interpreting the intense pressure features that appear in atomic core regions and (2) the need to divide space among pairs of interacting atoms in a meaningful way. In this article, we describe general solutions to these issues. In addressing the first issue, we explore the CP analysis of a test case in which no core pressures would be expected to arise: isolated atoms in large boxes. Our calculations reveal that intense core pressures do indeed arise in these virtually pressure-less model systems and allow us to trace the issue to the shifts in the voxel positions relative to atomic centers upon expanding and contracting the unit cell. A compensatory grid unwarping procedure is introduced to remedy this artifact. The second issue revolves around the difficulty of interpreting the pressure map in terms of interatomic interactions in a way that respects the size differences of the atoms and avoids artificial geometrical constraints. In approaching this challenge, we have developed a scheme for allocating the grid pressures to contacts inspired by the Hirshfeld charge analysis. Here, each voxel is allocated to the contact between the two atoms whose free atom electron densities show the largest values at that position. In this way, the differing sizes of atoms are naturally included in the division of space without resorting to empirical radii. The use of the improved DFT-CP method is illustrated through analyses of the applicability of radius ratio arguments to Laves phase structures and the structural preferences of AB5 intermetallics between the CaCu5 and AuBe5 structure types.

Structural consistency analysis of recombinant and wild-type human serum albumin

NASA Astrophysics Data System (ADS)

Cao, Hui-Ling; Sun, Li-Hua; Liu, Li; Li, Jian; Tang, Lin; Guo, Yun-Zhu; Mei, Qi-Bing; He, Jian-Hua; Yin, Da-Chuan

2017-01-01

Recombinant human serum albumin (rHSA) is potential alternatives for human serum albumin (HSA) which may ease severe shortage of HSA worldwide. In theory, rHSA and HSA are the same. Structure decides function. Therefore, the 3D structural consistency analysis of rHSA and HSA is outmost importance, which is the base of their function consistency. In this paper, the crystal structures of rHSA at resolution limit of 2.22 Å and HSA at 2.30 Å were determined by X-ray diffraction (XRD), which were deposited in the Protein Data Bank (PDB) with accession codes 4G03 (rHSA) and 4G04 (HSA). The differences between rHSA and HSA were systematically analyzed from the crystallization behavior, diffraction data and three-dimensional (3D) structure. The superimposed contrasted analysis indicated that rHSA and HSA achieved a structural similarity of 99% with an r.m.s. deviation of 0.397 Å for the corresponding overall Cα atoms. In addition, the number of α-helices in the rHSA or HSA molecule was verified to be 30. As a result, rHSA can potentially replace HSA. The study provides a theoretical and experimental basis for the clinical and additional applications of rHSA. Meanwhile, it is also a good example for applications of genetic engineering.

Thermal hydraulic-severe accident code interfaces for SCDAP/RELAP5/MOD3.2

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

Coryell, E.W.; Siefken, L.J.; Harvego, E.A.

1997-07-01

The SCDAP/RELAP5 computer code is designed to describe the overall reactor coolant system thermal-hydraulic response, core damage progression, and fission product release during severe accidents. The code is being developed at the Idaho National Engineering Laboratory under the primary sponsorship of the Office of Nuclear Regulatory Research of the U.S. Nuclear Regulatory Commission. The code is the result of merging the RELAP5, SCDAP, and COUPLE codes. The RELAP5 portion of the code calculates the overall reactor coolant system, thermal-hydraulics, and associated reactor system responses. The SCDAP portion of the code describes the response of the core and associated vessel structures.more » The COUPLE portion of the code describes response of lower plenum structures and debris and the failure of the lower head. The code uses a modular approach with the overall structure, input/output processing, and data structures following the pattern established for RELAP5. The code uses a building block approach to allow the code user to easily represent a wide variety of systems and conditions through a powerful input processor. The user can represent a wide variety of experiments or reactor designs by selecting fuel rods and other assembly structures from a range of representative core component models, and arrange them in a variety of patterns within the thermalhydraulic network. The COUPLE portion of the code uses two-dimensional representations of the lower plenum structures and debris beds. The flow of information between the different portions of the code occurs at each system level time step advancement. The RELAP5 portion of the code describes the fluid transport around the system. These fluid conditions are used as thermal and mass transport boundary conditions for the SCDAP and COUPLE structures and debris beds.« less

First-principles study of low-spin LaCoO3 with structurally consistent Hubbard U

NASA Astrophysics Data System (ADS)

Hsu, H.; Umemoto, K.; Cococcioni, M.; Wentzcovitch, R.

2008-12-01

We use the local density approximation + Hubbard U (LDA+U) method to calculate the structural and electronic properties of low-spin LaCoO3. The Hubbard U is obtained by first principles and consistent with each fully-optimized atomic structure at different pressures. With structurally consistent U, the fully-optimized atomic structure agrees with experimental data better than the calculations with fixed or vanishing U. A discussion on how the Hubbard U affects the electronic and atomic structure of LaCoO3 is also given.

Superimposition of protein structures with dynamically weighted RMSD.

PubMed

Wu, Di; Wu, Zhijun

2010-02-01

In protein modeling, one often needs to superimpose a group of structures for a protein. A common way to do this is to translate and rotate the structures so that the square root of the sum of squares of coordinate differences of the atoms in the structures, called the root-mean-square deviation (RMSD) of the structures, is minimized. While it has provided a general way of aligning a group of structures, this approach has not taken into account the fact that different atoms may have different properties and they should be compared differently. For this reason, when superimposed with RMSD, the coordinate differences of different atoms should be evaluated with different weights. The resulting RMSD is called the weighted RMSD (wRMSD). Here we investigate the use of a special wRMSD for superimposing a group of structures with weights assigned to the atoms according to certain thermal motions of the atoms. We call such an RMSD the dynamically weighted RMSD (dRMSD). We show that the thermal motions of the atoms can be obtained from several sources such as the mean-square fluctuations that can be estimated by Gaussian network model analysis. We show that the superimposition of structures with dRMSD can successfully identify protein domains and protein motions, and that it has important implications in practice, e.g., in aligning the ensemble of structures determined by nuclear magnetic resonance.

Molecular Simulations in Astrobiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.

2000-01-01

One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides exhibit orientational flexibility with changing conditions, which may have provided a mechanism of transmitting signals between the protocell and its environment. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations identify the mechanisms by which protons move through the gate.

