Impurity-doped Si10 cluster: Understanding the structural and electronic properties from first-principles calculations

NASA Astrophysics Data System (ADS)

Majumder, Chiranjib; Kulshreshtha, S. K.

2004-12-01

Structural and electronic properties of metal-doped silicon clusters ( MSi10 , M=Li , Be, B, C, Na, Mg, Al, and Si) have been investigated via ab initio molecular dynamics simulation under the formalism of the density functional theory. The exchange-correlation energy has been calculated using the generalized gradient approximation method. Several stable isomers of MSi10 clusters have been identified based on different initial configurations and their relative stabilities have been analyzed. From the results it is revealed that the location of the impurity atom depends on the nature of interaction between the impurity atom and the host cluster and the size of the impurty atom. Whereas Be and B atoms form stable isomers, the impurity atom being placed at the center of the bicapped tetragonal antiprism structure of the Si10 cluster, all other elements diffuse outside the cage of Si10 cluster. Further, to understand the stability and the chemical bonding, the LCAO-MO based all electron calculations have been carried out for the lowest energy isomers using the hybrid B3LYP energy functional. Based on the interaction energy of the M atoms with Si10 clusters it is found that p-p interaction dominates over the s-p interaction and smaller size atoms interact more strongly. Based on the binding energy, the relative stability of MSi10 clusters is found to follow the order of CSi10>BSi10>BeSi10>Si11>AlSi10>LiSi10>NaSi10>MgSi10 , leading one to infer that while the substitution of C, B and Be enhances the stability of the Si11 cluster, others have an opposite effect. The extra stability of the BeSi10 clusters is due to its encapsulated close packed structure and large energy gap between the HOMO and LUMO energy levels.

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

Shao, Jiahang; Antipov, Sergey P.; Baryshev, Sergey V.

Field emission from a solid metal surface has been continuously studied for a century over macroscopic to atomic scales. It is general knowledge that, other than the surface properties, the emitted current is governed solely by the applied electric field. A pin cathode has been used to study the dependence of field emission on stored energy in an L-band rf gun. The stored energy was changed by adjusting the axial position (distance between the cathode base and the gun back surface) of the cathode while the applied electric field on the cathode tip is kept constant. Avery strong correlation ofmore » the field-emission current with the stored energy has been observed. While eliminating all possible interfering sources, an enhancement of the current by a factor of 5 was obtained as the stored energy was increased by a factor of 3. It implies that under certain circumstances a localized field emission may be significantly altered by the global parameters in a system.« less

Defect structures induced by high-energy displacement cascades in γ uranium

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

Miao, Yinbin; Beeler, Benjamin; Deo, Chaitanya

Displacement cascade simulations were conducted for the c uranium system based on molecular dynamics. A recently developed modified embedded atom method (MEAM) potential was employed to replicate the atomic interactions while an embedded atom method (EAM) potential was adopted to help characterize the defect structures induced by the displacement cascades. The atomic displacement process was studied by providing primary knock-on atoms (PKAs) with kinetic energies from 1 keV to 50 keV. The influence of the PKA incident direction was examined. The defect structures were analyzed after the systems were fully relaxed. The states of the self-interstitial atoms (SIAs) were categorizedmore » into various types of dumbbells, the crowdion, and the octahedral interstitial. The voids were determined to have a polyhedral shape with {110} facets. The size distribution of the voids was also obtained. The results of this study not only expand the knowledge of the microstructural evolution in irradiated c uranium, but also provide valuable references for the radiation-induced defects in uranium alloy fuels.« less

Machine learning reveals orbital interaction in materials

NASA Astrophysics Data System (ADS)

Lam Pham, Tien; Kino, Hiori; Terakura, Kiyoyuki; Miyake, Takashi; Tsuda, Koji; Takigawa, Ichigaku; Chi Dam, Hieu

2017-12-01

We propose a novel representation of materials named an 'orbital-field matrix (OFM)', which is based on the distribution of valence shell electrons. We demonstrate that this new representation can be highly useful in mining material data. Experimental investigation shows that the formation energies of crystalline materials, atomization energies of molecular materials, and local magnetic moments of the constituent atoms in bimetal alloys of lanthanide metal and transition-metal can be predicted with high accuracy using the OFM. Knowledge regarding the role of the coordination numbers of the transition-metal and lanthanide elements in determining the local magnetic moments of the transition-metal sites can be acquired directly from decision tree regression analyses using the OFM.

Safe transport of radioactive materials in Egypt

NASA Astrophysics Data System (ADS)

El-Shinawy, Rifaat M. K.

1994-07-01

In Egypt the national regulations for safe transport of radioactive materials (RAM) are based on the International Atomic Energy Agency (IAEA) regulations. In addition, regulations for the safe transport of these materials through the Suez Canal (SC) were laid down by the Egyptian Atomic Energy Authority (EAEA) and the Suez Canal Authority (SCA). They are continuously updated to meet the increased knowledge and the gained experience. The technical and protective measures taken during transport of RAM through SC are mentioned. Assessment of the impact of transporting radioactive materials through the Suez Canal using the INTERTRAN computer code was carried out in cooperation with IAEA. The transported activities and empty containers, the number of vessels carrying RAM through the canal from 1963 to 1991 and their nationalities are also discussed. The protective measures are mentioned.A review of the present situation of the radioactive wastes storage facilities at the Atomic Energy site at Inshas is given along with the regulation for safe transportation and disposal of radioactive wastes

A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

PubMed

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

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.

Systematics of Rydberg Series of Diatomic Molecules and Correlation Diagrams

NASA Astrophysics Data System (ADS)

Lee, Chun-Woo

2015-06-01

Rydberg states are studied for H2, Li2, HeH, LiH and BeH using the multi-reference configuration interaction (MRCI) method. The systematics and regularities of the physical properties such as potential energies curves (PECs), quantum defect curves, permanent dipole moment and transition dipole moment curves of the Rydberg series are studied. They are explained using united atom perturbation theory by Bingel and Byers-Brown, Fermi model, Stark theory, and Mulliken's theory. Interesting mirror relationships of the dipole moments are observed between l-mixed Rydberg series, indicating that the members of the l-mixed Rydberg series have dipole moments with opposite directions, which are related to the reversal of the polarity of a dipole moment at the avoided crossing points. The assignment of highly excited states is difficult because of the usual absence of the knowledge on the behaviors of potential energy curves at small internuclear separation whereby the correlation between the united atom limit and separated atoms limit cannot be given. All electron MRCI calculations of PECs are performed to obtain the correlation diagrams between Rydberg orbitals at the united-atom and separated atoms limits.

Equilibrium geometries, electronic and magnetic properties of small AunNi- (n = 1-9) clusters

NASA Astrophysics Data System (ADS)

Tang, Cui-Ming; Chen, Xiao-Xu; Yang, Xiang-Dong

2014-05-01

Geometrical, electronic and magnetic properties of small AunNi- (n = 1-9) clusters have been investigated based on density functional theory (DFT) at PW91P86 level. An extensive structural search shows that the relative stable structures of AunNi- (n = 1-9) clusters adopt 2D structure for n = 1-5, 7 and 3D structure for n = 6, 8-9. And the substitution of a Ni atom for an Au atom in the Au-n+1 cluster obviously changes the structure of the host cluster. Moreover, an odd-even alternation phenomenon has been found for HOMO-LUMO energy gaps, indicating that the relative stable structures of the AunNi- clusters with odd-numbered gold atoms have a higher relative stability. Finally, the natural population analysis (NPA) and the vertical detachment energies (VDE) are studied, respectively. The theoretical values of VDE are reported for the first time to our best knowledge.

Quantum Chemical Topology: Knowledgeable atoms in peptides

NASA Astrophysics Data System (ADS)

Popelier, Paul L. A.

2012-06-01

The need to improve atomistic biomolecular force fields remains acute. Fortunately, the abundance of contemporary computing power enables an overhaul of the architecture of current force fields, which typically base their electrostatics on fixed atomic partial charges. We discuss the principles behind the electrostatics of a more realistic force field under construction, called QCTFF. At the heart of QCTFF lies the so-called topological atom, which is a malleable box, whose shape and electrostatics changes in response to a changing environment. This response is captured by a machine learning method called Kriging. Kriging directly predicts each multipole moment of a given atom (i.e. the output) from the coordinates of the nuclei surrounding this atom (i.e. the input). This procedure yields accurate interatomic electrostatic energies, which form the basis for future-proof progress in force field design.

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.

Current at Metal-Organic Interfaces

NASA Astrophysics Data System (ADS)

Kern, Klaus

2012-02-01

Charge transport through atomic and molecular constrictions greatly affects the operation and performance of organic electronic devices. Much of our understanding of the charge injection and extraction processes in these systems relays on our knowledge of the electronic structure at the metal-organic interface. Despite significant experimental and theoretical advances in studying charge transport in nanoscale junctions, a microscopic understanding at the single atom/molecule level is missing. In the present talk I will present our recent results to probe directly the nanocontact between single molecules and a metal electrode using scanning probe microscopy and spectroscopy. The experiments provide unprecedented microscopic details of single molecule and atom junctions and open new avenues to study quantum critical and many body phenomena at the atomic scale. Implications for energy conversion devices and carbon based nanoelectronics will also be discussed.

Multiloop atom interferometer measurements of chameleon dark energy in microgravity

NASA Astrophysics Data System (ADS)

Chiow, Sheng-wey; Yu, Nan

2018-02-01

Chameleon field is one of the promising candidates of dark energy scalar fields. As in all viable candidate field theories, a screening mechanism is implemented to be consistent with all existing tests of general relativity. The screening effect in the chameleon theory manifests its influence limited only to the thin outer layer of a bulk object, thus producing extra forces orders of magnitude weaker than that of the gravitational force of the bulk. For pointlike particles such as atoms, the depth of screening is larger than the size of the particle, such that the screening mechanism is ineffective and the chameleon force is fully expressed on the atomic test particles. Extra force measurements using atom interferometry are thus much more sensitive than bulk mass based measurements, and indeed have placed the most stringent constraints on the parameters characterizing chameleon field. In this paper, we present a conceptual measurement approach for chameleon force detection using atom interferometry in microgravity, in which multiloop atom interferometers exploit specially designed periodic modulation of chameleon fields. We show that major systematics of the dark energy force measurements, i.e., effects of gravitational forces and their gradients, can be suppressed below all hypothetical chameleon signals in the parameter space of interest.

Neutral-atom electron binding energies from relaxed-orbital relativistic Hartree-Fock-Slater calculations for Z between 2 and 106

NASA Technical Reports Server (NTRS)

Huang, K.-N.; Aoyagi, M.; Mark, H.; Chen, M. H.; Crasemann, B.

1976-01-01

Electron binding energies in neutral atoms have been calculated relativistically, with the requirement of complete relaxation. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first-order correction to the local approximation was thus included. Quantum-electrodynamic corrections were made. For all elements with atomic numbers ranging from 2 to 106, the following quantities are listed: total energies, electron kinetic energies, electron-nucleus potential energies, electron-electron potential energies consisting of electrostatic and Breit interaction (magnetic and retardation) terms, and vacuum polarization energies. Binding energies including relaxation are listed for all electrons in all atoms over the indicated range of atomic numbers. A self-energy correction is included for the 1s, 2s, and 2p(1/2) levels. Results for selected atoms are compared with energies calculated by other methods and with experimental values.

Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

PubMed Central

2015-01-01

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations. PMID:25290376

Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2014-10-16

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Determining Nuclear Fingerprints: Glove Boxes, Radiation Protection, and the International Atomic Energy Agency.

PubMed

Rentetzi, Maria

2017-06-01

In a nuclear laboratory, a glove box is a windowed, sealed container equipped with two flexible gloves that allow the user to manipulate nuclear materials from the outside in an ostensibly safe environment. As a routine laboratory device, it invites neglect from historians and storytellers of science. Yet, since especially the Gulf War, glove boxes have put the interdependence of science, diplomacy, and politics into clear relief. Standing at the intersection of history of science and international history, technological materials and devices such as the glove box can provide penetrating insight into the role of international diplomatic organizations to the global circulation and control of scientific knowledge. The focus here is on the International Atomic Energy Agency. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

A Technology-Enhanced Unit of Modeling Static Electricity: Integrating scientific explanations and everyday observations

NASA Astrophysics Data System (ADS)

Shen, Ji; Linn, Marcia C.

2011-08-01

What trajectories do students follow as they connect their observations of electrostatic phenomena to atomic-level visualizations? We designed an electrostatics unit, using the knowledge integration framework to help students link observations and scientific ideas. We analyze how learners integrate ideas about charges, charged particles, energy, and observable events. We compare learning enactments in a typical school and a magnet school in the USA. We use pre-tests, post-tests, embedded notes, and delayed post-tests to capture the trajectories of students' knowledge integration. We analyze how visualizations help students grapple with abstract electrostatics concepts such as induction. We find that overall students gain more sophisticated ideas. They can interpret dynamic, interactive visualizations, and connect charge- and particle-based explanations to interpret observable events. Students continue to have difficulty in applying the energy-based explanation.

School and the nuclear energy problems: Preliminary analysis of a questionnaire

NASA Astrophysics Data System (ADS)

Conforto, A. M.; Danusso, L.; Signorini, C.

1986-11-01

The feelings of Italian secondary school and university students toward the utilization of nuclear energy were explored, questioning 600 students aged 16 to 24. The study was carried on in 85/86, that is before the Chernobyl accident. The results show a relatively low level of knowledge about natural and radiation phenomena, and a weak correlation between atomic war possibility which is feared, and the attitude towards the pacific uses of atomic energy.

A Method to Estimate the Atomic Number and Mass Thickness of Intervening Materials in Uranium and Plutonium Gamma-Ray Spectroscopy Measurements

NASA Astrophysics Data System (ADS)

Streicher, Michael; Brown, Steven; Zhu, Yuefeng; Goodman, David; He, Zhong

2016-10-01

To accurately characterize shielded special nuclear materials (SNM) using passive gamma-ray spectroscopy measurement techniques, the effective atomic number and the thickness of shielding materials must be measured. Intervening materials between the source and detector may affect the estimated source isotopics (uranium enrichment and plutonium grade) for techniques which rely on raw count rates or photopeak ratios of gamma-ray lines separated in energy. Furthermore, knowledge of the surrounding materials can provide insight regarding the configuration of a device containing SNM. The described method was developed using spectra recorded using high energy resolution CdZnTe detectors, but can be expanded to any gamma-ray spectrometers with energy resolution of better than 1% FWHM at 662 keV. The effective atomic number, Z, and mass thickness of the intervening shielding material are identified by comparing the relative attenuation of different gamma-ray lines and estimating the proportion of Compton scattering interactions to photoelectric absorptions within the shield. While characteristic Kα x-rays can be used to identify shielding materials made of high Z elements, this method can be applied to all shielding materials. This algorithm has adequately estimated the effective atomic number for shields made of iron, aluminum, and polyethylene surrounding uranium samples using experimental data. The mass thicknesses of shielding materials have been estimated with a standard error of less than 1.3 g/cm2 for iron shields up to 2.5 cm thick. The effective atomic number was accurately estimated to 26 ± 5 for all iron thicknesses.

Laboratory Studies of Thermal Energy Charge Transfer of Multiply Charged Ions in Astrophysical Plasmas

NASA Technical Reports Server (NTRS)

Kwong, Victor H. S.

2003-01-01

The laser ablation/ion storage facility at the UNLV Physics Department has been dedicated to the study of atomic and molecular processes in low temperature plasmas. Our program focuses on the charge transfer (electron capture) of multiply charged ions and neutrals important in astrophysics. The electron transfer reactions with atoms and molecules is crucial to the ionization condition of neutral rich photoionized plasmas. With the successful deployment of the Far Ultraviolet Spectroscopic Explorer (FUSE) and the Chandra X-ray Observatory by NASA high resolution VUV and X-ray emission spectra fiom various astrophysical objects have been collected. These spectra will be analyzed to determine the source of the emission and the chemical and physical environment of the source. The proper interpretation of these spectra will require complete knowledge of all the atomic processes in these plasmas. In a neutral rich environment, charge transfer can be the dominant process. The rate coefficients need to be known accurately. We have also extended our charge transfer measurements to KeV region with a pulsed ion beam. The inclusion of this facility into our current program provides flexibility in extending the measurement to higher energies (KeV) if needed. This flexibility enables us to address issues of immediate interest to the astrophysical community as new observations are made by high resolution space based observatories.

Hydrocarbon-Fueled Scramjet Research at Hypersonic Mach Numbers

DTIC Science & Technology

2005-03-31

oxide O atomic oxygen 02 molecular oxygen OH hydroxyl radical ppm parts per million PD photodiode PLLF planar laser-induced fluorescence PMT...photomultiplier tube RAM random access memory RANS Reynolds-averaged Navier-Stokes RET rotational energy transfer TDLAS tunable diode laser absorption...here extend this knowledge base to flight at Mach 11.5. Griffiths (2004) used a tunable diode laser absorption spectroscopy ( TDLAS ) system to measure

Ab initio calculation of diffusion barriers for Cu adatom hopping on Cu(1 0 0) surface and evolution of atomic configurations

NASA Astrophysics Data System (ADS)

Zhang, Wei; Gan, Jie; Li, Qian; Gao, Kun; Sun, Jian; Xu, Ning; Ying, Zhifeng; Wu, Jiada

2011-06-01

The self-diffusion dynamics of Cu adatoms on Cu(1 0 0) surface has been studied based on the calculation of the energy barriers for various hopping events using lattice-gas based approach and a modified model. To simplify the description of the interactions and the calculation of the energy barrier, a three-tier hierarchy of description of atomic configurations was conceived in which the active adatom and its nearest atoms were chosen to constitute basic configuration and taken as a whole to study many-body interactions of the atoms in various atomic configurations, whereas the impacts of the next nearest atoms on the diffusion of the active adatom were considered as multi-site interactions. Besides the simple hopping of single adatoms, the movements of dimers and trimers as the results of multiple hopping events have also been examined. Taking into account the hopping events of all adatoms, the stability of atomic configurations has been examined and the evolution of atomic configurations has also been analyzed.

A NEW QUANTUM MECHANICAL THEORY OF EVOLUTION OF UNIVERSE AND LIFE

PubMed Central

Nigam, M C

1990-01-01

Based upon the principles of ancient science of Life, which admits both consciousness and matter, a new Quantum Mechanical theory of evolution of universe and life is propounded. The theory advocates: Right from the time, the evolution of universe takes place, life also starts evolving energies and ethereal – consciousness (subtler and real) in anti-electrons, as the complimentary partners. The material body acquires electrons for cordoning of atomic nuclei and displaying its manifestation, in the three spatial dimensions in scale of time. The ethereal consciousness acquires anti electrons for gaining necessary energy for superimposing itself over any of the manifested bodies of equivalent electronic energy and deriving the bliss of materialization. The theory is based upon the solid foundation of the ancient science (ethereal consciousness) laid down by the ancient seekers of knowledge like Kapila and Caraka who interpret many of the riddles of modern science on the frontiers of various disciplines of knowledge. PMID:22556513

Predicting protein complex geometries with a neural network.

PubMed

Chae, Myong-Ho; Krull, Florian; Lorenzen, Stephan; Knapp, Ernst-Walter

2010-03-01

A major challenge of the protein docking problem is to define scoring functions that can distinguish near-native protein complex geometries from a large number of non-native geometries (decoys) generated with noncomplexed protein structures (unbound docking). In this study, we have constructed a neural network that employs the information from atom-pair distance distributions of a large number of decoys to predict protein complex geometries. We found that docking prediction can be significantly improved using two different types of polar hydrogen atoms. To train the neural network, 2000 near-native decoys of even distance distribution were used for each of the 185 considered protein complexes. The neural network normalizes the information from different protein complexes using an additional protein complex identity input neuron for each complex. The parameters of the neural network were determined such that they mimic a scoring funnel in the neighborhood of the native complex structure. The neural network approach avoids the reference state problem, which occurs in deriving knowledge-based energy functions for scoring. We show that a distance-dependent atom pair potential performs much better than a simple atom-pair contact potential. We have compared the performance of our scoring function with other empirical and knowledge-based scoring functions such as ZDOCK 3.0, ZRANK, ITScore-PP, EMPIRE, and RosettaDock. In spite of the simplicity of the method and its functional form, our neural network-based scoring function achieves a reasonable performance in rigid-body unbound docking of proteins. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

A vacuum gauge based on an ultracold gas

NASA Astrophysics Data System (ADS)

Makhalov, V. B.; Turlapov, A. V.

2017-06-01

We report the design and application of a primary vacuum gauge based on an ultracold gas of atoms in an optical dipole trap. The pressure is calculated from the confinement time for atoms in the trap. The relationship between pressure and confinement time is established from the first principles owing to elimination of all channels introducing losses, except for knocking out an atom from the trap due to collisions with a residual gas particle. The method requires the knowledge of the gas chemical composition in the vacuum chamber, and, in the absence of this information, the systematic error is less than that of the ionisation sensor.

Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis.

PubMed

Wang, Feng; Islam, Shawkat; Vasilyev, Vladislav

2015-11-16

Two very different quantum mechanically based energy decomposition analyses (EDA) schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS) based on the Amsterdam Density Functional (ADF) package and the other is natural EDA (NEDA) based in the General Atomic and Molecular Electronic Structure System (GAMESS) package. It reveals that in addition to the model (theory and basis set), the fragmentation channels more significantly affect the interaction energy terms (Δ E ) between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel-the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative) polarization (POL) and charge transfer (CL) energies prefers the eclipsed ferrocene. The repulsive (positive) deformation (DEF) energy, which is dominated by the cyclopentadienyle (Cp) rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO) analysis indicates that all NBO energies, total Lewis (no Fe) and lone pair (LP) deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP) of the Fe atom and the acceptor antibond (BD*) NBOs of all C-C and C-H bonds in the ligand, LP(Fe)-BD*(C-C & C-H), which strongly stabilizes the eclipsed (D 5h ) conformation by -457.6 kcal·mol -1 .

Partitioning dynamic electron correlation energy: Viewing Møller-Plesset correlation energies through Interacting Quantum Atom (IQA) energy partitioning

NASA Astrophysics Data System (ADS)

McDonagh, James L.; Vincent, Mark A.; Popelier, Paul L. A.

2016-10-01

Here MP2, MP3 and MP4(SDQ) are energy-partitioned for the first time within the Interacting Quantum Atoms (IQA) context, as proof-of-concept for H2, He2 and HF. Energies are decomposed into four primary energy contributions: (i) atomic self-energies, and atomic interaction energies comprising of (ii) Coulomb, (iii) exchange and (iv) dynamic election correlation terms. We generate and partition one- and two-particle density-matrices to obtain all atomic energy components. This work suggests that, in terms of Van der Waals dispersion, the correlation energies represent an atomic stabilisation, by proximity to other atoms, as opposed to direct interactions with other nearby atoms.

XCOM intrinsic dimensionality for low-Z elements at diagnostic energies

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

Bornefalk, Hans

2012-02-15

Purpose: To determine the intrinsic dimensionality of linear attenuation coefficients (LACs) from XCOM for elements with low atomic number (Z = 1-20) at diagnostic x-ray energies (25-120 keV). H{sub 0}{sup q}, the hypothesis that the space of LACs is spanned by q bases, is tested for various q-values. Methods: Principal component analysis is first applied and the LACs are projected onto the first q principal component bases. The residuals of the model values vs XCOM data are determined for all energies and atomic numbers. Heteroscedasticity invalidates the prerequisite of i.i.d. errors necessary for bootstrapping residuals. Instead wild bootstrap is applied,more » which, by not mixing residuals, allows the effect of the non-i.i.d residuals to be reflected in the result. Credible regions for the eigenvalues of the correlation matrix for the bootstrapped LAC data are determined. If subsequent credible regions for the eigenvalues overlap, the corresponding principal component is not considered to represent true data structure but noise. If this happens for eigenvalues l and l + 1, for any l{<=}q, H{sub 0}{sup q} is rejected. Results: The largest value of q for which H{sub 0}{sup q} is nonrejectable at the 5%-level is q = 4. This indicates that the statistically significant intrinsic dimensionality of low-Z XCOM data at diagnostic energies is four. Conclusions: The method presented allows determination of the statistically significant dimensionality of any noisy linear subspace. Knowledge of such significant dimensionality is of interest for any method making assumptions on intrinsic dimensionality and evaluating results on noisy reference data. For LACs, knowledge of the low-Z dimensionality might be relevant when parametrization schemes are tuned to XCOM data. For x-ray imaging techniques based on the basis decomposition method (Alvarez and Macovski, Phys. Med. Biol. 21, 733-744, 1976), an underlying dimensionality of two is commonly assigned to the LAC of human tissue at diagnostic energies. The finding of a higher statistically significant dimensionality thus raises the question whether a higher assumed model dimensionality (now feasible with the advent of multibin x-ray systems) might also be practically relevant, i.e., if better tissue characterization results can be obtained.« less

Hybrid statistics-simulations based method for atom-counting from ADF STEM images.

PubMed

De Wael, Annelies; De Backer, Annick; Jones, Lewys; Nellist, Peter D; Van Aert, Sandra

2017-06-01

A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials. Copyright © 2017 Elsevier B.V. All rights reserved.

Calyx{trademark} EA implementation at AECB

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

NONE

1997-12-31

This report describes a project to examine the applicability of a knowledge-based decision support software for environmental assessment (Calyx) to assist the Atomic Energy Control Board in environmental screenings, assessment, management, and database searches. The report begins with background on the Calyx software and then reviews activities with regard to modification of the Calyx knowledge base for application to the nuclear sector. This is followed by lists of standard activities handled by the software and activities specific to the Board; the hierarchy of environmental components developed for the Board; details of impact rules that describe the conditions under which environmentalmore » impacts will occur (the bulk of the report); information on mitigation and monitoring rules and on instance data; and considerations for future work on implementing Calyx at the Board. Appendices include an introduction to expert systems and an overview of the Calyx knowledge base structure.« less

10 CFR 95.36 - Access by representatives of the International Atomic Energy Agency or by participants in other...

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2014-01-01

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2010-01-01

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28 CFR 13.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Administration DEPARTMENT OF JUSTICE ATOMIC WEAPONS AND SPECIAL NUCLEAR MATERIALS REWARDS REGULATIONS § 13.3 Definitions. Atomic energy means all forms of energy released in the course of nuclear fission or nuclear transformation. Atomic weapon means any device utilizing atomic energy, exclusive of the means for transporting...

28 CFR 13.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Administration DEPARTMENT OF JUSTICE ATOMIC WEAPONS AND SPECIAL NUCLEAR MATERIALS REWARDS REGULATIONS § 13.3 Definitions. Atomic energy means all forms of energy released in the course of nuclear fission or nuclear transformation. Atomic weapon means any device utilizing atomic energy, exclusive of the means for transporting...

28 CFR 13.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Administration DEPARTMENT OF JUSTICE ATOMIC WEAPONS AND SPECIAL NUCLEAR MATERIALS REWARDS REGULATIONS § 13.3 Definitions. Atomic energy means all forms of energy released in the course of nuclear fission or nuclear transformation. Atomic weapon means any device utilizing atomic energy, exclusive of the means for transporting...

28 CFR 13.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Administration DEPARTMENT OF JUSTICE ATOMIC WEAPONS AND SPECIAL NUCLEAR MATERIALS REWARDS REGULATIONS § 13.3 Definitions. Atomic energy means all forms of energy released in the course of nuclear fission or nuclear transformation. Atomic weapon means any device utilizing atomic energy, exclusive of the means for transporting...

28 CFR 13.3 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Administration DEPARTMENT OF JUSTICE ATOMIC WEAPONS AND SPECIAL NUCLEAR MATERIALS REWARDS REGULATIONS § 13.3 Definitions. Atomic energy means all forms of energy released in the course of nuclear fission or nuclear transformation. Atomic weapon means any device utilizing atomic energy, exclusive of the means for transporting...

On the application of accelerated molecular dynamics to liquid water simulations.

PubMed

de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew

2006-11-16

Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.

Relativistic calculations of atomic properties

NASA Astrophysics Data System (ADS)

Kaur, Jasmeet; Sahoo, B. K.; Arora, Bindiya

2017-04-01

Singly charged ions are engaging candidates in many areas of Physics. They are especially important in astrophysics for evaluating the radiative properties of stellar objects, in optical frequency standards and for fundamental physics studies such as searches for permanent electric dipole moments and atomic parity violation. Interpretation of these experiments often requires a knowledge of their transition wavelengths and electric dipole amplitudes. In this work, we discuss the calculation of various properties of alkaline earth ions. The relativistic all-order SD method in which all single and double excitations of the Dirac-Fock wave function are included, is used to calculate these atomic properties. We use this method for evaluation of electric dipole matrix elements of alkaline earth ions. Combination of these matrix elements with experimental energies allow to obtain the polarizabilities of ground and excited states of ions. We discuss the applications of estimated polarizabiities as a function of imaginary frequencies in the calculations of long-range atom-ion interactions. We have also located the magic wavelengths for nS1 / 2 - nD3 / 2 , 5 / 2 transitions of alkaline earth ions. These calculated properties will be highly valuable to atomic and astrophysics community. UGC-BSR Grant No. F.7-273/2009/BSR.

Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

PubMed

Wu, Guosheng; Robertson, Daniel H; Brooks, Charles L; Vieth, Michal

2003-10-01

The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated-annealing-based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid-based approximations to explicit all-atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all-atom representation of the protein (full force field) is used, while a lower accuracy of 66-76% is observed for grid-based methods. All docking experiments considered a 41-member protein-ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid-based docking is achieved if the explicit all-atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower-accuracy grid-based energy representations can be effectively used when followed with full force field minimization. The results of these grid-based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures. Copyright 2003 Wiley Periodicals, Inc.

Fifth Semiannual Report of the Commission to the Congress: Atomic Energy Development, 1947- 1948

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

Lilienthal, David E.; Bacher, Robert F.; Pike, Sumner T.

1949-01-01

The document represents the fifth semiannual report to Congress, covering specifically the various developments in atomic energy since the inception of the Atomic Energy Commission in 1946. This fifth report represents an expansion of effort in all phases of atomic energy development and is prepared against a background of world affairs.

High-resolution comparative modeling with RosettaCM.

PubMed

Song, Yifan; DiMaio, Frank; Wang, Ray Yu-Ruei; Kim, David; Miles, Chris; Brunette, Tj; Thompson, James; Baker, David

2013-10-08

We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%. Copyright © 2013 Elsevier Ltd. All rights reserved.

Change of Energy of the Cubic Subnanocluster of Iron Under Influence of Interstitial and Substitutional Atoms.

PubMed

Nedolya, Anatoliy V; Bondarenko, Natalya V

2016-12-01

Energy change of an iron face-centred cubic subnanocluster was evaluated using molecular mechanics method depending on the position of a carbon interstitial atom and substitutional atoms of nickel. Calculations of all possible positions of impurity atoms show that the energy change of the system are discrete and at certain positions of the atoms are close to continuous.In terms of energy, when all impurity atoms are on the same edge of an atomic cluster, their positions are more advantageous. The presence of nickel atoms on the edge of a cubic cluster resulted in decrease of potential barrier for a carbon atom and decrease in energy in the whole cluster. A similar drift of a carbon atom from central octahedral interstitial site to the surface in the direction <011> occurred under the influence of surface factors.Such configuration corresponds to decreasing symmetry and increasing the number of possible energy states of a subnanocluster, and it corresponds to the condition of spontaneous crystallization process in an isolated system.Taking into account accidental positions of the nickel atom in the iron cluster, such behaviour of the carbon atom can explain the mechanism of growth of a new phase and formation of new clusters in the presence of other kind of atoms because of surface influence.

Summation rules for a fully nonlocal energy-based quasicontinuum method

NASA Astrophysics Data System (ADS)

Amelang, J. S.; Venturini, G. N.; Kochmann, D. M.

2015-09-01

The quasicontinuum (QC) method coarse-grains crystalline atomic ensembles in order to bridge the scales from individual atoms to the micro- and mesoscales. A crucial cornerstone of all QC techniques, summation or quadrature rules efficiently approximate the thermodynamic quantities of interest. Here, we investigate summation rules for a fully nonlocal, energy-based QC method to approximate the total Hamiltonian of a crystalline atomic ensemble by a weighted sum over a small subset of all atoms in the crystal lattice. Our formulation does not conceptually differentiate between atomistic and coarse-grained regions and thus allows for seamless bridging without domain-coupling interfaces. We review traditional summation rules and discuss their strengths and weaknesses with a focus on energy approximation errors and spurious force artifacts. Moreover, we introduce summation rules which produce no residual or spurious force artifacts in centrosymmetric crystals in the large-element limit under arbitrary affine deformations in two dimensions (and marginal force artifacts in three dimensions), while allowing us to seamlessly bridge to full atomistics. Through a comprehensive suite of examples with spatially non-uniform QC discretizations in two and three dimensions, we compare the accuracy of the new scheme to various previous ones. Our results confirm that the new summation rules exhibit significantly smaller force artifacts and energy approximation errors. Our numerical benchmark examples include the calculation of elastic constants from completely random QC meshes and the inhomogeneous deformation of aggressively coarse-grained crystals containing nano-voids. In the elastic regime, we directly compare QC results to those of full atomistics to assess global and local errors in complex QC simulations. Going beyond elasticity, we illustrate the performance of the energy-based QC method with the new second-order summation rule by the help of nanoindentation examples with automatic mesh adaptation. Overall, our findings provide guidelines for the selection of summation rules for the fully nonlocal energy-based QC method.

Support effects on adsorption and catalytic activation of O2 in single atom iron catalysts with graphene-based substrates.

PubMed

Gao, Zheng-Yang; Yang, Wei-Jie; Ding, Xun-Lei; Lv, Gang; Yan, Wei-Ping

2018-03-07

The adsorption and catalytic activation of O 2 on single atom iron catalysts with graphene-based substrates were investigated systematically by density functional theory calculation. It is found that the support effects of graphene-based substrates have a significant influence on the stability of the single atom catalysts, the adsorption configuration, the electron transfer mechanism, the adsorption energy and the energy barrier. The differences in the stable adsorption configuration of O 2 on single atom iron catalysts with different graphene-based substrates can be well understood by the symmetrical matching principle based on frontier molecular orbital analysis. There are two different mechanisms of electron transfer, in which the Fe atom acts as the electron donor in single vacancy graphene-based substrates while the Fe atom mainly acts as the bridge for electron transfer in double vacancy graphene-based substrates. The Fermi softness and work function are good descriptors of the adsorption energy and they can well reveal the relationship between electronic structure and adsorption energy. This single atom iron catalyst with single vacancy graphene modified by three nitrogen atoms is a promising non-noble metal single atom catalyst in the adsorption and catalytic oxidation of O 2 . Furthermore, the findings can lay the foundation for the further study of graphene-based support effects and provide a guideline for the development and design of new non-noble-metal single atom catalysts.

Final Report on DTRA Basic Research Project #BRCALL08-Per3-C-2-0006 "High-Z Non-Equilibrium Physics and Bright X-ray Sources with New Laser Targets"

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

Colvin, Jeffrey D.

This project had two major goals. Final Goal: obtain spectrally resolved, absolutely calibrated x-ray emission data from uniquely uniform mm-scale near-critical-density high-Z plasmas not in local thermodynamic equilibrium (LTE) to benchmark modern detailed atomic physics models. Scientific significance: advance understanding of non-LTE atomic physics. Intermediate Goal: develop new nano-fabrication techniques to make suitable laser targets that form the required highly uniform non-LTE plasmas when illuminated by high-intensity laser light. Scientific significance: advance understanding of nano-science. The new knowledge will allow us to make x-ray sources that are bright at the photon energies of most interest for testing radiation hardening technologies,more » the spectral energy range where current x-ray sources are weak. All project goals were met.« less

Atomization Energies of SO and SO2; Basis Set Extrapolation Revisted

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Ricca, Alessandra; Arnold, James (Technical Monitor)

1998-01-01

The addition of tight functions to sulphur and extrapolation to the complete basis set limit are required to obtain accurate atomization energies. Six different extrapolation procedures are tried. The best atomization energies come from the series of basis sets that yield the most consistent results for all extrapolation techniques. In the variable alpha approach, alpha values larger than 4.5 or smaller than 3, appear to suggest that the extrapolation may not be reliable. It does not appear possible to determine a reliable basis set series using only the triple and quadruple zeta based sets. The scalar relativistic effects reduce the atomization of SO and SO2 by 0.34 and 0.81 kcal/mol, respectively, and clearly must be accounted for if a highly accurate atomization energy is to be computed. The magnitude of the core-valence (CV) contribution to the atomization is affected by missing diffuse valence functions. The CV contribution is much more stable if basis set superposition errors are accounted for. A similar study of SF, SF(+), and SF6 shows that the best family of basis sets varies with the nature of the S bonding.

Health and Environmental Science: A Brief Review

DOE R&D Accomplishments Database

1982-09-27

The detonation of the first atomic bomb heralded the beginning of a new age. Almost everyone agreed that the enormous energy released by the "atomic reaction" would create opportunities and problems far larger than man faced in previous history. However, few foresaw the explosion of knowledge that would also be part of this new age.

A new method to measure electron density and effective atomic number using dual-energy CT images

NASA Astrophysics Data System (ADS)

Ramos Garcia, Luis Isaac; Pérez Azorin, José Fernando; Almansa, Julio F.

2016-01-01

The purpose of this work is to present a new method to extract the electron density ({ρ\\text{e}} ) and the effective atomic number (Z eff) from dual-energy CT images, based on a Karhunen-Loeve expansion (KLE) of the atomic cross section per electron. This method was used to calibrate a Siemens Definition CT using the CIRS phantom. The predicted electron density and effective atomic number using 80 kVp and 140 kVp were compared with a calibration phantom and an independent set of samples. The mean absolute deviations between the theoretical and calculated values for all the samples were 1.7 %  ±  0.1 % for {ρ\\text{e}} and 4.1 %  ±  0.3 % for Z eff. Finally, these results were compared with other stoichiometric method. The application of the KLE to represent the atomic cross section per electron is a promising method for calculating {ρ\\text{e}} and Z eff using dual-energy CT images.

Microscopic modeling of gas-surface scattering: II. Application to argon atom adsorption on a platinum (111) surface

NASA Astrophysics Data System (ADS)

Filinov, A.; Bonitz, M.; Loffhagen, D.

2018-06-01

A new combination of first principle molecular dynamics (MD) simulations with a rate equation model presented in the preceding paper (paper I) is applied to analyze in detail the scattering of argon atoms from a platinum (111) surface. The combined model is based on a classification of all atom trajectories according to their energies into trapped, quasi-trapped and scattering states. The number of particles in each of the three classes obeys coupled rate equations. The coefficients in the rate equations are the transition probabilities between these states which are obtained from MD simulations. While these rates are generally time-dependent, after a characteristic time scale t E of several tens of picoseconds they become stationary allowing for a rather simple analysis. Here, we investigate this time scale by analyzing in detail the temporal evolution of the energy distribution functions of the adsorbate atoms. We separately study the energy loss distribution function of the atoms and the distribution function of in-plane and perpendicular energy components. Further, we compute the sticking probability of argon atoms as a function of incident energy, angle and lattice temperature. Our model is important for plasma-surface modeling as it allows to extend accurate simulations to longer time scales.

Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-Hydrogen-Bond Datasets for Noncovalent Interactions.

PubMed

Suárez, Dimas; Díaz, Natalia; Francisco, Evelio; Martín Pendás, Angel

2018-04-17

The interacting quantum atoms (IQA) method can assess, systematically and in great detail, the strength and physics of both covalent and noncovalent interactions. The lack of a pair density in density functional theory (DFT), which precludes the direct IQA decomposition of the characteristic exchange-correlation energy, has been recently overcome by means of a scaling technique, which can largely expand the applicability of the method. To better assess the utility of the augmented IQA methodology to derive quantum chemical decompositions at the atomic and molecular levels, we report the results of Hartree-Fock (HF) and DFT calculations on the complexes included in the S66 and the ionic H-bond databases of benchmark geometry and binding energies. For all structures, we perform single-point and geometry optimizations using HF and selected DFT methods with triple-ζ basis sets followed by full IQA calculations. Pairwise dispersion energies are accounted for by the D3 method. We analyze the goodness of the HF-D3 and DFT-D3 binding energies, the magnitude of numerical errors, the fragment and atomic distribution of formation energies, etc. It is shown that fragment-based IQA decomposes the formation energies in comparable terms to those of perturbative approaches and that the atomic IQA energies hold the promise of rigorously quantifying atomic and group energy contributions in larger biomolecular systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of the Substituents of Boron Atoms on Conjugated Polymers Containing B←N Units.

PubMed

Liu, Jun; Wang, Tao; Dou, Chuandong; Wang, Lixiang

2018-06-15

Organoboron chemistry is a new tool to tune the electronic structures and properties of conjugated polymers, which are important for applications in organic opto-electronic devices. To investigate the effects of substituents of boron atoms on conjugated polymers, we synthesized three conjugated polymers based on double B←N bridged bipyridine (BNBP) with various substituents on the boron atoms. By changing the substituents from four phenyl groups and two phenyl groups/two fluorine atoms to four fluorine atoms, the BNBP-based polymers show the blue-shifted absorption spectra, decreased LUMO/HOMO energy levels and enhanced electron affinities, as well as the increased electron mobilities. Moreover, these BNBP-based polymers can be used as electron acceptors for all-polymer solar cells. These results demonstrate that the substituents of boron atoms can effectively modulate the electronic properties and applications of conjugated polymers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Snoek Relaxation in Fe-Cr Alloys and Interstitial-Substitutional Interaction

NASA Astrophysics Data System (ADS)

Golovin, I. S.; Blanter, M. S.; Schaller, R.

1997-03-01

The internal friction (IF) spectra of -Fe, Fe-Cr ferritic alloys and Cr have been investigated in a frequency range of 0.01 to 10 Hz. A Snoek-type relaxation was found in all the investigated C doped Fe-Cr alloys, starting from pure Fe and finishing with pure Cr. The temperature location of the Snoek peak (Tmax) in -Fe was found to be 315 K (1 Hz). The activation energy deduced from the T - f shift was 0.81 eV. Tmax in Cr was 433 K with an activation energy of 1.11 eV. The Snoek-type peaks in Fe-Cr alloys are much wider than in pure Fe or pure Cr. The temperature location of the peak versus chromium content curve exhibits a maximum in the vicinity of 35 wt% Cr (Tmax was 573 to 578 K, f 1.2 Hz and the activation energy was about 1.45 eV). It is important that Cr atoms in α-Fe have a more pronounced influence on the temperature location of the peak than Fe atoms have in chromium. A new model based on the atomic interactions is proposed to explain the influence of composition on Snoek peak location. The internal friction has been simulated by a Monte Carlo method, using C-C and C-substitutional atom (s) interaction energies. A model of long-range strain-induced (elastic) interaction supplemented by the chemical interaction in the two nearest coordination shells around an immobile substitutional atom was used for the C-s interaction. The interatomic interaction was supposed to affect IF by changing both the carbon atom arrangement (short-range order) and the energy of C atoms in octahedral interstices, and therefore the activation energy of IF. The peak temperatue calculated coincides well with the experimental ones if the value for the chemical interaction in the first coordination shell (Hchem) for C-Cr in Fe is - 0.15 eV and for C-Fe in Cr +0.15 eV. The difference in the influence of Cr in α-Fe and Fe in Cr is accounted for by a difference in the elastic and chemical interaction both between the carbon atoms and the substitutional atoms. The relaxation process in chromium Fe-based alloys is due to the carbon atom diffusion under stress between octahedral interstices of first and second coordination shells around the Cr atoms, and in Cr-based alloys, between second and third shells around the Fe atoms.

Structural stability and electronic properties of β-tetragonal boron: A first-principles study

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

Hayami, Wataru, E-mail: hayami.wataru@nims.go.jp

2015-01-15

It is known that elemental boron has five polymorphs: α- and β-rhombohedral, α- and β-tetragonal, and the high-pressure γ phase. β-tetragonal (β-t) boron was first discovered in 1960, but there have been only a few studies since then. We have thoroughly investigated, using first-principles calculations, the atomic and electronic structures of β-t boron, the details of which were not known previously. The difficulty of calculation arises from the fact that β-t boron has a large unit cell that contains between 184 and 196 atoms, with 12 partially-occupied interstitial sites. This makes the number of configurations of interstitial atoms too greatmore » to calculate them all. By introducing assumptions based on symmetry and preliminary calculations, the number of configurations to calculate can be greatly reduced. It was eventually found that β-t boron has the lowest total energy, with 192 atoms (8 interstitial atoms) in an orthorhombic lattice. The total energy per atom was between those of α- and β-rhombohedral boron. Another tetragonal structure with 192 atoms was found to have a very close energy. The valence bands were fully filled and the gaps were about 1.16 to 1.54 eV, making it comparable to that of β-rhombohedral boron. - Graphical abstract: Electronic density distribution for the lowest-energy configuration (N=192) viewed from the 〈1 0 0〉 direction. Left: isosurface (yellow) at d=0.09 electrons/a.u.{sup 3} Right: isosurface (orange) at d=0.12 electrons/a.u.{sup 3}. - Highlights: • β-tetragonal boron was thoroughly investigated using first-principles calculations. • The lowest energy structure contains 192 atoms in an orthorhombic lattice. • Another tetragonal structure with 192 atoms has a very close energy. • The total energy per atom is between those of α- and β-rhombohedral boron. • The band gap of the lowest energy structure is about 1.16 to 1.54 eV.« less

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

PubMed

Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

2016-05-01

The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. Copyright © 2016 Elsevier Inc. All rights reserved.

Enhancing Conceptual Knowledge of Energy in Biology with Incorrect Representations

ERIC Educational Resources Information Center

Wernecke, Ulrike; Schütte, Kerstin; Schwanewedel, Julia; Harms, Ute

2018-01-01

Energy is an important concept in all natural sciences, and a challenging one for school science education. Students' conceptual knowledge of energy is often low, and they entertain misconceptions. Educational research in science and mathematics suggests that learning through depictive representations and learning from errors, based on the theory…

Overview of International Thermonuclear Experimental Reactor (ITER) engineering design activities*

NASA Astrophysics Data System (ADS)

Shimomura, Y.

1994-05-01

The International Thermonuclear Experimental Reactor (ITER) [International Thermonuclear Experimental Reactor (ITER) (International Atomic Energy Agency, Vienna, 1988), ITER Documentation Series, No. 1] project is a multiphased project, presently proceeding under the auspices of the International Atomic Energy Agency according to the terms of a four-party agreement among the European Atomic Energy Community (EC), the Government of Japan (JA), the Government of the Russian Federation (RF), and the Government of the United States (US), ``the Parties.'' The ITER project is based on the tokamak, a Russian invention, and has since been brought to a high level of development in all major fusion programs in the world. The objective of ITER is to demonstrate the scientific and technological feasibility of fusion energy for peaceful purposes. The ITER design is being developed, with support from the Parties' four Home Teams and is in progress by the Joint Central Team. An overview of ITER Design activities is presented.

Tomography of atomic number and density of materials using dual-energy imaging and the Alvarez and Macovski attenuation model

NASA Astrophysics Data System (ADS)

Paziresh, M.; Kingston, A. M.; Latham, S. J.; Fullagar, W. K.; Myers, G. M.

2016-06-01

Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073-2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127-135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260-1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.

Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111).

PubMed

Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J

2014-08-07

Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the range 0.2-0.3 eV due to ehp excitation, which should be possible to observe. The average non-adiabatic energy losses for non-penetrative scattering exceed the adiabatic losses to phonons by 0.9-1.0 eV. This suggests that for scattering of hyperthermal H-atoms from coinage metals the dominant energy dissipation channel should be to ehp excitation. These predictions can be tested by experiments that combine techniques for generating H-atom beams that are well resolved in translational energy and for detecting the scattered atoms with high energy-resolution.

USSR Report, Energy, No. 147.

DTIC Science & Technology

1983-05-18

based on low-temperature reactors ; atomic heat and electric power stations (ATETs); The restructuring of the energy balance for the 1980-2000 period...ASPT) based on low-temperature reactors ; atomic heat and electric power stations (TETs); industrial atomic power stations (AETS) based on high-temper...ature reactors ) and high-efficiency long-distance heat transport (in conjunc- tion with high-temperature nuclear power sources: ASDT). The

Monte Carlo Computational Modeling of the Energy Dependence of Atomic Oxygen Undercutting of Protected Polymers

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Stueber, Thomas J.; Norris, Mary Jo

1998-01-01

A Monte Carlo computational model has been developed which simulates atomic oxygen attack of protected polymers at defect sites in the protective coatings. The parameters defining how atomic oxygen interacts with polymers and protective coatings as well as the scattering processes which occur have been optimized to replicate experimental results observed from protected polyimide Kapton on the Long Duration Exposure Facility (LDEF) mission. Computational prediction of atomic oxygen undercutting at defect sites in protective coatings for various arrival energies was investigated. The atomic oxygen undercutting energy dependence predictions enable one to predict mass loss that would occur in low Earth orbit, based on lower energy ground laboratory atomic oxygen beam systems. Results of computational model prediction of undercut cavity size as a function of energy and defect size will be presented to provide insight into expected in-space mass loss of protected polymers with protective coating defects based on lower energy ground laboratory testing.

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

PubMed Central

Gallicchio, Emilio; Deng, Nanjie; He, Peng; Wickstrom, Lauren; Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Olson, Arthur J.; Levy, Ronald M.

2014-01-01

As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking and high level atomistic models to improve enrichment. The enrichment factor of our blind predictions ranked best among all of the computational submissions, and second best overall. This work represents to our knowledge the first example of the application of an all-atom physics-based binding free energy model to large scale virtual screening. A total of 285 parallel Hamiltonian replica exchange molecular dynamics absolute protein-ligand binding free energy simulations were conducted starting from docked poses. The setup of the simulations was fully automated, calculations were distributed on multiple computing resources and were completed in a 6-weeks period. The accuracy of the docked poses and the inclusion of intramolecular strain and entropic losses in the binding free energy estimates were the major factors behind the success of the method. Lack of sufficient time and computing resources to investigate additional protonation states of the ligands was a major cause of mispredictions. The experiment demonstrated the applicability of binding free energy modeling to improve hit rates in challenging virtual screening of focused ligand libraries during lead optimization. PMID:24504704

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

NASA Astrophysics Data System (ADS)

Reinhardt, Aleks; Doye, Jonathan P. K.; Noya, Eva G.; Vega, Carlos

2012-11-01

We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

Case-control study of prostatic cancer in employees of the United Kingdom Atomic Energy Authority.

PubMed Central

Rooney, C; Beral, V; Maconochie, N; Fraser, P; Davies, G

1993-01-01

OBJECTIVE--To investigate the relation between risk of prostatic cancer and occupational exposures, especially to radionuclides, in employees of the United Kingdom Atomic Energy Authority. DESIGN--Case-control study of men with prostatic cancer and matched controls. Information about sociodemographic factors and exposures to radionuclides and other substances was abstracted and classified for each subject from United Kingdom Atomic Energy Authority records without knowledge of who had cancer. SUBJECTS--136 men with prostatic cancer diagnosed between 1946 and 1986 and 404 matched controls, all employees of United Kingdom Atomic Energy Authority. MAIN OUTCOME MEASURES--Documented or possible contamination with specific radionuclides. RESULTS--Risk of prostatic cancer was significantly increased in men who were internally contaminated with or who worked in environments potentially contaminated by tritium, chromium-51, iron-59, cobalt-60, or zinc-65. Internal contamination with at least one of the five radionuclides was detected in 14 men with prostatic cancer (10%) and 12 controls (3%) (relative risk 5.32 (95% confidence interval 1.87 to 17.24). Altogether 28 men with prostatic cancer (21%) and 46 controls (11%) worked in environments potentially contaminated by at least one of the five radionuclides (relative risk 2.36 (1.26 to 4.43)); about two thirds worked at heavy water reactors (19 men with prostatic cancer and 32 controls (relative risk 2.13 (1.00 to 4.52)). Relative risk of prostatic cancer increased with increasing duration of work in places potentially contaminated by these radionuclides and with increasing level of probable contamination. Prostatic cancer was not associated with exposure to plutonium, uranium, cadmium, boron, beryllium, or organic or inorganic chemicals. CONCLUSIONS--Risk of prostatic cancer risk was increased in United Kingdom Atomic Energy Authority workers who were occupationally exposed to tritium, 51Cr, 59Fe, 60Co, or 65Zn. Exposure to these radionuclides was infrequent, and their separate effects could not be evaluated. PMID:8274891

Analysis of the Zeeman effect on D α spectra on the EAST tokamak

NASA Astrophysics Data System (ADS)

Gao, Wei; Huang, Juan; Wu, Chengrui; Xu, Zong; Hou, Yumei; Jin, Zhao; Chen, Yingjie; Zhang, Pengfei; Zhang, Ling; Wu, Zhenwei; EAST Team

2017-04-01

Based on the passive spectroscopy, the {{{D}}}α atomic emission spectra in the boundary region of the plasma have been measured by a high resolution optical spectroscopic multichannel analysis (OSMA) system in EAST tokamak. The Zeeman splitting of the {{{D}}}α spectral lines has been observed. A fitting procedure by using a nonlinear least squares method was applied to fit and analyze all polarization π and +/- σ components of the {{{D}}}α atomic spectra to acquire the information of the local plasma. The spectral line shape was investigated according to emission spectra from different regions (e.g., low-field side and high-field side) along the viewing chords. Each polarization component was fitted and classified into three energy categories (the cold, warm, and hot components) based on different atomic production processes, in consistent with the transition energy distribution by calculating the gradient of the {{{D}}}α spectral profile. The emission position, magnetic field intensity, and flow velocity of a deuterium atom were also discussed in the context. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275231 and 11575249) and the National Magnetic Confinement Fusion Energy Research Program of China (Grant No. 2015GB110005).

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

PubMed Central

Schmidt, Michael W.; Ivanic, Joseph; Ruedenberg, Klaus

2014-01-01

An analysis based on the variation principle shows that in the molecules H2+, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation. PMID:24880263

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion.

PubMed

Schmidt, Michael W; Ivanic, Joseph; Ruedenberg, Klaus

2014-05-28

An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

10 CFR 110.50 - Terms.

Code of Federal Regulations, 2010 CFR

2010-01-01

... provisions of the Atomic Energy Act and to all applicable rules, regulations, decisions and orders of the... conditions when required by amendments of the Atomic Energy Act or other applicable law, or by other rules, regulations, decisions or orders issued in accordance with the terms of the Atomic Energy Act or other...

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

Paziresh, M.; Kingston, A. M., E-mail: andrew.kingston@anu.edu.au; Latham, S. J.

Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski,more » Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073–2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127–135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260–1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.« less

Local Energies and Energy Fluctuations — Applied to the High Entropy Alloy CrFeCoNi

NASA Astrophysics Data System (ADS)

Fukushima, Tetsuya; Katayama-Yoshida, Hiroshi; Sato, Kazunori; Ogura, Masako; Zeller, Rudolf; Dederichs, Peter H.

2017-11-01

High entropy alloys show a variety of fascinating properties like high hardness, wear resistance, corrosion resistance, etc. They are random solid solutions of many components with rather high concentrations. We perform ab-initio calculations for the high entropy alloy CrFeCoNi, which equal concentration of 25% for each element. By the KKRnano program package, which is based on an order-N screened Korringa-Kohn-Rostoker Green's function method, we consider a face-centered cubic (FCC) supercell with 1372 randomly distributed elements, and in addition also smaller supercells with 500 and 256 atoms. It is found from our calculations that the local moments of the Cr atoms show a large environmental variation, ranging from -1.70 μB to +1.01 μB with an average of about -0.51 μB. We present a new method to calculate "local energies" of all atoms. This is based on the partitioning of the whole space into Voronoi cells and allows to calculate the energetic contribution of each atomic cell to the total energy of the supercell. The supercell calculations show very large variations of the local energies, analogous to the variations of the local moments. This shows that the random solid solution is not stable and has a tendency to form an L12-structure with the Cr-atoms ordered at the corner of the cube and the elements Fe, Co, and Ni randomly distributed on the three other FCC sublattices. For this structure the variation of the local moments are much smaller.

Accuracy of the raw-data-based effective atomic numbers and monochromatic CT numbers for contrast medium with a dual-energy CT technique.

PubMed

Kawahara, Daisuke; Ozawa, Shuichi; Yokomachi, Kazushi; Tanaka, Sodai; Higaki, Toru; Fujioka, Chikako; Suzuki, Tatsuhiko; Tsuneda, Masato; Nakashima, Takeo; Ohno, Yoshimi; Nagata, Yasushi

2018-02-01

To evaluate the accuracy of raw-data-based effective atomic number (Z eff ) values and monochromatic CT numbers for contrast material of varying iodine concentrations, obtained using dual-energy CT. We used a tissue characterization phantom and varying concentrations of iodinated contrast medium. A comparison between the theoretical values of Z eff and that provided by the manufacturer was performed. The measured and theoretical monochromatic CT numbers at 40-130 keV were compared. The average difference between the Z eff values of lung (inhale) inserts in the tissue characterization phantom was 81.3% and the average Z eff difference was within 8.4%. The average difference between the Z eff values of the varying concentrations of iodinated contrast medium was within 11.2%. For the varying concentrations of iodinated contrast medium, the differences between the measured and theoretical monochromatic CT values increased with decreasing monochromatic energy. The Z eff and monochromatic CT numbers in the tissue characterization phantom were reasonably accurate. The accuracy of the raw-data-based Z eff values was higher than that of image-based Z eff values in the tissue-equivalent phantom. The accuracy of Z eff values in the contrast medium was in good agreement within the maximum SD found in the iodine concentration range of clinical dynamic CT imaging. Moreover, the optimum monochromatic energy for human tissue and iodinated contrast medium was found to be 70 keV. Advances in knowledge: The accuracy of the Z eff values and monochromatic CT numbers of the contrast medium created by raw-data-based, dual-energy CT could be sufficient in clinical conditions.

Quaternary Chalcogenide-Based Misfit Nanotubes LnS(Se)-TaS(Se)2 (Ln = La, Ce, Nd, and Ho): Synthesis and Atomic Structural Studies.

PubMed

Lajaunie, Luc; Radovsky, Gal; Tenne, Reshef; Arenal, Raul

2018-01-16

We have synthesized quaternary chalcogenide-based misfit nanotubes LnS(Se)-TaS 2 (Se) (Ln = La, Ce, Nd, and Ho). None of the compounds described here were reported in the literature as a bulk compound. The characterization of these nanotubes, at the atomic level, has been developed via different transmission electron microscopy techniques, including high-resolution scanning transmission electron microscopy, electron diffraction, and electron energy-loss spectroscopy. In particular, quantification at sub-nanometer scale was achieved by acquiring high-quality electron energy-loss spectra at high energy (∼between 1000 and 2500 eV). Remarkably, the sulfur was found to reside primarily in the distorted rocksalt LnS lattice, while the Se is associated with the hexagonal TaSe 2 site. Consequently, these quaternary misfit layered compounds in the form of nanostructures possess a double superstructure of La/Ta and S/Se with the same periodicity. In addition, the interlayer spacing between the layers and the interatomic distances within the layer vary systematically in the nanotubes, showing clear reduction when going from the lightest (La atom) to the heaviest (Ho) atom. Amorphous layers, of different nature, were observed at the surface of the nanotubes. For La-based NTs, the thin external amorphous layer (inferior to 10 nm) can be ascribed to a Se deficiency. Contrarily, for Ho-based NTs, the thick amorphous layer (between 10 and 20 nm) is clearly ascribed to oxidation. All of these findings helped us to understand the atomic structure of these new compounds and nanotubes thereof.

The effect of energy and momentum transfer during magnetron sputter deposition of yttrium oxide thin films

NASA Astrophysics Data System (ADS)

Xia, Jinjiao; Liang, Wenping; Miao, Qiang; Depla, Diederik

2018-05-01

The influence of the ratio between the energy and the deposition flux, or the energy per arriving atom, on the growth of Y2O3 sputter deposited thin films has been studied. The energy per arriving atom has been varied by the adjustment of the discharge power, and/or the target-to-substrate distance. The relationship between the energy per arriving atom and the phase evolution, grain size, microstructure, packing density and residual stress was investigated in detail. At low energy per arriving atom, the films consist of the monoclinic B phase with a preferential (1 1 1) orientation. A minority cubic C phase appears at higher energy per arriving atom. A study of the thin film cross sections showed for all films straight columns throughout the thickness, typically for a zone II microstructure. The intrinsic stress is compressive, and increases with increasing energy per atom. The same trend is observed for the film density. Simulations show that the momentum transfer per arriving atom also scales with the energy per arriving atom. Hence, the interpretation of the observed trends as a function of the energy per arriving atom must be treated with care.

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

Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures.more » The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.« less

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity

NASA Astrophysics Data System (ADS)

Song, Chenchen; Martínez, Todd J.

2016-05-01

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N2.6 for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity.

PubMed

Song, Chenchen; Martínez, Todd J

2016-05-07

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N(2.6) for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111)

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

Kroes, Geert-Jan, E-mail: g.j.kroes@chem.leidenuniv.nl; Pavanello, Michele; Blanco-Rey, María

2014-08-07

Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of themore » incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction (“EF”) model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated “post” (“p”) the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the range 0.2-0.3 eV due to ehp excitation, which should be possible to observe. The average non-adiabatic energy losses for non-penetrative scattering exceed the adiabatic losses to phonons by 0.9-1.0 eV. This suggests that for scattering of hyperthermal H-atoms from coinage metals the dominant energy dissipation channel should be to ehp excitation. These predictions can be tested by experiments that combine techniques for generating H-atom beams that are well resolved in translational energy and for detecting the scattered atoms with high energy-resolution.« less

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

Morrow, Brian H.; Shen, Jana K.; Eike, David M.

Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pK{sub a}’s in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pK{sub a} of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pK{sub a} of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that inmore » the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs.« less

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

PubMed

Olson, Mark A; Feig, Michael; Brooks, Charles L

2008-04-15

This article examines ab initio methods for the prediction of protein loops by a computational strategy of multiscale conformational sampling and physical energy scoring functions. Our approach consists of initial sampling of loop conformations from lattice-based low-resolution models followed by refinement using all-atom simulations. To allow enhanced conformational sampling, the replica exchange method was implemented. Physical energy functions based on CHARMM19 and CHARMM22 parameterizations with generalized Born (GB) solvent models were applied in scoring loop conformations extracted from the lattice simulations and, in the case of all-atom simulations, the ensemble of conformations were generated and scored with these models. Predictions are reported for 25 loop segments, each eight residues long and taken from a diverse set of 22 protein structures. We find that the simulations generally sampled conformations with low global root-mean-square-deviation (RMSD) for loop backbone coordinates from the known structures, whereas clustering conformations in RMSD space and scoring detected less favorable loop structures. Specifically, the lattice simulations sampled basins that exhibited an average global RMSD of 2.21 +/- 1.42 A, whereas clustering and scoring the loop conformations determined an RMSD of 3.72 +/- 1.91 A. Using CHARMM19/GB to refine the lattice conformations improved the sampling RMSD to 1.57 +/- 0.98 A and detection to 2.58 +/- 1.48 A. We found that further improvement could be gained from extending the upper temperature in the all-atom refinement from 400 to 800 K, where the results typically yield a reduction of approximately 1 A or greater in the RMSD of the detected loop. Overall, CHARMM19 with a simple pairwise GB solvent model is more efficient at sampling low-RMSD loop basins than CHARMM22 with a higher-resolution modified analytical GB model; however, the latter simulation method provides a more accurate description of the all-atom energy surface, yet demands a much greater computational cost. (c) 2007 Wiley Periodicals, Inc.

How large are nonadiabatic effects in atomic and diatomic systems?

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

Yang, Yubo, E-mail: yyang173@illinois.edu, E-mail: normantubman2015@u.northwestern.edu; Tubman, Norm M., E-mail: yyang173@illinois.edu, E-mail: normantubman2015@u.northwestern.edu; Ceperley, David M.

2015-09-28

With recent developments in simulating nonadiabatic systems to high accuracy, it has become possible to determine how much energy is attributed to nuclear quantum effects beyond zero-point energy. In this work, we calculate the non-relativistic ground-state energies of atomic and molecular systems without the Born-Oppenheimer approximation. For this purpose, we utilize the fixed-node diffusion Monte Carlo method, in which the nodes depend on both the electronic and ionic positions. We report ground-state energies for all systems studied, ionization energies for the first-row atoms and atomization energies for the first-row hydrides. We find the ionization energies of the atoms to bemore » nearly independent of the Born-Oppenheimer approximation, within the accuracy of our results. The atomization energies of molecular systems, however, show small effects of the nonadiabatic coupling between electrons and nuclei.« less

How large are nonadiabatic effects in atomic and diatomic systems?

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

Yang, Yubo; Kylänpää, Ilkka; Tubman, Norm M.

2015-09-29

With recent developments in simulating nonadiabatic systems to high accuracy, it has become possible to determine how much energy is attributed to nuclear quantum effects beyond zero-point energy. Here, we calculate the non-relativistic ground-state energies of atomic and molecular systems without the Born-Oppenheimer approximation. For this purpose, we utilize the fixed-node diffusion Monte Carlo method, in which the nodes depend on both the electronic and ionic positions. Our report shows the ground-state energies for all systems studied, ionization energies for the first-row atoms and atomization energies for the first-row hydrides. We find the ionization energies of the atoms to bemore » nearly independent of the Born-Oppenheimer approximation, within the accuracy of our results. The atomization energies of molecular systems, however, show small effects of the nonadiabatic coupling between electrons and nuclei.« less

A first-principles study of He, Xe, Kr and O incorporation in thorium carbide

NASA Astrophysics Data System (ADS)

Pérez Daroca, D.; Llois, A. M.; Mosca, H. O.

2015-05-01

Thorium-based materials are currently being investigated in relation with their potential utilization in Generation-IV reactors as nuclear fuels. Understanding the incorporation of fission products and oxygen is very important to predict the behavior of nuclear fuels. A first approach to this goal is the study of the incorporation energies and stability of these elements in the material. By means of first-principles calculations within the framework of density functional theory, we calculate the incorporation energies of He, Xe, Kr and O atoms in Th and C vacancy sites, in tetrahedral interstitials and in Schottky defects along the 〈1 1 1〉 and 〈1 0 0〉 directions. We also analyze atomic displacements, volume modifications and Bader charges. This kind of results for ThC, to the best authors' knowledge, have not been obtained previously, neither experimentally, nor theoretically. This should deal as a starting point towards the study of the complex behavior of fission products in irradiated ThC.

Energy dependence of the trapping of uranium atoms by aluminum oxide surfaces

NASA Technical Reports Server (NTRS)

Librecht, K. G.

1979-01-01

The energy dependence of the trapping probability for sputtered U-235 atoms striking an oxidized aluminum collector surface at energies between 1 eV and 184 eV was measured. At the lowest energies, approximately 10% of the uranium atoms are not trapped, while above 10 eV essentially all of them stick. Trapping probabilities averaged over the sputtered energy distribution for uranium incident on gold and mica are also presented.

Efficient Procedure for the Numerical Calculation of Harmonic Vibrational Frequencies Based on Internal Coordinates

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

Miliordos, Evangelos; Xantheas, Sotiris S.

We propose a general procedure for the numerical calculation of the harmonic vibrational frequencies that is based on internal coordinates and Wilson’s GF methodology via double differentiation of the energy. The internal coordinates are defined as the geometrical parameters of a Z-matrix structure, thus avoiding issues related to their redundancy. Linear arrangements of atoms are described using a dummy atom of infinite mass. The procedure has been automated in FORTRAN90 and its main advantage lies in the nontrivial reduction of the number of single-point energy calculations needed for the construction of the Hessian matrix when compared to the corresponding numbermore » using double differentiation in Cartesian coordinates. For molecules of C 1 symmetry the computational savings in the energy calculations amount to 36N – 30, where N is the number of atoms, with additional savings when symmetry is present. Typical applications for small and medium size molecules in their minimum and transition state geometries as well as hydrogen bonded clusters (water dimer and trimer) are presented. Finally, in all cases the frequencies based on internal coordinates differ on average by <1 cm –1 from those obtained from Cartesian coordinates.« less

Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials

PubMed Central

Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

2009-01-01

Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all-atom distance-dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT-TS score, but decreased the Z-score of the native structure. The attractiveness of potential improved both the correlation and Z-score for template-based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states. PMID:19588493

Backscattering spectrometry device for identifying unknown elements present in a workpiece

DOEpatents

Doyle, Barney L.; Knapp, James A.

1991-01-01

A backscattering spectrometry method and device for identifying and quantifying impurities in a workpiece during processing and manufacturing of that workpiece. While the workpiece is implanted with an ion beam, that same ion beam backscatters resulting from collisions with known atoms and with impurities within the workpiece. Those ions backscatter along a predetermined scattering angle and are filtered using a self-supporting filter to stop the ions with a lower energy because they collided with the known atoms of the workpiece of a smaller mass. Those ions which pass through the filter have a greater energy resulting from impact with impurities having a greater mass than the known atoms of the workpiece. A detector counts the number and measures the energy of the ions which pass through the filter. From the energy determination and knowledge of the scattering angle, a mass calculation determines the identity, and from the number and solid angle of the scattering angle, a relative concentration of the impurity is obtained.

Relation between the Z-1 type expansion of the total energy of isoelectronic atoms and the many-electron theory on the electron correlation by Sinanoǧlu

NASA Astrophysics Data System (ADS)

Anno, Tosinobu; Teruya, Hirohide

1987-07-01

By applying the economical formula for the total energies of isoelectronic atoms presented by the present authors [J. Chem. Phys. 84, 6895 (1986)] to both the nonrelativistic exact energy and the Hartree-Fock energy, an expression of the Z-1 expansion type for the correlation energy is obtained for isoelectronic series involving the first-row atoms. Based upon the expression obtained, the following conclusions are derived on the relation between the Z-1 type expansion theory and Sinanoǧlu's many-electron theory (MET): (i) the Z2 term has nothing to do with the electron correlation; (ii) the term proportional to Z represents the internal correlation energy Eint in MET, at least when Z is large in comparison with the number of electrons N; (iii) the constant term in the Z-1 type expansion is the limiting value of the sum of the semi-internal and the all-external correlation energy (EF+Eu) when Z→∞ and its values for the ground-state atoms show a systematic trend when plotted against N; (iv) the sum of the Z-1 and the higher order terms in Z-1 represents the Z dependence of EF+Eu, although its small amount is attributable to a part of Eint when Z-N≲1.

High-energy e- /e+ spectrometer via coherent interaction in a bent crystal

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo; Howard, Alexander

2018-01-01

We propose a novel spectrometer based on the crystal channeling effect capable of discriminating between positive and negative particles well beyond the TeV energy scale. The atomic order of a crystalline structure generates an electrostatic field built up by all the atoms in the crystals, which confines charged particle trajectories between neighbouring atomic planes. Through such an interaction in a tiny curved crystal, the same dynamical action on the highest energy particles as that of a huge superconducting magnet is achieved. Depending on the charge sign, points of equilibrium of the oscillatory motion under channeling lie between or on atomic planes for positive and negative particles, respectively, forcing positive particles to stably oscillate far from the planes, while negative ones repeatedly cross them. The different interaction rate with atomic planes causes a tremendous discrepancy between the deflection efficiency of positive and negative particles under channeling. We suggest the use of interactions between charged particles and oriented bent crystals as a novel non-cryogenic passive charge spectrometer to aid the search for dark matter in the Universe in satellite-borne experiment. The limited angular acceptance makes this technique particularly suited for directional local sources of energetic charged particles.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity

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

Song, Chenchen; Martínez, Todd J.; SLAC National Accelerator Laboratory, Menlo Park, California 94025

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N{sup 2.6} for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 aremore » less than 0.5 kcal/mol for all systems tested (up to 162 atoms).« less

Recent Development of Advanced Electrode Materials by Atomic Layer Deposition for Electrochemical Energy Storage.

PubMed

Guan, Cao; Wang, John

2016-10-01

Electrode materials play a decisive role in almost all electrochemical energy storage devices, determining their overall performance. Proper selection, design and fabrication of electrode materials have thus been regarded as one of the most critical steps in achieving high electrochemical energy storage performance. As an advanced nanotechnology for thin films and surfaces with conformal interfacial features and well controllable deposition thickness, atomic layer deposition (ALD) has been successfully developed for deposition and surface modification of electrode materials, where there are considerable issues of interfacial and surface chemistry at atomic and nanometer scale. In addition, ALD has shown great potential in construction of novel nanostructured active materials that otherwise can be hardly obtained by other processing techniques, such as those solution-based processing and chemical vapor deposition (CVD) techniques. This review focuses on the recent development of ALD for the design and delivery of advanced electrode materials in electrochemical energy storage devices, where typical examples will be highlighted and analyzed, and the merits and challenges of ALD for applications in energy storage will also be discussed.

Recent Development of Advanced Electrode Materials by Atomic Layer Deposition for Electrochemical Energy Storage

PubMed Central

2016-01-01

Electrode materials play a decisive role in almost all electrochemical energy storage devices, determining their overall performance. Proper selection, design and fabrication of electrode materials have thus been regarded as one of the most critical steps in achieving high electrochemical energy storage performance. As an advanced nanotechnology for thin films and surfaces with conformal interfacial features and well controllable deposition thickness, atomic layer deposition (ALD) has been successfully developed for deposition and surface modification of electrode materials, where there are considerable issues of interfacial and surface chemistry at atomic and nanometer scale. In addition, ALD has shown great potential in construction of novel nanostructured active materials that otherwise can be hardly obtained by other processing techniques, such as those solution‐based processing and chemical vapor deposition (CVD) techniques. This review focuses on the recent development of ALD for the design and delivery of advanced electrode materials in electrochemical energy storage devices, where typical examples will be highlighted and analyzed, and the merits and challenges of ALD for applications in energy storage will also be discussed. PMID:27840793

Nanopores creation in boron and nitrogen doped polycrystalline graphene: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Izadifar, Mohammadreza; Abadi, Rouzbeh; Nezhad Shirazi, Ali Hossein; Alajlan, Naif; Rabczuk, Timon

2018-05-01

In the present paper, molecular dynamic simulations have been conducted to investigate the nanopores creation on 10% of boron and nitrogen doped polycrystalline graphene by silicon and diamond nanoclusters. Two types of nanoclusters based on silicon and diamond are used to investigate their effect for the fabrication of nanopores. Therefore, three different diameter sizes of the clusters with five kinetic energies of 10, 50, 100, 300 and 500 eV/atom at four different locations in boron or nitrogen doped polycrystalline graphene nanosheets have been perused. We also study the effect of 3% and 6% of boron doped polycrystalline graphene with the best outcome from 10% of doping. Our results reveal that the diamond cluster with diameter of 2 and 2.5 nm fabricates the largest nanopore areas on boron and nitrogen doped polycrystalline graphene, respectively. Furthermore, the kinetic energies of 10 and 50 eV/atom can not fabricate nanopores in some cases for silicon and diamond clusters on boron doped polycrystalline graphene nanosheets. On the other hand, silicon and diamond clusters fabricate nanopores for all locations and all tested energies on nitrogen doped polycrystalline graphene. The area sizes of nanopores fabricated by silicon and diamond clusters with diameter of 2 and 2.5 nm are close to the actual area size of the related clusters for the kinetic energy of 300 eV/atom in all locations on boron doped polycrystalline graphene. The maximum area and the average maximum area of nanopores are fabricated by the kinetic energy of 500 eV/atom inside the grain boundary at the center of the nanosheet and in the corner of nanosheet with diameters of 2 and 3 nm for silicon and diamond clusters on boron and nitrogen doped polycrystalline graphene.

Electronic Structure of Two-Dimensional Hydrocarbon Networks of sp2 and sp3 C Atoms

NASA Astrophysics Data System (ADS)

Fujii, Yasumaru; Maruyama, Mina; Wakabayashi, Katsunori; Nakada, Kyoko; Okada, Susumu

2018-03-01

Based on density functional theory with the generalized gradient approximation, we have investigated the geometric and electronic structures of two-dimensional hexagonal covalent networks consisting of oligoacenes and fourfold coordinated hydrocarbon atoms, which are alternately arranged in a hexagonal manner. All networks were semiconductors with a finite energy gap at the Γ point, which monotonically decreased with the increase of the oligoacene length. As a result of a Kagome network of oligoacene connected through sp3 C atoms, the networks possess peculiar electron states in their valence and conduction bands, which consist of a flat dispersion band and a Dirac cone. The total energy of the networks depends on the oligoacene length and has a minimum for the network comprising naphthalene.

Information Extraction Using Controlled English to Support Knowledge-Sharing and Decision-Making

DTIC Science & Technology

2012-06-01

or language variants. CE-based information extraction will greatly facilitate the processes in the cognitive and social domains that enable forces...terminology or language variants. CE-based information extraction will greatly facilitate the processes in the cognitive and social domains that...processor is run to turn the atomic CE into a more “ stylistically felicitous” CE, using techniques such as: aggregating all information about an entity

Dual-mode operation of 2D material-base hot electron transistors

PubMed Central

Lan, Yann-Wen; Torres, Jr., Carlos M.; Zhu, Xiaodan; Qasem, Hussam; Adleman, James R.; Lerner, Mitchell B.; Tsai, Shin-Hung; Shi, Yumeng; Li, Lain-Jong; Yeh, Wen-Kuan; Wang, Kang L.