The grasp2K relativistic atomic structure package

NASA Astrophysics Data System (ADS)

Jönsson, P.; He, X.; Froese Fischer, C.; Grant, I. P.

2007-10-01

This paper describes grasp2K, a general-purpose relativistic atomic structure package. It is a modification and extension of the GRASP92 package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The package includes a "make" facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the package will be given in some detail in this report. Program summaryProgram title: grasp2K Catalogue identifier: ADZL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 213 524 No. of bytes in distributed program, including test data, etc.: 1 328 588 Distribution format: tar.gz Programming language: Fortran and C Computer: Intel Xeon, 3.06 GHz Operating system: Suse LINUX RAM: 500 MB or more Classification: 2.1 Nature of problem: Prediction of atomic spectra—atomic energy levels, oscillator strengths, and radiative decay rates—using a 'fully relativistic' approach. Solution method: Atomic orbitals are assumed to be four-component spinor eigenstates of the angular momentum operator, j=l+s, and the parity operator Π=βπ. Configuration state functions (CSFs) are linear combinations of Slater determinants of atomic orbitals, and are simultaneous eigenfunctions of the atomic electronic angular momentum operator, J, and the atomic parity operator, P. Approximate atomic state functions (ASFs) are linear combinations of CSFs. A variational functional may be constructed by combining expressions for the energies of one or more ASFs. Average energy level (EAL) functionals are weighted sums of energies of all possible ASFs that may be constructed from a set of CSFs; the number of ASFs is then the same as the number of CSFs. Extended optimal level (EOL) functionals are weighted sums of energies of some subset of ASFs. Radial functions may be determined by numerically solving the multiconfiguration Dirac-Hartree-Fock (MCDHF) equations that define an extremum of the variational functional by the self-consistent-field (SCF) method. Lists of CSFs are generated from a set of reference CSFs and rules for deriving other CSFs from these. Expansion coefficients are obtained using sparse-matrix methods for solving the relativistic configuration interaction (CI) problem. Transition properties for pairs of ASFs are computed from matrix elements of multipole operators of the electromagnetic field. Biorthogonal transformation methods are employed so that all matrix elements between CSFs can be evaluated using Racah algebra. Restrictions: The maximum number of radial orbitals is limited to 120 by the packing algorithm used for 32-bit integers. The maximum size of a multiconfiguration (MC) calculation, as measured by the length of the configuration state function (CSF) list, is limited by numerical stability, processing time, or storage which may be either in memory or on disk. Numerical stability is the same as GRASP92 [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249] with a slight improvement in memory management for Version 2 codes. Sufficient disk space is needed to store angular data. In configuration interaction calculations the matrix may be either in memory or on disk. The tables of coefficients of fractional parentage, as in GRASP92, are limited to subshells with j⩽7/2; occupied subshells with j=9/2 are, therefore, restricted to a maximum of two electrons. Unusual features: The installation process has been simplified so that pre-processing of the raw code needed with GRASP92 can be eliminated. Dynamic memory allocation reduces the number of parameters needed to define fixed array dimensions to nine. The corrections discussed in [C. Froese Fischer, G. Gaigalas, Y. Ralchenko, Comput. Phys. Comm. 175 (2006) 739] have also been implemented. Environment variables are used to facilitate the compilation of the libraries, applications, and tools with different compilers on different platforms. Computationally intensive applications have been parallelized using the message passing interface (MPI). When standard output is redirected, prompts and critical information about the progress of a calculation or convergence are still directed to the screen through the standard error output unit. Running time: CPU time required to execute test cases: 5 min ( n=4 calculation with 2190 CSFs) and 52.7 minutes ( n=5 calculation with 6752 CSFs)

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Local structure and polarization resistance of Ce doped SrMnO{sub 3} using extended x-ray fine structure analysis

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

Ryu, Jiseung; Lee, Heesoo, E-mail: heesoo@pusan.ac.kr

2014-09-15

Changes to the local structure of Sr and Mn atoms in Sr{sub 1−x}Ce{sub x}MnO{sub 3} (SCM) according to increasing Ce content and the effect of the structural change on the polarization resistance of SCM were investigated. The reduction of manganese was confirmed by the absorption edge shift of the Mn K-edge toward lower energies. The noise of oscillation in extended X-ray absorption fine structure k{sup 3}χ data at Mn K-edge reveals the distortion of the local structure of Mn atoms, and the peak that indicates the bonding length of Mn-O, Sr/Ce, and -Mn decreased with the addition of Ce contentmore » in Fourier transformations of the Mn K-edge. The distortion of the local structure at Mn atoms was affected by the reduced manganese ions having larger ionic radii than Mn{sup 4+}. Meanwhile, few distortions of local atomic structures of Sr atoms occurred, and the average nearest neighboring distances of Sr-O and Sr-Mn are ∼2.13 Å and ∼2.95 Å, respectively. The average bonding lengths of the Ce-O and Ce-Mn increased because the ionic radius of substituted Ce ion with 12 coordination number is smaller than that of Sr ion, which leads the reduction of Mn ions and the distortion of local structure at the substituted A-site. Therefore, we reasoned that the distortion of the local atomic structure at Mn atoms in MnO{sub 6} and Ce atoms in A-site is one of the causes for interrupting oxygen ion transfers as a geometric factor, which results in an increase in the polarization resistance of SCM within the Ce composition range from 10 mol. % to 30 mol. %.« less

A basin-hopping Monte Carlo investigation of the structural and energetic properties of 55- and 561-atom bimetallic nanoclusters: the examples of the ZrCu, ZrAl, and CuAl systems.

PubMed

De Souza, Douglas G; Cezar, Henrique M; Rondina, Gustavo G; de Oliveira, Marcelo F; Da Silva, Juarez L F

2016-05-05

We report a basin-hopping Monte Carlo investigation within the embedded-atom method of the structural and energetic properties of bimetallic ZrCu, ZrAl, and CuAl nanoclusters with 55 and 561 atoms. We found that unary Zr55, Zr561, Cu55, Cu561, Al55, and Al561 systems adopt the well known compact icosahedron (ICO) structure. The excess energy is negative for all systems and compositions, which indicates an energetic preference for the mixing of both chemical species. The ICO structure is preserved if a few atoms of the host system are replaced by different species, however, the composition limit in which the ICO structure is preserved depends on both the host and new chemical species. Using several structural analyses, three classes of structures, namely ideal ICO, nearly ICO, and distorted ICO structures, were identified. As the amounts of both chemical species change towards a more balanced composition, configurations far from the ICO structure arise and the dominant structures are nearly spherical, which indicates a strong minimization of the surface energy by decreasing the number of atoms with lower coordination on the surface. The average bond lengths follow Vegard's law almost exactly for ZrCu and ZrAl, however, this is not the case for CuAl. Furthermore, the radial distribution allowed us to identify the presence of an onion-like behavior in the surface of the 561-atom CuAl nanocluster with the Al atoms located in the outermost surface shell, which can be explained by the lower surface energies of the Al surfaces compared with the Cu surfaces. In ZrCu and ZrAl the radial distribution indicates a nearly homogeneous distribution for the chemical species, however, with a slightly higher concentration of Al atoms on the ZrAl surface, which can also be explained by the lower surface energy.

Voronoi analysis of the short–range atomic structure in iron and iron–carbon melts

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

Sobolev, Andrey; Mirzoev, Alexander

2015-08-17

In this work, we simulated the atomic structure of liquid iron and iron–carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short–range atomic order of iron atoms — it remains effectively the same as in pure iron melts.

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

Unusual Features of Crystal Structures of Some Simple Copper Compounds

ERIC Educational Resources Information Center

Douglas, Bodie

2009-01-01

Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

DOE PAGES

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto; ...

2017-09-15

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

ELSI: A unified software interface for Kohn-Sham electronic structure solvers

NASA Astrophysics Data System (ADS)

Yu, Victor Wen-zhe; Corsetti, Fabiano; García, Alberto; Huhn, William P.; Jacquelin, Mathias; Jia, Weile; Lange, Björn; Lin, Lin; Lu, Jianfeng; Mi, Wenhui; Seifitokaldani, Ali; Vázquez-Mayagoitia, Álvaro; Yang, Chao; Yang, Haizhao; Blum, Volker

2018-01-01

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.

PLIP: fully automated protein-ligand interaction profiler.

PubMed

Salentin, Sebastian; Schreiber, Sven; Haupt, V Joachim; Adasme, Melissa F; Schroeder, Michael

2015-07-01

The characterization of interactions in protein-ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community. Here, we present the protein-ligand interaction profiler (PLIP), a novel web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures, freely available at projects.biotec.tu-dresden.de/plip-web. The input is either a Protein Data Bank structure, a protein or ligand name, or a custom protein-ligand complex (e.g. from docking). In contrast to other tools, the rule-based PLIP algorithm does not require any structure preparation. It returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. The full python source code is available for download on the website. PLIP's command-line mode allows for high-throughput interaction profiling. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

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

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

Colloquium: Laser probing of neutron-rich nuclei in light atoms

NASA Astrophysics Data System (ADS)

Lu, Z.-T.; Mueller, P.; Drake, G. W. F.; Nörtershäuser, W.; Pieper, Steven C.; Yan, Z.-C.

2013-10-01

The neutron-rich He6 and He8 isotopes exhibit an exotic nuclear structure that consists of a tightly bound He4-like core with additional neutrons orbiting at a relatively large distance, forming a halo. Recent experimental efforts have succeeded in laser trapping and cooling these short-lived, rare helium atoms and have measured the atomic isotope shifts along the He4-He6-He8 chain by performing laser spectroscopy on individual trapped atoms. Meanwhile, the few-electron atomic structure theory, including relativistic and QED corrections, has reached a comparable degree of accuracy in the calculation of the isotope shifts. In parallel efforts, also by measuring atomic isotope shifts, the nuclear charge radii of lithium and beryllium isotopes have been studied. The techniques employed were resonance ionization spectroscopy on neutral, thermal lithium atoms and collinear laser spectroscopy on beryllium ions. Combining advances in both atomic theory and laser spectroscopy, the charge radii of these light halo nuclei have now been determined for the first time independent of nuclear structure models. The results are compared with the values predicted by a number of nuclear structure calculations and are used to guide our understanding of the nuclear forces in the extremely neutron-rich environment.

Interpolation schemes for peptide rearrangements.

PubMed

Bauer, Marianne S; Strodel, Birgit; Fejer, Szilard N; Koslover, Elena F; Wales, David J

2010-02-07

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.

1,2-Dibenzyl and -Diaryltetradimethylamido-dimolybdenum and -Ditungsten Compounds: M2R2(NMe2)4 (M=M). Structural Effects of Me2N-to-M Alpha-Bonding.

DTIC Science & Technology

1982-07-07

CHETCUTI, M H CHISHOLM. K FOLTING N00OON 79-C 00144 UNCL’ASS IF IED INDU/DC/TR-82/2-MC NL mh~hEhEEo. OFFICE OF NAVAL RESEARCH Contract No. N00014-79...ldo i, n,.aowy a"d Identf ’ mko.) ’ / a, From the reactions between RMgCI (R = CH C H and CH-p-tolyl) or LiR.(R C6H, ~~,-- ;n 6o5 C"-tolyl) (2euv . 6...ligands u-donate to metal atomic Availability Codes V Avail and/or D special 4 orbitals which would otherwise be available for mischevious M--- H -C

The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility

PubMed Central

Bashan, Anat; Yonath, Ada

2009-01-01

Crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. For the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. This cluster played a dual role in ribosomal crystallography: providing anomalous phasing power and dramatically increased the resolution, by stabilization of a selected functional conformation. Thus, four out of the fourteen clusters that bind to each of the crystallized small subunits are attached to a specific ribosomal protein in a fashion that may control a significant component of the subunit internal flexibility, by “gluing” symmetrical related subunits. Here we highlight basic issues in the relationship between metal ions and macromolecules and present common traits controlling in the interactions between polymetalates and various macromolecules, which may be extended towards the exploitation of polymetalates for therapeutical treatment. PMID:19915655

Ab-initio study on electronic properties of rocksalt SnAs

NASA Astrophysics Data System (ADS)

Babariya, Bindiya; Vaghela, M. V.; Gajjar, P. N.