2016-01-01

Vertical hot electron transistors incorporating atomically-thin 2D materials, such as graphene or MoS2, in the base region have been proposed and demonstrated in the development of electronic and optoelectronic applications. To the best of our knowledge, all previous 2D material-base hot electron transistors only considered applying a positive collector-base potential (VCB > 0) as is necessary for the typical unipolar hot-electron transistor behavior. Here we demonstrate a novel functionality, specifically a dual-mode operation, in our 2D material-base hot electron transistors (e.g. with either graphene or MoS2 in the base region) with the application of a negative collector-base potential (VCB < 0). That is, our 2D material-base hot electron transistors can operate in either a hot-electron or a reverse-current dominating mode depending upon the particular polarity of VCB. Furthermore, these devices operate at room temperature and their current gains can be dynamically tuned by varying VCB. We anticipate our multi-functional dual-mode transistors will pave the way towards the realization of novel flexible 2D material-based high-density and low-energy hot-carrier electronic applications. PMID:27581550

Dual-mode operation of 2D material-base hot electron transistors.

PubMed

Lan, Yann-Wen; Torres, Carlos M; Zhu, Xiaodan; Qasem, Hussam; Adleman, James R; Lerner, Mitchell B; Tsai, Shin-Hung; Shi, Yumeng; Li, Lain-Jong; Yeh, Wen-Kuan; Wang, Kang L

2016-09-01

Vertical hot electron transistors incorporating atomically-thin 2D materials, such as graphene or MoS2, in the base region have been proposed and demonstrated in the development of electronic and optoelectronic applications. To the best of our knowledge, all previous 2D material-base hot electron transistors only considered applying a positive collector-base potential (VCB > 0) as is necessary for the typical unipolar hot-electron transistor behavior. Here we demonstrate a novel functionality, specifically a dual-mode operation, in our 2D material-base hot electron transistors (e.g. with either graphene or MoS2 in the base region) with the application of a negative collector-base potential (VCB < 0). That is, our 2D material-base hot electron transistors can operate in either a hot-electron or a reverse-current dominating mode depending upon the particular polarity of VCB. Furthermore, these devices operate at room temperature and their current gains can be dynamically tuned by varying VCB. We anticipate our multi-functional dual-mode transistors will pave the way towards the realization of novel flexible 2D material-based high-density and low-energy hot-carrier electronic applications.

The helium effect at grain boundaries in Fe-Cr alloys: A first-principles study

NASA Astrophysics Data System (ADS)

Zemła, M. R.; Wróbel, J. S.; Wejrzanowski, T.; Nguyen-Manh, D.; Kurzydłowski, K. J.

2017-02-01

Helium is produced in the structural materials in nuclear power plants by nuclear transmutation following neutron irradiation. Since the solubility of helium in all metals is extremely low, helium tends to be trapped at defects such as vacancies, dislocations and grain boundaries, which cause material embrittlement. Density functional theory (DFT) calculations were performed in order to investigate the helium effect at grain boundaries (GBs) in iron-chromium alloys. Both cohesive energy and magnetic properties at symmetric Σ3(1 1 1) and Σ5(2 1 0) tilt Fe GBs are studied in the presence of Cr and He atoms. It is found that the presence of Cr atoms increases cohesive energy, at different He concentrations, and strongly influences magnetic properties at the GBs. The effect of the segregation energy of helium atom as a function of the different positions of Cr atoms located inside/outside a GB has been considered. Results of the present first-principles study enable one to clarify the role of Cr in understanding the helium effect in Fe-Cr-based alloys.

A Comprehensive X-Ray Absorption Model for Atomic Oxygen

NASA Technical Reports Server (NTRS)

Gorczyca, T. W.; Bautista, M. A.; Hasoglu, M. F.; Garcia, J.; Gatuzz, E.; Kaastra, J. S.; Kallman, T. R.; Manson, S. T.; Mendoza, C.; Raassen, A. J. J.;

Visualising reacting single atoms under controlled conditions: Advances in atomic resolution in situ Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM)

NASA Astrophysics Data System (ADS)

Boyes, Edward D.; Gai, Pratibha L.

2014-02-01

Advances in atomic resolution Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM) for probing gas-solid catalyst reactions in situ at the atomic level under controlled reaction conditions of gas environment and temperature are described. The recent development of the ESTEM extends the capability of the ETEM by providing the direct visualisation of single atoms and the atomic structure of selected solid state heterogeneous catalysts in their working states in real-time. Atomic resolution E(S)TEM provides a deeper understanding of the dynamic atomic processes at the surface of solids and their mechanisms of operation. The benefits of atomic resolution-E(S)TEM to science and technology include new knowledge leading to improved technological processes with substantial economic benefits, improved healthcare, reductions in energy needs and the management of environmental waste generation. xml:lang="fr"

Conceptual Integration of Covalent Bond Models by Algerian Students

ERIC Educational Resources Information Center

Salah, Hazzi; Dumon, Alain

2014-01-01

The concept of covalent bonding is characterized by an interconnected knowledge framework based on Lewis and quantum models of atoms and molecules. Several research studies have shown that students at all levels of chemistry learning find the quantum model to be one of the most difficult subjects to understand. We have tried in this paper to…

Recovery of a Charred Painting Using Atomic Oxygen Treatment

NASA Technical Reports Server (NTRS)

Rutledge, Sharon K.; Banks, Bruce A.; Chichernea, Virgil A.

1999-01-01

A noncontact method is described which uses atomic oxygen to remove soot and char from the surface of a painting. The atomic oxygen was generated by the dissociation of oxygen in low pressure air using radio frequency energy. The treatment, which is an oxidation process, allows control of the amount of material to be removed. The effectiveness of char removal from half of a fire-damaged oil painting was studied using reflected light measurements from selected areas of the painting and by visual and photographic observation. The atomic oxygen was able to effectively remove char and soot from the treated half of the painting. The remaining loosely bound pigment was lightly sprayed with a mist to replace the binder and then varnish was reapplied. Caution should he used when treating an untested paint medium using atomic oxygen. A representative edge or corner should he tested first in order to determine if the process would be safe for the pigments present. As more testing occurs, a greater knowledge base will be developed as to what types of paints and varnishes can or cannot be treated using this technique. With the proper precautions, atomic oxygen treatment does appear to be a technique with great potential for allowing very charred, previously unrestorable art to be salvaged.

Effective Atomic Number, Mass Attenuation Coefficient Parameterization, and Implications for High-Energy X-Ray Cargo Inspection Systems

NASA Astrophysics Data System (ADS)

Langeveld, Willem G. J.

The most widely used technology for the non-intrusive active inspection of cargo containers and trucks is x-ray radiography at high energies (4-9 MeV). Technologies such as dual-energy imaging, spectroscopy, and statistical waveform analysis can be used to estimate the effective atomic number (Zeff) of the cargo from the x-ray transmission data, because the mass attenuation coefficient depends on energy as well as atomic number Z. The estimated effective atomic number, Zeff, of the cargo then leads to improved detection capability of contraband and threats, including special nuclear materials (SNM) and shielding. In this context, the exact meaning of effective atomic number (for mixtures and compounds) is generally not well-defined. Physics-based parameterizations of the mass attenuation coefficient have been given in the past, but usually for a limited low-energy range. Definitions of Zeff have been based, in part, on such parameterizations. Here, we give an improved parameterization at low energies (20-1000 keV) which leads to a well-defined Zeff. We then extend this parameterization up to energies relevant for cargo inspection (10 MeV), and examine what happens to the Zeff definition at these higher energies.

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.

Coupled-cluster based basis sets for valence correlation calculations

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

Claudino, Daniel; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu; Gargano, Ricardo

Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These newmore » sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via 〈r{sup n}〉 (−3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within “chemical accuracy” of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.« less

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

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).

Accuracy of free energies of hydration using CM1 and CM3 atomic charges.

PubMed

Udier-Blagović, Marina; Morales De Tirado, Patricia; Pearlman, Shoshannah A; Jorgensen, William L

2004-08-01

Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water. Copyright 2004 Wiley Periodicals, Inc.

Lamb Shift of n = 1 and n = 2 States of Hydrogen-like Atoms, 1 ≤ Z ≤ 110

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

Yerokhin, V. A.; Shabaev, V. M.

2015-09-15

Theoretical energy levels of the n = 1 and n = 2 states of hydrogen-like atoms with the nuclear charge numbers 1 ≤ Z ≤ 110 are tabulated. The tabulation is based on ab initio quantum electrodynamics calculations performed to all orders in the nuclear binding strength parameter Zα, where α is the fine structure constant. Theoretical errors due to various effects are critically examined and estimated.

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

[Living without atomic power? Carl Friedrich von Weizsäcker as expert in the nuclear energy debate of the 1970's].

PubMed

Seefried, Elke

2014-01-01

Carl Friedrich von Weizsäcker crossed the boundaries separating science, politics and the public sphere. In this he was led by the conviction that scientists in the modern 'technical age' are responsible for consequences resulting from their applied knowledge. Weizsäcker tried to introduce his knowledge into the policy process by advising politicians or by using the public sphere, thus applying pressure on politics. This was not only true for the 'Göttinger Erklärung' in 1957 but also for his engagement in the nuclear energy debate of the 1970s. Influenced by the 'Limits to Growth' discourse, Weizsäcker more and more gravitated towards an ecological world view and increasingly questioned material growth as well as a techno-scientific based understanding of progress. Weizsäcker thought about risks of the technical age in general and of the use of nuclear energy in particular. In the light of a growing fragmentation of scientific authority, Weizsäcker revealed uncertainty as he became fully aware that expertise cannot be based on scientific reason and cannot code the problems in terms of truth, but is inextricably linked with value spheres and contingencies. Nevertheless, his expertise was utilized as he encouraged parts of the Social Democratic Party (SPD) around Erhard Eppler to think about alternatives in energy policy.

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.

Z-dependence of mean excitation energies for second and third row atoms and their ions

NASA Astrophysics Data System (ADS)

Sauer, Stephan P. A.; Sabin, John R.; Oddershede, Jens

2018-05-01

All mean excitation energies for second and third row atoms and their ions are calculated in the random-phase approximation using large basis sets. To a very good approximation, it turns out that mean excitation energies within an isoelectronic series are a quadratic function of the nuclear charge. It is demonstrated that this behavior is linked to the fact that the contributions from continuum electronic states give the dominate contributions to the mean excitation energies and that these contributions for atomic ions appear hydrogen-like. We argue that this finding may present a method to get a first estimate of mean excitation energies also for other non-relativistic atomic ions.

The key energy scales of Gd-based metallofullerene determined by resonant inelastic x-ray scattering spectroscopy

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

Shao, Yu-Cheng; Wray, L. Andrew; Huang, Shih-Wen

Endohedral metallofullerenes, formed by encaging Gd inside fullerenes like C 80, can exhibit enhanced proton relaxitivities compared with other Gd-chelates, making them the promising contrast agents for magnetic resonance imaging (MRI). However, the underlying key energy scales of Gd x Sc 3-xN@C 80 (x = 1–3) remain unclear. Here, we carry out resonant inelastic x-ray scattering (RIXS) experiments on Gd xSc 3-xN@C 80 at Gd N 4,5-edges to directly study the electronic structure and spin flip excitations of Gd 4f electrons. Compared with reference Gd 2O 3 and contrast agent Gadodiamide, the features in the RIXS spectra of all metallofullerenesmore » exhibit broader spectral lineshape and noticeable energy shift. Using atomic multiplet calculations, we have estimated the key energy scales such as the inter-site spin exchange field, intra-atomic 4f–4f Coulomb interactions, and spin-orbit coupling. The implications of these parameters to the 4f states of encapsulated Gd atoms are discussed.« less

The key energy scales of Gd-based metallofullerene determined by resonant inelastic x-ray scattering spectroscopy

DOE PAGES

Shao, Yu-Cheng; Wray, L. Andrew; Huang, Shih-Wen; ...

2017-08-15

Endohedral metallofullerenes, formed by encaging Gd inside fullerenes like C 80, can exhibit enhanced proton relaxitivities compared with other Gd-chelates, making them the promising contrast agents for magnetic resonance imaging (MRI). However, the underlying key energy scales of Gd x Sc 3-xN@C 80 (x = 1–3) remain unclear. Here, we carry out resonant inelastic x-ray scattering (RIXS) experiments on Gd xSc 3-xN@C 80 at Gd N 4,5-edges to directly study the electronic structure and spin flip excitations of Gd 4f electrons. Compared with reference Gd 2O 3 and contrast agent Gadodiamide, the features in the RIXS spectra of all metallofullerenesmore » exhibit broader spectral lineshape and noticeable energy shift. Using atomic multiplet calculations, we have estimated the key energy scales such as the inter-site spin exchange field, intra-atomic 4f–4f Coulomb interactions, and spin-orbit coupling. The implications of these parameters to the 4f states of encapsulated Gd atoms are discussed.« less

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

On the atomic-number similarity of the binding energies of electrons in filled shells of elements of the periodic table

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

Karpov, V. Ya.; Shpatakovskaya, G. V., E-mail: shpagalya@yandex.ru

An expression for the binding energies of electrons in the ground state of an atom is derived on the basis of the Bohr–Sommerfeld quantization rule within the Thomas–Fermi model. The validity of this relation for all elements from neon to uranium is tested within a more perfect quantum-mechanical model with and without the inclusion of relativistic effects, as well as with experimental binding energies. As a result, the ordering of electronic levels in filled atomic shells is established, manifested in an approximate atomic-number similarity. It is proposed to use this scaling property to analytically estimate the binding energies of electronsmore » in an arbitrary atom.« less

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

PubMed

Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

2015-05-12

We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the extensive analysis of conformational properties of glycoprotein structures reported in the Protein Data Bank. Use of the BPMC search leads to significant improvements in sampling efficiency for glycan simulations. Moreover, good agreement with the X-ray glycoprotein structures is achieved for all glycan chain lengths. Thus, average/median RMSDs are 0.81/0.68 Å for one-residue glycans and 1.32/1.47 Å for three-residue glycans. RMSD from the native structure for the lowest-energy conformation of the 12-residue glycan chain (PDB ID 3og2) is 1.53 Å. Additionally, results obtained for free short oligosaccharides using the new force field are in line with the available experimental data, i.e., the most populated conformations in solution are predicted to be the lowest energy ones. The newly developed parameters allow for the accurate modeling of linear and branched hexopyranose glycosides in heterogeneous systems.

Studies on an ultrasonic atomization feed direct methanol fuel cell.

PubMed

Wu, Chaoqun; Liu, Linghao; Tang, Kai; Chen, Tao

2017-01-01

Direct methanol fuel cell (DMFC) is promising as an energy conversion device for the replacement of conventional chemical cell in future, owing to its convenient fuel storage, high energy density and low working temperature. The development of DMFC technology is currently limited by catalyst poison and methanol crossover. To alleviate the methanol crossover, a novel fuel supply system based on ultrasonic atomization is proposed. Experimental investigations on this fuel supply system to evaluate methanol permeation rates, open circuit voltages (OCVs) and polarization curves under a series of conditions have been carried out and reported in this paper. In comparison with the traditional liquid feed DMFC system, it can be found that the methanol crossover under the ultrasonic atomization feed system was significantly reduced because the DMFC reaches a large stable OCV value. Moreover, the polarization performance does not vary significantly with the liquid feed style. Therefore, the cell fed by ultrasonic atomization can be operated with a high concentration methanol to improve the energy density of DMFC. Under the supply condition of relatively high concentration methanol such as 4M and 8M, the maximum power density fed by ultrasonic atomization is higher than liquid by 6.05% and 12.94% respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

ITFITS model for vibration--translation energy partitioning in atom-- polyatomic molecule collisions

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

Shobatake, K.; Rice, S.A.; Lee, Y.T.

1973-09-01

A model for vibration-translation energy partitioning in the collinear collision of an atom and an axially symmetric polyatonaic molecule is proposed. The model is based on an extension of the ideas of Mahan and Heidrich, Wilson, and Rapp. Comparison of energy transfers computed from classical trajesctory calculations and the model proposed indicate good agreement when the mass of the free atom is small relative to the mass of the bound atom it strikes. The agreement is less satisfactory when that mass ratio becomes large. (auth)

Hall Determination of Atomic Radii of Alkali Metals

ERIC Educational Resources Information Center

Houari, Ahmed

2008-01-01

I will propose here an alternative method for determining atomic radii of alkali metals based on the Hall measurements of their free electron densities and the knowledge of their crystal structure. (Contains 2 figures.)

Evaluation of Analysis Conditions for Laser-Pulsed Atom Probe Tomography: Example of Cemented Tungsten Carbide.

PubMed

Peng, Zirong; Choi, Pyuck-Pa; Gault, Baptiste; Raabe, Dierk

2017-04-01

Cemented tungsten carbide has been analyzed using laser-pulsed atom probe tomography (APT). The influence of experimental parameters, including laser pulse energy, pulse repetition rate, and specimen base temperature, on the acquired data were evaluated from different aspects, such as mass spectrum, chemical composition, noise-to-signal ratio, and multiple events. Within all the applied analysis conditions, only 1 MHz pulse repetition rate led to a strong detector saturation effect, resulting in a largely biased chemical composition. A comparative study of the laser energy settings showed that an ~12 times higher energy was required for the less focused green laser of the LEAPTM 3000X HR system to achieve a similar evaporation field as the finer spot ultraviolet laser of the LEAPTM 5000 XS system.

Embedded-atom-method interatomic potentials from lattice inversion.

PubMed

Yuan, Xiao-Jian; Chen, Nan-Xian; Shen, Jiang; Hu, Wangyu

2010-09-22

The present work develops a physically reliable procedure for building the embedded-atom-method (EAM) interatomic potentials for the metals with fcc, bcc and hcp structures. This is mainly based on Chen-Möbius lattice inversion (Chen et al 1997 Phys. Rev. E 55 R5) and first-principles calculations. Following Baskes (Baskes et al 2007 Phys. Rev. B 75 094113), this new version of the EAM eliminates all of the prior arbitrary choices in the determination of the atomic electron density and pair potential functions. Parameterizing the universal form deduced from the calculations within the density-functional scheme for homogeneous electron gas as the embedding function, the new-type EAM potentials for Cu, Fe and Ti metals have successfully been constructed by considering interatomic interactions up to the fifth neighbor, the third neighbor and the seventh neighbor, respectively. The predictions of elastic constants, structural energy difference, vacancy formation energy and migration energy, activation energy of vacancy diffusion, latent heat of melting and relative volume change on melting all satisfactorily agree with the experimental results available or first-principles calculations. The predicted surface energies for low-index crystal faces and the melting point are in agreement with the experimental data to the same extent as those calculated by other EAM-type potentials such as the FBD-EAM, 2NN MEAM and MS-EAM. In addition, the order among the predicted low-index surface energies is also consistent with the experimental information.

Influence of Parameters of a Reactive Interatomic Potential on the Properties of Saturated Hydrocarbons

DTIC Science & Technology

2017-01-01

Methodology 3 2.1 Modified Embedded-Atom Method Theory 3 2.1.1 Embedding Energy Function 3 2.1.2 Screening Factor 8 2.1.3 Modified Embedded-Atom...Simulation Methodology 2.1 Modified Embedded-Atom Method Theory In the EAM and MEAM formalisms1,2,5 the total energy of a system of atoms (Etot) is...An interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a semiempirical many-body potential based on

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

NASA Astrophysics Data System (ADS)

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-10-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.

Comparison Between Self-Guided Langevin Dynamics and Molecular Dynamics Simulations for Structure Refinement of Protein Loop Conformations

DTIC Science & Technology

2011-01-01

SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18 . NUMBER OF PAGES 9 19a. NAME OF RESPONSIBLE PERSON a. REPORT...unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39- 18 sampling is based on...atom distance-scaled ideal-gas reference state (DFIRE-AA) statistical potential func- tion.[ 18 ] The third approach is the Rosetta all-atom energy func

Deuterium supersaturation in low-energy plasma-loaded tungsten surfaces

NASA Astrophysics Data System (ADS)

Gao, L.; Jacob, W.; von Toussaint, U.; Manhard, A.; Balden, M.; Schmid, K.; Schwarz-Selinger, T.

2017-01-01

Fundamental understanding of hydrogen-metal interactions is challenging due to a lack of knowledge on defect production and/or evolution upon hydrogen ingression, especially for metals undergoing hydrogen irradiation with ion energy below the displacement thresholds reported in literature. Here, applying a novel low-energy argon-sputter depth profiling method with significantly improved depth resolution for tungsten (W) surfaces exposed to deuterium (D) plasma at 300 K, we show the existence of a 10 nm thick D-supersaturated surface layer (DSSL) with an unexpectedly high D concentration of ~10 at.% after irradiation with ion energy of 215 eV. Electron back-scatter diffraction reveals that the W lattice within this DSSL is highly distorted, thus strongly blurring the Kikuchi pattern. We explain this strong damage by the synergistic interaction of energetic D ions and solute D atoms with the W lattice. Solute D atoms prevent the recombination of vacancies with interstitial W atoms, which are produced by collisions of energetic D ions with W lattice atoms (Frenkel pairs). This proposed damaging mechanism could also be active on other hydrogen-irradiated metal surfaces. The present work provides deep insight into hydrogen-induced lattice distortion at plasma-metal interfaces and sheds light on its modelling work.

On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

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

Zhu, Xiaolei, E-mail: virtualzx@gmail.com; Yarkony, David R., E-mail: yarkony@jhu.edu

2016-01-14

In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} to describe the photodissociation of phenolmore » from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 10{sup 6} configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct H{sup d}, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm{sup −1} for electronic energies <60 000 cm{sup −1}.« less

Spreadsheet-Based Program for Simulating Atomic Emission Spectra

ERIC Educational Resources Information Center

Flannigan, David J.

2014-01-01

A simple Excel spreadsheet-based program for simulating atomic emission spectra from the properties of neutral atoms (e.g., energies and statistical weights of the electronic states, electronic partition functions, transition probabilities, etc.) is described. The contents of the spreadsheet (i.e., input parameters, formulas for calculating…

Trapping hydrogen atoms from a neon-gas matrix: a theoretical simulation.

PubMed

Bovino, S; Zhang, P; Kharchenko, V; Dalgarno, A

2009-08-07

Hydrogen is of critical importance in atomic and molecular physics and the development of a simple and efficient technique for trapping cold and ultracold hydrogen atoms would be a significant advance. In this study we simulate a recently proposed trap-loading mechanism for trapping hydrogen atoms released from a neon matrix. Accurate ab initio quantum calculations are reported of the neon-hydrogen interaction potential and the energy- and angular-dependent elastic scattering cross sections that control the energy transfer of initially cold atoms are obtained. They are then used to construct the Boltzmann kinetic equation, describing the energy relaxation process. Numerical solutions of the Boltzmann equation predict the time evolution of the hydrogen energy distribution function. Based on the simulations we discuss the prospects of the technique.

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 Oxygen Durability Evaluation of Protected Polymers Using Thermal Energy Plasma Systems

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Rutledge, Sharon K.; Degroh, Kim K.; Stidham, Curtis R.; Gebauer, Linda; Lamoreaux, Cynthia M.

1995-01-01

The durability evaluation of protected polymers intended for use in low Earth orbit (LEO) has necessitated the use of large-area, high-fluence, atomic oxygen exposure systems. Two thermal energy atomic oxygen exposure systems which are frequently used for such evaluations are radio frequency (RF) plasma ashers and electron cyclotron resonance plasma sources. Plasma source testing practices such as ample preparation, effective fluence prediction, atomic oxygen flux determination, erosion measurement, operational considerations, and erosion yield measurements are presented. Issues which influence the prediction of in-space durability based on ground laboratory thermal energy plasma system testing are also addressed.

State of knowledge about energy development impacts on North American rangelands: An integrative approach.

PubMed

Kreuter, Urs P; Iwaasa, Alan D; Theodori, Gene L; Ansley, R James; Jackson, Robert B; Fraser, Lauchlan H; Naeth, M Anne; McGillivray, Susan; Moya, Edmundo Garcia

2016-09-15

To reduce dependence on foreign oil reserves, there has been a push in North America to develop alternative domestic energy resources. Relatively undeveloped renewable energy resources include biofuels and wind and solar energy, many of which occur predominantly on rangelands. Rangelands are also key areas for natural gas development from shales and tight sand formations. Accordingly, policies aimed at greater energy independence are likely to affect the delivery of crucial ecosystem services provided by rangelands. Assessing and dealing with the biophysical and socio-economic effects of energy development on rangeland ecosystems require an integrative and systematic approach that is predicated on a broad understanding of diverse issues related to energy development. In this article, we present a road map for developing an integrative assessment of energy development on rangelands in North America. We summarize current knowledge of socio-economic and biophysical aspects of rangeland based energy development, and we identify knowledge gaps and monitoring indicators to fill these knowledge gaps. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lorentz and CPT Tests with Atoms

NASA Astrophysics Data System (ADS)

Vargas Silva, Arnaldo J.

The prospects for using atomic-spectroscopy experiments to test Lorentz and CPT symmetry are investigated. Phenomenological models for Lorentz violation studied in this work include ones with contributions from all quadratic operators for a Dirac fermion in the Lagrange density of the Standard-Model Extension (SME), without restriction on the operator mass dimension. The systems considered include atoms composed of conventional matter, antimatter, and second-generation particles. Generic expressions for the Lorentz-violating energy shifts applicable to a broad range of atomic transitions are obtained. Signals for Lorentz violation that can in principle be studied in spectroscopic experiments are identified from the theoretical corrections to the spectrum. Some of these signals include sidereal and annual variations of atomic transition frequencies measured in a laboratory on the surface of the Earth. Other possibilities include effects produced by changing the orientation of the applied magnetic field or by realizing space-based experiments. Discrepancies in the experimental values for fundamental constants and energy levels based on self-consistent predictions from the Standard Model also offer potential signals for Lorentz violation. The sensitivities of different experiments to distinct sets of coefficients for Lorentz violation are considered. Using atoms composed of different particle species allows measurements of coefficients for Lorentz violation in different fermion sectors of the SME. Experiments comparing hydrogen and antihydrogen can discriminate between coefficients for Lorentz violation that are associated with CPT-odd or CPT-even operators. Additionally, certain systems and transitions are more sensitive to nonminimal operators, while others are particularly sensitive to minimal ones.

Monolayer Nickel Cobalt Hydroxyl Carbonate for High Performance All-Solid-State Asymmetric Supercapacitors.

PubMed

Zhao, Yufeng; Ma, Hongnan; Huang, Shifei; Zhang, Xuejiao; Xia, Meirong; Tang, Yongfu; Ma, Zi-Feng

2016-09-07

The emergence of atomically thick nanolayer materials, which feature a short ion diffusion channel and provide more exposed atoms in the electrochemical reactions, offers a promising occasion to optimize the performance of supercapacitors on the atomic level. In this work, a novel monolayer Ni-Co hydroxyl carbonate with an average thickness of 1.07 nm is synthesized via an ordinary one-pot hydrothermal route for the first time. This unique monolayer structure can efficiently rise up the exposed electroactive sites and facilitate the surface dependent electrochemical reaction processes, and thus results in outstanding specific capacitance of 2266 F g(-1). Based on this material, an all-solid-state asymmetric supercapacitor is developed adopting alkaline PVA (poly(vinyl alcohol)) gel (PVA/KOH) as electrolyte, which performs remarkable cycling stability (no capacitance fade after 19 000 cycles) together with promising energy density of 50 Wh kg(-1) (202 μWh cm(-2)) and high power density of 8.69 kW kg(-1) (35.1 mW cm(-2)). This as-assembled all-solid-state asymmetric supercapacitor (AASC) holds great potential in the field of portable energy storage devices.

Learning molecular energies using localized graph kernels.

PubMed

Ferré, Grégoire; Haut, Terry; Barros, Kipton

2017-03-21

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

Learning molecular energies using localized graph kernels

NASA Astrophysics Data System (ADS)

Ferré, Grégoire; Haut, Terry; Barros, Kipton

2017-03-01

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

Free-energy landscape of the villin headpiece in an all-atom force field.

PubMed

Herges, Thomas; Wenzel, Wolfgang

2005-04-01

We investigate the landscape of the internal free-energy of the 36 amino acid villin headpiece with a modified basin hopping method in the all-atom force field PFF01, which was previously used to predictively fold several helical proteins with atomic resolution. We identify near native conformations of the protein as the global optimum of the force field. More than half of the twenty best simulations started from random initial conditions converge to the folding funnel of the native conformation, but several competing low-energy metastable conformations were observed. From 76,000 independently generated conformations we derived a decoy tree which illustrates the topological structure of the entire low-energy part of the free-energy landscape and characterizes the ensemble of metastable conformations. These emerge as similar in secondary content, but differ in tertiary arrangement.

XZP + 1d and XZP + 1d-DKH basis sets for second-row elements: application to CCSD(T) zero-point vibrational energy and atomization energy calculations.

PubMed

Campos, Cesar T; Jorge, Francisco E; Alves, Júlia M A

2012-09-01

Recently, segmented all-electron contracted double, triple, quadruple, quintuple, and sextuple zeta valence plus polarization function (XZP, X = D, T, Q, 5, and 6) basis sets for the elements from H to Ar were constructed for use in conjunction with nonrelativistic and Douglas-Kroll-Hess Hamiltonians. In this work, in order to obtain a better description of some molecular properties, the XZP sets for the second-row elements were augmented with high-exponent d "inner polarization functions," which were optimized in the molecular environment at the second-order Møller-Plesset level. At the coupled cluster level of theory, the inclusion of tight d functions for these elements was found to be essential to improve the agreement between theoretical and experimental zero-point vibrational energies (ZPVEs) and atomization energies. For all of the molecules studied, the ZPVE errors were always smaller than 0.5 %. The atomization energies were also improved by applying corrections due to core/valence correlation and atomic spin-orbit effects. This led to estimates for the atomization energies of various compounds in the gaseous phase. The largest error (1.2 kcal mol(-1)) was found for SiH(4).

Measurements of Excitation Functions and Line Polarizations for Electron Impact Excitation of the n = 2, 3 States of Atomic Hydrogen in the Energy Range 11 - 2000 eV

NASA Technical Reports Server (NTRS)

James, G. K.; Ajello, J. M.; Kanik, I.; Slevin, J.; Franklin, B.; Shemansky, D.

1993-01-01

The electron-atomic hydrogen scattering system is an important testing ground for theoretical models and has received a great deal of attention from experimentalists and theoreticians alike over the years. A complete description of the excitation process requires a knowledge of many different parameters, and experimental measurements of these parameters have been performed in various laboratories around the world. As far as total cross section data are concerned it has been noted that the discrepancy between the data of Long et al. and Williams for n = 2 excitations needs to be resolved in the interests of any further refinement of theory. We report new measurements of total cross sections and atomic line polarizations for both n=2 and n=3 excitations at energies from threshold to 2000 eV...

First-principles calculation of defect free energies: General aspects illustrated in the case of bcc Fe

NASA Astrophysics Data System (ADS)

Murali, D.; Posselt, M.; Schiwarth, M.

2015-08-01

Modeling of nanostructure evolution in solids requires comprehensive data on the properties of defects such as the vacancy and foreign atoms. Since most processes occur at elevated temperatures, not only the energetics of defects in the ground state, but also their temperature-dependent free energies must be known. The first-principles calculation of contributions of phonon and electron excitations to free formation, binding, and migration energies of defects is illustrated in the case of bcc Fe. First of all, the ground-state properties of the vacancy, the foreign atoms Cu, Y, Ti, Cr, Mn, Ni, V, Mo, Si, Al, Co, O, and the O-vacancy pair are determined under constant volume (CV) as well as zero-pressure (ZP) conditions, and relations between the results of both kinds of calculations are discussed. Second, the phonon contribution to defect free energies is calculated within the harmonic approximation using the equilibrium atomic positions determined in the ground state under CV and ZP conditions. In most cases, the ZP-based free formation energy decreases monotonously with temperature, whereas for CV-based data both an increase and a decrease were found. The application of a quasiharmonic correction to the ZP-based data does not modify this picture significantly. However, the corrected data are valid under zero-pressure conditions at higher temperatures than in the framework of the purely harmonic approach. The difference between CV- and ZP-based data is mainly due to the volume change of the supercell since the relative arrangement of atoms in the environment of the defects is nearly identical in the two cases. A simple transformation similar to the quasiharmonic approach is found between the CV- and ZP-based frequencies. Therefore, it is not necessary to calculate these quantities and the corresponding defect free energies separately. In contrast to ground-state energetics, the CV- and ZP-based defect free energies do not become equal with increasing supercell size. Third, it was found that the contribution of electron excitations to the defect free energy can lead to an additional deviation of the total free energy from the ground-state value or can compensate the deviation caused by the phonon contribution. Finally, self-diffusion via the vacancy mechanism is investigated. The ratio of the respective CV- and ZP-based results for the vacancy diffusivity is nearly equal to the reciprocal of that for the equilibrium concentration. This behavior leads to almost identical CV- and ZP-based values for the self-diffusion coefficient. Obviously, this agreement is accidental. The consideration of the temperature dependence of the magnetization yields self-diffusion data in very good agreement with experiments.

A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments

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

Li, Tong; Gu, YuanTong, E-mail: yuantong.gu@qut.edu.au

As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grainedmore » level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.« less

Operation of the computer model for direct atomic oxygen exposure of Earth satellites

NASA Technical Reports Server (NTRS)

Bourassa, R. J.; Gruenbaum, P. E.; Gillis, J. R.; Hargraves, C. R.

1995-01-01

One of the primary causes of material degradation in low Earth orbit (LEO) is exposure to atomic oxygen. When atomic oxygen molecules collide with an orbiting spacecraft, the relative velocity is 7 to 8 km/sec and the collision energy is 4 to 5 eV per atom. Under these conditions, atomic oxygen may initiate a number of chemical and physical reactions with exposed materials. These reactions contribute to material degradation, surface erosion, and contamination. Interpretation of these effects on materials and the design of space hardware to withstand on-orbit conditions requires quantitative knowledge of the atomic oxygen exposure environment. Atomic oxygen flux is a function of orbit altitude, the orientation of the orbit plan to the Sun, solar and geomagnetic activity, and the angle between exposed surfaces and the spacecraft heading. We have developed a computer model to predict the atomic oxygen exposure of spacecraft in low Earth orbit. The application of this computer model is discussed.

Interpreting atom probe data from chromium oxide scales.

PubMed

La Fontaine, Alexandre; Gault, Baptiste; Breen, Andrew; Stephenson, Leigh; Ceguerra, Anna V; Yang, Limei; Nguyen, Thuan Dinh; Zhang, Jianqiang; Young, David J; Cairney, Julie M

2015-12-01

Picosecond-pulsed ultraviolet-laser (UV-355 nm) assisted atom probe tomography (APT) was used to analyze protective, thermally grown chromium oxides formed on stainless steel. The influence of analysis parameters on the thermal tail observed in the mass spectra and the chemical composition is investigated. A new parameter termed "laser sensitivity factor" is introduced in order to quantify the effect of laser energy on the extent of the thermal tail. This parameter is used to compare the effect of increasing laser energy on thermal tails in chromia and chromite samples. Also explored is the effect of increasing laser energy on the measured oxygen content and the effect of specimen base temperature and laser pulse frequency on the mass spectrum. Finally, we report a preliminary analysis of molecular ion dissociations in chromia. Copyright © 2015 Elsevier B.V. All rights reserved.

The Hyperfine Structure of the Ground State in the Muonic Helium Atoms

NASA Astrophysics Data System (ADS)

Aznabayev, D. T.; Bekbaev, A. K.; Korobov, V. I.

2018-05-01

Non-relativistic ionization energies 3He2+μ-e- and 4He2+μ-e- of helium-muonic atoms are calculated for ground states. The calculations are based on the variational method of the exponential expansion. Convergence of the variational energies is studied by an increasing of a number of the basis functions N. This allows to claim that the obtained energy values have 26 significant digits for ground states. With the obtained results we calculate hyperfine splitting of the muonic helium atoms.

TOUCHSTONE II: a new approach to ab initio protein structure prediction.

PubMed

Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey

2003-08-01

We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These procedures are readily automated and are being implemented on a genomic scale.

Low cost estimation of the contribution of post-CCSD excitations to the total atomization energy using density functional theory calculations

NASA Astrophysics Data System (ADS)

Sánchez, H. R.; Pis Diez, R.

2016-04-01

Based on the Aλ diagnostic for multireference effects recently proposed [U.R. Fogueri, S. Kozuch, A. Karton, J.M. Martin, Theor. Chem. Acc. 132 (2013) 1], a simple method for improving total atomization energies and reaction energies calculated at the CCSD level of theory is proposed. The method requires a CCSD calculation and two additional density functional theory calculations for the molecule. Two sets containing 139 and 51 molecules are used as training and validation sets, respectively, for total atomization energies. An appreciable decrease in the mean absolute error from 7-10 kcal mol-1 for CCSD to about 2 kcal mol-1 for the present method is observed. The present method provides atomization energies and reaction energies that compare favorably with relatively recent scaled CCSD methods.

Photon interaction study of organic nonlinear optical materials in the energy range 122-1330 keV

NASA Astrophysics Data System (ADS)

Awasarmol, Vishal V.; Gaikwad, Dhammajyot K.; Raut, Siddheshwar D.; Pawar, Pravina P.

2017-01-01

In the present study, the mass attenuation coefficient (μm) of six organic nonlinear optical materials has been calculated in the energy range 122-1330 keV and compared with the obtained values from the WinXCOM program. It is found that there is a good agreement between theoretical and experimental values (<3%). The linear attenuation coefficients (μ) total atomic cross section (σt, a), and total electronic cross section (σt, el) have also been calculated from the obtained μm values and their variations with photon energy have been plotted. From the present work, it is observed that the variation of obtained values of μm, μ, σt, a, and σt, el strongly depends on the photon energy and decreases or increases due to chemical composition and density of the sample. All the samples have been studied extensively using transmission method with a view to utilize the material for radiation dosimetry. Investigated samples are good material for radiation dosimetry due their low effective atomic number. The mass attenuation coefficient (μm), linear attenuation coefficients (μ), total atomic cross section (σt, a), total electronic cross section (σt, el), effective atomic numbers (Zeff), molar extinction coefficient (ε), mass energy absorption coefficient (μen/ρ) and effective atomic energy absorption cross section (σa, en) of all sample materials have been carried out and transmission curves have been plotted. The transmission curve shows that the variation of all sample materials decreases with increasing photon energy.

Long-range interactions between metastable rare gases atoms

NASA Astrophysics Data System (ADS)

Vrinceanu, D.; Marinescu, M.; Flannery, M. R.

1998-10-01

Knowledge of the long-range interaction between atoms and molecules is of fundamental importance for low-energy and low-temperature collisions. The electronic interaction between the charge distributions of two metastable rare gases atoms can be expanded in inverse powers of R, the internuclear distance. The coefficients C_6, C_8, and C_10 of, respectively, the R-6, R-8, and R-10 terms are calculated by integrating the products of the dynamic electric polarizabilities of the individual atoms at imaginary frequencies, which are in turn obtained by solving a system of coupled inhomogeneous differential equations. The triplet state spectrum of the rare gases atoms is described by precise l-dependent one-electron model potentials. Numerical results for the C_6, C_8, and C_10 dispersion coefficients for homonuclear and heteronuclear metastable rare gases diatoms are presented.

Long-range interactions between metastable rare gases atoms

NASA Astrophysics Data System (ADS)

Vrinceanu, D.; Marinescu, M.; Flannery, M. R.