2018-05-01

Within the frame work of Local Density Approximation of Exchange and Correlation, ab-initio method of density functional theory with Abinit code is used to compute electronic energy band structure, density of States and charge density of SnAs in rocksalt phase. Our result after optimization for lattice constant agrees with experimental value within 0.59% deviation. The computed electronic energy bands in high symmetry directions Γ→K→X→Γ→L→X→W→L→U shown metallic nature. The lowest band in the electronic band structure is showing band-gap approximately 1.70 eV from next higher band and no crossing between lowest two bands are seen. The density of states revels p-p orbit hybridization between Sn and As atoms. The spherical contour around Sn and As in the charge density plot represent partly ionic and partly covalent bonding. Fermi surface topology is the resultant effect of the single band crossing along L direction at Ef.

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

PubMed

Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

2011-07-30

MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

First-principles calculations on the four phases of BaTiO3.

PubMed

Evarestov, Robert A; Bandura, Andrei V

2012-04-30

The calculations based on linear combination of atomic orbitals basis functions as implemented in CRYSTAL09 computer code have been performed for cubic, tetragonal, orthorhombic, and rhombohedral modifications of BaTiO(3) crystal. Structural and electronic properties as well as phonon frequencies were obtained using local density approximation, generalized gradient approximation, and hybrid exchange-correlation density functional theory (DFT) functionals for four stable phases of BaTiO(3). A comparison was made between the results of different DFT techniques. It is concluded that the hybrid PBE0 [J. P. Perdew, K. Burke, M. Ernzerhof, J. Chem. Phys. 1996, 105, 9982.] functional is able to predict correctly the structural stability and phonon properties both for cubic and ferroelectric phases of BaTiO(3). The comparative phonon symmetry analysis in BaTiO(3) four phases has been made basing on the site symmetry and irreducible representation indexes for the first time. Copyright © 2012 Wiley Periodicals, Inc.

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Interplay of weak interactions in the atom-by-atom condensation of xenon within quantum boxes

PubMed Central

Nowakowska, Sylwia; Wäckerlin, Aneliia; Kawai, Shigeki; Ivas, Toni; Nowakowski, Jan; Fatayer, Shadi; Wäckerlin, Christian; Nijs, Thomas; Meyer, Ernst; Björk, Jonas; Stöhr, Meike; Gade, Lutz H.; Jung, Thomas A.

2015-01-01

Condensation processes are of key importance in nature and play a fundamental role in chemistry and physics. Owing to size effects at the nanoscale, it is conceptually desired to experimentally probe the dependence of condensate structure on the number of constituents one by one. Here we present an approach to study a condensation process atom-by-atom with the scanning tunnelling microscope, which provides a direct real-space access with atomic precision to the aggregates formed in atomically defined ‘quantum boxes’. Our analysis reveals the subtle interplay of competing directional and nondirectional interactions in the emergence of structure and provides unprecedented input for the structural comparison with quantum mechanical models. This approach focuses on—but is not limited to—the model case of xenon condensation and goes significantly beyond the well-established statistical size analysis of clusters in atomic or molecular beams by mass spectrometry. PMID:25608225

Atomic oxygen protective coating with resistance to undercutting at defect sites

NASA Technical Reports Server (NTRS)

Banks, Bruce A. (Inventor); Rutledge, Sharon K. (Inventor)

1994-01-01

Structures composed at least partially of an organic substrate may be protected from oxidation by applying a catalyst onto said substrate for promoting the combination of atomic oxygen to molecular oxygen. The structure may also be protected by applying both a catalyst and an atomic oxygen shielding layer onto the substrate. The structures to be protected include spacecraft surfaces.

Atomic Structure of Au 329(SR) 84 Faradaurate Plasmonic Nanomolecules

DOE PAGES

Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; ...

2015-04-03

To design novel nanomaterials, it is important to precisely control the composition, determine the atomic structure, and manipulate the structure to tune the materials property. Here we present a comprehensive characterization of the material whose composition is Au 329(SR) 84 precisely, therefore referred to as a nanomolecule. The size homogeneity was shown by electron microscopy, solution X-ray scattering, and mass spectrometry. We proposed its atomic structure to contain the Au 260 core using experiments and modeling of a total-scattering-based atomic-pair distribution functional analysis. HAADF-STEM images shows fcc-like 2.0 ± 0.1 nm diameter nanomolecules.

NC-AFM observation of atomic scale structure of rutile-type TiO2(110) surface prepared by wet chemical process.

PubMed

Namai, Yoshimichi; Matsuoka, Osamu

2006-04-06

We succeeded in observing the atomic scale structure of a rutile-type TiO2(110) single-crystal surface prepared by the wet chemical method of chemical etching in an acid solution and surface annealing in air. Ultrahigh vacuum noncontact atomic force microscopy (UHV-NC-AFM) was used for observing the atomic scale structures of the surface. The UHV-NC-AFM measurements at 450 K, which is above a desorption temperature of molecularly adsorbed water on the TiO2(110) surface, enabled us to observe the atomic scale structure of the TiO2(110) surface prepared by the wet chemical method. In the UHV-NC-AFM measurements at room temperature (RT), however, the atomic scale structure of the TiO2(110) surface was not observed. The TiO2(110) surface may be covered with molecularly adsorbed water after the surface was prepared by the wet chemical method. The structure of the TiO2(110) surface that was prepared by the wet chemical method was consistent with the (1 x 1) bulk-terminated model of the TiO2(110) surface.

Atomic scale chemical tomography of human bone

NASA Astrophysics Data System (ADS)

Langelier, Brian; Wang, Xiaoyue; Grandfield, Kathryn

2017-01-01

Human bone is a complex hierarchical material. Understanding bone structure and its corresponding composition at the nanometer scale is critical for elucidating mechanisms of biomineralization under healthy and pathological states. However, the three-dimensional structure and chemical nature of bone remains largely unexplored at the nanometer scale due to the challenges associated with characterizing both the structural and chemical integrity of bone simultaneously. Here, we use correlative transmission electron microscopy and atom probe tomography for the first time, to our knowledge, to reveal structures in human bone at the atomic level. This approach provides an overlaying chemical map of the organic and inorganic constituents of bone on its structure. This first use of atom probe tomography on human bone reveals local gradients, trace element detection of Mg, and the co-localization of Na with the inorganic-organic interface of bone mineral and collagen fibrils, suggesting the important role of Na-rich organics in the structural connection between mineral and collagen. Our findings provide the first insights into the hierarchical organization and chemical heterogeneity in human bone in three-dimensions at its smallest length scale - the atomic level. We demonstrate that atom probe tomography shows potential for new insights in biomineralization research on bone.

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

PubMed Central

Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

2011-01-01

Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909

Methodology trends on gamma and electron radiation damage simulation studies in solids under high fluency irradiation environments

NASA Astrophysics Data System (ADS)

Cruz Inclán, Carlos M.; González Lazo, Eduardo; Rodríguez Rodríguez, Arturo; Guzmán Martínez, Fernando; Abreu Alfonso, Yamiel; Piñera Hernández, Ibrahin; Leyva Fabelo, Antonio

2017-09-01

The present work deals with the numerical simulation of gamma and electron radiation damage processes under high brightness and radiation particle fluency on regard to two new radiation induced atom displacement processes, which concern with both, the Monte Carlo Method based numerical simulation of the occurrence of atom displacement process as a result of gamma and electron interactions and transport in a solid matrix and the atom displacement threshold energies calculated by Molecular Dynamic methodologies. The two new radiation damage processes here considered in the framework of high brightness and particle fluency irradiation conditions are: 1) The radiation induced atom displacement processes due to a single primary knockout atom excitation in a defective target crystal matrix increasing its defect concentrations (vacancies, interstitials and Frenkel pairs) as a result of a severe and progressive material radiation damage and 2) The occurrence of atom displacements related to multiple primary knockout atom excitations for the same or different atomic species in an perfect target crystal matrix due to subsequent electron elastic atomic scattering in the same atomic neighborhood during a crystal lattice relaxation time. In the present work a review numeral simulation attempts of these two new radiation damage processes are presented, starting from the former developed algorithms and codes for Monte Carlo simulation of atom displacements induced by electron and gamma in

Effect of the electric field on buckled and puckered arsenene

NASA Astrophysics Data System (ADS)

Chavez, Victor Hugo; Fernandez-Escamilla, Hector Noe; Martínez-Guerra, Edgar

With the emergence of new 2D materials, more recently phosphorene, arsenene appears as a new candidate to be explored for electronic devices. We have studied the stability of arsenene pristine and the effect of a transversal electric field on its electronic properties. The calculations were performed using the SIESTA code, with the GGA exchange-correlation functional in the PBE form. We have used numerical atomic orbitals as the basis set for the valence wavefunctions employing a double ζ-polarized basis. We use the Perdew-Becke pseudopotential for an As atom that includes the scalar-relativistic effect and Troullier-Martins parametrization. We adopt the Monkhorst-Pack scheme for k-point sampling of Brillouin zone integrations with 25 ×25 ×1 and 25 ×25 ×1 for the buckled/planar and puckered systems, respectively. We found that buckled and puckered arsenenes are stable and posses indirect gap. The effect of the electric field on the electronic structure of the buckled arsenene is the modulation of indirect to direct gap, while in puckered arsenene the gap linearly decreases as electric field is increased. This research was supported by Consejo Nacional de Ciencia y Tecnología (Conacyt) under Grant No. 43830-F.

Positron states and annihilation characteristics of surface-trapped positrons at the oxidized Cu(110) surface

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Olenga, Antoine; Weiss, A. H.

2013-03-01

The process by which oxide layers are formed on metal surfaces is still not well understood. In this work we present the results of theoretical studies of positron states and annihilation characteristics of surface-trapped positrons at the oxidized Cu(110) surface. An ab-initio investigation of stability and associated electronic properties of different adsorption phases of oxygen on Cu(110) has been performed on the basis of density functional theory and using DMOl3 code. The changes in the positron work function and the surface dipole moment when oxygen atoms occupy on-surface and sub-surface sites have been attributed to charge redistribution within the first two layers, buckling effects within each layer and interlayer expansion. The computed positron binding energy, positron surface state wave function, and annihilation probabilities of surface trapped positrons with relevant core electrons demonstrate their sensitivity to oxygen coverage, elemental content, atomic structure of the topmost layers of surfaces, and charge transfer effects. Theoretical results are compared with experimental data obtained from studies of oxidized transition metal surfaces using positron annihilation induced Auger electron spectroscopy. This work was supported in part by the National Science Foundation Grant DMR-0907679.

Composition Dependence of the Properties of Noble-metal Nanoalloys

NASA Astrophysics Data System (ADS)

Fernández Seivane, Lucas; Barrón, Héctor; Benson, James; Weissker, Hans-Christian; López-Lozano, Xochitl

2012-03-01

Bimetallic nanostructured materials are of greater interest both from the scientific and technological points of view due to their potential to improve the catalytic properties of novel materials. Their applicability as well as the performance depends critically on their size, shape and composition, either as alloy or core-shell. In this work, the structural, electronic, magnetic and optical properties of bimetallic Au-Ag nanoclusters have been investigated through density-functional-theory-based calculations with the Siesta and Octopus codes. Different symmetries -tetrahedral, bipyramidal, decahedral and icosahedral- of bimetallic nanoparticles of 4-, 5-, 7- and 13-atoms, were taken into account including all the possibly different Au:Ag ratio concentrations. In combination with a statistical analysis of the performed calculations and the concepts of the Enthalpy of Mixing and Energy Excess, we have been able to predict the most probable gap and magnetic moment for all the composition stoichiometries. This approach allows us to understand the energy differences due to cluster shape effects, the stoichiometry and segregation. In addition, we can also obtain the bulk energy and surface energy of Au-Ag nanoalloys by looking at fixed number of atoms and fixed morphologies.

Pseudopotentials for quantum Monte Carlo studies of transition metal oxides

DOE PAGES

Krogel, Jaron T.; Santana Palacio, Juan A.; Reboredo, Fernando A.