1998-05-01

Knowledge of the long-range interaction between atoms and molecules is of fundamental importance for low-energy and low-temperature collisions. The electronic interaction between the charge distributions of two metastable rare gases atoms can be expanded in inverse powers of R, the internuclear distance. The coefficients C_6, C_8, and C_10 of, respectively, the R-6, R-8, and R-10 terms are calculated by integrating the products of the dynamic electric polarizabilities of the individual atoms at imaginary frequencies, which are in turn obtained by solving a system of coupled inhomogeneous differential equations. The triplet state spectrum of the rare gases atoms is described by precise l-dependent one-electron model potentials. Numerical results for the C_6, C_8, and C_10 dispersion coefficients for homonuclear and heteronuclear metastable rare gases diatoms are presented.

Phenomenology of break-up modes in contact free externally heated nanoparticle laden fuel droplets

NASA Astrophysics Data System (ADS)

Pathak, Binita; Basu, Saptarshi

2016-12-01

We study thermally induced atomization modes in contact free (acoustically levitated) nanoparticle laden fuel droplets. The initial droplet size, external heat supplied, and suspended particle concentration (wt. %) in droplets govern the stability criterion which ultimately determines the dominant mode of atomization. Pure fuel droplets exhibit two dominant modes of breakup namely primary and secondary. Primary modes are rather sporadic and normally do not involve shape oscillations. Secondary atomization however leads to severe shape deformations and catastrophic intense breakup of the droplets. The dominance of these modes has been quantified based on the external heat flux, dynamic variation of surface tension, acoustic pressure, and droplet size. Addition of particles alters the regimes of the primary and secondary atomization and introduces bubble induced boiling and bursting. We analyze this new mode of atomization and estimate the time scale of bubble growth up to the point of bursting using energy balance to determine the criterion suitable for parent droplet rupture. All the three different modes of breakup have been well identified in a regime map determined in terms of Weber number and the heat utilization rate which is defined as the energy utilized for transient heating, vaporization, and boiling in droplets.

Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing

NASA Astrophysics Data System (ADS)

Farrell, Kathryn; Oden, J. Tinsley

2014-07-01

Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and methods through applications to representative atomic structures and we discuss extensions to the validation process for molecular models of polymer structures encountered in certain semiconductor nanomanufacturing processes. The powerful method of model plausibility as a means for selecting interaction potentials for coarse-grained models is discussed in connection with a coarse-grained hexane molecule. Discussions of how all-atom information is used to construct priors are contained in an appendix.

An equation of state for partially ionized plasmas: The Coulomb contribution to the free energy

NASA Astrophysics Data System (ADS)

Kilcrease, D. P.; Colgan, J.; Hakel, P.; Fontes, C. J.; Sherrill, M. E.

2015-09-01

We have previously developed an equation of state (EOS) model called ChemEOS (Hakel and Kilcrease, Atomic Processes in Plasmas, Eds., J. Cohen et al., AIP, 2004) for a plasma of interacting ions, atoms and electrons. It is based on a chemical picture of the plasma and is derived from an expression for the Helmholtz free energy of the interacting species. All other equilibrium thermodynamic quantities are then obtained by minimizing this free energy subject to constraints, thus leading to a thermodynamically consistent EOS. The contribution to this free energy from the Coulomb interactions among the particles is treated using the method of Chabrier and Potekhin (Phys. Rev. E 58, 4941 (1998)) which we have adapted for partially ionized plasmas. This treatment is further examined and is found to give rise to unphysical behavior for various elements at certain values of the density and temperature where the Coulomb coupling begins to become significant and the atoms are partially ionized. We examine the source of this unphysical behavior and suggest corrections that produce acceptable results. The sensitivity of the thermodynamic properties and frequency-dependent opacity of iron is examined with and without these corrections. The corrected EOS is used to determine the fractional ion populations and level populations for a new generation of OPLIB low-Z opacity tables currently being prepared at Los Alamos National Laboratory with the ATOMIC code.

In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field.

PubMed

Herges, T; Wenzel, W

2005-01-14

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 A backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

NASA Astrophysics Data System (ADS)

Herges, T.; Wenzel, W.

2005-01-01

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

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

Wales, D. J., E-mail: dw34@cam.ac.uk

This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. Themore » effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of “friction” effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.« less

Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

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

Kamberaj, Hiqmet, E-mail: hkamberaj@ibu.edu.mk

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, andmore » 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.« less

Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2015-09-01

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

PubMed

Olson, Mark A; Lee, Michael S

2014-01-01

A central problem of computational structural biology is the refinement of modeled protein structures taken from either comparative modeling or knowledge-based methods. Simulations are commonly used to achieve higher resolution of the structures at the all-atom level, yet methodologies that consistently yield accurate results remain elusive. In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population and exchanges near steep energetic barriers. This approach is compared to earlier work of applying the conventional method of static temperature clients to refine a dataset of conformational decoys. Our results show that, while an adaptive method has many theoretical advantages over a static distribution of client temperatures, only limited improvement was gained from this strategy in excursions of the downhill refinement regime leading to an increase in the fraction of native contacts. To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.

NIST Databases on Atomic Spectra

NASA Astrophysics Data System (ADS)

Reader, J.; Wiese, W. L.; Martin, W. C.; Musgrove, A.; Fuhr, J. R.

2002-11-01

The NIST atomic and molecular spectroscopic databases now available on the World Wide Web through the NIST Physics Laboratory homepage include Atomic Spectra Database, Ground Levels and Ionization Energies for the Neutral Atoms, Spectrum of Platinum Lamp for Ultraviolet Spectrograph Calibration, Bibliographic Database on Atomic Transition Probabilities, Bibliographic Database on Atomic Spectral Line Broadening, and Electron-Impact Ionization Cross Section Database. The Atomic Spectra Database (ASD) [1] offers evaluated data on energy levels, wavelengths, and transition probabilities for atoms and atomic ions. Data are given for some 950 spectra and 70,000 energy levels. About 91,000 spectral lines are included, with transition probabilities for about half of these. Additional data resulting from our ongoing critical compilations will be included in successive new versions of ASD. We plan to include, for example, our recently published data for some 16,000 transitions covering most ions of the iron-group elements, as well as Cu, Kr, and Mo [2]. Our compilations benefit greatly from experimental and theoretical atomic-data research being carried out in the NIST Atomic Physics Division. A new compilation covering spectra of the rare gases in all stages of ionization, for example, revealed a need for improved data in the infrared. We have thus measured these needed data with our high-resolution Fourier transform spectrometer [3]. An upcoming new database will give wavelengths and intensities for the stronger lines of all neutral and singly-ionized atoms, along with energy levels and transition probabilities for the persistent lines [4]. A critical compilation of the transition probabilities of Ba I and Ba II [5] has been completed and several other compilations of atomic transition probabilities are nearing completion. These include data for all spectra of Na, Mg, Al, and Si [6]. Newly compiled data for selected ions of Ne, Mg, Si and S, will form the basis for a new database intended to assist interpretation of soft x-ray astronomical spectra, such as from the Chandra X-ray Observatory. These data will be available soon on the World Wide Web [7].

An accurate full-dimensional potential energy surface for H-Au(111): Importance of nonadiabatic electronic excitation in energy transfer and adsorption.

PubMed

Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander

2015-09-28

We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.

Adsorption and diffusion of Au atoms on the (001) surface of Ti, Zr, Hf, V, Nb, Ta, and Mo carbides.

PubMed

Florez, Elizabeth; Viñes, Francesc; Rodriguez, Jose A; Illas, Francesc

2009-06-28

The adsorption of atomic Au on the (001) surface of TiC, ZrC, HfC, VC, NbC, TaC, and delta-MoC and the mechanism of diffusion of this adatom through the surface have been studied in terms of a periodic density functional theory based approach. In all the cases, the Au adsorption energies are in the range of 1.90-2.35 eV. The moderately large adsorption energies allow the Au diffusion before desorption could take place. For TiC(001), ZrC(001), and HfC(001), atomic Au is adsorbed directly on top of C atoms and diffusion takes place along the diagonal of the squares formed by M-C-M-C atoms with the transition state located above the hollow sites. For the rest of transition metal carbides the situation is less simple with the appearance of more than one stable adsorption site, as for NbC and TaC, of a small energy barrier for diffusion around the most stable adsorption site and of a more complex diffusion pathway. The small energy barrier for diffusion around the most stable site will result in a highly mobile Au species which could be observed in scanning tunnel microscope experiments. After depositing Au on metal-carbide surfaces, there is a noticeable charge transfer from the substrate to the adsorbed Au atom. The electronic perturbations on Au increase when going from TiC to ZrC or TaC. Our results indicate that metal carbides should be better supports for the chemical activation of Au than metal oxides.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Wang, Yimin; Braams, Bastiaan J.; Bowman, Joel M.; Carter, Stuart; Tew, David P.

2008-06-01

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and ``exact'' full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased ``fixed-node'' diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm-1 in Cartesian coordinates and 22.6 cm-1 in normal coordinates, with an uncertainty of 2-3 cm-1. This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm-1. The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm-1. These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm-1, and agree well with the experimental values of 21.6 and 2.9 cm-1 for the H and D transfer, respectively.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

PubMed

Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

2008-06-14

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

Adsorption Energies of Carbon, Nitrogen, and Oxygen Atoms on the Low-temperature Amorphous Water Ice: A Systematic Estimation from Quantum Chemistry Calculations

NASA Astrophysics Data System (ADS)

Shimonishi, Takashi; Nakatani, Naoki; Furuya, Kenji; Hama, Tetsuya

2018-03-01

We propose a new simple computational model to estimate the adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3 P), nitrogen (4 S), and oxygen (3 P) atoms based on quantum chemistry calculations. The adsorption energies were estimated to be 14,100 ± 420 K for carbon, 400 ± 30 K for nitrogen, and 1440 ± 160 K for oxygen. The adsorption energy of oxygen is consistent with experimentally reported values. We found that the binding of a nitrogen atom is purely physisorption, while that of a carbon atom is chemisorption, in which a chemical bond to an O atom of a water molecule is formed. That of an oxygen atom has a dual character, with both physisorption and chemisorption. The chemisorption of atomic carbon also implies the possibility of further chemical reactions to produce molecules bearing a C–O bond, though this may hinder the formation of methane on water ice via sequential hydrogenation of carbon atoms. These properties would have a large impact on the chemical evolution of carbon species in interstellar environments. We also investigated the effects of newly calculated adsorption energies on the chemical compositions of cold dense molecular clouds with the aid of gas-ice astrochemical simulations. We found that abundances of major nitrogen-bearing molecules, such as N2 and NH3, are significantly altered by applying the calculated adsorption energy, because nitrogen atoms can thermally diffuse on surfaces, even at 10 K.

Hydrogen rearrangements in the fragmentation of anthracene by low-energy electron impact

NASA Astrophysics Data System (ADS)

van der Burgt, Peter J. M.; Dunne, Melissa; Gradziel, Marcin L.

2018-02-01

We have measured mass spectra for positive ions produced by low-energy electron impact on anthracene using a reflectron time-of-flight mass spectrometer. The electron impact energy has been varied from 0 to 100 eV in steps of 0.5 eV. Ion yield curves of most of the fragment ions have been determined by fitting groups of adjacent peaks in the mass spectra with sequences of normalized Gaussians. Appearance energies for all these ions have been determined, and we report the first direct measurement of the triple ionization energy of anthracene at 45.5±0.5 eV. The groups of fragments containing 8-13 carbon atoms provide evidence for hydrogen rearrangements during the fragmentation, involving retention or loss of one or two additional hydrogen atoms. Groups of fragments with 6 and 7 carbon atoms clearly show the presence of doubly-charged fragments. The smaller fragments with 1-4 carbon atoms all show broadened peaks, and these fragments may be partly or mostly due to energetic charge-separation fragmentations of doubly-charged anthracene.

Nanoalloy catalysts inside fuel cells: An atomic-level perspective on the functionality by combined in operando x-ray spectroscopy and total scattering

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

Petkov, Valeri; Maswadeh, Yazan; Zhao, Yinguang

We introduce an experimental approach for structural characterization of catalysts for fuel cells combining synchrotron x-ray spectroscopy and total scattering. The approach allows probing catalysts inside operating fuel cells with atomic-level precision (~ 0.02 Å) and element specificity (~ 2–3 at%) in both time (~ 1 min) and space (~ μm) resolved manner. The approach is demonstrated on exemplary Pd-Sn and Pt-Ni-Cu nanoalloy catalysts for the oxygen reduction reaction (ORR) deposited on the cathode of an operating proton exchange membrane fuel cell. In operando x-ray data show that under operating conditions, the catalyst particles can undergo specific structural changes, rangingmore » from sub-Å atomic fluctuations and sharp nanophase transitions to a gradual strain relaxation and growth, which inflict significant losses in their ORR activity. Though triggered electrochemically, the changes are not driven solely by differences in the reduction potential and surface energy of the metallic species constituting the nanoalloys but also by the formation energy of competing nanophases, mismatch between the size of individual atomic species and their ability to interdiffuse fast in search of energetically favorable configurations. Given their complexity, the changes are difficult to predict and so the resulting ORR losses remain difficult to limit. We show that in operando knowledge of the structural evolution of nanoalloy catalysts helps create strategies for improving their activity and stability. In particular, we show that shaping Pd-Sn nanoalloys rich in Pd as cubes reduces the interdiffusion of atoms at their surface and so makes them better catalysts for ORR in fuel cells in comparison to other Pd-Sn nanoalloys. In addition, we demonstrate that the approach introduced here can provide knowledge of other major factors affecting the performance of fuel cells such as operating temperature and the overall catalyst utilization, in particular the evolution of elemental and mass distribution of catalyst particles over the cells’ cathode. Last but not least, we discuss how in operando x-ray spectroscopy and total x-ray scattering can bridge the knowledge gap between the widely used in situ SAXS, EXAFS and monocrystal surface XRD techniques for structural characterization of nanoalloy catalysts explored for energy related applications.« less

Nanoalloy catalysts inside fuel cells: An atomic-level perspective on the functionality by combined in operando x-ray spectroscopy and total scattering

DOE PAGES

Petkov, Valeri; Maswadeh, Yazan; Zhao, Yinguang; ...

2018-04-18

We introduce an experimental approach for structural characterization of catalysts for fuel cells combining synchrotron x-ray spectroscopy and total scattering. The approach allows probing catalysts inside operating fuel cells with atomic-level precision (~ 0.02 Å) and element specificity (~ 2–3 at%) in both time (~ 1 min) and space (~ μm) resolved manner. The approach is demonstrated on exemplary Pd-Sn and Pt-Ni-Cu nanoalloy catalysts for the oxygen reduction reaction (ORR) deposited on the cathode of an operating proton exchange membrane fuel cell. In operando x-ray data show that under operating conditions, the catalyst particles can undergo specific structural changes, rangingmore » from sub-Å atomic fluctuations and sharp nanophase transitions to a gradual strain relaxation and growth, which inflict significant losses in their ORR activity. Though triggered electrochemically, the changes are not driven solely by differences in the reduction potential and surface energy of the metallic species constituting the nanoalloys but also by the formation energy of competing nanophases, mismatch between the size of individual atomic species and their ability to interdiffuse fast in search of energetically favorable configurations. Given their complexity, the changes are difficult to predict and so the resulting ORR losses remain difficult to limit. We show that in operando knowledge of the structural evolution of nanoalloy catalysts helps create strategies for improving their activity and stability. In particular, we show that shaping Pd-Sn nanoalloys rich in Pd as cubes reduces the interdiffusion of atoms at their surface and so makes them better catalysts for ORR in fuel cells in comparison to other Pd-Sn nanoalloys. In addition, we demonstrate that the approach introduced here can provide knowledge of other major factors affecting the performance of fuel cells such as operating temperature and the overall catalyst utilization, in particular the evolution of elemental and mass distribution of catalyst particles over the cells’ cathode. Last but not least, we discuss how in operando x-ray spectroscopy and total x-ray scattering can bridge the knowledge gap between the widely used in situ SAXS, EXAFS and monocrystal surface XRD techniques for structural characterization of nanoalloy catalysts explored for energy related applications.« less

When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms.

PubMed

Petković, Milena; Nakarada, Đura; Etinski, Mihajlo

2018-05-25

Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

The 2012 Atomic Mass Evaluation and the Mass Tables

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

Audi, G., E-mail: amdc.audi@gmail.com; Wang, M.; MPI-K, D-69117 Heidelberg

The new evaluation of the Atomic Masses, Ame2012, has just been released. It represents a major step in the history of the 60 year old Atomic Mass Evaluation based on the method developed by Wapstra. This new publication includes all material available to date. Some of the policies and procedures used in our evaluation are reported, together with an illustration of one specially difficult case, the energy available for the {sup 102}Pd double-electron capture. The observation of the mass surface reveals many important new features. We illustrate this statement by the double magicity of {sup 270}Hs at N = 162more » and Z = 108.« less

A fully-nonlocal energy-based formulation and high-performance realization of the quasicontinuum method

NASA Astrophysics Data System (ADS)

Amelang, Jeff

The quasicontinuum (QC) method was introduced to coarse-grain crystalline atomic ensembles in order to bridge the scales from individual atoms to the micro- and mesoscales. Though many QC formulations have been proposed with varying characteristics and capabilities, a crucial cornerstone of all QC techniques is the concept of summation rules, which attempt to efficiently approximate the total Hamiltonian of a crystalline atomic ensemble by a weighted sum over a small subset of atoms. In this work we propose a novel, fully-nonlocal, energy-based formulation of the QC method with support for legacy and new summation rules through a general energy-sampling scheme. Our formulation does not conceptually differentiate between atomistic and coarse-grained regions and thus allows for seamless bridging without domain-coupling interfaces. Within this structure, we introduce a new class of summation rules which leverage the affine kinematics of this QC formulation to most accurately integrate thermodynamic quantities of interest. By comparing this new class of summation rules to commonly-employed rules through analysis of energy and spurious force errors, we find that the new rules produce no residual or spurious force artifacts in the large-element limit under arbitrary affine deformation, while allowing us to seamlessly bridge to full atomistics. We verify that the new summation rules exhibit significantly smaller force artifacts and energy approximation errors than all comparable previous summation rules through a comprehensive suite of examples with spatially non-uniform QC discretizations in two and three dimensions. Due to the unique structure of these summation rules, we also use the new formulation to study scenarios with large regions of free surface, a class of problems previously out of reach of the QC method. Lastly, we present the key components of a high-performance, distributed-memory realization of the new method, including a novel algorithm for supporting unparalleled levels of deformation. Overall, this new formulation and implementation allows us to efficiently perform simulations containing an unprecedented number of degrees of freedom with low approximation error.

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

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

Yang, Xiu; Lei, Huan; Gao, Peiyuan

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a method for quantifying this uncertainty in solvation energies using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many moremore » types of atomic charges; therefore, construction of surrogate models for the charge parameter space required compressed sensing combined with an iterative rotation method to enhance problem sparsity. We present results for the uncertainty in small molecule solvation energies based on these approaches. Additionally, we explore the correlation between uncertainties due to radii and charges which motivates the need for future work in uncertainty quantification methods for high-dimensional parameter spaces.« less

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

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

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

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

PubMed Central

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-01-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into “alpha helix” and “beta sheet” structures. The 5-residue polyalanine displays a substantial increase in the “beta strand” fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. PMID:22029338

Ultrashort soliton switching based on coherent energy hiding.

PubMed

Romagnoli, M; Wabnitz, S; Zoccolotti, L

1991-08-15

Coherent coupling between light and atoms may be exploited for conceiving a novel class of all-optical signalprocessing devices without a direct counterpart in the continuous-wave regime. We show that the self-switching of ultrashort soliton pulses on resonance with a transition of doping centers in a slab waveguide directional coupler is based on nonlinear group-velocity (instead of the usual phase-velocity) changes.

All-atom ab initio native structure prediction of a mixed fold (1FME): A comparison of structural and folding characteristics of various ββα miniproteins

NASA Astrophysics Data System (ADS)

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2009-11-01

We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold ββα miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other ββα miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue ββα miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1→Glu1 and Ile7→Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I' turn (1FME) was well reproduced with the present simulation.

Kinetic Energy Distribution of H(2p) Atoms from Dissociative Excitation of H2

NASA Technical Reports Server (NTRS)

Ajello, Joseph M.; Ahmed, Syed M.; Kanik, Isik; Multari, Rosalie

1995-01-01

The kinetic energy distribution of H(2p) atoms resulting from electron impact dissociation of H2 has been measured for the first time with uv spectroscopy. A high resolution uv spectrometer was used for the measurement of the H Lyman-alpha emission line profiles at 20 and 100 eV electron impact energies. Analysis of the deconvolved 100 eV line profile reveals the existence of a narrow line peak and a broad pedestal base. Slow H(2p) atoms with peak energy near 80 meV produce the peak profile, which is nearly independent of impact energy. The wings of H Lyman-alpha arise from dissociative excitation of a series of doubly excited Q(sub 1) and Q(sub 2) states, which define the core orbitals. The fast atom energy distribution peaks at 4 eV.

Green Chemistry: An Introductory Text (Mike Lancaster)

NASA Astrophysics Data System (ADS)

Rosan, Alan M.

2003-10-01

With the unrealistic and irreconcilable choice of either technical or environmental performance still dominating the consumer view, the need for green teaching, green thinking, and green practice is paramount. Replete with extensive and varied examples, detailed analyses, and critical comparisons, this text is an important contribution to the training of future chemists and chemical engineers who will need to work together to plan and conduct syntheses requiring atom economy, energy efficiency, waste minimization, safe reactor design and operation all linked by an overarching environmental ethic. If these laudable goals are ever attained it will be as a consequence of the insightful knowledge and forthright teachings of texts like this one.

Oxidation-driven surface dynamics on NiAl(100)

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

Qin, Hailang; Chen, Xidong; Li, Liang

Atomic steps, a defect common to all crystal surfaces, can play an important role in many physical and chemical processes. However, attempts to predict surface dynamics under nonequilibrium conditions are usually frustrated by poor knowledge of the atomic processes of surface motion arising from mass transport from/to surface steps. Using low-energy electron microscopy that spatially and temporally resolves oxide film growth during the oxidation of NiAl(100) we demonstrate that surface steps are impermeable to oxide film growth. The advancement of the oxide occurs exclusively on the same terrace and requires the coordinated migration of surface steps. The resulting piling upmore » of surface steps ahead of the oxide growth front progressively impedes the oxide growth. This process is reversed during oxide decomposition. The migration of the substrate steps is found to be a surface-step version of the well-known Hele-Shaw problem, governed by detachment (attachment) of Al atoms at step edges induced by the oxide growth (decomposition). As a result, by comparing with the oxidation of NiAl(110) that exhibits unimpeded oxide film growth over substrate steps, we suggest that whenever steps are the source of atoms used for oxide growth they limit the oxidation process; when atoms are supplied from the bulk, the oxidation rate is not limited by the motion of surface steps.« less

Oxidation-driven surface dynamics on NiAl(100)

DOE PAGES

Qin, Hailang; Chen, Xidong; Li, Liang; ...

2014-12-29

Atomic steps, a defect common to all crystal surfaces, can play an important role in many physical and chemical processes. However, attempts to predict surface dynamics under nonequilibrium conditions are usually frustrated by poor knowledge of the atomic processes of surface motion arising from mass transport from/to surface steps. Using low-energy electron microscopy that spatially and temporally resolves oxide film growth during the oxidation of NiAl(100) we demonstrate that surface steps are impermeable to oxide film growth. The advancement of the oxide occurs exclusively on the same terrace and requires the coordinated migration of surface steps. The resulting piling upmore » of surface steps ahead of the oxide growth front progressively impedes the oxide growth. This process is reversed during oxide decomposition. The migration of the substrate steps is found to be a surface-step version of the well-known Hele-Shaw problem, governed by detachment (attachment) of Al atoms at step edges induced by the oxide growth (decomposition). As a result, by comparing with the oxidation of NiAl(110) that exhibits unimpeded oxide film growth over substrate steps, we suggest that whenever steps are the source of atoms used for oxide growth they limit the oxidation process; when atoms are supplied from the bulk, the oxidation rate is not limited by the motion of surface steps.« less

Ab initio theory of noble gas atoms in bcc transition metals.

PubMed

Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; Gan, Jian

2018-06-18

Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe). Our charge density analysis indicates that the strong polarization of nearest-neighbor metal atoms by noble gas interstitials is the electronic origin of their high formation energies. Such polarization becomes more significant with an increasing gas atom size and interstitial charge density in the host bcc metal, which explains the similar trend followed by the unrelaxed formation energies of noble gas interstitials. Upon allowing for local relaxation, nearby metal atoms move farther away from gas interstitials in order to decrease polarization, albeit at the expense of increasing the elastic strain energy. Such atomic relaxation is found to play an important role in governing both the energetics and site preference of noble gas atoms in bcc metals. Our most notable finding is that the fully relaxed formation energies of noble gas interstitials are strongly correlated with the elastic shear modulus of the bcc metal, and the physical origin of this unexpected correlation has been elucidated by our theoretical analysis based on the effective-medium theory. The kinetic behavior of noble gas atoms and their interaction with pre-existing vacancies in bcc transition metals have also been discussed in this work.

Calculation of low-Z impurity pellet induced fluxes of charge exchange neutral particles escaping from magnetically confined toroidal plasmas.

PubMed

Goncharov, P R; Ozaki, T; Sudo, S; Tamura, N; Tolstikhina, I Yu; Sergeev, V Yu

2008-10-01

Measurements of energy- and time-resolved neutral hydrogen and helium fluxes from an impurity pellet ablation cloud, referred to as pellet charge exchange or PCX experiments, can be used to study local fast ion energy distributions in fusion plasmas. The estimation of the local distribution function f(i)(E) of fast ions entering the cloud requires knowledge of both the fraction F(0)(E) of incident ions exiting the cloud as neutral atoms and the attenuation factor A(E,rho) describing the loss of fast atoms in the plasma. Determination of A(E,rho), in turn, requires the total stopping cross section sigma(loss) of neutral atoms in the plasma and the Jacobian reflecting the measurement geometry and the magnetic surface shape. The obtained functions F(0)(E) and A(E,rho) enter multiplicatively into the probability density for escaping neutral particle kinetic energy. A general calculation scheme has been developed and realized as a FORTRAN code, which is to be applied for the calculation of f(i)(E) from PCX experimental results obtained with low-Z impurity pellets.

Double photoionization of atoms

NASA Astrophysics Data System (ADS)

Wiedenhoeft, Marco

2003-10-01

Double photoionization studies of atoms and molecules are new state-of-the-art studies providing a deeper knowledge of multi-electron excitations. This type of work advances the understanding of many-body problems. Double photoionization of atoms is of great interest to learn about electron-electron correlation and relaxation effects in atoms and molecules. In order to study double photoionization processes, a new electron-electron coincidence apparatus was built to carry out the measurements. I will present the apparatus I built as well as the results of the measurement of the triply-differential-cross-section (TDCS) for the predicted interference and Post-Collision-Interaction (PCI) effects in the Xenon N5O2,3 O2,3 Auger decay after 4d5/2 photoionization. Furthermore I present measurements for direct double photoionization of Helium at various photon energies.

Multipolar electrostatics for proteins: atom-atom electrostatic energies in crambin.

PubMed

Yuan, Yongna; Mills, Matthew J L; Popelier, Paul L A

2014-02-15

Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom-atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom-atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ℓA+ ℓB + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom-atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels are only slightly larger than those calculated at HF/6-31G(d,p) level. This convergence behavior is transferable to the well-known amyloid beta polypeptide Aβ1-42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. Copyright © 2013 Wiley Periodicals, Inc.

EMR-based medical knowledge representation and inference via Markov random fields and distributed representation learning.

PubMed

Zhao, Chao; Jiang, Jingchi; Guan, Yi; Guo, Xitong; He, Bin

2018-05-01

Electronic medical records (EMRs) contain medical knowledge that can be used for clinical decision support (CDS). Our objective is to develop a general system that can extract and represent knowledge contained in EMRs to support three CDS tasks-test recommendation, initial diagnosis, and treatment plan recommendation-given the condition of a patient. We extracted four kinds of medical entities from records and constructed an EMR-based medical knowledge network (EMKN), in which nodes are entities and edges reflect their co-occurrence in a record. Three bipartite subgraphs (bigraphs) were extracted from the EMKN, one to support each task. One part of the bigraph was the given condition (e.g., symptoms), and the other was the condition to be inferred (e.g., diseases). Each bigraph was regarded as a Markov random field (MRF) to support the inference. We proposed three graph-based energy functions and three likelihood-based energy functions. Two of these functions are based on knowledge representation learning and can provide distributed representations of medical entities. Two EMR datasets and three metrics were utilized to evaluate the performance. As a whole, the evaluation results indicate that the proposed system outperformed the baseline methods. The distributed representation of medical entities does reflect similarity relationships with respect to knowledge level. Combining EMKN and MRF is an effective approach for general medical knowledge representation and inference. Different tasks, however, require individually designed energy functions. Copyright © 2018 Elsevier B.V. All rights reserved.

Nuclear astrophysics lessons from INTEGRAL.

PubMed

Diehl, Roland

2013-02-01

Measurements of high-energy photons from cosmic sources of nuclear radiation through ESA's INTEGRAL mission have advanced our knowledge: new data with high spectral resolution showed that characteristic gamma-ray lines from radioactive decays occur throughout the Galaxy in its interstellar medium. Although the number of detected sources and often the significance of the astrophysical results remain modest, conclusions derived from this unique astronomical window of radiation originating from nuclear processes are important, complementing the widely-employed atomic-line based spectroscopy. We review the results and insights obtained in the past decade from gamma-ray line measurements of cosmic sources in the context of their astrophysical questions.

Energy Levels and Spectral Lines of Li Atoms in White Dwarf Strength Magnetic Fields

NASA Astrophysics Data System (ADS)

Zhao, L. B.

2018-04-01

A theoretical approach based on B-splines has been developed to calculate atomic structures and discrete spectra of Li atoms in a strong magnetic field typical of magnetic white dwarf stars. Energy levels are presented for 20 electronic states with the symmetries 20+, 20‑, 2(‑1)+, 2(‑1)‑, and 2(‑2)+. The magnetic field strengths involved range from 0 to 2350 MG. The wavelengths and oscillator strengths for the electric dipole transitions relevant to these magnetized atomic states are reported. The current results are compared to the limited theoretical data in the literature. A good agreement has been found for the lower energy levels, but a significant discrepancy is clearly visible for the higher energy levels. The existing discrepancies of the wavelengths and oscillator strengths are also discussed. Our investigation shows that the spectrum data of magnetized Li atoms previously published are obviously far from meeting requirements of analyzing discrete atomic spectra of magnetic white dwarfs with lithium atmospheres.

A DFT based analysis of adsorption of Hg2+ ion on chitosan monomer and its citralidene and salicylidene derivatives: Prior to the removal of Hg toxicity.

PubMed

Hassan, Basila; Rajan, Vijisha K; Mujeeb, V M Abdul; K, Muraleedharan

2017-06-01

A Density functional theory based study of adsorption of the toxic metal Hg (II) ion by chitosan monomer and two of its derivatives; citralidene and salicylidene chitosan, has been performed. The effect of structural features on the stability of studied complexes has been analyzed by using Gaussian03 software package. All the possible conformations of these adsorbents were studied using the global minimum geometries. All the adsorbing sites were studied by placing the metal ion on the centroid of the atoms and the stable conformer of the adsorbent-metal ion complex was identified. Interaction between Hg (II) and the adsorbents is found to be electrostatic. Metal ion binding with nitrogen atom is stronger than that with oxygen atoms in all the cases as the charge density of nitrogen is enhanced on Schiff base formation. The advantage of derivatives over chitosan monomer is their stability in acidic media. ΔE value of the complexes are in the order SC-Hg (II)>chitosan-Hg (II)>CC-Hg (II) which indicates that the stability of complexes increases with increase in energy gap. The study reveals that aromatic Schiff base derivatives of chitosan is better for Hg(II) intake than aliphatic derivatives. Copyright © 2017 Elsevier B.V. All rights reserved.

A Free-Energy Approach for All-Atom Protein Simulation

PubMed Central

Verma, Abhinav; Wenzel, Wolfgang

2009-01-01

All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 Å to the native conformation and an average Z-score of −3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded β-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger ββα motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 Å to their respective experimental conformations. PMID:19413955

A free-energy approach for all-atom protein simulation.

PubMed

Verma, Abhinav; Wenzel, Wolfgang

2009-05-06

All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 A to the native conformation and an average Z-score of -3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded beta-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger beta beta alpha motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 A to their respective experimental conformations.

Molecular dynamics of bacteriorhodopsin.

PubMed

Lupo, J A; Pachter, R

1997-02-01

A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.

Hierarchical atom type definitions and extensible all-atom force fields.

PubMed

Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

2016-03-15

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Learning molecular energies using localized graph kernels

DOE PAGES

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

2017-03-21

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

Learning molecular energies using localized graph kernels

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

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

A method for determination mass absorption coefficient of gamma rays by Compton scattering.

PubMed

El Abd, A

2014-12-01

A method was proposed for determination mass absorption coefficient of gamma rays for compounds, alloys and mixtures. It is based on simulating interaction processes of gamma rays with target elements having atomic numbers from Z=1 to Z=92 using the MCSHAPE software. Intensities of Compton scattered gamma rays at saturation thicknesses and at a scattering angle of 90° were calculated for incident gamma rays of different energies. The obtained results showed that the intensity of Compton scattered gamma rays at saturations and mass absorption coefficients can be described by mathematical formulas. These were used to determine mass absorption coefficients for compound, alloys and mixtures with the knowledge of their Compton scattered intensities. The method was tested by calculating mass absorption coefficients for some compounds, alloys and mixtures. There is a good agreement between obtained results and calculated ones using WinXom software. The advantages and limitations of the method were discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Laboratory Studies Offer New Insights for Mesospheric Nightglow

NASA Astrophysics Data System (ADS)

Kalogerakis, K. S.; Matsiev, D.

2017-12-01

The hydroxyl radical has a key role in the chemistry and energetics of the Earth's middle atmosphere. A detailed knowledge of the rate constants and relevant pathways for OH(high v) vibrational relaxation by atomic and molecular oxygen and their temperature dependence is absolutely critical for understanding mesospheric OH and extracting reliable chemical heating rates from atmospheric observations. We have developed laser-based experimental approaches to study the complex collisional energy transfer processes involving the OH radical and other relevant atmospheric species. Work in our laboratory indicated that the total removal rate constant for OH(v = 9) + O at room temperature is more than one order of magnitude larger than that for removal by O2. Thus, O atoms are expected to significantly influence the intensity and vibrational distribution extracted from the Meinel OH(v) emissions. Our recent laboratory measurements corroborated the aforementioned result for OH(v = 9) + O and provided important new insights on the multi-quantum energy transfer pathways involved. We will discuss relevant atmospheric implications, including warranted revisions of mesospheric nightglow models. Research supported by SRI International Internal R&D and NSF Aeronomy Grant AGS-1441896. Previously funded by NASA Geospace Science Grant NNX12AD09G.

Implementation of an approximate self-energy correction scheme in the orthogonalized linear combination of atomic orbitals method of band-structure calculations

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

Gu, Z.; Ching, W.Y.

Based on the Sterne-Inkson model for the self-energy correction to the single-particle energy in the local-density approximation (LDA), we have implemented an approximate energy-dependent and [bold k]-dependent [ital GW] correction scheme to the orthogonalized linear combination of atomic orbital-based local-density calculation for insulators. In contrast to the approach of Jenkins, Srivastava, and Inkson, we evaluate the on-site exchange integrals using the LDA Bloch functions throughout the Brillouin zone. By using a [bold k]-weighted band gap [ital E][sub [ital g

Atom-Dependent Edge-Enhanced Second-Harmonic Generation on MoS2 Monolayers.

PubMed

Lin, Kuang-I; Ho, Yen-Hung; Liu, Shu-Bai; Ciou, Jian-Jhih; Huang, Bo-Ting; Chen, Christopher; Chang, Han-Ching; Tu, Chien-Liang; Chen, Chang-Hsiao

2018-02-14

Edge morphology and lattice orientation of single-crystal molybdenum disulfide (MoS 2 ) monolayers, a transition metal dichalcogenide (TMD), possessing a triangular shape with different edges grown by chemical vapor deposition are characterized by atomic force microscopy and transmission electron microscopy. Multiphoton laser scanning microscopy is utilized to study one-dimensional atomic edges of MoS 2 monolayers with localized midgap electronic states, which result in greatly enhanced optical second-harmonic generation (SHG). Microscopic S-zigzag edge and S-Mo Klein edge (bare Mo atoms protruding from a S-zigzag edge) terminations and the edge-atom dependent resonance energies can therefore be deduced based on SHG images. Theoretical calculations based on density functional theory clearly explain the lower energy of the S-zigzag edge states compared to the corresponding S-Mo Klein edge states. Characterization of the atomic-scale variation of edge-enhanced SHG is a step forward in this full-optical and high-yield technique of atomic-layer TMDs.

Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

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

Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at

Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy ismore » constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.« less

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

PubMed Central

Trnka, Tomáš; Kozmon, Stanislav; Tvaroška, Igor; Koča, Jaroslav

2015-01-01

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals. PMID:25849117

Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2.

PubMed

Trnka, Tomáš; Kozmon, Stanislav; Tvaroška, Igor; Koča, Jaroslav

2015-04-01

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals.

ProQ3: Improved model quality assessments using Rosetta energy terms

PubMed Central

Uziela, Karolis; Shu, Nanjiang; Wallner, Björn; Elofsson, Arne

2016-01-01

Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/. PMID:27698390

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

Probing the Quantum States of a Single Atom Transistor at Microwave Frequencies.

PubMed

Tettamanzi, Giuseppe Carlo; Hile, Samuel James; House, Matthew Gregory; Fuechsle, Martin; Rogge, Sven; Simmons, Michelle Y

2017-03-28

The ability to apply gigahertz frequencies to control the quantum state of a single P atom is an essential requirement for the fast gate pulsing needed for qubit control in donor-based silicon quantum computation. Here, we demonstrate this with nanosecond accuracy in an all epitaxial single atom transistor by applying excitation signals at frequencies up to ≈13 GHz to heavily phosphorus-doped silicon leads. These measurements allow the differentiation between the excited states of the single atom and the density of states in the one-dimensional leads. Our pulse spectroscopy experiments confirm the presence of an excited state at an energy ≈9 meV, consistent with the first excited state of a single P donor in silicon. The relaxation rate of this first excited state to the ground state is estimated to be larger than 2.5 GHz, consistent with theoretical predictions. These results represent a systematic investigation of how an atomically precise single atom transistor device behaves under radio frequency excitations.

Reaction and Protection of Electrical Wire Insulators in Atomic-oxygen Environments

NASA Technical Reports Server (NTRS)

Hung, Ching-Cheh; Cantrell, Gidget

1994-01-01

Atomic-oxygen erosion on spacecraft in low Earth orbit is an issue which is becoming increasingly important because of the growing number of spacecraft that will fly in the orbits which have high concentrations of atomic oxygen. In this investigation, the atomic-oxygen durability of three types of electrical wire insulation (carbon-based, fluoropolymer, and polysiloxane elastomer) were evaluated. These insulation materials were exposed to thermal-energy atomic oxygen, which was obtained by RF excitation of air at a pressure of 11-20 Pa. The effects of atomic-oxygen exposure on insulation materials indicate that all carbon-based materials erode at about the same rate as polyamide Kapton and, therefore, are not atomic-oxygen durable. However, the durability of fluoropolymers needs to be evaluated on a case by case basis because the erosion rates of fluoropolymers vary widely. For example, experimental data suggest the formation of atomic fluorine during atomic-oxygen amorphous-fluorocarbon reactions. Dimethyl polysiloxanes (silicone) do not lose mass during atomic-oxygen exposure, but develop silica surfaces which are under tension and frequently crack as a result of loss of methyl groups. However, if the silicone sample surfaces were properly pretreated to provide a certain roughness, atomic oxygen exposure resulted in a sturdy, non-cracked atomic-oxygen durable SiO2 layer. Since the surface does not crack during such silicone-atomic oxygen reaction, the crack-induced contamination by silicone can be reduced or completely stopped. Therefore, with proper pretreatment, silicone can be either a wire insulation material or a coating on wire insulation materials to provide atomic-oxygen durability.

Multi-energy x-ray detectors to improve air-cargo security

NASA Astrophysics Data System (ADS)

Paulus, Caroline; Moulin, Vincent; Perion, Didier; Radisson, Patrick; Verger, Loïck

2017-05-01

X-ray based systems have been used for decades to screen luggage or cargo to detect illicit material. The advent of energy-sensitive photon-counting x-ray detectors mainly based on Cd(Zn)Te semi-conductor technology enables to improve discrimination between materials compared to single or dual energy technology. The presented work is part of the EUROSKY European project to develop a Single European Secure Air-Cargo Space. "Cargo" context implies the presence of relatively heavy objects and with potentially high atomic number. All the study is conducted on simulations with three different detectors: a typical dual energy sandwich detector, a realistic model of the commercial ME100 multi-energy detector marketed by MULTIX, and a ME100 "Cargo": a not yet existing modified multi-energy version of the ME100 more suited to air freight cargo inspection. Firstly, a comparison on simulated measurements shows the performances improvement of the new multi-energy detectors compared to the current dual-energy one. The relative performances are evaluated according to different criteria of separability or contrast-to-noise ratio and the impact of different parameters is studied (influence of channel number, type of materials and tube voltage). Secondly, performances of multi-energy detectors for overlaps processing in a dual-view system is accessed: the case of orthogonal projections has been studied, one giving dimensional values, the other one providing spectral data to assess effective atomic number. A method of overlap correction has been proposed and extended to multi-layer objects case. Therefore, Calibration and processing based on bi-material decomposition have been adapted for this purpose.

Teaching Energy Using an Integrated Science Approach

ERIC Educational Resources Information Center

Poggi, Valeria; Miceli, Cristina; Testa, Italo

2017-01-01

Despite its relevance to all scientific domains, the debate surrounding the teaching of energy is still open. The main point remains the problems students have in understanding some aspects of the energy concept and in applying their knowledge to the comprehension of natural phenomena. In this paper, we present a research-based interdisciplinary…

Requirements for Simulating Space Radiation With Particle Accelerators

NASA Technical Reports Server (NTRS)

Schimmerling, W.; Wilson, J. W.; Cucinotta, F.; Kim, M-H Y.

2004-01-01

Interplanetary space radiation consists of fully ionized nuclei of atomic elements with high energy for which only the few lowest energy ions can be stopped in shielding materials. The health risk from exposure to these ions and their secondary radiations generated in the materials of spacecraft and planetary surface enclosures is a major limiting factor in the management of space radiation risk. Accurate risk prediction depends on a knowledge of basic radiobiological mechanisms and how they are modified in the living tissues of a whole organism. To a large extent, this knowledge is not currently available. It is best developed at ground-based laboratories, using particle accelerator beams to simulate the components of space radiation. Different particles, in different energy regions, are required to study different biological effects, including beams of argon and iron nuclei in the energy range 600 to several thousand MeV/nucleon and carbon beams in the energy range of approximately 100 MeV/nucleon to approximately 1000 MeV/nucleon. Three facilities, one each in the United States, in Germany and in Japan, currently have the partial capability to satisfy these constraints. A facility has been proposed using the Brookhaven National Laboratory Booster Synchrotron in the United States; in conjunction with other on-site accelerators, it will be able to provide the full range of heavy ion beams and energies required. International cooperation in the use of these facilities is essential to the development of a safe international space program.

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.

In Situ Atomic-Scale Observation of Electrochemical Delithiation Induced Structure Evolution of LiCoO2 Cathode in a Working All-Solid-State Battery.

PubMed

Gong, Yue; Zhang, Jienan; Jiang, Liwei; Shi, Jin-An; Zhang, Qinghua; Yang, Zhenzhong; Zou, Dongli; Wang, Jiangyong; Yu, Xiqian; Xiao, Ruijuan; Hu, Yong-Sheng; Gu, Lin; Li, Hong; Chen, Liquan

2017-03-29

We report a method for in situ atomic-scale observation of electrochemical delithiation in a working all-solid-state battery using a state-of-the-art chip based in situ transmission electron microscopy (TEM) holder and focused ion beam milling to prepare an all-solid-state lithium-ion battery sample. A battery consisting of LiCoO 2 cathode, LLZO solid state electrolyte and gold anode was constructed, delithiated and observed in an aberration corrected scanning transmission electron microscope at atomic scale. We found that the pristine single crystal LiCoO 2 became nanosized polycrystal connected by coherent twin boundaries and antiphase domain boundaries after high voltage delithiation. This is different from liquid electrolyte batteries, where a series of phase transitions take place at LiCoO 2 cathode during delithiation. Both grain boundaries become more energy favorable along with extraction of lithium ions through theoretical calculation. We also proposed a lithium migration pathway before and after polycrystallization. This new methodology could stimulate atomic scale in situ scanning/TEM studies of battery materials and provide important mechanistic insight for designing better all-solid-state battery.

Nuclear Science.

ERIC Educational Resources Information Center

Pennsylvania State Dept. of Education, Harrisburg. Bureau of Curriculum Services.

This document is a report on a course in nuclear science for the high school curriculum. The course is designed to provide a basic but comprehensive understanding of the atom in the light of modern knowledge, and to show how people attempt to harness the tremendous energy liberated through fission and fusion reactions. The course crosses what are…

A physically interpretable quantum-theoretic QSAR for some carbonic anhydrase inhibitors with diverse aromatic rings, obtained by a new QSAR procedure.

PubMed

Clare, Brian W; Supuran, Claudiu T

2005-03-15

A QSAR based almost entirely on quantum theoretically calculated descriptors has been developed for a large and heterogeneous group of aromatic and heteroaromatic carbonic anhydrase inhibitors, using orbital energies, nodal angles, atomic charges, and some other intuitively appealing descriptors. Most calculations have been done at the B3LYP/6-31G* level of theory. For the first time we have treated five-membered rings by the same means that we have used for benzene rings in the past. Our flip regression technique has been expanded to encompass automatic variable selection. The statistical quality of the results, while not equal to those we have had with benzene derivatives, is very good considering the noncongeneric nature of the compounds. The most significant correlation was with charge on the atoms of the sulfonamide group, followed by the nodal orientation and the solvation energy calculated by COSMO and the charge polarization of the molecule calculated as the mean absolute Mulliken charge over all atoms.

Effectiveness of an Asynchronous Online Module on University Students' Understanding of the Bohr Model of the Hydrogen Atom

ERIC Educational Resources Information Center

Farina, William J., Jr.; Bodzin, Alec M.

2018-01-01

Web-based learning is a growing field in education, yet empirical research into the design of high quality Web-based university science instruction is scarce. A one-week asynchronous online module on the Bohr Model of the atom was developed and implemented guided by the knowledge integration framework. The unit design aligned with three identified…

Atom-chip-based interferometry with Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Gebbe, Martina; Abend, Sven; Gersemann, Matthias; Ahlers, Holger; Muentinga, Hauke; Herrmann, Sven; Laemmerzahl, Claus; Ertmer, Wolfgang; Rasel, Ernst M.; Quantus Collaboration

2017-04-01

Due to their small spatial and momentum width ultracold Bose-Einstein condensates (BEC) or even delta-kick collimated (DKC) atomic ensembles are very well suited for high precision atom interferometry and measure, for example, inertial forces with high accuracy. We generate such an ensemble in a miniaturized atom-chip setup, where BEC generation and DKC can be performed in a fast and reliable way. Using the chip as a retroreflector we have realized the first atom-chip-based gravimeter. All atom-optical operations including detection take place inside a volume of a one centimeter cube. In order to investigate new geometries we studied symmetric double Bragg diffraction as well as the coherent acceleration of atoms with Bloch oscillations. By combining both techniques we developed a novel relaunch mechanism, which we use to span a fountain geometry within our gravimeter. The relaunch increases the free fall time and, thus, enhances the device's sensitivity. Additionally, we employ these techniques to implement symmetric scalable large momentum beam splitters. This work is supported by the CRC 1128 geo-Q and the DLR with funds provided by the Federal Ministry of Economic Affairs and Energy (BMWi) due to an enactment of the German Bundestag under Grant No. DLR 50WM1552-1557 (QUANTUS-IV-Fallturm).

State of the art for ab initio vs empirical potentials for HeH+ (2e-), BeH+ (4e-), BeH (5e-), Li2 (6e-) and BH (6e-)

NASA Astrophysics Data System (ADS)

Dattani, Nike

For large internuclear distances, the potential energy between two atoms is known analytically, based on constants that are calculated from atomic ab initio rather than molecular ab initio. This analytic form can be built into models for molecular potentials that are fitted to spectroscopic data. Such empirical potentials constitute the most accurate molecular potentials known. For HeH+, and BeH+, the long-range form of the potential is based only on the polarizabilities for He and H respectively, for which we have included up to 4th order QED corrections. For BeH, the best ab initio potential matches all but one observed vibrational spacing to < 1 cm- accuracy, and for Li2 the discrepancy in the spacings is < 0.08 cm-1 for all vibrational levels. But experimental methods such as photoassociation require the absolute energies, not spacings, and these are still several in several cm-1 disagreement. So empirical potentials are still the only reliable way to predict energies for few-electron systems. We also give predictions for various unobserved ''halo nucleonic molecules'' containing the ''halo'' isotopes: 6,8He, 11Li, 11,14Be and 8 , 17 , 19B.

Atomic structure of a decagonal Al-Pd-Mn phase

NASA Astrophysics Data System (ADS)

Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

2017-12-01

We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

New statistical potential for quality assessment of protein models and a survey of energy functions

PubMed Central

2010-01-01

Background Scoring functions, such as molecular mechanic forcefields and statistical potentials are fundamentally important tools in protein structure modeling and quality assessment. Results The performances of a number of publicly available scoring functions are compared with a statistical rigor, with an emphasis on knowledge-based potentials. We explored the effect on accuracy of alternative choices for representing interaction center types and other features of scoring functions, such as using information on solvent accessibility, on torsion angles, accounting for secondary structure preferences and side chain orientation. Partially based on the observations made, we present a novel residue based statistical potential, which employs a shuffled reference state definition and takes into account the mutual orientation of residue side chains. Atom- and residue-level statistical potentials and Linux executables to calculate the energy of a given protein proposed in this work can be downloaded from http://www.fiserlab.org/potentials. Conclusions Among the most influential terms we observed a critical role of a proper reference state definition and the benefits of including information about the microenvironment of interaction centers. Molecular mechanical potentials were also tested and found to be over-sensitive to small local imperfections in a structure, requiring unfeasible long energy relaxation before energy scores started to correlate with model quality. PMID:20226048

Combined Film Catalog, 1972, United States Atomic Energy Commission.

ERIC Educational Resources Information Center

Atomic Energy Commission, Washington, DC.

A comprehensive listing of all current United States Atomic Energy Commission (USAEC) films, this catalog describes 232 films in two major film collections. Part One: Education-Information contains 17 subject categories and two series and describes 134 films with indicated understanding levels on each film for use by schools. The categories…

MoFvAb: Modeling the Fv region of antibodies

PubMed Central

Bujotzek, Alexander; Fuchs, Angelika; Qu, Changtao; Benz, Jörg; Klostermann, Stefan; Antes, Iris; Georges, Guy

2015-01-01

Knowledge of the 3-dimensional structure of the antigen-binding region of antibodies enables numerous useful applications regarding the design and development of antibody-based drugs. We present a knowledge-based antibody structure prediction methodology that incorporates concepts that have arisen from an applied antibody engineering environment. The protocol exploits the rich and continuously growing supply of experimentally derived antibody structures available to predict CDR loop conformations and the packing of heavy and light chain quickly and without user intervention. The homology models are refined by a novel antibody-specific approach to adapt and rearrange sidechains based on their chemical environment. The method achieves very competitive all-atom root mean square deviation values in the order of 1.5 Å on different evaluation datasets consisting of both known and previously unpublished antibody crystal structures. PMID:26176812

An equation of state for partially ionized plasmas: The Coulomb contribution to the free energy

DOE PAGES

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

2015-06-20

We have previously developed an equation of state (EOS) model called ChemEOS (Hakel and Kilcrease, Atomic Processes in Plasmas, Eds., J. Cohen et al., AIP, 2004) for a plasma of interacting ions, atoms and electrons. It is based on a chemical picture of the plasma and is derived from an expression for the Helmholtz free energy of the interacting species. All other equilibrium thermodynamic quantities are then obtained by minimizing this free energy subject to constraints, thus leading to a thermodynamically consistent EOS. The contribution to this free energy from the Coulomb interactions among the particles is treated using themore » method of Chabrier and Potekhin (Phys. Rev. E 58, 4941 (1998)) which we have adapted for partially ionized plasmas. This treatment is further examined and is found to give rise to unphysical behavior for various elements at certain values of the density and temperature where the Coulomb coupling begins to become significant and the atoms are partially ionized. We examine the source of this unphysical behavior and suggest corrections that produce acceptable results. The sensitivity of the thermodynamic properties and frequency-dependent opacity of iron is examined with and without these corrections. Lastly, the corrected EOS is used to determine the fractional ion populations and level populations for a new generation of OPLIB low-Z opacity tables currently being prepared at Los Alamos National Laboratory with the ATOMIC code.« less

Kinetic-energy matrix elements for atomic Hylleraas-CI wave functions.

PubMed

Harris, Frank E

2016-05-28

Hylleraas-CI is a superposition-of-configurations method in which each configuration is constructed from a Slater-type orbital (STO) product to which is appended (linearly) at most one interelectron distance rij. Computations of the kinetic energy for atoms by this method have been difficult due to the lack of formulas expressing these matrix elements for general angular momentum in terms of overlap and potential-energy integrals. It is shown here that a strategic application of angular-momentum theory, including the use of vector spherical harmonics, enables the reduction of all atomic kinetic-energy integrals to overlap and potential-energy matrix elements. The new formulas are validated by showing that they yield correct results for a large number of integrals published by other investigators.

Studies of dispersion energy in hydrogen-bonded systems. H2O-HOH, H2O-HF, H3N-HF, HF-HF

NASA Astrophysics Data System (ADS)

Szcześniak, M. M.; Scheiner, Steve

1984-02-01

Dispersion energy is calculated in the systems H2O-HOH, H2O-HF, H3N-HF, and HF-HF as a function of the intermolecular separation using a variety of methods. M≂ller-Plesset perturbation theory to second and third orders is applied in conjunction with polarized basis sets of 6-311G** type and with an extended basis set including a second set of polarization functions (DZ+2P). These results are compared to a multipole expansion of the dispersion energy, based on the Unsöld approximation, carried out to the inverse tenth power of the intermolecular distance. Pairwise evaluation is also carried out using both atom-atom and bond-bond formulations. The MP3/6-311G** results are in generally excellent accord with the leading R-6 term of the multipole expansion. This expansion, if carried out to the R-10 term, reproduces extremely well previously reported dispersion energies calculated via variation-perturbation theory. Little damping of the expansion is required for intermolecular distances equal to or greater than the equilibrium separation. Although the asymptotic behavior of the MP2 dispersion energy is somewhat different than that of the other methods, augmentation of the basis set by a second diffuse set of d functions leads to quite good agreement in the vicinity of the minima. Both the atom-atom and bond-bond parametrization schemes are in good qualitative agreement with the other methods tested. All approaches produce similar dependence of the dispersion energy upon the angular orientation between the two molecules involved in the H bond.

Atomic Defects and Doping of Monolayer NbSe2.

PubMed

Nguyen, Lan; Komsa, Hannu-Pekka; Khestanova, Ekaterina; Kashtiban, Reza J; Peters, Jonathan J P; Lawlor, Sean; Sanchez, Ana M; Sloan, Jeremy; Gorbachev, Roman V; Grigorieva, Irina V; Krasheninnikov, Arkady V; Haigh, Sarah J

2017-03-28

We have investigated the structure of atomic defects within monolayer NbSe 2 encapsulated in graphene by combining atomic resolution transmission electron microscope imaging, density functional theory (DFT) calculations, and strain mapping using geometric phase analysis. We demonstrate the presence of stable Nb and Se monovacancies in monolayer material and reveal that Se monovacancies are the most frequently observed defects, consistent with DFT calculations of their formation energy. We reveal that adventitious impurities of C, N, and O can substitute into the NbSe 2 lattice stabilizing Se divacancies. We further observe evidence of Pt substitution into both Se and Nb vacancy sites. This knowledge of the character and relative frequency of different atomic defects provides the potential to better understand and control the unusual electronic and magnetic properties of this exciting two-dimensional material.

A knowledge-based control system for air-scour optimisation in membrane bioreactors.

PubMed

Ferrero, G; Monclús, H; Sancho, L; Garrido, J M; Comas, J; Rodríguez-Roda, I

2011-01-01

Although membrane bioreactors (MBRs) technology is still a growing sector, its progressive implementation all over the world, together with great technical achievements, has allowed it to reach a mature degree, just comparable to other more conventional wastewater treatment technologies. With current energy requirements around 0.6-1.1 kWh/m3 of treated wastewater and investment costs similar to conventional treatment plants, main market niche for MBRs can be areas with very high restrictive discharge limits, where treatment plants have to be compact or where water reuse is necessary. Operational costs are higher than for conventional treatments; consequently there is still a need and possibilities for energy saving and optimisation. This paper presents the development of a knowledge-based decision support system (DSS) for the integrated operation and remote control of the biological and physical (filtration and backwashing or relaxation) processes in MBRs. The core of the DSS is a knowledge-based control module for air-scour consumption automation and energy consumption minimisation.

Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

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

Deshlahra, Prashant; Iglesia, Enrique

The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accuratemore » and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.« less

Toward the identification of molecular cogs.

PubMed

Dziubiński, Maciej; Lesyng, Bogdan

2016-04-05

Computer simulations of molecular systems allow determination of microscopic interactions between individual atoms or groups of atoms, as well as studies of intramolecular motions. Nevertheless, description of structural transformations at the mezoscopic level and identification of causal relations associated with these transformations is very difficult. Structural and functional properties are related to free energy changes. Therefore, to better understand structural and functional properties of molecular systems, it is required to deepen our knowledge of free energy contributions arising from molecular subsystems in the course of structural transformations. The method presented in this work quantifies the energetic contribution of each pair of atoms to the total free energy change along a given collective variable. Next, with the help of a genetic clustering algorithm, the method proposes a division of the system into two groups of atoms referred to as molecular cogs. Atoms which cooperate to push the system forward along a collective variable are referred to as forward cogs, and those which work in the opposite direction as reverse cogs. The procedure was tested on several small molecules for which the genetic clustering algorithm successfully found optimal partitionings into molecular cogs. The primary result of the method is a plot depicting the energetic contributions of the identified molecular cogs to the total Potential of Mean Force (PMF) change. Case-studies presented in this work should help better understand the implications of our approach, and were intended to pave the way to a future, publicly available implementation. © 2015 Wiley Periodicals, Inc.

Localized overlap algorithm for unexpanded dispersion energies

NASA Astrophysics Data System (ADS)

Rob, Fazle; Misquitta, Alston J.; Podeszwa, Rafał; Szalewicz, Krzysztof

2014-03-01

First-principles-based, linearly scaling algorithm has been developed for calculations of dispersion energies from frequency-dependent density susceptibility (FDDS) functions with account of charge-overlap effects. The transition densities in FDDSs are fitted by a set of auxiliary atom-centered functions. The terms in the dispersion energy expression involving products of such functions are computed using either the unexpanded (exact) formula or from inexpensive asymptotic expansions, depending on the location of these functions relative to the dimer configuration. This approach leads to significant savings of computational resources. In particular, for a dimer consisting of two elongated monomers with 81 atoms each in a head-to-head configuration, the most favorable case for our algorithm, a 43-fold speedup has been achieved while the approximate dispersion energy differs by less than 1% from that computed using the standard unexpanded approach. In contrast, the dispersion energy computed from the distributed asymptotic expansion differs by dozens of percent in the van der Waals minimum region. A further increase of the size of each monomer would result in only small increased costs since all the additional terms would be computed from the asymptotic expansion.

SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

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

Khabibullin, A.R.; Woods, L.M.; Karolak, A.

2016-06-15

Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis setmore » in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA-based-radiopharmaceuticals and will enhance our understanding of processes occurring at subatomic levels.« less

Exploration of the Tavis-Cummings Model with Multiple Qubits in Circuit QED

NASA Astrophysics Data System (ADS)

Fink, J. M.; Blais, A.; Wallraff, A.

2009-03-01

Superconducting qubits in coplanar waveguide resonators provide an unprecedentedly large dipole coupling strength to microwave frequency photons confined in an on-chip waveguide resonator [1]. In contrast to atoms in traditional cavity QED a controlled number of qubits remain at fixed positions with constant coupling to the cavity field at all times. Utilizing these properties we have performed measurements with up to three independently flux-tunable qubits to study cavity mediated multi-qubit interactions. By tuning the qubits in resonance with the cavity field individually, we demonstrate the square root of N scaling of the collective dipole coupling strength with the number of resonant atoms N as described by the Tavis-Cummings model. To our knowledge this is the first observation of this nonlinearity in a system in which the atom number can be changed one by one in a discrete fashion. In addition, the energies of both bright and dark coupled multi-qubit / photon states are well explained by the Tavis-Cummings model over a wide range of detunings. On resonance we obtain an equal superposition of a photon and a Dicke state with an excitation equally shared among the N qubits.[1] J. M. Fink et al. Nature 454, 315 (2008).

Chemical trends for acceptor impurities in GaN

NASA Astrophysics Data System (ADS)

Neugebauer, Jörg; Van de Walle, Chris G.

1999-03-01

We present a comprehensive investigation of acceptor impurities in GaN, based on first-principles total-energy calculations. Two main factors are identified that determine acceptor incorporation: the strength of chemical bonding between the acceptor and its neighbors (which can be assessed by comparison with existing compounds) and the atomic size match between the acceptor and the host atom for which it substitutes. None of the candidates (Li, Na, K, Be, Zn, and Ca) exhibits characteristics which surpass those of Mg in all respects. Only Be emerges as a potential alternative dopant, although it may suffer from compensation by Be interstitial donors.

Lasers, Cold Atoms and Atomic Clocks: Realizing the Second Today

NASA Astrophysics Data System (ADS)

Calonico, Davide

2013-09-01

The time is the physical quantity that mankind could measure with the best accuracy, thanks to the properties of the atomic physics, as the present definition of time is based on atomic energy transitions. This short review gives some basic information on the heart of the measurement of time in the contemporary world, i.e. the atomic clocks, and some trends related.

A detailed evaluation of heating processes in the middle atmosphere

NASA Technical Reports Server (NTRS)

Mlynczak, Martin; Solomon, Susan

1994-01-01

A fundamental problem in the study of the terrestrial middle atmosphere is to calculate accurately the local heating due to the absorption of solar radiation. Knowledge of the heat budget is essential to understanding the atmospheric thermal structure, atmospheric motions, atmospheric chemistry, and their coupling. The evaluation of heating rates is complicated (especially above the stratopause) by the fact that the heating is not a simple one-step process. That is, the absorbed solar energy does not all immediately appear as heat. Rather, substantial portions of the incident energy may appear as internal energy of excited photolysis products (e.g., O(1D) or O2(1 delta)) or as chemical potential energy of product species such as atomic oxygen. The ultimate disposition of the internal and chemical energy possessed by the photolysis products determines the efficiency and thus the rate at which the middle atmosphere is heated. In studies of the heat budget, it is also vitally important to consider transport of long lived chemical species such as atomic oxygen above approximately 80 km. In such cases, the chemical potential energy may be transported great distances (horizontally or vertically) before undergoing a reaction to release the heat. Atomic oxygen influences the heating not only by reactions with itself and with O2 but also by reactions with odd-hydrogen species, especially those involving OH (Mlynczak and Solomon, 1991a). Consequently, absorbed solar energy may finally by converted to heat a long time after and at a location far from the original deposition. The purpose of this paper is to examine the solar and chemical heating processes and to present parameterizations for the heating efficiencies readily applicable for use in numerical models and heat budget studies. In the next two sections the processes relevant to the heating efficiencies for ozone and molecular oxygen will be reviewed. In section 4 the processes for the exothermic reactions will be reviewed and parameterizations for the heating efficiencies for both the solar and chemical processes will be presented in Section 5.

Koopmans' theorem in the Hartree-Fock method. General formulation

NASA Astrophysics Data System (ADS)

Plakhutin, Boris N.

2018-03-01

This work presents a general formulation of Koopmans' theorem (KT) in the Hartree-Fock (HF) method which is applicable to molecular and atomic systems with arbitrary orbital occupancies and total electronic spin including orbitally degenerate (OD) systems. The new formulation is based on the full set of variational conditions imposed upon the HF orbitals by the variational principle for the total energy and the conditions imposed by KT on the orbitals of an ionized electronic shell [B. N. Plakhutin and E. R. Davidson, J. Chem. Phys. 140, 014102 (2014)]. Based on these conditions, a general form of the restricted open-shell HF method is developed, whose eigenvalues (orbital energies) obey KT for the whole energy spectrum. Particular attention is paid to the treatment of OD systems, for which the new method gives a number of unexpected results. For example, the present method gives four different orbital energies for the triply degenerate atomic level 2p in the second row atoms B to F. Based on both KT conditions and a parallel treatment of atoms B to F within a limited configuration interaction approach, we prove that these four orbital energies, each of which is triply degenerate, are related via KT to the energies of different spin-dependent ionization and electron attachment processes (2p)N → (2p ) N ±1. A discussion is also presented of specific limitations of the validity of KT in the HF method which arise in OD systems. The practical applicability of the theory is verified by comparing KT estimates of the ionization potentials I2s and I2p for the second row open-shell atoms Li to F with the relevant experimental data.

Unique Reactivity of Transition Metal Atoms Embedded in Graphene to CO, NO, O₂ and O Adsorption: A First-Principles Investigation.

PubMed

Chu, Minmin; Liu, Xin; Sui, Yanhui; Luo, Jie; Meng, Changgong

2015-10-27

Taking the adsorption of CO, NO, O₂ and O as probes, we investigated the electronic structure of transition metal atoms (TM, TM = Fe, Co, Ni, Cu and Zn) embedded in graphene by first-principles-based calculations. We showed that these TM atoms can be effectively stabilized on monovacancy defects on graphene by forming plausible interactions with the C atoms associated with dangling bonds. These interactions not only give rise to high energy barriers for the diffusion and aggregation of the embedded TM atoms to withstand the interference of reaction environments, but also shift the energy levels of TM-d states and regulate the reactivity of the embedded TM atoms. The adsorption of CO, NO, O₂ and O correlates well with the weight averaged energy level of TM-d states, showing the crucial role of interfacial TM-C interactions on manipulating the reactivity of embedded TM atoms. These findings pave the way for the developments of effective monodispersed atomic TM composites with high stability and desired performance for gas sensing and catalytic applications.

Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts

NASA Astrophysics Data System (ADS)

Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

2015-04-01

An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ~ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified.An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ~ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modelling methodology. See DOI: 10.1039/c5nr00800j

Peculiarities of FeSi phonon spectrum induced by a change of atomic volume

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

Parshin, P. P., E-mail: Parshin-PP@nrcki.ru, E-mail: neupar45@yandex.ru; Chumakov, A. I.; Alekseev, P. A.

2016-12-15

We analyze in detail the results of experimental investigations of the evolution of the thermal vibration spectra for iron atoms in iron monosilicide FeSi depending on two external parameters, viz., temperature T (in the range 46–297 K at pressure P = 0.1 MPa) and pressure P (in the range 0.1 MPa–43 GPa at temperature T = 297 K), obtained by nuclear inelastic scattering of synchrotron radiation. The decrease of the atomic volume is accompanied by a rearrangement of the phonon spectrum, which is manifested, in particular, in the splitting of the low-energy peak in the spectrum and in an increasemore » of the energy for all phonons. The changes of the average energy of the iron atom vibrational spectrum and of the Debye energy with decreasing atomic volume are analyzed. Different versions of FeSi electron spectrum variation, which can be used to explain the observed phonon anomalies, are considered.« less

Towards a rational approach for heavy-atom derivative screening in protein crystallography

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

Agniswamy, Johnson; Joyce, M. Gordon; Hammer, Carl H.

2008-04-01

Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity ofmore » more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Met-, Cys- and His-containing peptides were derivatized against Hg, Au and Pt compounds, while Tyr-, Glu-, Asp-, Asn- and Gln-containing peptides were assessed against Pb compounds. A total of 1668 reactive conditions were examined using mass spectrometry and were compiled into heavy-atom reactivity tables. The results showed that heavy-atom derivatization reactions are highly linked to buffer and pH, with the most accommodating buffer being MES at pH 6. A group of 21 compounds were identified as most successful irrespective of ligand or buffer/pH conditions. To assess the applicability of the peptide heavy-atom reactivity to proteins, lysozyme crystals were derivatized with a list of peptide-reactive compounds that included both known and new compounds for lysozyme derivatization. The results showed highly consistent heavy-atom reactivities between the peptides and lysozyme.« less

An overview of the Evaluation of Oxygen Interactions with Materials 3 experiment: Space Shuttle Mission 46, July-August 1992

NASA Technical Reports Server (NTRS)

Koontz, Steven L.; Leger, Lubert J.; Visentine, James T.; Hunton, Don E.; Cross, Jon B.; Hakes, Charles L.

1995-01-01

The Evaluation of Oxygen Interactions with Materials 3 (EOIM-3) flight experiment was developed to obtain benchmark atomic oxygen reactivity data and was conducted during Space Transportation System Mission 46 (STS-46), July 31 to August 7, 1992. In this paper, we present an overview of EOIM-3 and the results of the Lyndon B. Johnson Space Center (JSC) materials reactivity and mass spectrometer/carousel experiments. Mass spectrometer calibration methods are discussed briefly, as a prelude to a detailed discussion of the mass spectrometric results produced during STS-46. Mass spectrometric measurements of ambient O-atom flux and fluence are in good agreement with the values calculated using the MSIS-86 model of the thermosphere as well as estimates based on the extent of O-atom reaction with Kapton polyimide. Mass spectrometric measurements of gaseous products formed by O-atom reaction with C(13) labeled Kapton revealed CO, CO2, H2O, NO, and NO2. Finally, by operating the mass spectrometer so as to detect naturally occurring ionospheric species, we characterized the ambient ionosphere at various times during EOIM-3 and detected the gaseous reaction products formed when ambient ions interacted with the C(13) Kapton carousel sector. By direct comparison of the results of on-orbit O-atom exposures with those conducted in ground-based laboratory systems, which provide known O-atom fluences and translational energies, we have demonstrated the strong translational energy dependence of O-atom reactions with a variety of polymers. A 'line-of-centers' reactive scattering model was shown to provide a reasonably accurate description of the translational energy dependence of polymer reactions with O atoms at high atom kinetic energies while a Beckerle-Ceyer model provided an accurate description of O-atom reactivity over a three order-of-magnitude range in translational energy and a four order-of-magnitude range in reaction efficiency. Postflight studies of the polymer samples by x-ray photoelectron spectroscopy and infrared spectroscopy demonstrate that O-atom attack is confined to the near-surface region of the sample, i.e. within 50 to 100 A of the surface.

New energy levels of atomic niobium (Nb I) discovered by laser-spectroscopic investigations

NASA Astrophysics Data System (ADS)

Kröger, S.; Windholz, L.; Başar, Gü.; Başar, Gö.

2018-06-01

We report the discovery of 9 previously unknown energy levels of the atomic niobium, all having even parity. Two levels have energies below 19,500 cm-1 and angular momentum J = 3/2, while the energies of the others are located between 39,700 and 43,420 cm-1. The levels were discovered by laser excitation of several unclassified spectral lines in the wavelength range between 554 nm and 650 nm and detection of laser-induced fluorescence with a monochromator.

In situ disordering of monoclinic titanium monoxide Ti5O5 studied by transmission electron microscope TEM.

PubMed

Rempel, А А; Van Renterghem, W; Valeeva, А А; Verwerft, M; Van den Berghe, S

2017-09-07

The superlattice and domain structures exhibited by ordered titanium monoxide Ti 5 O 5 are disrupted by low energy electron beam irradiation. The effect is attributed to the disordering of the oxygen and titanium sublattices. This disordering is caused by the displacement of both oxygen and titanium atoms by the incident electrons and results in a phase transformation of the monoclinic phase Ti 5 O 5 into cubic B1 titanium monoxide. In order to determine the energies required for the displacement of titanium or oxygen atoms, i.e. threshold displacement energies, a systematic study of the disappearance of superstructure reflections with increasing electron energy and electron bombardment dose has been performed in situ in a transmission electron microscope (TEM). An incident electron energy threshold between 120 and 140 keV has been observed. This threshold can be ascribed to the displacements of titanium atoms with 4 as well as with 5 oxygen atoms as nearest neighbors. The displacement threshold energy of titanium atoms in Ti 5 O 5 corresponding with the observed incident electron threshold energy lies between 6.0 and 7.5 eV. This surprisingly low value can be explained by the presence of either one or two vacant oxygen lattice sites in the nearest neighbors of all titanium atoms.

PLASS: Protein-ligand affinity statistical score a knowledge-based force-field model of interaction derived from the PDB

NASA Astrophysics Data System (ADS)

Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.

2004-04-01

We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

Atomic oxygen beam source for erosion simulation

NASA Technical Reports Server (NTRS)

Cuthbertson, J. W.; Langer, W. D.; Motley, R. W.; Vaughn, J. A.

1991-01-01

A device for the production of low energy (3 to 10 eV) neutral atomic beams for surface modification studies is described that reproduces the flux of atomic oxygen in low Earth orbit. The beam is produced by the acceleration of plasma ions onto a negatively biased plate of high-Z metal; the ions are neutralized and reflected by the surface, retaining some fraction of their incident kinetic energy, forming a beam of atoms. The plasma is generated by a coaxial RF exciter which produces a magnetically-confined (4 kG) plasma column. At the end of the column, ions fall through the sheath to the plate, whose bias relative to the plasma can be varied to adjust the beam energy. The source provides a neutral flux approximately equal to 5 x 10(exp 16)/sq cm at a distance of 9 cm and a fluence approximately equal to 10(exp 20)/sq cm in five hours. The composition and energy of inert gas beams was diagnosed using a mass spectometer/energy analyzer. The energy spectra of the beams demonstrate energies in the range 5 to 15 eV, and qualitatively show expected dependences upon incident and reflecting atom species and potential drop. Samples of carbon film, carbon-based paint, Kapton, mylar, and teflon exposed to atomic O beams show erosion quite similar to that observed in orbit on the space shuttle.

Accuracy of Lagrange-sinc functions as a basis set for electronic structure calculations of atoms and molecules

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

Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook

2015-03-07

We developed a self-consistent field program based on Kohn-Sham density functional theory using Lagrange-sinc functions as a basis set and examined its numerical accuracy for atoms and molecules through comparison with the results of Gaussian basis sets. The result of the Kohn-Sham inversion formula from the Lagrange-sinc basis set manifests that the pseudopotential method is essential for cost-effective calculations. The Lagrange-sinc basis set shows faster convergence of the kinetic and correlation energies of benzene as its size increases than the finite difference method does, though both share the same uniform grid. Using a scaling factor smaller than or equal tomore » 0.226 bohr and pseudopotentials with nonlinear core correction, its accuracy for the atomization energies of the G2-1 set is comparable to all-electron complete basis set limits (mean absolute deviation ≤1 kcal/mol). The same basis set also shows small mean absolute deviations in the ionization energies, electron affinities, and static polarizabilities of atoms in the G2-1 set. In particular, the Lagrange-sinc basis set shows high accuracy with rapid convergence in describing density or orbital changes by an external electric field. Moreover, the Lagrange-sinc basis set can readily improve its accuracy toward a complete basis set limit by simply decreasing the scaling factor regardless of systems.« less

Generalizing Atoms in Constraint Logic

NASA Technical Reports Server (NTRS)

Page, C. David, Jr.; Frisch, Alan M.

1991-01-01

This paper studies the generalization of atomic formulas, or atoms, that are augmented with constraints on or among their terms. The atoms may also be viewed as definite clauses whose antecedents express the constraints. Atoms are generalized relative to a body of background information about the constraints. This paper first examines generalization of atoms with only monadic constraints. The paper develops an algorithm for the generalization task and discusses algorithm complexity. It then extends the algorithm to apply to atoms with constraints of arbitrary arity. The paper also presents semantic properties of the generalizations computed by the algorithms, making the algorithms applicable to such problems as abduction, induction, and knowledge base verification. The paper emphasizes the application to induction and presents a pac-learning result for constrained atoms.

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".

Positrons in the Galaxy: Their Births, Marriages and Deaths

NASA Technical Reports Server (NTRS)

Skinner, Gerald K.

2010-01-01

High energy (approximately GeV) positrons are seen within cosmic rays and observation of a narrow line at 511 keV shows that positrons are annihilating in the galaxy after slowing down to approximately keV energies or less. Our state of knowledge of the origin of these positrons, of the formation of positronium 'atoms', and of the circumstances of their annihilation or escape from the galaxy are reviewed and the question of whether the two phenomena are linked is discussed.

Molecular mechanism of direct proflavine-DNA intercalation: evidence for drug-induced minimum base-stacking penalty pathway.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2012-10-11

DNA intercalation, a biophysical process of enormous clinical significance, has surprisingly eluded molecular understanding for several decades. With appropriate configurational restraint (to prevent dissociation) in all-atom metadynamics simulations, we capture the free energy surface of direct intercalation from minor groove-bound state for the first time using an anticancer agent proflavine. Mechanism along the minimum free energy path reveals that intercalation happens through a minimum base stacking penalty pathway where nonstacking parameters (Twist→Slide/Shift) change first, followed by base stacking parameters (Buckle/Roll→Rise). This mechanism defies the natural fluctuation hypothesis and provides molecular evidence for the drug-induced cavity formation hypothesis. The thermodynamic origin of the barrier is found to be a combination of entropy and desolvation energy.