2016-02-22

Quantum Monte Carlo (QMC) calculations of transition metal oxides are partially limited by the availability of high-quality pseudopotentials that are both accurate in QMC and compatible with major plane-wave electronic structure codes. We have generated a set of neon-core pseudopotentials with small cutoff radii for the early transition metal elements Sc to Zn within the local density approximation of density functional theory. The pseudopotentials have been directly tested for accuracy within QMC by calculating the first through fourth ionization potentials of the isolated transition metal (M) atoms and the binding curve of each M-O dimer. We find the ionization potentialsmore » to be accurate to 0.16(1) eV, on average, relative to experiment. The equilibrium bond lengths of the dimers are within 0.5(1)% of experimental values, on average, and the binding energies are also typically accurate to 0.18(3) eV. The level of accuracy we find for atoms and dimers is comparable to what has recently been observed for bulk metals and oxides using the same pseudopotentials. Our QMC pseudopotential results compare well with the findings of previous QMC studies and benchmark quantum chemical calculations.« less

IR investigation on silicon oxycarbide structure obtained from precursors with 1:1 silicon to carbon atoms ratio and various carbon atoms distribution

NASA Astrophysics Data System (ADS)

Niemiec, Wiktor; Szczygieł, Przemysław; Jeleń, Piotr; Handke, Mirosław

2018-07-01

Silicon oxycarbide is a material with a number of advantageous properties that strongly depend on its structure. The most common approach to its tailoring is based on varying the silicon to carbon atoms ratio in the preceramic polymeric precursor. This work is the first comparison of the materials obtained from precursors with the same Si to C atoms ratio, but with various distribution of these atoms in the preceramic polymer. In addition to standard mixtures of monomers containing single silicon atom, a number of monomers with high molar masses and well defined structure was used. The IR was used to investigate the structure of the precursors and materials obtained after their annealing in 800 °C. The results show, that not only the distribution of carbon containing groups among the monomers is important, but also the (in)ability of these groups to end up in each other vicinity in the precursor as well as the degree of condensation of each structural unit.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

DOE PAGES

Zhang, S.; Univ. of Helsinki; Nordlund, Kai; ...

2016-10-25

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms,more » Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.« less

Raman Scattered He II 4332 and Photoionization Model in the Symbiotic Star V1016 Cygni

NASA Astrophysics Data System (ADS)

Lee, H.-W.; Heo, J.-E.; Lee, B.-C.

2014-08-01

Symbiotic stars are wide binary systems of a white dwarf and a mass losing giant. They exhibit unique Raman scattered features as a result of inelastic scattering of far UV line photons by atomic hydrogen. Co-existence of a far UV He II emission region and a thick H I region in symbiotic stars is necessary for the formation of Raman-scattered features blueward of hydrogen Balmer emission lines. Being a single electron atom, He II has the same atomic structure as the hydrogen atom and hence emits far UV emission lines that are slightly blueward of hydrogen Lyman lines. These far UV He II emission lines can be Raman scattered to appear blueward of hydrogen Balmer lines. In particular, the symbiotic star V1016 Cyg is found to exhibit Raman scattered He II 4332 feature in the BOES high resolution spectrum. Our profile fitting of Raman scattered He II 4332 is consistent with the mass loss geometry proposed by Jung & Lee (2004). We use the photoionization code ‘ CLOUDY' to estimate the far UV He II emission lines and make comparisons with the observed Raman scattered He II 4332 blueward of Hγ in the high resolution echelle V1016 Cyg. The emission nebula is assumed to be of uniform density of 108 cm-3 that is illuminated by a black body characterized by its temperature and total luminosity. With our comparisons we conclude that the Raman scattered He II features are consistent with the existence of a photoionized nebula by a hot black body source with temperature 7-8× 104 K with a luminosity 1038erg s-1.

Density functional theory study of nitrogen atoms and molecules interacting with Fe(1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Nosir, M. A.; Martin-Gondre, L.; Bocan, G. A.; Díez Muiño, R.

2016-09-01

We present Density functional theory (DFT) calculations for the investigation of the structural relaxation of Fe(1 1 1), as well as for the study of the interaction of nitrogen atoms and molecules with this surface. We perform spin polarized DFT calculations using VASP (Vienna Ab-initio Simulation Package) code. We use the supercell approach and up to 19 slab layers for the relaxation of the Fe(1 1 1) surface. We find a contraction of the first two interlayer distances with a relative value of Δ12 = - 7.8 % and Δ23 = - 21.7 % with respect to the bulk reference. The third interlayer distance is however expanded with a relative change of Δ34 = 9.7 % . Early experimental studies of the surface relaxation using Low Energy Electron Diffraction (LEED) and Medium Energy Ion Scattering (MEIS) showed contradictory results, even on the relaxation general trend. Our current theoretical results support the LEED conclusions and are consistent qualitatively with other recent theoretical calculations. In addition, we study the interaction energy of nitrogen atoms and molecules on the Fe(1 1 1) surface. The nitrogen atoms are adsorbed in the hollow site of the unit cell, with an adsorption energy consistent with the one found in previous studies. In addition, we find the three molecularly adsorbed states that are observed experimentally. Two of them correspond to the adsorbed molecule oriented normal to the surface and a third one corresponds to the molecule adsorbed parallel to the surface. We conclude that our results are accurate enough to be used to build a full six-dimensional potential energy surface for the N2 system.

Analyzing non-LTE Kr plasmas produced in high energy density experiments: from the Z machine to the National Ignition Facility

NASA Astrophysics Data System (ADS)

Dasgupta, Arati

2015-11-01

Designing high fluence photon sources above 10 keV are a challenge for High Energy Density plasmas. This has motivated radiation source development investigations of Kr with K-shell energies around 13 keV. Recent pulsed power driven gas-puff experiments on the refurbished Z machine at Sandia have produced intense X-rays in the multi-keV photon energy range. K-shell radiative yields and efficiencies are very high for Ar, but rapidly decrease for higher atomic number (ZA) elements such as Kr. It has been suggested that an optimum exists corresponding to a trade-off between the increase of photon energy for higher ZA elements and the corresponding fall off in radiative power. However the conversion efficiency on NIF, where the drive, energy deposition process, and target dynamics are different, does not fall off with higher ZA as rapidly as on Z. We have developed detailed atomic structure and collisional data for the full K-, L- and partial M-shell of Kr using the Flexible Atomic Code (FAC). Our non-LTE atomic model includes all collisional and recombination processes, including state-specific dielectronic recombination (DR), that significantly affect ionization balance and spectra of Kr plasmas at the temperatures and densities of concern. The model couples ionization physics, radiation production and transport, and magnetohydrodynamics. In this talk, I will give a detailed description of the model and discuss 1D Kr simulations employing a multifrequency radiation transport scheme. Synthetic K- and L-shell spectra will be compared with available experimental data. This talk will analyze experimental data indicative of the differences between Z and NIF experimental data and discuss how they affect the K-shell radiative output of Kr plasma. Work supported by DOE/NNSA.