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

Rydberg blockade in three-atom systems

NASA Astrophysics Data System (ADS)

Barredo, Daniel; Ravets, Sylvain; Labuhn, Henning; Beguin, Lucas; Vernier, Aline; Chicireanu, Radu; Nogrette, Florence; Lahaye, Thierry; Browaeys, Antoine

2014-05-01

The control of individual neutral atoms in arrays of optical tweezers is a promising avenue for quantum science and technology. Here we demonstrate unprecedented control over a system of three Rydberg atoms arranged in linear and triangular configurations. The interaction between Rydberg atoms results in the observation of an almost perfect van der Waals blockade. When the single-atom Rabi frequency for excitation to the Rydberg state is comparable to the interaction energy, we directly observe the anisotropy of the interaction between nD-states. Using the independently measured two-body interaction energy shifts we fully reproduce the dynamics of the three-atom system with a model based on a master equation without any adjustable parameter. Combined with our ability to trap single atoms in arbitrary patterns of 2D arrays of up to 100 traps separated by a few microns, these results are very promising for a scalable implementation of quantum simulation of frustrated quantum magnetism with Rydberg atoms.

Kinetic-energy matrix elements for atomic Hylleraas-CI wave functions

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

Harris, Frank E., E-mail: harris@qtp.ufl.edu

Hylleraas-CI is a superposition-of-configurations method in which each configuration is constructed from a Slater-type orbital (STO) product to which is appended (linearly) at most one interelectron distance r{sub ij}. Computations of the kinetic energy for atoms by this method have been difficult due to the lack of formulas expressing these matrix elements for general angular momentum in terms of overlap and potential-energy integrals. It is shown here that a strategic application of angular-momentum theory, including the use of vector spherical harmonics, enables the reduction of all atomic kinetic-energy integrals to overlap and potential-energy matrix elements. The new formulas are validatedmore » by showing that they yield correct results for a large number of integrals published by other investigators.« less

Extracting the σ-term from low-energy pion-nucleon scattering

NASA Astrophysics Data System (ADS)

Ruiz de Elvira, Jacobo; Hoferichter, Martin; Kubis, Bastian; Meißner, Ulf-G.

2018-02-01

We present an extraction of the pion-nucleon (π N) scattering lengths from low-energy π N scattering, by fitting a representation based on Roy-Steiner equations to the low-energy data base. We show that the resulting values confirm the scattering-length determination from pionic atoms, and discuss the stability of the fit results regarding electromagnetic corrections and experimental normalization uncertainties in detail. Our results provide further evidence for a large π N σ-term, {σ }π N=58(5) {{MeV}}, in agreement with, albeit less precise than, the determination from pionic atoms.

Python-Based Tool for Universal Nuclear Data Extraction

NASA Astrophysics Data System (ADS)

McDonald, William; Blair, Hayden; Consalvi, Peter; Garbiso, Markus; Grover, Hannah; Harget, Alex; Martin, Matthew; Natzke, Connor; Leach, Kyle

2017-09-01

Over the past 70 years, nuclear physics experiments have provided a vast wealth of experimental data on both ground and excited state properties across the nuclear chart. In many cases, searching for and parsing the relevant nuclear structure data from previous work can be tedious and difficult. Although the compilation, evaluation, and digitization of this data by multiple groups around the world over the past several decades has helped dramatically in this respect, the process of performing systematic studies using this data can still be cumbersome and limited. We are in the process of creating a python-based program to extract, sort, and manipulate nuclear and atomic data efficiently. In its current state, the program is able to extract all atomic-shell ionization energies, excited- and ground-state nuclear properties, and all beta-decay rates and ratios. As a part of this ongoing project, we plan to use this tool to examine beta-decay rates in extreme astrophysical environments.

Cucurbit[6]uril: A Possible Host for Noble Gas Atoms.

PubMed

Pan, Sudip; Mandal, Subhajit; Chattaraj, Pratim K

2015-08-27

Density functional and ab initio molecular dynamics studies are carried out to investigate the stability of noble gas encapsulated cucurbit[6]uril (CB[6]) systems. Interaction energy, dissociation energy and dissociation enthalpy are calculated to understand the efficacy of CB[6] in encapsulating noble gas atoms. CB[6] could encapsulate up to three Ne atoms having dissociation energy (zero-point energy corrected) in the range of 3.4-4.1 kcal/mol, whereas due to larger size, only one Ar or Kr atom encapsulated analogues would be viable. The dissociation energy value for the second Ar atom is only 1.0 kcal/mol. On the other hand, the same for the second Kr is -0.5 kcal/mol, implying the instability of the system. The noble gas dissociation processes are endothermic in nature, which increases gradually along Ne to Kr. Kr encapsulated analogue is found to be viable at room temperature. However, low temperature is needed for Ne and Ar encapsulated analogues. The temperature-pressure phase diagram highlights the region in which association and dissociation processes of Kr@CB[6] would be favorable. At ambient temperature and pressure, CB[6] may be used as an effective noble gas carrier. Wiberg bond indices, noncovalent interaction indices, electron density, and energy decomposition analyses are used to explore the nature of interaction between noble gas atoms and CB[6]. Dispersion interaction is found to be the most important term in the attraction energy. Ne and Ar atoms in one Ng entrapped analogue are found to stay inside the cavity of CB[6] throughout the simulation at 298 K. However, during simulation Ng2 units in Ng2@CB[6] flip toward the open faces of CB[6]. After 1 ps, one Ne atom of Ne3@CB[6] almost reaches the open face keeping other two Ne atoms inside. At lower temperature (77 K), all the Ng atoms in Ngn@CB[6] remain well inside the cavity of CB[6] throughout the simulation time (1 ps).

Axial to transverse energy mixing dynamics in octupole-based magnetostatic antihydrogen traps

NASA Astrophysics Data System (ADS)

Zhong, M.; Fajans, J.; Zukor, A. F.

2018-05-01

The nature of the trajectories of antihydrogen atoms confined in an octupole minimum-B trap is of great importance for upcoming spectroscopy, cooling, and gravity experiments. Of particular interest is the mixing time between the axial and transverse energies for the antiatoms. Here, using computer simulations, we establish that almost all trajectories are chaotic, and then quantify the characteristic mixing time between the axial and transverse energies. We find that there are two classes of trajectories: for trajectories whose axial energy is higher than about 20% of the total energy, the axial energy substantially mixes within about 10 s, whereas for trajectories whose axial energy is lower than about 10% of the total energy, the axial energy remains nearly constant for 1000 s or longer.

Guiding Conformation Space Search with an All-Atom Energy Potential

PubMed Central

Brunette, TJ; Brock, Oliver

2009-01-01

The most significant impediment for protein structure prediction is the inadequacy of conformation space search. Conformation space is too large and the energy landscape too rugged for existing search methods to consistently find near-optimal minima. To alleviate this problem, we present model-based search, a novel conformation space search method. Model-based search uses highly accurate information obtained during search to build an approximate, partial model of the energy landscape. Model-based search aggregates information in the model as it progresses, and in turn uses this information to guide exploration towards regions most likely to contain a near-optimal minimum. We validate our method by predicting the structure of 32 proteins, ranging in length from 49 to 213 amino acids. Our results demonstrate that model-based search is more effective at finding low-energy conformations in high-dimensional conformation spaces than existing search methods. The reduction in energy translates into structure predictions of increased accuracy. PMID:18536015

Tuning of electronic band gaps and optoelectronic properties of binary strontium chalcogenides by means of doping of magnesium atom(s)- a first principles based theoretical initiative with mBJ, B3LYP and WC-GGA functionals

NASA Astrophysics Data System (ADS)

Debnath, Bimal; Sarkar, Utpal; Debbarma, Manish; Bhattacharjee, Rahul; Chattopadhyaya, Surya

2018-02-01

First principle based theoretical initiative is taken to tune the optoelectronic properties of binary strontium chalcogenide semiconductors by doping magnesium atom(s) into their rock-salt unit cells at specific concentrations x = 0.0, 0.25, 0.50, 0.75 and 1.0 and such tuning is established by studying structural, electronic and optical properties of designed binary compounds and ternary alloys employing WC-GGA, B3LYP and mBJ exchange-correlation functionals. Band structure of each compound is constructed and respective band gaps under all the potential schemes are measured. The band gap bowing and its microscopic origin are calculated using quadratic fit and Zunger's approach, respectively. The atomic and orbital origins of electronic states in the band structure of any compound are explored from its density of states. The nature of chemical bonds between the constituent atoms in each compound is explored from the valence electron density contour plots. Optical properties of any specimen are explored from the computed spectra of its dielectric function, refractive index, extinction coefficient, normal incidence reflectivity, optical conductivity optical absorption and energy loss function. Several calculated results are compared with available experimental and earlier theoretical data.

Is Einstein the Father of the Atomic Bomb

NASA Astrophysics Data System (ADS)

Lustig, Harry

2009-05-01

Soon after the American atomic bombs were dropped on Hiroshima and Nagasaki, the notion took hold in the popular mind that Albert Einstein was ``the father of the bomb.'' The claim of paternity rests on the belief that E=mc2 is what makes the release of enormous amounts of energy in the fission process possible and that the atomic bomb could not have been built without it. This is a misapprehension. Most physicists have known that all along. Nevertheless in his reaction to the opera Dr. Atomic, a prominent physicist claimed that Einstein's discovery that matter can be transformed into energy ``is precisely what made the bomb possible.'' In fact what makes the fission reaction and one of its applications,the atomic bomb, possible is the smaller binding energies of fission products compared to the binding energies of the nuclei that undergo fission.The binding energies of nuclei are a well understood consequence of the numbers and arrangements of protons and neutrons in the nucleus and of quantum-mechanical effects. The realization that composite systems have binding energies predates relativity. In the 19th century they were ascribed to potential and other forms of energy that reside in the system. With Einstein they became rest mass energy. While E=mc2 is not the cause of fission, measuring the masses of the participants in the reaction does permit an easy calculation of the kinetic energy that is released.

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites.

PubMed

Hadadi, Noushin; Hafner, Jasmin; Soh, Keng Cher; Hatzimanikatis, Vassily

2017-01-01

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely available in the literature. The understanding of metabolic pathways at the atomic level is of great importance as it can deconvolute the overlapping catabolic/anabolic pathways resulting in the observed metabolic phenotype. The automated identification of atom transitions within a metabolic network is a very challenging task since the degree of complexity of metabolic networks dramatically increases when we transit from metabolite-level studies to atom-level studies. Despite being studied extensively in various approaches, the field of atom mapping of metabolic networks is lacking an automated approach, which (i) accounts for the information of reaction mechanism for atom mapping and (ii) is extendable from individual atom-mapped reactions to atom-mapped reaction networks. Hereby, we introduce a computational framework, iAM.NICE (in silico Atom Mapped Network Integrated Computational Explorer), for the systematic atom-level reconstruction of metabolic networks from in silico labelled substrates. iAM.NICE is to our knowledge the first automated atom-mapping algorithm that is based on the underlying enzymatic biotransformation mechanisms, and its application goes beyond individual reactions and it can be used for the reconstruction of atom-mapped metabolic networks. We illustrate the applicability of our method through the reconstruction of atom-mapped reactions of the KEGG database and we provide an example of an atom-level representation of the core metabolic network of E. coli. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Energy: A Cross-Curricular Approach.

ERIC Educational Resources Information Center

Lalonde, Christine

This guide is based on the premise that lives (and lifestyles) revolve around the production, consumption, and conversion of energy. Yet for such an all-encompassing concept little accompanying factual knowledge exists at the grade-school level. The objectives (and the resulting activities and extensions) are focused on the needs of the upper…

Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments.

PubMed

Darley, Michael G; Handley, Chris M; Popelier, Paul L A

2008-09-09

Intramolecular polarization is the change to the electron density of a given atom upon variation in the positions of the neighboring atoms. We express the electron density in terms of multipole moments. Using glycine and N-methylacetamide (NMA) as pilot systems, we show that neural networks can capture the change in electron density due to polarization. After training, modestly sized neural networks successfully predict the atomic multipole moments from the nuclear positions of all atoms in the molecule. Accurate electrostatic energies between two atoms can be then obtained via a multipole expansion, inclusive of polarization effects. As a result polarization is successfully modeled at short-range and without an explicit polarizability tensor. This approach puts charge transfer and multipolar polarization on a common footing. The polarization procedure is formulated within the context of quantum chemical topology (QCT). Nonbonded atom-atom interactions in glycine cover an energy range of 948 kJ mol(-1), with an average energy difference between true and predicted energy of 0.2 kJ mol(-1), the largest difference being just under 1 kJ mol(-1). Very similar energy differences are found for NMA, which spans a range of 281 kJ mol(-1). The current proof-of-concept enables the construction of a new protein force field that incorporates electron density fragments that dynamically respond to their fluctuating environment.

Fast and accurate grid representations for atom-based docking with partner flexibility.

PubMed

de Vries, Sjoerd J; Zacharias, Martin

2017-06-30

Macromolecular docking methods can broadly be divided into geometric and atom-based methods. Geometric methods use fast algorithms that operate on simplified, grid-like molecular representations, while atom-based methods are more realistic and flexible, but far less efficient. Here, a hybrid approach of grid-based and atom-based docking is presented, combining precalculated grid potentials with neighbor lists for fast and accurate calculation of atom-based intermolecular energies and forces. The grid representation is compatible with simultaneous multibody docking and can tolerate considerable protein flexibility. When implemented in our docking method ATTRACT, grid-based docking was found to be ∼35x faster. With the OPLSX forcefield instead of the ATTRACT coarse-grained forcefield, the average speed improvement was >100x. Grid-based representations may allow atom-based docking methods to explore large conformational spaces with many degrees of freedom, such as multiple macromolecules including flexibility. This increases the domain of biological problems to which docking methods can be applied. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The nuclear size and mass effects on muonic hydrogen-like atoms embedded in Debye plasma

NASA Astrophysics Data System (ADS)

Poszwa, A.; Bahar, M. K.; Soylu, A.

2016-10-01

Effects of finite nuclear size and finite nuclear mass are investigated for muonic atoms and muonic ions embedded in the Debye plasma. Both nuclear charge radii and nuclear masses are taken into account with experimentally determined values. In particular, isotope shifts of bound state energies, radial probability densities, transition energies, and binding energies for several atoms are studied as functions of Debye length. The theoretical model based on semianalytical calculations, the Sturmian expansion method, and the perturbative approach has been constructed, in the nonrelativistic frame. For some limiting cases, the comparison with previous most accurate literature results has been made.

Helium behavior in oxide dispersion strengthened (ODS) steel: Insights from ab initio modeling

NASA Astrophysics Data System (ADS)

Sun, Dan; Li, Ruihuan; Ding, Jianhua; Huang, Shaosong; Zhang, Pengbo; Lu, Zheng; Zhao, Jijun

2018-02-01

Using first-principles calculations, we systemically investigate the energetics and stability behavior of helium (He) atoms and small Hen (n = 2-4) clusters inside oxide dispersion strengthened (ODS) steel, as well as the incorporation of large amount of He atoms inside Y2O3 crystal. From the energetic point of view, He atom inside Y2O3 cluster is most stable, followed by the interstitial sites at the α-Fe/Y2O3 interface, and the tetrahedral interstitial sites inside α-Fe region. We further consider Hen (n = 2-4) clusters at the tetrahedral interstitial site surrounded by four Y atoms, which is the most stable site in the ODS steel model. The incorporation energies of all these Hen clusters are lower than that of single He atom in α-Fe, while the binding energy between two He atoms is relatively small. With insertion of 15 He atoms into 80-atom unit cell of Y2O3 crystal, the incorporation energy of He atoms is still lower than that of He4 cluster in α-Fe crystal. These theoretical results suggest that He atoms tend to aggregate inside Y2O3 clusters or at the α-Fe/Y2O3 interface, which is beneficial to prevent the He embrittlement in ODS steels.

Theoretical study of Ag doping-induced vacancies defects in armchair graphene

NASA Astrophysics Data System (ADS)

Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

2018-06-01

We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

A new semiclassical decoupling scheme for electronic transitions in molecular collisions - Application to vibrational-to-electronic energy transfer

NASA Technical Reports Server (NTRS)

Lee, H.-W.; Lam, K. S.; Devries, P. L.; George, T. F.

1980-01-01

A new semiclassical decoupling scheme (the trajectory-based decoupling scheme) is introduced in a computational study of vibrational-to-electronic energy transfer for a simple model system that simulates collinear atom-diatom collisions. The probability of energy transfer (P) is calculated quasiclassically using the new scheme as well as quantum mechanically as a function of the atomic electronic-energy separation (lambda), with overall good agreement between the two sets of results. Classical mechanics with the new decoupling scheme is found to be capable of predicting resonance behavior whereas an earlier decoupling scheme (the coordinate-based decoupling scheme) failed. Interference effects are not exhibited in P vs lambda results.

Characterizing structural transitions using localized free energy landscape analysis.

PubMed

Banavali, Nilesh K; Mackerell, Alexander D

2009-01-01

Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes. Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom. The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

Sources of Information on Atomic Energy, International Series of Monographs in Library and Information Science, Volume 2.

ERIC Educational Resources Information Center

Anthony, L. J.

This book provides a comprehensive survey of the principal national and international organizations which are sources of information on atomic and nuclear energy and of the published literature in this field. Organizations in all the major nuclear countries such as the United States, Britain, the Soviet Union, France, and Japan are described, and…

Solvation and Spectral Line Shifts of Chromium Atoms in Helium Droplets Based on a Density Functional Theory Approach

PubMed Central

2014-01-01

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y7P, a5S, and y5P excited states. The necessary Cr–He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z7P ← a7S, y7P ← a7S, z5P ← a5S, and y5P ← a5S are compared to recent fluorescence and photoionization experiments. PMID:24906160

Solvation and spectral line shifts of chromium atoms in helium droplets based on a density functional theory approach.

PubMed

Ratschek, Martin; Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2014-08-21

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y(7)P, a(5)S, and y(5)P excited states. The necessary Cr-He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z(7)P ← a(7)S, y(7)P ← a(7)S, z(5)P ← a(5)S, and y(5)P ← a(5)S are compared to recent fluorescence and photoionization experiments.

Role of codeposited impurities during growth. II. Dependence of morphology on binding and barrier energies

NASA Astrophysics Data System (ADS)

Sathiyanarayanan, Rajesh; Hamouda, Ajmi Bh.; Pimpinelli, A.; Einstein, T. L.

2011-01-01

In an accompanying article we showed that surface morphologies obtained through codeposition of a small quantity (2%) of impurities with Cu during growth (step-flow mode, θ = 40 ML) significantly depends on the lateral nearest-neighbor binding energy (ENN) to Cu adatom and the diffusion barrier (Ed) of the impurity atom on Cu(0 0 1). Based on these two energy parameters, ENN and Ed, we classify impurity atoms into four sets. We study island nucleation and growth in the presence of codeposited impurities from different sets in the submonolayer (θ⩽ 0.7 ML) regime. Similar to growth in the step-flow mode, we find different nucleation and growth behavior for impurities from different sets. We characterize these differences through variations of the number of islands (Ni) and the average island size with coverage (θ). Further, we compute the critical nucleus size (i) for all of these cases from the distribution of capture-zone areas using the generalized Wigner distribution.

Multiscale modeling for ferroelectric materials: identification of the phase-field model’s free energy for PZT from atomistic simulations

NASA Astrophysics Data System (ADS)

Völker, Benjamin; Landis, Chad M.; Kamlah, Marc

2012-03-01

Within a knowledge-based multiscale simulation approach for ferroelectric materials, the atomic level can be linked to the mesoscale by transferring results from first-principles calculations into a phase-field model. A recently presented routine (Völker et al 2011 Contin. Mech. Thermodyn. 23 435-51) for adjusting the Helmholtz free energy coefficients to intrinsic and extrinsic ferroelectric material properties obtained by DFT calculations and atomistic simulations was subject to certain limitations: caused by too small available degrees of freedom, an independent adjustment of the spontaneous strains and piezoelectric coefficients was not possible, and the elastic properties could only be considered in cubic instead of tetragonal symmetry. In this work we overcome such restrictions by expanding the formulation of the free energy function, i.e. by motivating and introducing new higher-order terms that have not appeared in the literature before. Subsequently we present an improved version of the adjustment procedure for the free energy coefficients that is solely based on input parameters from first-principles calculations performed by Marton and Elsässer, as documented in Völker et al (2011 Contin. Mech. Thermodyn. 23 435-51). Full sets of adjusted free energy coefficients for PbTiO3 and tetragonal Pb(Zr,Ti)O3 are presented, and the benefits of the newly introduced higher-order free energy terms are discussed.

Surface conversion techniques for low energy neutral atom imagers

NASA Technical Reports Server (NTRS)

Quinn, J. M.

1995-01-01

This investigation has focused on development of key technology elements for low energy neutral atom imaging. More specifically, we have investigated the conversion of low energy neutral atoms to negatively charged ions upon reflection from specially prepared surfaces. This 'surface conversion' technique appears to offer a unique capability of detecting, and thus imaging, neutral atoms at energies of 0.01 - 1 keV with high enough efficiencies to make practical its application to low energy neutral atom imaging in space. Such imaging offers the opportunity to obtain the first instantaneous global maps of macroscopic plasma features and their temporal variation. Through previous in situ plasma measurements, we have a statistical picture of large scale morphology and local measurements of dynamic processes. However, with in situ techniques it is impossible to characterize or understand many of the global plasma transport and energization processes. A series of global plasma images would greatly advance our understanding of these processes and would provide the context for interpreting previous and future in situ measurements. Fast neutral atoms, created from ions that are neutralized in collisions with exospheric neutrals, offer the means for remotely imaging plasma populations. Energy and mass analysis of these neutrals provides critical information about the source plasma distribution. The flux of neutral atoms available for imaging depends upon a convolution of the ambient plasma distribution with the charge exchange cross section for the background neutral population. Some of the highest signals are at relatively low energies (well below 1 keV). This energy range also includes some of the most important plasma populations to be imaged, for example the base of the cleft ion fountain.

Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids

NASA Astrophysics Data System (ADS)

Anatole von Lilienfeld, O.; Tkatchenko, Alexandre

2010-06-01

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C6 and C9, are computed "on the fly" from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C60 dimer, a peptide (Ala10), an intercalated drug-DNA model [ellipticine-d(CG)2], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.

Two and three-body interatomic dispersion energy contributions to binding in molecules and solids.

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

von Lilienfeld-Toal, Otto Anatole; Tkatchenko, Alexandre

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C{sub 6} and C{sub 9}, are computed 'on the fly' from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiriciallymore » determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C{sub 60} dimer, a peptide (Ala{sub 10}), an intercalated drug-DNA model [ellipticine-d(CG){sub 2}], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.« less

Probing the effect of electron channelling on atomic resolution energy dispersive X-ray quantification.

PubMed

MacArthur, Katherine E; Brown, Hamish G; Findlay, Scott D; Allen, Leslie J

2017-11-01

Advances in microscope stability, aberration correction and detector design now make it readily possible to achieve atomic resolution energy dispersive X-ray mapping for dose resilient samples. These maps show impressive atomic-scale qualitative detail as to where the elements reside within a given sample. Unfortunately, while electron channelling is exploited to provide atomic resolution data, this very process makes the images rather more complex to interpret quantitatively than if no electron channelling occurred. Here we propose small sample tilt as a means for suppressing channelling and improving quantification of composition, whilst maintaining atomic-scale resolution. Only by knowing composition and thickness of the sample is it possible to determine the atomic configuration within each column. The effects of neighbouring atomic columns with differing composition and of residual channelling on our ability to extract exact column-by-column composition are also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

A first principle study for the adsorption and absorption of carbon atom and the CO dissociation on Ir(100) surface

NASA Astrophysics Data System (ADS)

Erikat, I. A.; Hamad, B. A.

2013-11-01

We employ density functional theory to examine the adsorption and absorption of carbon atom as well as the dissociation of carbon monoxide on Ir(100) surface. We find that carbon atoms bind strongly with Ir(100) surface and prefer the high coordination hollow site for all coverages. In the case of 0.75 ML coverage of carbon, we obtain a bridging metal structure due to the balance between Ir-C and Ir-Ir interactions. In the subsurface region, the carbon atom prefers the octahedral site of Ir(100) surface. We find large diffusion barrier for carbon atom into Ir(100) surface (2.70 eV) due to the strong bonding between carbon atom and Ir(100) surface, whereas we find a very small segregation barrier (0.22 eV) from subsurface to the surface. The minimum energy path and energy barrier for the dissociation of CO on Ir(100) surface are obtained by using climbing image nudge elastic band. The energy barrier of CO dissociation on Ir(100) surface is found to be 3.01 eV, which is appreciably larger than the association energy (1.61 eV) of this molecule.

A first principle study for the adsorption and absorption of carbon atom and the CO dissociation on Ir(100) surface.

PubMed

Erikat, I A; Hamad, B A

2013-11-07

We employ density functional theory to examine the adsorption and absorption of carbon atom as well as the dissociation of carbon monoxide on Ir(100) surface. We find that carbon atoms bind strongly with Ir(100) surface and prefer the high coordination hollow site for all coverages. In the case of 0.75 ML coverage of carbon, we obtain a bridging metal structure due to the balance between Ir-C and Ir-Ir interactions. In the subsurface region, the carbon atom prefers the octahedral site of Ir(100) surface. We find large diffusion barrier for carbon atom into Ir(100) surface (2.70 eV) due to the strong bonding between carbon atom and Ir(100) surface, whereas we find a very small segregation barrier (0.22 eV) from subsurface to the surface. The minimum energy path and energy barrier for the dissociation of CO on Ir(100) surface are obtained by using climbing image nudge elastic band. The energy barrier of CO dissociation on Ir(100) surface is found to be 3.01 eV, which is appreciably larger than the association energy (1.61 eV) of this molecule.

Quantum theory of atoms in molecules: results for the SR-ZORA Hamiltonian.

PubMed

Anderson, James S M; Ayers, Paul W

2011-11-17

The quantum theory of atoms in molecules (QTAIM) is generalized to include relativistic effects using the popular scalar-relativistic zeroth-order regular approximation (SR-ZORA). It is usually assumed that the definition of the atom as a volume bounded by a zero-flux surface of the electron density is closely linked to the form of the kinetic energy, so it is somewhat surprising that the atoms corresponding to the relativistic kinetic-energy operator in the SR-ZORA Hamiltonian are also bounded by zero-flux surfaces. The SR-ZORA Hamiltonian should be sufficient for qualitative descriptions of molecular electronic structure across the periodic table, which suggests that QTAIM-based analysis can be useful for molecules and solids containing heavy atoms.

Coupled channel effects on resonance states of positronic alkali atom

NASA Astrophysics Data System (ADS)

Yamashita, Takuma; Kino, Yasushi

2018-01-01

S-wave Feshbach resonance states belonging to dipole series in positronic alkali atoms (e+Li, e+Na, e+K, e+Rb and e+Cs) are studied by coupled-channel calculations within a three-body model. Resonance energies and widths below a dissociation threshold of alkali-ion and positronium are calculated with a complex scaling method. Extended model potentials that provide positronic pseudo-alkali-atoms are introduced to investigate the relationship between the resonance states and dissociation thresholds based on a three-body dynamics. Resonances of the dipole series below a dissociation threshold of alkali-atom and positron would have some associations with atomic energy levels that results in longer resonance lifetimes than the prediction of the analytical law derived from the ion-dipole interaction.

Universal sensor based on the spectroscopy of glow discharge for the detection of traces of atoms or molecules in air

NASA Astrophysics Data System (ADS)

Atutov, S. N.; Galeyev, A. E.; Plekhanov, A. I.; Yakovlev, A. V.

2018-03-01

A sensitive and versatile sensor for the detection of traces of atoms or molecules in air based on the emission spectroscopy of glow discharge in air has been developed and studied. The advantages of this sensor compared to other well-known methods are that it renders the use of ultrahigh vacuum or cryogenic temperatures superfluous. The sensor is insensitive to the presence of water vapor (for example, in exhaled air) because of the absence of strong water lines in the visible spectral range. It has a high spectral selectivity limited only by Doppler broadening of the emission lines. The high selectivity of the sensor combined with a wide spectral range allows the detection of many toxic impurities, which can be present in air. Moreover, the spectral range used covers almost all biomarkers in exhaled air, making the proposed sensor extremely interesting for medical applications. To our knowledge, the proposed method is the first based on a glow discharge in air.

Modeling DNA bubble formation at the atomic scale

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

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

History of nuclear technology development in Japan

NASA Astrophysics Data System (ADS)

Yamashita, Kiyonobu

2015-04-01

Nuclear technology development in Japan has been carried out based on the Atomic Energy Basic Act brought into effect in 1955. The nuclear technology development is limited to peaceful purposes and made in a principle to assure their safety. Now, the technologies for research reactors radiation application and nuclear power plants are delivered to developing countries. First of all, safety measures of nuclear power plants (NPPs) will be enhanced based on lesson learned from TEPCO Fukushima Daiichi NPS accident.

History of nuclear technology development in Japan

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

Yamashita, Kiyonobu, E-mail: yamashita.kiyonobu@jaea.go.jp; General Advisor Nuclear HRD Centre, Japan Atomic Energy Agency, TOKAI-mura, NAKA-gun, IBARAKI-ken, 319-1195

2015-04-29

Nuclear technology development in Japan has been carried out based on the Atomic Energy Basic Act brought into effect in 1955. The nuclear technology development is limited to peaceful purposes and made in a principle to assure their safety. Now, the technologies for research reactors radiation application and nuclear power plants are delivered to developing countries. First of all, safety measures of nuclear power plants (NPPs) will be enhanced based on lesson learned from TEPCO Fukushima Daiichi NPS accident.

Charge transfer in low-energy collisions of H with He+ and H+ with He in excited states

NASA Astrophysics Data System (ADS)

Loreau, J.; Ryabchenko, S.; Muñoz Burgos, J. M.; Vaeck, N.

2018-04-01

The charge transfer process in collisions of excited (n = 2, 3) hydrogen atoms with He+ and in collisions of excited helium atoms with H+ is studied theoretically. A combination of a fully quantum-mechanical method and a semi-classical approach is employed to calculate the charge-exchange cross sections at collision energies from 0.1 eV u‑1 up to 1 keV u‑1. These methods are based on accurate ab initio potential energy curves and non-adiabatic couplings for the molecular ion HeH+. Charge transfer can occur either in singlet or in triplet states, and the differences between the singlet and triplet spin manifolds are discussed. The dependence of the cross section on the quantum numbers n and l of the initial state is demonstrated. The isotope effect on the charge transfer cross sections, arising at low collision energy when H is substituted by D or T, is investigated. Rate coefficients are calculated for all isotopes up to 106 K. Finally, the impact of the present calculations on models of laboratory plasmas is discussed.

Hydrogen collisions with transition metal surfaces: Universal electronically nonadiabatic adsorption

NASA Astrophysics Data System (ADS)

Dorenkamp, Yvonne; Jiang, Hongyan; Köckert, Hansjochen; Hertl, Nils; Kammler, Marvin; Janke, Svenja M.; Kandratsenka, Alexander; Wodtke, Alec M.; Bünermann, Oliver

2018-01-01

Inelastic scattering of H and D atoms from the (111) surfaces of six fcc transition metals (Au, Pt, Ag, Pd, Cu, and Ni) was investigated, and in each case, excitation of electron-hole pairs dominates the inelasticity. The results are very similar for all six metals. Differences in the average kinetic energy losses between metals can mainly be attributed to different efficiencies in the coupling to phonons due to the different masses of the metal atoms. The experimental observations can be reproduced by molecular dynamics simulations based on full-dimensional potential energy surfaces and including electronic excitations by using electronic friction in the local density friction approximation. The determining factors for the energy loss are the electron density at the surface, which is similar for all six metals, and the mass ratio between the impinging atoms and the surface atoms. Details of the electronic structure of the metal do not play a significant role. The experimentally validated simulations are used to explore sticking over a wide range of incidence conditions. We find that the sticking probability increases for H and D collisions near normal incidence—consistent with a previously reported penetration-resurfacing mechanism. The sticking probability for H or D on any of these metals may be represented as a simple function of the incidence energy, Ein, metal atom mass, M, and incidence angle, 𝜗i n. S =(S0+a ṡEi n+b ṡM ) *(1 -h (𝜗i n-c ) (1 -cos(𝜗 i n-c ) d ṡh (Ei n-e ) (Ei n-e ) ) ) , where h is the Heaviside step function and for H, S0 = 1.081, a = -0.125 eV-1, b =-8.40 ṡ1 0-4 u-1, c = 28.88°, d = 1.166 eV-1, and e = 0.442 eV; whereas for D, S0 = 1.120, a = -0.124 eV-1, b =-1.20 ṡ1 0-3 u-1, c = 28.62°, d = 1.196 eV-1, and e = 0.474 eV.

Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

NASA Astrophysics Data System (ADS)

Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

2017-10-01

Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

Nonperturbative theory of atom-surface interaction: corrections at short separations

NASA Astrophysics Data System (ADS)

Bordag, M.; Klimchitskaya, G. L.; Mostepanenko, V. M.

2018-02-01

The nonperturbative expressions for the free energy and force of interaction between a ground-state atom and a real-material surface at any temperature are presented. The transition to the Matsubara representation is performed, whereupon the comparison is made with the commonly used perturbative results based on the standard Lifshitz theory. It is shown that the Lifshitz formulas for the free energy and force of an atom-surface interaction follow from the nonperturbative ones in the lowest order of the small parameter. Numerical computations of the free energy and force for the atoms of He{\\hspace{0pt}}\\ast and Na interacting with a surface of an Au plate have been performed using the frequency-dependent dielectric permittivity of Au and highly accurate dynamic atomic polarizabilities in the framework of both the nonperturbative and perturbative theories. According to our results, the maximum deviations between the two theories are reached at the shortest atom-surface separations of about 1 nm. Simple analytic expressions for the atom-surface free energy are derived in the classical limit and for an ideal-metal plane. In the lowest order of the small parameter, they are found in agreement with the perturbative ones following from the standard Lifshitz theory. Possible applications of the obtained results in the theory of van der Waals adsorption are discussed.

Effects of an energy balance educational intervention and the COPE cognitive behavioral therapy intervention for Division I U.S. Air Force Academy female athletes.

PubMed

Buffington, Brenda C; Melnyk, Bernadette M; Morales, Shelly; Lords, Amanda; Zupan, Michael R

2016-04-01

Female athletes struggle harder than male athletes to lose body fat and maintain a leaner physique. The purpose of this study was to determine the effects of an educational and cognitive behavioral therapy (CBT)-based intervention on knowledge, body composition, anxiety, stress, and nutritional intake. A randomized controlled trial was conducted with 153 female athletes from the U.S. Air Force Academy (USAFA). Participants were assigned to one of three groups: (a) a combined energy balance and CBT-based intervention (E1); (b) a CBT-based intervention alone (E2); and (c) a control group (C). Main outcomes included a DXA scan for body composition, a knowledge test, the GAD-7 for anxiety, the brief inventory of perceived stress (BIPS) for stress, and a 24-h food recall. Significant improvement on knowledge of energy balance occurred in all three groups E1 (p < .001), E2, and C (p < .05). Significant reductions in percentage of body fat occurred in E1 (p < .001) and E2 (p < .05). There also were significant reductions in the percent of fat consumed by E1 (p < .05) and saturated fat consumed by both E1 and E2 (p < .05). The control group only demonstrated a significant increase in stress as measured by the BIPS (p < .05). A combined energy balance and CBT-based intervention improves knowledge and body fat. The importance to assess knowledge, anxiety, stress, nutrition intake, and percentage of body fat in female athletes and to deliver evidence-based interventions to improve their health outcomes. ©2016 American Association of Nurse Practitioners.

The American atom: A documentary history of nuclear policies from the discovery of fission to the present

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

Williams, R.C.; Cantelon, P.L.

1984-01-01

In selecting these historical documents the authors have applied three general tests: first, does the document help tell the story of the development of American nuclear policy in a nontechnical way; second, is the source primary rather than secondary, written by an actor in the drama rather than by a member of the audience; third, does the document provide coverage of the major chapters in the story. The Manhattan Project was America's $2 billion secret project to build an atomic bomb. Many documents associated with the project have come to light only in recent years. In Section II they usemore » the letters of J. Robert Oppenheimer and the recently declassified minutes of policy committees to tell the story of how the bomb was designed and built and how the decision was made to drop the first uranium and plutonium devices on the Japanese cities of Hiroshima and Nagasaki in 1945. How did a weapon of war become the key to a peacetime industry. In considering atomic energy after World War II, they focus in Section III on the legislative enabling acts that established the Atomic Energy Commission, the short-lived dream of international control of nuclear weapons under the Baruch Plan, and the ''atoms for peace'' program of President Dwight D. Eisenhower. By 1954 the highly classified work on nuclear weapons paralleled a new development of nuclear energy and power reactors. Knowledge was shared with both private industry and other countries. The fruits of this program are considered in the later section on nuclear power.« less

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

PubMed

Lara, A; Riquelme, M; Vöhringer-Martinez, E

2018-05-11

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Controlled dipole-dipole interactions between K Rydberg atoms in a laser-chopped effusive beam

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

Kutteruf, M. R.; Jones, R. R.

2010-12-15

We explore pulsed-field control of resonant dipole-dipole interactions between K Rydberg atoms. A laser-based atomic beam chopper is used to reduce the relative velocities of Rydberg atoms excited from an effusive thermal source. Resonant energy transfer (RET) between pairs of atoms is controlled via Stark tuning of the relevant Rydberg energy levels. Resonance line shapes in the electric field dependence of the RET probability are used to determine the effective temperature of the sample. We demonstrate that the relative atom velocities can be reduced to the point where the duration of the electric-field tuning pulses, and not the motion ofmore » neighboring atoms, defines the interaction time for each pair within the ensemble. Coherent, transform-limited broadening of the resonance line shape is observed as the tuning pulse duration is reduced below the natural time scale for collisions.« less

Free energy landscapes of a highly structured β-hairpin peptide and its single mutant

NASA Astrophysics Data System (ADS)

Kim, Eunae; Yang, Changwon; Jang, Soonmin; Pak, Youngshang

2008-10-01

We investigated the free energy landscapes of a highly structured β-hairpin peptide (MBH12) and a less structured peptide with a single mutation of Tyr6 to Asp6 (MBH10). For the free energy mapping, starting from an extended conformation, the replica exchange molecular dynamic simulations for two β-hairpins were performed using a modified version of an all-atom force field employing an implicit solvation (param99MOD5/GBSA). With the present simulation approach, we demonstrated that detailed stability changes associated with the sequence modification from MBH12 to MBH10 are quantitatively well predicted at the all-atom level.

Prediction of In-Space Durability of Protected Polymers Based on Ground Laboratory Thermal Energy Atomic Oxygen

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; deGroh, Kim K.; Rutledge, Sharon; DiFilippo, Frank J.

1996-01-01

The probability of atomic oxygen reacting with polymeric materials is orders of magnitude lower at thermal energies (greater than O.1 eV) than at orbital impact energies (4.5 eV). As a result, absolute atomic oxygen fluxes at thermal energies must be orders of magnitude higher than orbital energy fluxes, to produce the same effective fluxes (or same oxidation rates) for polymers. These differences can cause highly pessimistic durability predictions for protected polymers and polymers which develop protective metal oxide surfaces as a result of oxidation if one does not make suitable calibrations. A comparison was conducted of undercut cavities below defect sites in protected polyimide Kapton samples flown on the Long Duration Exposure Facility (LDEF) with similar samples exposed in thermal energy oxygen plasma. The results of this comparison were used to quantify predicted material loss in space based on material loss in ground laboratory thermal energy plasma testing. A microindent hardness comparison of surface oxidation of a silicone flown on the Environmental Oxygen Interaction with Materials-III (EOIM-III) experiment with samples exposed in thermal energy plasmas was similarly used to calibrate the rate of oxidation of silicone in space relative to samples in thermal energy plasmas exposed to polyimide Kapton effective fluences.

Efficient grid-based techniques for density functional theory

NASA Astrophysics Data System (ADS)

Rodriguez-Hernandez, Juan Ignacio

Understanding the chemical and physical properties of molecules and materials at a fundamental level often requires quantum-mechanical models for these substance's electronic structure. This type of many body quantum mechanics calculation is computationally demanding, hindering its application to substances with more than a few hundreds atoms. The supreme goal of many researches in quantum chemistry---and the topic of this dissertation---is to develop more efficient computational algorithms for electronic structure calculations. In particular, this dissertation develops two new numerical integration techniques for computing molecular and atomic properties within conventional Kohn-Sham-Density Functional Theory (KS-DFT) of molecular electronic structure. The first of these grid-based techniques is based on the transformed sparse grid construction. In this construction, a sparse grid is generated in the unit cube and then mapped to real space according to the pro-molecular density using the conditional distribution transformation. The transformed sparse grid was implemented in program deMon2k, where it is used as the numerical integrator for the exchange-correlation energy and potential in the KS-DFT procedure. We tested our grid by computing ground state energies, equilibrium geometries, and atomization energies. The accuracy on these test calculations shows that our grid is more efficient than some previous integration methods: our grids use fewer points to obtain the same accuracy. The transformed sparse grids were also tested for integrating, interpolating and differentiating in different dimensions (n = 1,2,3,6). The second technique is a grid-based method for computing atomic properties within QTAIM. It was also implemented in deMon2k. The performance of the method was tested by computing QTAIM atomic energies, charges, dipole moments, and quadrupole moments. For medium accuracy, our method is the fastest one we know of.

Atomic structure and domain wall pinning in samarium-cobalt-based permanent magnets.

PubMed

Duerrschnabel, M; Yi, M; Uestuener, K; Liesegang, M; Katter, M; Kleebe, H-J; Xu, B; Gutfleisch, O; Molina-Luna, L

2017-07-04

A higher saturation magnetization obtained by an increased iron content is essential for yielding larger energy products in rare-earth Sm 2 Co 17 -type pinning-controlled permanent magnets. These are of importance for high-temperature industrial applications due to their intrinsic corrosion resistance and temperature stability. Here we present model magnets with an increased iron content based on a unique nanostructure and -chemical modification route using Fe, Cu, and Zr as dopants. The iron content controls the formation of a diamond-shaped cellular structure that dominates the density and strength of the domain wall pinning sites and thus the coercivity. Using ultra-high-resolution experimental and theoretical methods, we revealed the atomic structure of the single phases present and established a direct correlation to the macroscopic magnetic properties. With further development, this knowledge can be applied to produce samarium cobalt permanent magnets with improved magnetic performance.Understanding the factors that determine the properties of permanent magnets, which play a central role in many industrial applications, can help in improving their performance. Here, the authors study how changes in the iron content affect the microstructure of samarium cobalt magnets.

Kinetic Energy and Angular Distributions of He and Ar Atoms Evaporating from Liquid Dodecane.

PubMed

Patel, Enamul-Hasan; Williams, Mark A; Koehler, Sven P K

2017-01-12

We report both kinetic energy and angular distributions for He and Ar atoms evaporating from C 12 H 26 . All results were obtained by performing molecular dynamics simulations of liquid C 12 H 26 with around 10-20 noble gas atoms dissolved in the liquid and by subsequently following the trajectories of the noble gas atoms after evaporation from the liquid. Whereas He evaporates with a kinetic energy distribution of (1.05 ± 0.03) × 2RT (corrected for the geometry used in experiments: (1.08 ± 0.03) × 2RT, experimentally obtained value: (1.14 ± 0.01) × 2RT), Ar displays a kinetic energy distribution that better matches a Maxwell-Boltzmann distribution at the temperature of the liquid ((0.99 ± 0.04) × 2RT). This behavior is also reflected in the angular distributions, which are close to a cosine distribution for Ar but slightly narrower, especially for faster atoms, in the case of He. This behavior of He is most likely due to the weak interaction potential between He and the liquid hydrocarbon.

Charge-equilibrium and radiation of low-energy cosmic rays passing through interstellar medium

NASA Technical Reports Server (NTRS)

Rule, D. W.; Omidvar, K.

1977-01-01

The charge equilibrium and radiation of an oxygen and an iron beam in the MeV per nucleon energy range, representing a typical beam of low-energy cosmic rays passing through the interstellar medium, is considered. Electron loss of the beam has been taken into account by means of the First Born approximation allowing for the target atom to remain unexcited, or to be excited to all possible states. Electron capture cross sections have been calculated by means of the scaled Oppenheimer-Brinkman-Kramers approximation, taking into account all atomic shells of the target atoms. Radiation of the beam due to electron capture into the excited states of the ion, collisional excitation and collisional inner-shell ionization of the ions has been considered. Effective X-ray production cross sections and multiplicities for the most energetic X-ray lines emitted by the Fe and O beams have been calculated.

The photodissociation dynamics of alkyl radicals

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

Giegerich, Jens; Fischer, Ingo, E-mail: ingo.fischer@uni-wuerzburg.de

2015-01-28

The photodisscociation dynamics of the alkyl radicals i-propyl (CH(CH{sub 3}){sub 2}) and t-butyl (C(CH{sub 3}){sub 3}) are investigated by H-atom photofragment imaging. While i-propyl is excited at 250 nm, the photodynamics of t-butyl are explored over a large energy range using excitation wavelengths between 347 nm and 233 nm. The results are compared to those obtained previously for ethyl, CH{sub 3}CH{sub 2}, and to those reported for t-butyl using 248 nm excitation. The translational energy (E{sub T}) distribution of the H-atom photofragments is bimodal and appears rather similar for all three radicals. The low E{sub T} part of the distributionmore » shows an isotropic photofragment angular distribution, while the high E{sub T} part is associated with a considerable anisotropy. Thus, for t-butyl, two H-atom loss channels of roughly equal importance have been identified in addition to the CH{sub 3}-loss channel reported previously. A mechanism for the photodissociation of alkyl radicals is suggested that is based on interactions between Rydberg- and valence states.« less

Quantum defect theory for the orbital Feshbach resonance

NASA Astrophysics Data System (ADS)

Cheng, Yanting; Zhang, Ren; Zhang, Peng

2017-01-01

In the ultracold gases of alkali-earth-metal-like atoms, a new type of Feshbach resonance, i.e., the orbital Feshbach resonance (OFR), has been proposed and experimentally observed in ultracold 173Yb atoms [R. Zhang et al., Phys. Rev. Lett. 115, 135301 (2015), 10.1103/PhysRevLett.115.135301]. When the OFR of the 173Yb atoms occurs, the energy gap between the open and closed channels is smaller by two orders of magnitude than the van der Waals energy. As a result, quantitative accurate results for the low-energy two-body problems can be obtained via multichannel quantum defect theory (MQDT), which is based on the exact solution of the Schrödinger equation with the van der Waals potential. In this paper we use MQDT to calculate the two-atom scattering length, effective range, and binding energy of two-body bound states for the systems with OFR. With these results we further study the clock-transition spectrum for the two-body bound states, which can be used to experimentally measure the binding energy. Our results are helpful for the quantitative theoretical and experimental research for the ultracold gases of alkali-earth-metal-like atoms with OFR.

Quantitative Electron-Excited X-Ray Microanalysis of Borides, Carbides, Nitrides, Oxides, and Fluorides with Scanning Electron Microscopy/Silicon Drift Detector Energy-Dispersive Spectrometry (SEM/SDD-EDS) and NIST DTSA-II.

PubMed

Newbury, Dale E; Ritchie, Nicholas W M

2015-10-01

A scanning electron microscope with a silicon drift detector energy-dispersive X-ray spectrometer (SEM/SDD-EDS) was used to analyze materials containing the low atomic number elements B, C, N, O, and F achieving a high degree of accuracy. Nearly all results fell well within an uncertainty envelope of ±5% relative (where relative uncertainty (%)=[(measured-ideal)/ideal]×100%). Quantification was performed with the standards-based "k-ratio" method with matrix corrections calculated based on the Pouchou and Pichoir expression for the ionization depth distribution function, as implemented in the NIST DTSA-II EDS software platform. The analytical strategy that was followed involved collection of high count (>2.5 million counts from 100 eV to the incident beam energy) spectra measured with a conservative input count rate that restricted the deadtime to ~10% to minimize coincidence effects. Standards employed included pure elements and simple compounds. A 10 keV beam was employed to excite the K- and L-shell X-rays of intermediate and high atomic number elements with excitation energies above 3 keV, e.g., the Fe K-family, while a 5 keV beam was used for analyses of elements with excitation energies below 3 keV, e.g., the Mo L-family.

Exploring a potential energy surface by machine learning for characterizing atomic transport

NASA Astrophysics Data System (ADS)

Kanamori, Kenta; Toyoura, Kazuaki; Honda, Junya; Hattori, Kazuki; Seko, Atsuto; Karasuyama, Masayuki; Shitara, Kazuki; Shiga, Motoki; Kuwabara, Akihide; Takeuchi, Ichiro

2018-03-01

We propose a machine-learning method for evaluating the potential barrier governing atomic transport based on the preferential selection of dominant points for atomic transport. The proposed method generates numerous random samples of the entire potential energy surface (PES) from a probabilistic Gaussian process model of the PES, which enables defining the likelihood of the dominant points. The robustness and efficiency of the method are demonstrated on a dozen model cases for proton diffusion in oxides, in comparison with a conventional nudge elastic band method.

Improved modification for the density-functional theory calculation of thermodynamic properties for C-H-O composite compounds.

PubMed

Liu, Min Hsien; Chen, Cheng; Hong, Yaw Shun

2005-02-08

A three-parametric modification equation and the least-squares approach are adopted to calibrating hybrid density-functional theory energies of C(1)-C(10) straight-chain aldehydes, alcohols, and alkoxides to accurate enthalpies of formation DeltaH(f) and Gibbs free energies of formation DeltaG(f), respectively. All calculated energies of the C-H-O composite compounds were obtained based on B3LYP6-311++G(3df,2pd) single-point energies and the related thermal corrections of B3LYP6-31G(d,p) optimized geometries. This investigation revealed that all compounds had 0.05% average absolute relative error (ARE) for the atomization energies, with mean value of absolute error (MAE) of just 2.1 kJ/mol (0.5 kcal/mol) for the DeltaH(f) and 2.4 kJ/mol (0.6 kcal/mol) for the DeltaG(f) of formation.

Atomic-like high-harmonic generation from two-dimensional materials.

PubMed

Tancogne-Dejean, Nicolas; Rubio, Angel

2018-02-01

The generation of high-order harmonics from atomic and molecular gases enables the production of high-energy photons and ultrashort isolated pulses. Obtaining efficiently similar photon energy from solid-state systems could lead, for instance, to more compact extreme ultraviolet and soft x-ray sources. We demonstrate from ab initio simulations that it is possible to generate high-order harmonics from free-standing monolayer materials, with an energy cutoff similar to that of atomic and molecular gases. In the limit in which electrons are driven by the pump laser perpendicularly to the monolayer, they behave qualitatively the same as the electrons responsible for high-harmonic generation (HHG) in atoms, where their trajectories are described by the widely used semiclassical model, and exhibit real-space trajectories similar to those of the atomic case. Despite the similarities, the first and last steps of the well-established three-step model for atomic HHG are remarkably different in the two-dimensional materials from gases. Moreover, we show that the electron-electron interaction plays an important role in harmonic generation from monolayer materials because of strong local-field effects, which modify how the material is ionized. The recombination of the accelerated electron wave packet is also found to be modified because of the infinite extension of the material in the monolayer plane, thus leading to a more favorable wavelength scaling of the harmonic yield than in atomic HHG. Our results establish a novel and efficient way of generating high-order harmonics based on a solid-state device, with an energy cutoff and a more favorable wavelength scaling of the harmonic yield similar to those of atomic and molecular gases. Two-dimensional materials offer a unique platform where both bulk and atomic HHG can be investigated, depending on the angle of incidence. Devices based on two-dimensional materials can extend the limit of existing sources.

Fast divide-and-conquer algorithm for evaluating polarization in classical force fields

NASA Astrophysics Data System (ADS)

Nocito, Dominique; Beran, Gregory J. O.

2017-03-01

Evaluation of the self-consistent polarization energy forms a major computational bottleneck in polarizable force fields. In large systems, the linear polarization equations are typically solved iteratively with techniques based on Jacobi iterations (JI) or preconditioned conjugate gradients (PCG). Two new variants of JI are proposed here that exploit domain decomposition to accelerate the convergence of the induced dipoles. The first, divide-and-conquer JI (DC-JI), is a block Jacobi algorithm which solves the polarization equations within non-overlapping sub-clusters of atoms directly via Cholesky decomposition, and iterates to capture interactions between sub-clusters. The second, fuzzy DC-JI, achieves further acceleration by employing overlapping blocks. Fuzzy DC-JI is analogous to an additive Schwarz method, but with distance-based weighting when averaging the fuzzy dipoles from different blocks. Key to the success of these algorithms is the use of K-means clustering to identify natural atomic sub-clusters automatically for both algorithms and to determine the appropriate weights in fuzzy DC-JI. The algorithm employs knowledge of the 3-D spatial interactions to group important elements in the 2-D polarization matrix. When coupled with direct inversion in the iterative subspace (DIIS) extrapolation, fuzzy DC-JI/DIIS in particular converges in a comparable number of iterations as PCG, but with lower computational cost per iteration. In the end, the new algorithms demonstrated here accelerate the evaluation of the polarization energy by 2-3 fold compared to existing implementations of PCG or JI/DIIS.

Effect of energy transfer from atomic electron shell to an α particle emitted by decaying nucleus

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

Igashov, S. Yu., E-mail: igashov@theor.mephi.ru; Tchuvil’sky, Yu. M.

2016-12-15

The process of energy transfer from the electron shell of an atom to an α particle propagating through the shell is formulated mathematically. Using the decay of the {sup 226}Ra nucleus as an example, it is demonstrated that this phenomenon increases the α-decay intensity in contrast with other known effects of similar type. Moreover, the α decay of the nucleus is more strongly affected by the energy transfer than by all other effects taken together.

Visualisation and orbital-free parametrisation of the large-Z scaling of the kinetic energy density of atoms

NASA Astrophysics Data System (ADS)

Cancio, Antonio C.; Redd, Jeremy J.

2017-03-01

The scaling of neutral atoms to large Z, combining periodicity with a gradual trend to homogeneity, is a fundamental probe of density functional theory, one that has driven recent advances in understanding both the kinetic and exchange-correlation energies. Although research focus is normally upon the scaling of integrated energies, insights can also be gained from energy densities. We visualise the scaling of the positive-definite kinetic energy density (KED) in closed-shell atoms, in comparison to invariant quantities based upon the gradient and Laplacian of the density. We notice a striking fit of the KED within the core of any atom to a gradient expansion using both the gradient and the Laplacian, appearing as an asymptotic limit around which the KED oscillates. The gradient expansion is qualitatively different from that derived from first principles for a slowly varying electron gas and is correlated with a nonzero Pauli contribution to the KED near the nucleus. We propose and explore orbital-free meta-GGA models for the kinetic energy to describe these features, with some success, but the effects of quantum oscillations in the inner shells of atoms make a complete parametrisation difficult. We discuss implications for improved orbital-free description of molecular properties.

Si(111) strained layers on Ge(111): Evidence for c (2 ×4 ) domains

NASA Astrophysics Data System (ADS)

Zhachuk, R.; Coutinho, J.; Dolbak, A.; Cherepanov, V.; Voigtländer, B.

2017-08-01

The tensile-strained Si (111 ) layers grown on top of Ge (111 ) substrates are studied by combining scanning tunneling microscopy, low-energy electron diffraction, and first-principles calculations. It is shown that the layers exhibit c (2 ×4 ) domains, which are separated by domain walls along <1 ¯10 > directions. A model structure for the c (2 ×4 ) domains is proposed, which shows low formation energy and good agreement with the experimental data. The results of our calculations suggest that Ge atoms are likely to replace Si atoms with dangling bonds on the surface (rest-atoms and adatoms), thus significantly lowering the surface energy and inducing the formation of domain walls. The experiments and calculations demonstrate that when surface strain changes from compressive to tensile, the (111) reconstruction converts from dimer-adatom-stacking fault-based to adatom-based structures.

Energy Levels of Hydrogen and Deuterium

National Institute of Standards and Technology Data Gateway

SRD 142 NIST Energy Levels of Hydrogen and Deuterium (Web, free access)   This database provides theoretical values of energy levels of hydrogen and deuterium for principle quantum numbers n = 1 to 200 and all allowed orbital angular momenta l and total angular momenta j. The values are based on current knowledge of the revelant theoretical contributions including relativistic, quantum electrodynamic, recoil, and nuclear size effects.

Reaction of hydrogen with Ag(111): binding states, minimum energy paths, and kinetics.

PubMed

Montoya, Alejandro; Schlunke, Anna; Haynes, Brian S

2006-08-31

The interaction of atomic and molecular hydrogen with the Ag(111) surface is studied using periodic density functional total-energy calculations. This paper focuses on the site preference for adsorption, ordered structures, and energy barriers for H diffusion and H recombination. Chemisorbed H atoms are unstable with respect to the H(2) molecule in all adsorption sites below monolayer coverage. The three-hollow sites are energetically the most favorable for H chemisorption. The binding energy of H to the surface decreases slightly up to one monolayer, suggesting a small repulsive H-H interaction on nonadjacent sites. Subsurface and vacancy sites are energetically less favorable for H adsorption than on-top sites. Recombination of chemisorbed H atoms leads to the formation of gas-phase H(2) with no molecular chemisorbed state. Recombination is an exothermic process and occurs on the bridge site with a pronounced energy barrier. This energy barrier is significantly higher than that inferred from experimental temperature-programmed desorption (TPD) studies. However, there is significant permeability of H atoms through the recombination energy barrier at low temperatures, thus increasing the rate constant for H(2) desorption due to quantum tunneling effects, and improving the agreement between experiment and theory.

A novel knowledge-based potential for RNA 3D structure evaluation

NASA Astrophysics Data System (ADS)

Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang

2018-03-01

Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).

Chapter 6 Quantum Mechanical Methods for Loss-Excitation and Loss-Ionization in Fast Ion-Atom Collisions

NASA Astrophysics Data System (ADS)

Belkic, Dzevad

Inelastic collisions between bare nuclei and hydrogen-like atomic systems are characterized by three main channels: electron capture, excitation, and ionization. Capture dominates at lower energies, whereas excitation and ionization prevail at higher impact energies. At intermediate energies and in the region of resonant scattering near the Massey peak, all three channels become competitive. For dressed or clothed nuclei possessing electrons, such as hydrogen-like ions, several additional channels open up, including electron loss (projectile ionization or stripping). The most important aspect of electron loss is the competition between one- and two-electron processes. Here, in a typical one-electron process, the projectile emits an electron, whereas the target final and initial states are the same. A prototype of double-electron transitions in loss processes is projectile ionization accompanied with an alteration of the target state. In such a two-electron process, the target could be excited or ionized. The relative importance of these loss channels with single- and double-electron transitions involving collisions of dressed projectiles with atomic systems is also strongly dependent on the value of the impact energy. Moreover, impact energies determine which theoretical method is likely to be more appropriate to use for predictions of cross sections. At low energies, an expansion of total scattering wave functions in terms of molecular orbitals is adequate. This is because the projectile spends considerable time in the vicinity of the target, and as a result, a compound system comprised of the projectile and the target can be formed in a metastable molecular state which is prone to decay. At high energies, a perturbation series expansion is more appropriate in terms of powers of interaction potentials. In the intermediate energy region, atomic orbitals are often used with success while expanding the total scattering wave functions. The present work is focused on quantum mechanical perturbation theories applied to electron loss collisions involving two hydrogen-like atoms. Both the one- and two-electron transitions (target unaffected by collision, as well as loss-ionization) are thoroughly examined in various intervals of impact energies varying from the threshold via the Massey peak to the Bethe asymptotic region. Systematics are established for the fast, simple, and accurate computations of cross sections for loss-excitation and loss-ionization accounting for the entire spectra of all four particles, including two free electrons and two free protons. The expounded algorithmic strategy of quantum mechanical methodologies is of great importance for wide applications to particle transport physics, especially in fusion research and hadron radiotherapy. This should advantageously replace the current overwhelming tendency in these fields for using phenomenological modeling with artificial functions extracted from fitting the existing experimental/theoretical data bases for cross sections.

Atomic-scale luminescence measurement and theoretical analysis unveiling electron energy dissipation at a p-type GaAs(110) surface.

PubMed

Imada, Hiroshi; Miwa, Kuniyuki; Jung, Jaehoon; Shimizu, Tomoko K; Yamamoto, Naoki; Kim, Yousoo

2015-09-11

Luminescence of p-type GaAs was induced by electron injection from the tip of a scanning tunnelling microscope into a GaAs(110) surface. Atomically-resolved photon maps revealed a significant reduction in luminescence intensity at surface electronic states localized near Ga atoms. Theoretical analysis based on first principles calculations and a rate equation approach was performed to describe the perspective of electron energy dissipation at the surface. Our study reveals that non-radiative recombination through the surface states (SS) is a dominant process for the electron energy dissipation at the surface, which is suggestive of the fast scattering of injected electrons into the SS.

Double-image storage optimized by cross-phase modulation in a cold atomic system

NASA Astrophysics Data System (ADS)

Qiu, Tianhui; Xie, Min

2017-09-01

A tripod-type cold atomic system driven by double-probe fields and a coupling field is explored to store double images based on the electromagnetically induced transparency (EIT). During the storage time, an intensity-dependent signal field is applied further to extend the system with the fifth level involved, then the cross-phase modulation is introduced for coherently manipulating the stored images. Both analytical analysis and numerical simulation clearly demonstrate a tunable phase shift with low nonlinear absorption can be imprinted on the stored images, which effectively can improve the visibility of the reconstructed images. The phase shift and the energy retrieving rate of the probe fields are immune to the coupling intensity and the atomic optical density. The proposed scheme can easily be extended to the simultaneous storage of multiple images. This work may be exploited toward the end of EIT-based multiple-image storage devices for all-optical classical and quantum information processings.

Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

PubMed

Torres, A E; Fomine, S

2015-04-28

The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.

First-Principles Prediction of Densities of Amorphous Materials: The Case of Amorphous Silicon

NASA Astrophysics Data System (ADS)

Furukawa, Yoritaka; Matsushita, Yu-ichiro

2018-02-01

A novel approach to predict the atomic densities of amorphous materials is explored on the basis of Car-Parrinello molecular dynamics (CPMD) in density functional theory. Despite the determination of the atomic density of matter being crucial in understanding its physical properties, no first-principles method has ever been proposed for amorphous materials until now. We have extended the conventional method for crystalline materials in a natural manner and pointed out the importance of the canonical ensemble of the total energy in the determination of the atomic densities of amorphous materials. To take into account the canonical distribution of the total energy, we generate multiple amorphous structures with several different volumes by CPMD simulations and average the total energies at each volume. The density is then determined as the one that minimizes the averaged total energy. In this study, this approach is implemented for amorphous silicon (a-Si) to demonstrate its validity, and we have determined the density of a-Si to be 4.1% lower and its bulk modulus to be 28 GPa smaller than those of the crystal, which are in good agreement with experiments. We have also confirmed that generating samples through classical molecular dynamics simulations produces a comparable result. The findings suggest that the presented method is applicable to other amorphous systems, including those for which experimental knowledge is lacking.

International Atomic Energy Agency study with referring physicians on patient radiation exposure and its tracking: a prospective survey using a web-based questionnaire

PubMed Central

Rehani, Madan M; Berris, Theocharis

2012-01-01

Objectives To assess the following themes among referring physicians: (A) importance of acquiring information about previous diagnostic exposures; (B) knowledge about radiation doses involved, familiarity with radiation units and, age-related radiosensitivity; (C) opinion on whether patients should be provided information about radiation dose and (D) self-assessment of appropriateness of referrals. Design A prospective survey using a web-based questionnaire. Setting International survey among referring physicians. Participants Referring physicians from 28 countries. Main outcome measures Knowledge, opinion and practice of the four themes of the survey. Results All 728 responses from 28 countries (52.3% from developed and 47.7% from developing countries) indicated that while the vast majority (71.7%) of physicians feel that being aware of history of CT scans would always or mostly lead them to a better decision on referring patients for CT scans, only 43.4% often enquire about it. The majority of referring physicians (60.5%) stated that having a system that provides quick information about patient exposure history would be useful. The knowledge about radiation doses involved is poor, as only one-third (34.7%) of respondents chose the correct option of the number of chest x-rays with equivalence of a CT scan. In total, 70.9% of physicians stated that they do not feel uncomfortable when patients ask about radiation risk from CT scans they prescribe. Most physicians (85.6%) assessed that they have rarely prescribed CT scans of no clinical use in patient management. Conclusions This first ever multinational survey among referring physicians from 28 countries indicates support for a system that provides radiation exposure history of the patient, demonstrates poor knowledge about radiation doses, supports radiation risk communication with patients and mandatory provisions for justification of a CT examination. PMID:22997065

Modern Spectroscopy

ERIC Educational Resources Information Center

Barrow, Gordon M.

1970-01-01

Presents the basic ideas of modern spectroscopy. Both the angular momenta and wave-nature approaches to the determination of energy level patterns for atomic and molecular systems are discussed. The interpretation of spectra, based on atomic and molecular models, is considered. (LC)

Generation and acceleration of neutral atoms in intense laser plasma experiments

NASA Astrophysics Data System (ADS)

Tata, Sheroy; Mondal, Angana; Sarkar, Shobhik; Ved, Yash; Lad, Amit D.; Pasley, John; Colgan, James; Krishnamurthy, M.

2017-10-01

The interaction of a high intensity (>=1018 W/cm2), high contrast (>=109), ultra-short (30fs) laser with solid targets generates a highly dense hot plasma. The quasi-static electric fields in such plasmas are well known for ion acceleration via the target normal sheath acceleration process. Under such conditions charge reduction to generate fast neutral atoms is almost inhibited. Improvised Thomson parabola spectrometry with improved signal to noise ratio has enabled us to measure the signals of fast neutral atoms and negative ions having energies in excess of tens of keV. A study on the neutralization of accelerated protons in plasma shows that the neutral atom to all particle ratio rises sharply from a few percent at the highest detectable energy to 50 % at 15 keV. Using usual charge transfer reactions the generation of neutral atoms can not be explained, thus we conjecture that the neutralization of the accelerated ions is not from the hot dense region of the plasma but neutral atom formation takes place by co-propagating ions with low energy electrons enhancing the effective neutral ratio.

Applications of atom interferometry - from ground to space

NASA Astrophysics Data System (ADS)

Schubert, Christian; Rasel, Ernst Maria; Gaaloul, Naceur; Ertmer, Wolfgang

2016-07-01

Atom interferometry is utilized for the measurement of rotations [1], accelerations [2] and for tests of fundamental physics [3]. In these devices, three laser light pulses separated by a free evolution time coherently manipulate the matter waves which resembles the Mach-Zehnder geometry in optics. Atom gravimeters demonstrated an accuracy of few microgal [2,4], and atom gradiometers showed a noise floor of 30 E Hz^{-1/2} [5]. Further enhancements of atom interferometers are anticipated by the integration of novel source concepts providing ultracold atoms, extending the free fall time of the atoms, and enhanced techniques for coherent manipulation. Sources providing Bose-Einstein condensates recently demontrated a flux compatible with precision experiments [6]. All of these aspects are studied in the transportable quantum gravimeter QG-1 and the very long baseline atom interferometry teststand in Hannover [7] with the goal of surpassing the microgal regime. Going beyond ground based setups, the QUANTUS collaboration exploits the unique features of a microgravity environment in drop tower experiments [8] and in a sounding rocket mission. The payloads are compact and robust atom optics experiments based on atom chips [6], enabling technology for transportable sensors on ground as a byproduct. More prominently, they are pathfinders for proposed satellite missions as tests of the universality of free fall [9] and gradiometry based on atom interferometers [10]. This work is supported by the German Space Agency (DLR) with funds provided by the Federal Ministry for Economic Affairs and Energy (BMWi) due to an enactment of the German Bundestag under grant numbers DLR 50WM1552-1557 (QUANTUS-IV-Fallturm) and by the Deutsche Forschungsgemeinschaft in the framework of the SFB 1128 geo-Q. [1] PRL 114 063002 2015 [2] Nature 400 849 1999 [3] PRL 112 203002 2014 [4] NJP 13 065026 2011 [5] PRA 65 033608 2002 [6] NJP 17 065001 2015 [7] NJP 17 035011 2015 [8] PRL 110 093602 2013 [9] CQG 31 115010 2014 [10] MST 26 139 2014.

Structural, electronic and vibrational properties of GexCy (x+y=2-5) nanoclusters: A B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Goswami, Sohini; Saha, Sushmita; Yadav, R. K.

2015-11-01

An ab-initio study of the stability, structural and electronic properties has been made for 84 germanium carbide nanoclusters, GexCy (x+y=2-5). The configuration possessing the maximum value of final binding energy (FBE), among the various configurations corresponding to a fixed x+y=n value, is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize fully the geometries of the nanoclusters. The binding energies (BE), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps have been obtained for all the clusters and the bond lengths have been reported for the most stable clusters. We have considered the zero point energy (ZPE) corrections. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have also been investigated for the most stable structures. The configurations containing the carbon atoms in majority are seen to be the most stable structures. The strong C-C bond has important role in stabilizing the clusters. For the clusters containing one germanium atom and all the other as carbon atoms, the BE increases monotonically with the number of the carbon atoms. The HOMO-LUMO gap, IPs and EAs fluctuates with increase in the number of atoms. The nanoclusters containing even number of carbon atoms have large HOMO-LUMO gaps and IPs, whereas the nanoclusters containing even number of carbon atoms have small EAs. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA). The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in the experiments.

Quantum Computation by Optically Coupled Steady Atoms/Quantum-Dots Inside a Quantum Cavity

NASA Technical Reports Server (NTRS)

Pradhan, P.; Wang, K. L.; Roychowdhury, V. P.; Anantram, M. P.; Mor, T.; Saini, Subhash (Technical Monitor)

1999-01-01

We present a model for quantum computation using $n$ steady 3-level atoms kept inside a quantum cavity, or using $n$ quantum-dots (QDs) kept inside a quantum cavity. In this model one external laser is pointed towards all the atoms/QDs, and $n$ pairs of electrodes are addressing the atoms/QDs, so that each atom is addressed by one pair. The energy levels of each atom/QD are controlled by an external Stark field given to the atom/QD by its external pair of electrodes. Transition between two energy levels of an individual atom/ QD are controlled by the voltage on its electrodes, and by the external laser. Interactions between two atoms/ QDs are performed with the additional help of the cavity mode (using on-resonance condition). Laser frequency, cavity frequency, and energy levels are far off-resonance most of the time, and they are brought to the resonance (using the Stark effect) only at the time of operations. Steps for a controlled-NOT gate between any two atoms/QDs have been described for this model. Our model demands some challenging technological efforts, such as manufacturing single-electron QDs inside a cavity. However, it promises big advantages over other existing models which are currently implemented, and might enable a much easier scale-up, to compute with many more qubits.

Magnetic properties of Mg12O12 nanocage doped with transition metal atoms (Mn, Fe, Co and Ni): DFT study

NASA Astrophysics Data System (ADS)

Javan, Masoud Bezi

2015-07-01

Binding energy of the Mg12O12 nanocage doped with transition metals (TM=Mn, Fe, Co and Ni) in endohedrally, exohedrally and substitutionally forms were studied using density functional theory with the generalized gradient approximation exchange-correlation functional along 6 different paths inside and outside of the Mg12O12 nanocage. The most stable structures were determined with full geometry optimization near the minimum of the binding energy curves of all the examined paths inside and outside of the Mg12O12 nanocage. The results reveal that for all stable structures, the Ni atom has a larger binding energy than the other TM atoms. It is also found that for all complexes additional peaks contributed by TM-3d, 4s and 4p states appear in the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) gap of the host MgO cluster. The mid-gap states are mainly due to the hybridization between TM-3d, 4s and 4p orbitals and the cage π orbitals. The magnetic moment of the endohedrally doped TM atoms in the Mg12O12 are preserved to some extent due to the interaction between the TM and Mg12O12 nanocage, in contrast to the completely quenched magnetic moment of the Fe and Ni atoms in the Mg11(TM)O12 complexes. Furthermore, charge population analysis shows that charge transfer occurs from TM atom to the cage for endohedrally and substitutionally doping.

Analysis of Surface and Bulk Behavior in Ni-Pd Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Noebe, Rondald D.

2003-01-01

The most salient features of the surface structure and bulk behavior of Ni-Pd alloys have been studied using the BFS method for alloys. Large-scale atomistic simulations were performed to investigate surface segregation profiles as a function of temperature, crystal face, and composition. Pd enrichment of the first layer was observed in (111) and (100) surfaces, and enrichment of the top two layers occurred for (110) surfaces. In all cases, the segregation profile shows alternate planes enriched and depleted in Pd. In addition, the phase structure of bulk Ni-Pd alloys as a function of temperature and composition was studied. A weak ordering tendency was observed at low temperatures, which helps explain the compositional oscillations in the segregation profiles. Finally, based on atom-by-atom static energy calculations, a comprehensive explanation for the observed surface and bulk features will be presented in terms of competing chemical and strain energy effects.

Nuclear energy in postwar Japan and anti-nuclear movements in the 1950s.

PubMed

Yamazaki, Masakatsu

2009-01-01

The atomic bombings of Hiroshima and Nagasaki in August 1945 revealed the most destructive power to-date of man-made weapons. Their impact was so great that Japanese scientists thought that a bigger disaster could be prevented only if war was abolished. Thus they welcomed the international control of atomic energy. It was, however, only after the occupation that the Japanese general public began to learn about the horror of these atomic disasters due to the censorship imposed by the occupational forces. The hydrogen bomb test by the US in the Bikini atoll on March 1, 1954 renewed fears of nuclear weapons. The crew of a Japanese fishing vessel, the "Daigo Fukuryu Maru" (Lucky Dragon No. 5) suffered from exposure to radiation from the test. Even after the incident the US did not stop nuclear tests which continued to radioactively contaminate fish and rains in Japan. As a result, the petition movement for the ban of nuclear trials suddenly spread all over the country. By the summer of 1955 the number of the signatures grew to more than one third of Japan's population at the time. Under the strong influence of anti-nuclear Japanese public opinion the Science Council of Japan announced the so-called three principles of atomic energy: "openness," "democracy," and "independence" to ensure atomic energy was used for peaceful uses only. These principles were included in the Atomic Energy Basic Law established in December 1955. With this law, military uses of nuclear energy were strictly forbidden.

[Nuclear energy and environment: review of the IAEA environmental projects].

PubMed

Fesenko, S; Fogt, G

2012-01-01

The review of the environmental projects of the International Atomic Energy Agency is presented. Basic IAEA documents intended to protect humans and the Environment are considered and their main features are discussed. Some challenging issues in the area of protection of the Environment and man, including the impact of nuclear facilities on the environment, radioactive waste management, and remediation of the areas affected by radiological accidents, nuclear testing and sites of nuclear facilities are also discussed. The need to maintain the existing knowledge in radioecology and protection of the environment is emphasised.

Computing many-body wave functions with guaranteed precision: the first-order Møller-Plesset wave function for the ground state of helium atom.

PubMed

Bischoff, Florian A; Harrison, Robert J; Valeev, Edward F

2012-09-14

We present an approach to compute accurate correlation energies for atoms and molecules using an adaptive discontinuous spectral-element multiresolution representation for the two-electron wave function. Because of the exponential storage complexity of the spectral-element representation with the number of dimensions, a brute-force computation of two-electron (six-dimensional) wave functions with high precision was not practical. To overcome the key storage bottlenecks we utilized (1) a low-rank tensor approximation (specifically, the singular value decomposition) to compress the wave function, and (2) explicitly correlated R12-type terms in the wave function to regularize the Coulomb electron-electron singularities of the Hamiltonian. All operations necessary to solve the Schrödinger equation were expressed so that the reconstruction of the full-rank form of the wave function is never necessary. Numerical performance of the method was highlighted by computing the first-order Møller-Plesset wave function of a helium atom. The computed second-order Møller-Plesset energy is precise to ~2 microhartrees, which is at the precision limit of the existing general atomic-orbital-based approaches. Our approach does not assume special geometric symmetries, hence application to molecules is straightforward.

Ab initio local-energy and local-stress analysis of tensile behaviours of tilt grain boundaries in Al and Cu

NASA Astrophysics Data System (ADS)

Wang, Hao; Kohyama, Masanori; Tanaka, Shingo; Shiihara, Yoshinori

2017-01-01

Tensile deformation and failure of Σ9 tilt grain boundaries (GBs) in Al and Cu have been examined by first-principles tensile tests (FPTTs). Local-energy and local-stress schemes were applied to clarify the variations of local energies and local hydrostatic stresses for all atoms during the deformation process. The GBs in Al and Cu exhibited quite different tensile behaviours in the FPTTs, despite their similar initial configurations. For the Al GB, there are two stages of deformation before failure. In the first stage, the back bonds of the interfacial bonds are mainly stretched, due to special high strength of the interfacial reconstructed bonds. In the second stage, the interfacial bonds begin to be significantly stretched due to high concentrated stresses, while stretching of the back bonds is suppressed. The atoms at the interfacial, back and bulk bonds have very different variations of local energies and local stresses during each stage, because the behaviour of each atom is significantly dependent on each local structural change due to the high sensitivity of sp electrons to the local environment in Al. The Cu GB has much higher tensile strength, and a natural introduction of stacking faults (SFs) occurs via the {111}< 112> shear slip in the bulk regions between the interfaces before the maximum stress is reached. This is caused by the smaller SF energy and lower ideal shear strength of Cu than Al, and is triggered by highly accumulated local energies and stress at the interface atoms. The local-energy distribution around the SF is consistent with the previous theoretical estimation. After the introduction of the SF, the local energies and stresses of all the atoms in the Cu GB supercell tend to become similar to each other during the tensile process, in contrast to the inhomogeneity in the Al GB. The origins of the different tensile behaviours observed for Al and Cu GBs are discussed with respect to the different bonding natures of Al and Cu, which are dominated by three sp valence electrons per atom for Al and by fully occupied d bands and s electrons for Cu.