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

Atomic structure and dynamics properties of Cu50Zr50 films

NASA Astrophysics Data System (ADS)

Chen, Heng; Qu, Bingyan; Li, Dongdong; Zhou, Rulong; Zhang, Bo

2018-01-01

In this paper, the structural and dynamic properties of Cu50Zr50 films are investigated by molecular dynamics simulations. Our results show that the dynamics of the surface atoms are much faster than those of the bulk. Especially, the diffusion coefficient of the surface atoms is about forty times larger than that of the bulk at 600 K, which qualitatively agrees with the experimental results. Meanwhile, we find that the population of the icosahedral (-like) clusters in the surface region is obviously higher than that of the bulk, which prevents the surface from crystallization. A new method to determine the string-like collective atomic motion is introduced in the paper, and it suggests a possible connection between the glass formation ability and collective atomic motion. By using the method, the effects of surface on collective motion are illustrated. Our results show that the string-like collective atomic motion of surface atoms is weakened while that of the interior atoms is strengthened. The studies clearly explain the effects of surface on the structural and dynamic properties of Cu50Zr50 films from the atomic scale.

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

PubMed Central

Theobald, Douglas L.; Wuttke, Deborah S.

2008-01-01

Summary THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. PMID:16777907

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

PubMed

Masso, Majid

2018-09-14

Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Probing Single Pt Atoms in Complex Intermetallic Al13Fe4.

PubMed

Yamada, Tsunetomo; Kojima, Takayuki; Abe, Eiji; Kameoka, Satoshi; Murakami, Yumi; Gille, Peter; Tsai, An Pang

2018-03-21

The atomic structure of a 0.2 atom % Pt-doped complex metallic alloy, monoclinic Al 13 Fe 4 , was investigated using a single crystal prepared by the Czochralski method. High-angle annular dark-field scanning transmission electron microscopy showed that the Pt atoms were dispersed as single atoms and substituted at Fe sites in Al 13 Fe 4 . Single-crystal X-ray structural analysis revealed that the Pt atoms preferentially substitute at Fe(1). Unlike those that have been reported, Pt single atoms in the surface layers showed lower activity and selectivity than those of Al 2 Pt and bulk Pt for propyne hydrogenation, indicating that the active state of a given single-atom Pt site is strongly dominated by the bonding to surrounding Al atoms.

Pb chains on reconstructed Si(335) surface

NASA Astrophysics Data System (ADS)

Krawiec, Mariusz

2009-04-01

The structural and electronic properties of Si(335)-Au surface decorated with Pb atoms are studied by means of density-functional theory. The resulting structural model features Pb atoms bonded to neighboring Si and Au surface atoms, forming monoatomic chain located 0.2 nm above the surface. The presence of Pb chain leads to a strong rebonding of Si atoms at the step edge. The fact that Pb atoms occupy positions in the middle of terrace is consistent with scanning tunneling microscopy (STM) data and also confirmed by simulated STM images. The calculated band structure clearly shows one-dimensional metallic character. The calculated electronic bands remain in very good agreement with photoemission data.

Optimal atomic structure of amorphous silicon obtained from density functional theory calculations

NASA Astrophysics Data System (ADS)

Pedersen, Andreas; Pizzagalli, Laurent; Jónsson, Hannes

2017-06-01

Atomic structure of amorphous silicon consistent with several reported experimental measurements has been obtained from annealing simulations using electron density functional theory calculations and a systematic removal of weakly bound atoms. The excess energy and density with respect to the crystal are well reproduced in addition to radial distribution function, angular distribution functions, and vibrational density of states. No atom in the optimal configuration is locally in a crystalline environment as deduced by ring analysis and common neighbor analysis, but coordination defects are present at a level of 1%-2%. The simulated samples provide structural models of this archetypal disordered covalent material without preconceived notion of the atomic ordering or fitting to experimental data.

Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Saini, Subhash (Technical Monitor)

1998-01-01

Adatom chains, precise structures artificially created on an atomically regulated surface, are the smallest possible candidates for future nanoelectronics. Since all the devices are created by combining adatom chains precisely prepared with atomic precision, device characteristics are predictable, and free from deviations due to accidental structural defects. In this atomic dimension, however, an analogy to the current semiconductor devices may not work. For example, Si structures are not always semiconducting. Adatom states do not always localize at the substrate surface when adatoms form chemical bonds to the substrate atoms. Transport properties are often determined for the entire system of the chain and electrodes, and not for chains only. These fundamental issues are discussed, which will be useful for future device considerations.

Structural basis for the mechanism of inhibition of uridine phosphorylase from Salmonella typhimurium

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

Lashkov, A. A.; Zhukhlistova, N. E.; Sotnichenko, S. E.

2010-01-15

The three-dimensional structures of three complexes of Salmonella typhimurium uridine phosphorylase with the inhibitor 2,2'-anhydrouridine, the substrate PO{sub 4}, and with both the inhibitor 2,2'-anhydrouridine and the substrate PO{sub 4} (a binary complex) were studied in detail by X-ray diffraction. The structures of the complexes were refined at 2.38, 1.5, and 1.75 A resolution, respectively. Changes in the three-dimensional structure of the subunits in different crystal structures are considered depending on the presence or absence of the inhibitor molecule and (or) the phosphate ion in the active site of the enzyme. The presence of the phosphate ion in the phosphate-bindingmore » site was found to substantially change the orientations of the side chains of the amino-acid residues Arg30, Arg91, and Arg48 coordinated to this ion. A comparison showed that the highly flexible loop L9 is unstable. The atomic coordinates of the refined structures of the complexes and the corresponding structure factors were deposited in the Protein Data Bank (their PDB ID codes are 3DD0 and 3C74). The experimental data on the spatial reorganization of the active site caused by changes in its functional state from the unligated to the completely inhibited state suggest the structural basis for the mechanism of inhibition of Salmonella typhimurium uridine phosphorylase.« less

Parallel Grand Canonical Monte Carlo (ParaGrandMC) Simulation Code

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin I.

2016-01-01

This report provides an overview of the Parallel Grand Canonical Monte Carlo (ParaGrandMC) simulation code. This is a highly scalable parallel FORTRAN code for simulating the thermodynamic evolution of metal alloy systems at the atomic level, and predicting the thermodynamic state, phase diagram, chemical composition and mechanical properties. The code is designed to simulate multi-component alloy systems, predict solid-state phase transformations such as austenite-martensite transformations, precipitate formation, recrystallization, capillary effects at interfaces, surface absorption, etc., which can aid the design of novel metallic alloys. While the software is mainly tailored for modeling metal alloys, it can also be used for other types of solid-state systems, and to some degree for liquid or gaseous systems, including multiphase systems forming solid-liquid-gas interfaces.

Atomistic Simulations of Surface Cross-Slip Nucleation in Face-Centered Cubic Nickel and Copper (Postprint)

DTIC Science & Technology

2013-02-15

molecular dynamics code, LAMMPS [9], developed at Sandia National Laboratory. The simulation cell is a rectangular parallelepiped, with the z-axis...with assigned energies within LAMMPs of greater than 4.42 eV (Ni) or 3.52 eV (Cu) (the energy of atoms in the stacking fault region), the partial...molecular dynamics code LAMMPS , which was developed at Sandia National Laboratory by Dr. Steve Plimpton and co-workers. This work was supported by the

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

PubMed

Vaguine, A A; Richelle, J; Wodak, S J

1999-01-01

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

Structural Investigation of the (010) Surface of the Al13Fe4 Catalyst

NASA Astrophysics Data System (ADS)

Ledieu, J.; Gaudry, É.; Loli, L. N. Serkovic; Villaseca, S. Alarcón; de Weerd, M.-C.; Hahne, M.; Gille, P.; Grin, Y.; Dubois, J.-M.; Fournée, V.

2013-02-01

We have investigated the structure of the Al13Fe4(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as “glue” atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al13Fe4 catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster , Nat. Mater. 11, 690 (2012)NMAACR1476-1122].

Changing optical band structure with single photons

NASA Astrophysics Data System (ADS)

Albrecht, Andreas; Caneva, Tommaso; Chang, Darrick E.

2017-11-01

Achieving strong interactions between individual photons enables a wide variety of exciting possibilities in quantum information science and many-body physics. Cold atoms interfaced with nanophotonic structures have emerged as a platform to realize novel forms of nonlinear interactions. In particular, when atoms are coupled to a photonic crystal waveguide, long-range atomic interactions can arise that are mediated by localized atom-photon bound states. We theoretically show that in such a system, the absorption of a single photon can change the band structure for a subsequent photon. This occurs because the first photon affects the atoms in the chain in an alternating fashion, thus leading to an effective period doubling of the system and a new optical band structure for the composite atom-nanophotonic system. We demonstrate how this mechanism can be engineered to realize a single-photon switch, where the first incoming photon switches the system from being highly transmissive to highly reflective, and analyze how signatures can be observed via non-classical correlations of the outgoing photon field.

A microscopic study investigating the structure of SnSe surfaces

NASA Astrophysics Data System (ADS)

Kim, Sang-ui; Duong, Anh-Tuan; Cho, Sunglae; Rhim, S. H.; Kim, Jungdae

2016-09-01

SnSe has been widely studied due to its many potential applications that take advantage of its excellent thermoelectric, photovoltaic, and optoelectronic properties. However, experimental investigations into the microscopic structure of SnSe remain largely unexplored. Herein, for the first time, the atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM) and density functional theory (DFT) calculations. The cleaved surface of SnSe is comprised of covalently bonded Se and Sn atoms in zigzag patterns. However, rectangular periodicity was observed in the atomic images of SnSe surfaces for filled and empty state probing. Detailed atomic structures are analyzed by DFT calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms.

Multibillion-atom Molecular Dynamics Simulations of Plasticity, Spall, and Ejecta

NASA Astrophysics Data System (ADS)

Germann, Timothy C.

2007-06-01

Modern supercomputing platforms, such as the IBM BlueGene/L at Lawrence Livermore National Laboratory and the Roadrunner hybrid supercomputer being built at Los Alamos National Laboratory, are enabling large-scale classical molecular dynamics simulations of phenomena that were unthinkable just a few years ago. Using either the embedded atom method (EAM) description of simple (close-packed) metals, or modified EAM (MEAM) models of more complex solids and alloys with mixed covalent and metallic character, simulations containing billions to trillions of atoms are now practical, reaching volumes in excess of a cubic micron. In order to obtain any new physical insights, however, it is equally important that the analysis of such systems be tractable. This is in fact possible, in large part due to our highly efficient parallel visualization code, which enables the rendering of atomic spheres, Eulerian cells, and other geometric objects in a matter of minutes, even for tens of thousands of processors and billions of atoms. After briefly describing the BlueGene/L and Roadrunner architectures, and the code optimization strategies that were employed, results obtained thus far on BlueGene/L will be reviewed, including: (1) shock compression and release of a defective EAM Cu sample, illustrating the plastic deformation accompanying void collapse as well as the subsequent void growth and linkup upon release; (2) solid-solid martensitic phase transition in shock-compressed MEAM Ga; and (3) Rayleigh-Taylor fluid instability modeled using large-scale direct simulation Monte Carlo (DSMC) simulations. I will also describe our initial experiences utilizing Cell Broadband Engine processors (developed for the Sony PlayStation 3), and planned simulation studies of ejecta and spall failure in polycrystalline metals that will be carried out when the full Petaflop Opteron/Cell Roadrunner supercomputer is assembled in mid-2008.

Atomic and electronic structure of the silicon and silicon-metal Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, KSi{sub 20} nanoparticles

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

Borshch, N. A., E-mail: ssd18@phys.vsu.ru; Pereslavtseva, N. S.; Kurganskii, S. I.

The results of atomic-structure optimization and calculation of the electronic structure of the Si{sub 20}, Si{sub 20}{sup -}, NaSi{sub 20}, and KSi{sub 20} clusters are reported. The PM3 and AM1 semiempirical methods were used in the calculations. It is shown that the Na and K atoms stabilize the fullerene-like silicon structure. The effect of configuration of the clusters on their electronic structure is analyzed.

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

NASA Astrophysics Data System (ADS)

Thompson, A. P.; Swiler, L. P.; Trott, C. R.; Foiles, S. M.; Tucker, G. J.

2015-03-01

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109