Hydrogen-impurity complexes in III V semiconductors

NASA Astrophysics Data System (ADS)

Ulrici, W.

2004-12-01

This review summarizes the presently available knowledge concerning hydrogen-impurity complexes in III-V compounds. The impurities form shallow acceptors on group III sites (Be, Zn, Cd) and on group V sites (C, Si, Ge) as well as shallow donors on group V sites (S, Se, Te) and on group III sites (Si, Sn). These complexes are mainly revealed by their hydrogen stretching modes. Therefore, nearly all information about their structure and dynamic properties is derived from vibrational spectroscopy. The complexes of shallow impurities with hydrogen have been most extensively investigated in GaAs, GaP and InP. This holds also for Mg-H in GaN. The complexes exhibit a different microscopic structure, which is discussed in detail. The isoelectronic impurity nitrogen, complexed with one hydrogen atom, is investigated in detail in GaAs and GaP. Those complexes can exist in different charge states. The experimental results such as vibrational frequencies, the microscopic structure and the activation energy for reorientation for many of these complexes are in very good agreement with results of ab initio calculations. Different types of oxygen-hydrogen complexes in GaAs and GaP are described, with one hydrogen atom or two hydrogen atoms bonded to oxygen. Three of these complexes in GaAs were found to be electrically active.

Interfacial metal and antibody recognition.

PubMed

Zhou, Tongqing; Hamer, Dean H; Hendrickson, Wayne A; Sattentau, Quentin J; Kwong, Peter D

2005-10-11

The unique ligation properties of metal ions are widely exploited by proteins, with approximately one-third of all proteins estimated to be metalloproteins. Although antibodies use various mechanisms for recognition, to our knowledge, none has ever been characterized that uses an interfacial metal. We previously described a family of CD4-reactive antibodies, the archetype being Q425. CD4:Q425 engagement does not interfere with CD4:HIV-1 gp120 envelope glycoprotein binding, but it blocks subsequent steps required for viral entry. Here, we use surface-plasmon resonance to show that Q425 requires calcium for recognition of CD4. Specifically, Q425 binding of calcium resulted in a 55,000-fold enhancement in affinity for CD4. X-ray crystallographic analyses of Q425 in the presence of Ca(2+), Ba(2+), or EDTA revealed an exposed metal-binding site, partially coordinated by five atoms contributed from four antibody complementarity-determining regions. The results suggest that Q425 recognition of CD4 involves direct ligation of antigen by the Q425-held calcium, with calcium binding each ligating atom of CD4 with approximately 1.5 kcal/mol of binding energy. This energetic contribution, which is greater than that from a typical protein atom, demonstrates how interfacial metal ligation can play a unique role in antigen recognition.

Interfacial metal and antibody recognition

PubMed Central

Zhou, Tongqing; Hamer, Dean H.; Hendrickson, Wayne A.; Sattentau, Quentin J.; Kwong, Peter D.

2005-01-01

The unique ligation properties of metal ions are widely exploited by proteins, with approximately one-third of all proteins estimated to be metalloproteins. Although antibodies use various mechanisms for recognition, to our knowledge, none has ever been characterized that uses an interfacial metal. We previously described a family of CD4-reactive antibodies, the archetype being Q425. CD4:Q425 engagement does not interfere with CD4:HIV-1 gp120 envelope glycoprotein binding, but it blocks subsequent steps required for viral entry. Here, we use surface-plasmon resonance to show that Q425 requires calcium for recognition of CD4. Specifically, Q425 binding of calcium resulted in a 55,000-fold enhancement in affinity for CD4. X-ray crystallographic analyses of Q425 in the presence of Ca2+, Ba2+, or EDTA revealed an exposed metal-binding site, partially coordinated by five atoms contributed from four antibody complementarity-determining regions. The results suggest that Q425 recognition of CD4 involves direct ligation of antigen by the Q425-held calcium, with calcium binding each ligating atom of CD4 with ≈1.5 kcal/mol of binding energy. This energetic contribution, which is greater than that from a typical protein atom, demonstrates how interfacial metal ligation can play a unique role in antigen recognition. PMID:16195378

Universal aspects of brittle fracture, adhesion, and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Ferrante, John; Smith, John R.

1989-01-01

This universal relation between binding energy and interatomic separation was originally discovered for adhesion at bimetallic interfaces involving the simple metals Al, Zn, Mg, and Na. It is shown here that the same universal relation extends to adhesion at transition-metal interfaces. Adhesive energies have been computed for the low-index interfaces of Al, Ni, Cu, Ag, Fe, and W, using the equivalent-crystal theory (ECT) and keeping the atoms in each semiinfinite slab fixed rigidly in their equilibrium positions. These adhesive energy curves can be scaled onto each other and onto the universal adhesion curve. The effect of tip shape on the adhesive forces in the atomic-force microscope (AFM) is studied by computing energies and forces using the ECT. While the details of the energy-distance and force-distance curves are sensitive to tip shape, all of these curves can be scaled onto the universal adhesion curve.

Beam shaping assembly optimization for (7)Li(p,n)(7)Be accelerator based BNCT.

PubMed

Minsky, D M; Kreiner, A J

2014-06-01

Within the framework of accelerator-based BNCT, a project to develop a folded Tandem-ElectroStatic-Quadrupole accelerator is under way at the Atomic Energy Commission of Argentina. The proposed accelerator is conceived to deliver a proton beam of 30mA at about 2.5MeV. In this work we explore a Beam Shaping Assembly (BSA) design based on the (7)Li(p,n)(7)Be neutron production reaction to obtain neutron beams to treat deep seated tumors. © 2013 Elsevier Ltd. All rights reserved.

Hyperfine excitation of CH in collisions with atomic and molecular hydrogen

NASA Astrophysics Data System (ADS)

Dagdigian, Paul J.

2018-04-01

We investigate here the excitation of methylidene (CH) induced by collisions with atomic and molecular hydrogen (H and H2). The hyperfine-resolved rate coefficients were obtained from close coupling nuclear-spin-free scattering calculations. The calculations are based upon recent, high-accuracy calculations of the CH(X2Π)-H(2S) and CH(X2Π)-H2 potential energy surfaces. Cross-sections and rate coefficients for collisions with atomic H, para-H2, and ortho-H2 were computed for all transitions between the 32 hyperfine levels for CH(X2Π) involving the n ≤ 4 rotational levels for temperatures between 10 and 300 K. These rate coefficients should significantly aid in the interpretation of astronomical observations of CH spectra. As a first application, the excitation of CH is simulated for conditions in typical molecular clouds.

10 CFR 810.4 - Communications.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Communications. 810.4 Section 810.4 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.4 Communications. (a) All communications concerning the regulations in this part should be addressed to: U.S. Department of Energy, Washington, DC...

10 CFR 810.4 - Communications.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Communications. 810.4 Section 810.4 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.4 Communications. (a) All communications concerning the regulations in this part should be addressed to: U.S. Department of Energy, Washington, DC...

Ultrafast triggered transient energy storage by atomic layer deposition into porous silicon for integrated transient electronics

NASA Astrophysics Data System (ADS)

Douglas, Anna; Muralidharan, Nitin; Carter, Rachel; Share, Keith; Pint, Cary L.

2016-03-01

Here we demonstrate the first on-chip silicon-integrated rechargeable transient power source based on atomic layer deposition (ALD) coating of vanadium oxide (VOx) into porous silicon. A stable specific capacitance above 20 F g-1 is achieved until the device is triggered with alkaline solutions. Due to the rational design of the active VOx coating enabled by ALD, transience occurs through a rapid disabling step that occurs within seconds, followed by full dissolution of all active materials within 30 minutes of the initial trigger. This work demonstrates how engineered materials for energy storage can provide a basis for next-generation transient systems and highlights porous silicon as a versatile scaffold to integrate transient energy storage into transient electronics.Here we demonstrate the first on-chip silicon-integrated rechargeable transient power source based on atomic layer deposition (ALD) coating of vanadium oxide (VOx) into porous silicon. A stable specific capacitance above 20 F g-1 is achieved until the device is triggered with alkaline solutions. Due to the rational design of the active VOx coating enabled by ALD, transience occurs through a rapid disabling step that occurs within seconds, followed by full dissolution of all active materials within 30 minutes of the initial trigger. This work demonstrates how engineered materials for energy storage can provide a basis for next-generation transient systems and highlights porous silicon as a versatile scaffold to integrate transient energy storage into transient electronics. Electronic supplementary information (ESI) available: (i) Experimental details for ALD and material fabrication, ellipsometry film thickness, preparation of gel electrolyte and separator, details for electrochemical measurements, HRTEM image of VOx coated porous silicon, Raman spectroscopy for VOx as-deposited as well as annealed in air for 1 hour at 450 °C, SEM and transient behavior dissolution tests of uniformly coated VOx on porous silicon, dissolution tests for 0.1 M and 0.01 M NaOH trigger solutions, EIS analysis for VOx coated devices, and EDS compositional analysis of VOx. (ii) Video showing transient behavior of integrated VOx/porous silicon scaffolds. See DOI: 10.1039/c5nr09095d

Environmental knowledge and attitudes and behaviours towards energy consumption.

PubMed

Paço, Arminda; Lavrador, Tânia

2017-07-15

Numerous investigations have arisen in order to study and characterise environmentally friendly consumer profiles, with some authors applying the relationship between knowledge, attitudes and behaviour to this end. The present research approach, based upon the Theory of Reasoned Action (TRA), seeks to verify the existence of relationships between knowledge and attitudes and between knowledge and environmental behaviour. In this instance, data collection involved a questionnaire aimed at assessing the overall environmental knowledge of respondents as well as their attitudes and behaviours regarding energy issues (savings, consumption, interest, use). The results pointed to the lack of relationship between knowledge and attitudes, and between knowledge and behaviour whilst the relationship between attitudes and behaviour proved to be only weak. The results also found that males, older students and those studying Engineering and the Social and Human Sciences are those reporting higher levels of environmental knowledge. However, when it comes to attitudes and behaviours, females seem to display more awareness around these issues. Copyright © 2017 Elsevier Ltd. All rights reserved.

Model-based local density sharpening of cryo-EM maps

PubMed Central

Jakobi, Arjen J; Wilmanns, Matthias

2017-01-01

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

Quantization of Differences Between Atomic and Nuclear Rest Masses and Self-organization of Atoms and Nuclei

NASA Astrophysics Data System (ADS)

Gareev, F. A.; Zhidkova, I. E.

2007-03-01

We come to the conclusion that all atomic models based on either the Newton equation and the Kepler laws, or the Maxwell equations, or the Schrodinger and Dirac equations are in reasonable agreement with experimental data. We can only suspect that these equations are grounded on the same fundamental principle(s) which is (are) not known or these equations can be transformed into each other. We proposed a new mechanism of LENR: cooperative processes in the whole system nuclei + atoms + condensed matter - nuclear reactions in plasma - can occur at smaller threshold energies than the corresponding ones on free constituents. We were able to quantize phenomenologically the first time the differences between atomic and nuclear rest masses by the formula: δδM =n1/n2 X 0.0076294 (in MeV/ c^2), ni=1,2,3,.... Note that this quantization rule is justified for atoms and nuclei with different A, N and Z and the nuclei and atoms represent a coherent synchronized systems - a complex of coupled oscillators (resonators). The cooperative resonance synchronization mechanisms can explain how electron volt (atomic-) scale processes can induce and control nuclear MeV (nuclear-) scale processes and reactions., F.A. Gareev, I.E. Zhidkova, E-print arXiv Nucl-th/ 0610002 2006.

Dissipation of 'dark energy' by cortex in knowledge retrieval.

PubMed

Capolupo, Antonio; Freeman, Walter J; Vitiello, Giuseppe

2013-03-01

We have devised a thermodynamic model of cortical neurodynamics expressed at the classical level by neural networks and at the quantum level by dissipative quantum field theory. Our model is based on features in the spatial images of cortical activity newly revealed by high-density electrode arrays. We have incorporated the mechanism and necessity for so-called dark energy in knowledge retrieval. We have extended the model first using the Carnot cycle to define our measures for energy, entropy and temperature, and then using the Rankine cycle to incorporate criticality and phase transitions. We describe the dynamics of two interactive fields of neural activity that express knowledge, one at high and the other at low energy density, and the two operators that create and annihilate the fields. We postulate that the extremely high density of energy sequestered briefly in cortical activity patterns can account for the vividness, richness of associations, and emotional intensity of memories recalled by stimuli. Copyright © 2013 Elsevier B.V. All rights reserved.

Spectral artefacts post sputter-etching and how to cope with them - A case study of XPS on nitride-based coatings using monoatomic and cluster ion beams

NASA Astrophysics Data System (ADS)

Lewin, Erik; Counsell, Jonathan; Patscheider, Jörg

2018-06-01

The issue of artefacts due to sputter-etching has been investigated for a group of AlN-based thin film materials with varying thermodynamical stability. Stability of the materials was controlled by alloying AlN with the group 14 elements Si, Ge or Sn in two different concentrations. The coatings were sputter-etched with monoatomic Ar+ with energies between 0.2 and 4.0 keV to study the sensitivity of the materials for sputter damage. The use of Arn+ clusters to remove an oxidised surface layer was also evaluated for a selected sample. The spectra were compared to pristine spectra obtained after in-vacuo sample transfer from the synthesis chamber to the analysis instrument. It was found that the all samples were affected by high energy (4 keV) Ar+ ions to varying degrees. The determining factors for the amount of observed damage were found to be the materials' enthalpy of formation, where a threshold value seems to exist at approximately -1.25 eV/atom (∼-120 kJ/mol atoms). For each sample, the observed amount of damage was found to have a linear dependence to the energy deposited by the ion beam per volume removed material. Despite the occurrence of sputter-damage in all samples, etching settings that result in almost artefact-free spectral data were found; using either very low energy (i.e. 200 eV) monoatomic ions, or an appropriate combination of ion cluster size and energy. The present study underlines that analysis post sputter-etching must be carried out with an awareness of possible sputter-induced artefacts.

Ultrafast Coulomb explosion of a diiodomethane molecule induced by an X-ray free-electron laser pulse.

PubMed

Takanashi, Tsukasa; Nakamura, Kosuke; Kukk, Edwin; Motomura, Koji; Fukuzawa, Hironobu; Nagaya, Kiyonobu; Wada, Shin-Ichi; Kumagai, Yoshiaki; Iablonskyi, Denys; Ito, Yuta; Sakakibara, Yuta; You, Daehyun; Nishiyama, Toshiyuki; Asa, Kazuki; Sato, Yuhiro; Umemoto, Takayuki; Kariyazono, Kango; Ochiai, Kohei; Kanno, Manabu; Yamazaki, Kaoru; Kooser, Kuno; Nicolas, Christophe; Miron, Catalin; Asavei, Theodor; Neagu, Liviu; Schöffler, Markus; Kastirke, Gregor; Liu, Xiao-Jing; Rudenko, Artem; Owada, Shigeki; Katayama, Tetsuo; Togashi, Tadashi; Tono, Kensuke; Yabashi, Makina; Kono, Hirohiko; Ueda, Kiyoshi

2017-08-02

Coulomb explosion of diiodomethane CH 2 I 2 molecules irradiated by ultrashort and intense X-ray pulses from SACLA, the Japanese X-ray free electron laser facility, was investigated by multi-ion coincidence measurements and self-consistent charge density-functional-based tight-binding (SCC-DFTB) simulations. The diiodomethane molecule, containing two heavy-atom X-ray absorbing sites, exhibits a rather different charge generation and nuclear motion dynamics compared to iodomethane CH 3 I with only a single heavy atom, as studied earlier. We focus on charge creation and distribution in CH 2 I 2 in comparison to CH 3 I. The release of kinetic energy into atomic ion fragments is also studied by comparing SCC-DFTB simulations with the experiment. Compared to earlier simulations, several key enhancements are made, such as the introduction of a bond axis recoil model, where vibrational energy generated during charge creation processes induces only bond stretching or shrinking. We also propose an analytical Coulomb energy partition model to extract the essential mechanism of Coulomb explosion of molecules from the computed and the experimentally measured kinetic energies of fragment atomic ions by partitioning each pair Coulomb interaction energy into two ions of the pair under the constraint of momentum conservation. Effective internuclear distances assigned to individual fragment ions at the critical moment of the Coulomb explosion are then estimated from the average kinetic energies of the ions. We demonstrate, with good agreement between the experiment and the SCC-DFTB simulation, how the more heavily charged iodine fragments and their interplay define the characteristic features of the Coulomb explosion of CH 2 I 2 . The present study also confirms earlier findings concerning the magnitude of bond elongation in the ultrashort X-ray pulse duration, showing that structural damage to all but C-H bonds does not develop to a noticeable degree in the pulse length of ∼10 fs.

Permeability of two-dimensional graphene and hexagonal-boron nitride to hydrogen atom

NASA Astrophysics Data System (ADS)

Gupta, Varun; Kumar, Ankit; Ray, Nirat

2018-05-01

The permeability of atomic hydrogen in monolayer hexagonal Boron Nitride(h-BN) and graphene has been studied using first-principles density functional theory based simulations. For the specific cases of physisorption and chemisoroption, barrier heights are calculated using the nudged elastic band approach. We find that the barrier potential for physisorption through the ring is lower for graphene than h-BN. In the case of chemisorption, where the H atom passes through by making bonds with the atoms in the ring, the barrier potential for the graphene was found to be higher than that of h-BN. We conclude that the penetration of H atom with notable kinetic energy (<3eV) through physiosorption is more probable for graphene as compared to h-BN. Whereas through chemisorption, lower kinetic energy (>3eV) H-atoms have a higher chance to penetrate through h-BN than graphene.

A molecular modeling based method to predict elution behavior and binding patches of proteins in multimodal chromatography.

PubMed

Banerjee, Suvrajit; Parimal, Siddharth; Cramer, Steven M

2017-08-18

Multimodal (MM) chromatography provides a powerful means to enhance the selectivity of protein separations by taking advantage of multiple weak interactions that include electrostatic, hydrophobic and van der Waals interactions. In order to increase our understanding of such phenomena, a computationally efficient approach was developed that combines short molecular dynamics simulations and continuum solvent based coarse-grained free energy calculations in order to study the binding of proteins to Self Assembled Monolayers (SAM) presenting MM ligands. Using this method, the free energies of protein-MM SAM binding over a range of incident orientations of the protein can be determined. The resulting free energies were then examined to identify the more "strongly bound" orientations of different proteins with two multimodal surfaces. The overall free energy of protein-MM surface binding was then determined and correlated to retention factors from isocratic chromatography. This correlation, combined with analytical expressions from the literature, was then employed to predict protein gradient elution salt concentrations as well as selectivity reversals with different MM resin systems. Patches on protein surfaces that interacted strongly with MM surfaces were also identified by determining the frequency of heavy atom contacts with the atoms of the MM SAMs. A comparison of these patches to Electrostatic Potential and hydrophobicity maps indicated that while all of these patches contained significant positive charge, only the highest frequency sites also possessed hydrophobicity. The ability to identify key binding patches on proteins may have significant impact on process development for the separation of bioproduct related impurities. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Structural properties and diffusion processes of the Cu 3Au (0 0 1) surface

NASA Astrophysics Data System (ADS)

Wang, Fang; Zhang, Jian-Min; Zhang, Yan; Ji, Vincent

2010-09-01

The surface relaxation and surface energy of both the mixed AuCu and pure Cu terminated Cu 3Au (0 0 1) surfaces are simulated and calculated by using the modified analytical embedded-atom method. We find that the mixed AuCu termination is energetically preferred over the pure Cu termination thereby the mono-vacancy diffusion is also investigated in the topmost few layers of the mixed AuCu terminated Cu 3Au (0 0 1) surface. In the mixed AuCu terminated surface the relaxed Au atoms are raised above Cu atoms for 0.13 Å in the topmost layer. All the surface atoms displace outwards, this effect occurs in the first three layers and changes the first two inter-layer spacing. For mono-vacancy migration in the first layer, the migration energies of Au and Cu mono-vacancy via two-type in-plane displace: the nearest neighbor jump (NNJ) and the second nearest neighbor jump (2NNJ), are calculated and the results show that the NNJ requires a much lower energy than 2NNJ. For the evolution of the energy requirements for successive nearest neighbor jumps (SNNJ) along three different paths: circularity, zigzag and beeline, we find that the circularity path is preferred over the other two paths due to its minimum energy barriers and final energies. In the second layer, the NN jumps in intra- and inter-layer of the Cu mono-vacancy are investigated. The calculated energy barriers and final energies show that the vacancy prefer jump up to a proximate Cu site. This replacement between the Cu vacancy in the second layer and Cu atom in the first layer is remunerative for the Au atoms enrichment in the topmost layer.

Nanostructured Fe-Cr Alloys for Advanced Nuclear Energy Applications

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

Scattergood, Ronald O.

2016-04-26

We have completed research on the grain-size stabilization of model nanostructured Fe14Cr base alloys at high temperatures by the addition of non-equilibrium solutes. Fe14Cr base alloys are representative for nuclear reactor applications. The neutron flux in a nuclear reactor will generate He atoms that coalesce to form He bubbles. These can lead to premature failure of the reactor components, limiting their lifetime and increasing the cost and capacity for power generation. In order to mitigate such failures, Fe14Cr base alloys have been processed to contain very small nano-size oxide particles (less than 10 nm in size) that trap He atomsmore » and reduce bubble formation. Theoretical and experimental results indicate that the grain boundaries can also be very effective traps for He atoms and bubble formation. An optimum grain size will be less than 100 nm, ie., nanocrystalline alloys must be used. Powder metallurgy methods based on high-energy ball milling can produce Fe-Cr base nanocrystalline alloys that are suitable for nuclear energy applications. The problem with nanocrystalline alloys is that excess grain-boundary energy will cause grains to grow at higher temperatures and their propensity for He trapping will be lost. The nano-size oxide particles in current generation nuclear alloys provide some grain size stabilization by reducing grain-boundary mobility (Zener pinning – a kinetic effect). However the current mitigation strategy minimizing bubble formation is based primarily on He trapping by nano-size oxide particles. An alternate approach to nanoscale grain size stabilization has been proposed. This is based on the addition of small amounts of atoms that are large compared to the base alloy. At higher temperatures these will diffuse to the grain boundaries and will produce an equilibrium state for the grain size at higher temperatures (thermodynamic stabilization – an equilibrium effect). This would be preferred compared to a kinetic effect, which is not based on an equilibrium state. The PI and coworkers have developed thermodynamic-based models that can be used to select appropriate solute additions to Fe14Cr base alloys to achieve a contribution to grain-size stabilization and He bubble mitigation by the thermodynamic effect. All such models require approximations and the proposed research was aimed at alloy selection, processing and detailed atomic-level microstructure evaluations to establish the efficacy of the thermodynamic effect. The outcome of this research shows that appropriate alloy additions can produce a contribution from the thermodynamic stabilization effect. Furthermore, due to the oxygen typically present in nominally high purity elemental powders used for powder metallurgy processing, the optimum results obtained appeared as a synergistic combination of nano-size oxide particle pinning kinetic effect and the grain-boundary segregation thermodynamic effect.« less

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

PubMed Central

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

2010-01-01

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

Critical evaluation of dipolar, acid-base and charge interactions I. Electron displacement within and between molecules, liquids and semiconductors.

PubMed

Rosenholm, Jarl B

2017-09-01

Specific dipolar, acid-base and charge interactions involve electron displacements. For atoms, single bonds and molecules electron displacement is characterized by electronic potential, absolute hardness, electronegativity and electron gap. In addition, dissociation, bonding, atomization, formation, ionization, affinity and lattice enthalpies are required to quantify the electron displacement in solids. Semiconductors are characterized by valence and conduction band energies, electron gaps and average Fermi energies which in turn determine Galvani potentials of the bulk, space charge layer and surface states. Electron displacement due to interaction between (probe) molecules, liquids and solids are characterized by parameters such as Hamaker constant, solubility parameter, exchange energy density, surface tension, work of adhesion and immersion. They are determined from permittivity, refractive index, enthalpy of vaporization, molar volume, surface pressure and contact angle. Moreover, acidic and basic probes may form adducts which are adsorbed on target substrates in order to establish an indirect measure of polarity, acidity, basicity or hydrogen bonding. Acidic acceptor numbers (AN), basic donor numbers (DN), acidic and basic "electrostatic" (E) and "covalent" (C) parameters determined by enthalpy of adduct formation are considered as general acid-base scales. However, the formal grounds for assignments as dispersive, Lifshitz-van der Waals, polar, acid, base and hydrogen bond interactions are inconsistent. Although correlations are found no of the parameters are mutually fully compatible and moreover the enthalpies of acid-base interaction do not correspond to free energies. In this review the foundations of different acid-base parameters relating to electron displacement within and between (probe) molecules, liquids and (semiconducting) solids are thoroughly investigated and their mutual relationships are evaluated. Copyright © 2017 Elsevier B.V. All rights reserved.

Collisional quenching of atoms and molecules on spacecraft thermal protection surfaces

NASA Technical Reports Server (NTRS)

Marinelli, W. J.; Green, B. D.

1988-01-01

Preliminary results of a research program to determine energy partitioning in spacecraft thermal protection materials due to atom recombination at the gas-surface interface are presented. The primary focus of the research is to understand the catalytic processes which determine heat loading on Shuttle, Aeroassisted OTV, and NASP thermal protection surfaces in nonequilibrium flight regimes. Highly sensitive laser diagnostics based on laser-induced fluorescence and resonantly-enhanced multiphoton ionization spectroscopy are used to detect atoms and metastable molecules. At low temperatures, a discharge flow reactor is employed to measure deactivation/recombination coefficients for O-atoms, N-atoms, and O2. Detection methods are presented for measuring O-atoms, O2 and N2, and results for deactivation of O2 and O-atoms on reaction-cured glass and Ni surfaces. Both atom recombination and metastable product formation are examined. Radio-frequency discharges are used to produce highly dissociated beams of atomic species at energies characteristic of the surface temperature. Auger electron spectroscopy is employed as a diagnostic of surface composition in order to accurately define and control measurement conditions.

H(D) → D(H) + Cu(111) collision system: Molecular dynamics study of surface temperature effects

PubMed Central

Vurdu, Can D.; Güvenç, Ziya B.

2011-01-01

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London–Eyring–Polanyi–Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. PMID:21528959

H(D) → D(H) + Cu(111) collision system: molecular dynamics study of surface temperature effects.

PubMed

Vurdu, Can D; Güvenç, Ziya B

2011-04-28

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London-Eyring-Polanyi-Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures.

Atomic adsorption on pristine graphene along the Periodic Table of Elements - From PBE to non-local functionals

NASA Astrophysics Data System (ADS)

Pašti, Igor A.; Jovanović, Aleksandar; Dobrota, Ana S.; Mentus, Slavko V.; Johansson, Börje; Skorodumova, Natalia V.

2018-04-01

The understanding of atomic adsorption on graphene is of high importance for many advanced technologies. Here we present a complete database of the atomic adsorption energies for the elements of the Periodic Table up to the atomic number 86 (excluding lanthanides) on pristine graphene. The energies have been calculated using the projector augmented wave (PAW) method with PBE, long-range dispersion interaction corrected PBE (PBE+D2, PBE+D3) as well as non-local vdW-DF2 approach. The inclusion of dispersion interactions leads to an exothermic adsorption for all the investigated elements. Dispersion interactions are found to be of particular importance for the adsorption of low atomic weight earth alkaline metals, coinage and s-metals (11th and 12th groups), high atomic weight p-elements and noble gases. We discuss the observed adsorption trends along the groups and rows of the Periodic Table as well some computational aspects of modelling atomic adsorption on graphene.

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.

10 CFR 810.4 - Communications.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Communications. 810.4 Section 810.4 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.4 Communications. (a) All communications... and Nonproliferation. Telephone: (202) 586-2331. (b) Communications also may be delivered to the...

10 CFR 810.4 - Communications.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Communications. 810.4 Section 810.4 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.4 Communications. (a) All communications... and Nonproliferation. Telephone: (202) 586-2331. (b) Communications also may be delivered to the...

10 CFR 810.4 - Communications.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Communications. 810.4 Section 810.4 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.4 Communications. (a) All communications... and Nonproliferation. Telephone: (202) 586-2331. (b) Communications also may be delivered to the...

Above-threshold scattering about a Feshbach resonance for ultracold atoms in an optical collider.

PubMed

Horvath, Milena S J; Thomas, Ryan; Tiesinga, Eite; Deb, Amita B; Kjærgaard, Niels

2017-09-06

Ultracold atomic gases have realized numerous paradigms of condensed matter physics, where control over interactions has crucially been afforded by tunable Feshbach resonances. So far, the characterization of these Feshbach resonances has almost exclusively relied on experiments in the threshold regime near zero energy. Here, we use a laser-based collider to probe a narrow magnetic Feshbach resonance of rubidium above threshold. By measuring the overall atomic loss from colliding clouds as a function of magnetic field, we track the energy-dependent resonance position. At higher energy, our collider scheme broadens the loss feature, making the identification of the narrow resonance challenging. However, we observe that the collisions give rise to shifts in the center-of-mass positions of outgoing clouds. The shifts cross zero at the resonance and this allows us to accurately determine its location well above threshold. Our inferred resonance positions are in excellent agreement with theory.Studies on energy-dependent scattering of ultracold atoms were previously carried out near zero collision energies. Here, the authors observe a magnetic Feshbach resonance in ultracold Rb collisions for above-threshold energies and their method can also be used to detect higher partial wave resonances.

78 FR 56944 - Strata Energy, Inc. (Ross In Situ Recovery Uranium Project); Notice of Atomic Safety and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-16

..., Inc. (Ross In Situ Recovery Uranium Project); Notice of Atomic Safety and Licensing Board Reconstitution Pursuant to 10 CFR 2.313(c) and 2.321(b), the Atomic Safety and Licensing Board (Board) in the... Craig M. White to serve on the Board in place of Administrative Judge Kenneth L. Mossman. All...

ISPE: A knowledge-based system for fluidization studies

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

Reddy, S.

1991-01-01

Chemical engineers use mathematical simulators to design, model, optimize and refine various engineering plants/processes. This procedure requires the following steps: (1) preparation of an input data file according to the format required by the target simulator; (2) excecuting the simulation; and (3) analyzing the results of the simulation to determine if all specified goals'' are satisfied. If the goals are not met, the input data file must be modified and the simulation repeated. This multistep process is continued until satisfactory results are obtained. This research was undertaken to develop a knowledge based system, IPSE (Intelligent Process Simulation Environment), that canmore » enhance the productivity of chemical engineers/modelers by serving as an intelligent assistant to perform a variety tasks related to process simulation. ASPEN, a widely used simulator by the US Department of Energy (DOE) at Morgantown Energy Technology Center (METC) was selected as the target process simulator in the project. IPSE, written in the C language, was developed using a number of knowledge-based programming paradigms: object-oriented knowledge representation that uses inheritance and methods, rulebased inferencing (includes processing and propagation of probabilistic information) and data-driven programming using demons. It was implemented using the knowledge based environment LASER. The relationship of IPSE with the user, ASPEN, LASER and the C language is shown in Figure 1.« less

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

PubMed

Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

2016-06-30

In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level

PubMed Central

Olsson, Martin A.; Söderhjelm, Pär

2016-01-01

In this article, the convergence of quantum mechanical (QM) free‐energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa‐acid deep‐cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158–224 atoms). We use single‐step exponential averaging (ssEA) and the non‐Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi‐empirical PM6‐DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free‐energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27117350

Computer Model Of Fragmentation Of Atomic Nuclei

NASA Technical Reports Server (NTRS)

Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.

1995-01-01

High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.

Energetic ion bombardment of Ag surfaces by C60+ and Ga+ projectiles.

PubMed

Sun, Shixin; Szakal, Christopher; Winograd, Nicholas; Wucher, Andreas

2005-10-01

The ion bombardment-induced release of particles from a metal surface is investigated using energetic fullerene cluster ions as projectiles. The total sputter yield as well as partial yields of neutral and charged monomers and clusters leaving the surface are measured and compared with corresponding data obtained with atomic projectile ions of similar impact kinetic energy. It is found that all yields are enhanced by about one order of magnitude under bombardment with the C60+ cluster projectiles compared with Ga+ ions. In contrast, the electronic excitation processes determining the secondary ion formation probability are unaffected. The kinetic energy spectra of sputtered particles exhibit characteristic differences which reflect the largely different nature of the sputtering process for both types of projectiles. In particular, it is found that under C60+ impact (1) the energy spectrum of sputtered atoms peaks at significantly lower kinetic energies than for Ga+ bombardment and (2) the velocity spectra of monomers and dimers are virtually identical, a finding which is in pronounced contrast to all published data obtained for atomic projectiles. The experimental findings are in reasonable agreement with recent molecular dynamics simulations.

The AME2016 atomic mass evaluation (II). Tables, graphs and references

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

Wang, Meng; Audi, G.; Kondev, F. G.

This paper is the second part of the new evaluation of atomic masses, Ame2016. Using least-squares adjustments to all evaluated and accepted experimental data, described in Part I, we derive tables with numerical values and graphs to replace those given in Ame2012. The first table lists the recommended atomic mass values and their uncertainties. It is followed by a table of the influences of data on primary nuclides, a table of various reaction and decay energies, and finally, a series of graphs of separation and decay energies. The last section of this paper lists all references of the input datamore » used in the Ame2016 and the Nubase2016 evaluations (first paper in this issue). Amdc: http://amdc.impcas.ac.cn/« less

DFT study of conformational and vibrational characteristics of 2-(2-hydroxyphenyl)benzothiazole molecule.

PubMed

Pandey, Urmila; Srivastava, Mayuri; Singh, R P; Yadav, R A

2014-08-14

The conformational and IR and Raman spectral studies of 2-(2-hydroxyphenyl)benzothiazole have been carried out by using the DFT method at the B3LYP/6-311++G(**) level. The detailed vibrational assignments have been done on the basis of calculated potential energy distributions. Comparative studies of molecular geometries, atomic charges and vibrational fundamentals of all the conformers have been made. There are four possible conformers for this molecule. The optimized geometrical parameters obtained by B3LYP/6-311++G(**) method showed good agreement with the experimental X-ray data. The atomic polar tensor (APT) charges, Mulliken atomic charges, natural bond orbital (NBO) analysis and HOMO-LUMO energy gap of HBT and its conformers were also computed. Copyright © 2014 Elsevier B.V. All rights reserved.

Dark Matter Detection Using Helium Evaporation and Field Ionization

NASA Astrophysics Data System (ADS)

Maris, Humphrey J.; Seidel, George M.; Stein, Derek

2017-11-01

We describe a method for dark matter detection based on the evaporation of helium atoms from a cold surface and their subsequent detection using field ionization. When a dark matter particle scatters off a nucleus of the target material, elementary excitations (phonons or rotons) are produced. Excitations which have an energy greater than the binding energy of helium to the surface can result in the evaporation of helium atoms. We propose to detect these atoms by ionizing them in a strong electric field. Because the binding energy of helium to surfaces can be below 1 meV, this detection scheme opens up new possibilities for the detection of dark matter particles in a mass range down to 1 MeV /c2 .

Dark Matter Detection Using Helium Evaporation and Field Ionization.

PubMed

Maris, Humphrey J; Seidel, George M; Stein, Derek

2017-11-03

We describe a method for dark matter detection based on the evaporation of helium atoms from a cold surface and their subsequent detection using field ionization. When a dark matter particle scatters off a nucleus of the target material, elementary excitations (phonons or rotons) are produced. Excitations which have an energy greater than the binding energy of helium to the surface can result in the evaporation of helium atoms. We propose to detect these atoms by ionizing them in a strong electric field. Because the binding energy of helium to surfaces can be below 1 meV, this detection scheme opens up new possibilities for the detection of dark matter particles in a mass range down to 1  MeV/c^{2}.

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

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

PubMed Central

Frappier, Vincent; Najmanovich, Rafael J.

2014-01-01

Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. PMID:24762569

Last results of DIRAC experiment on study hadronic hydrogen-like atoms at PS CERN

NASA Astrophysics Data System (ADS)

Afanasyev, Leonid

2016-04-01

Results on study the hydrogen-like atoms consisting of charged pions and Kaons are presented. The first measurement of K+ π and Kπ+ atoms lifetime was fulfilled basing on identification of 178 ± 49 Kπ pairs from the atom breakup. The measured lifetime is τ = (2.5-1.8+3.0) fs. This value is dictated by properties of the strong πK-interaction at low energy, namely S-wave πK scattering length. The first experimental value of the isospin-odd combination of S-wave πK scattering length was obtained | a0- | =1/3 |a/2 -a3/2 | = (0.11-0.04+0.09) Mπ-1 (ai for isospin I). A dedicated experiment with π+ π atoms allows further study of these already observed atoms. The preliminary results on observation of the long-lived (metastable) states of π+ π atoms are presented. The observation of long-lived states opens the possibility to measure the energy difference between ns and np states - the Lamb shift.

High translational energy release in H2 (D2) associative desorption from H (D) chemisorbed on C(0001).

PubMed

Baouche, S; Gamborg, G; Petrunin, V V; Luntz, A C; Baurichter, A; Hornekaer, L

2006-08-28

Highly energetic translational energy distributions are reported for hydrogen and deuterium molecules desorbing associatively from the atomic chemisorption states on highly oriented pyrolytic graphite (HOPG). Laser assisted associative desorption is used to measure the time of flight of molecules desorbing from a hydrogen (deuterium) saturated HOPG surface produced by atomic exposure from a thermal atom source at around 2100 K. The translational energy distributions normal to the surface are very broad, from approximately 0.5 to approximately 3 eV, with a peak at approximately 1.3 eV. The highest translational energy measured is close to the theoretically predicted barrier height. The angular distribution of the desorbing molecules is sharply peaked along the surface normal and is consistent with thermal broadening contributing to energy release parallel to the surface. All results are in qualitative agreement with recent density functional theory calculations suggesting a lowest energy para-type dimer recombination path.

Simple method for determining binding energies of fullerene and complex atomic negative ions

NASA Astrophysics Data System (ADS)

Felfli, Zineb; Msezane, Alfred

2017-04-01

A robust potential which embeds fully the vital core polarization interaction has been used in the Regge pole method to explore low-energy electron scattering from C60, Eu and Nb through the total cross sections (TCSs) calculations. From the characteristic dramatically sharp resonances in the TCSs manifesting negative ion formation in these systems, we extracted the binding energies for the C60, Euand Nbanions they are found to be in outstanding agreement with the measured electron affinities of C60, Eu and Nb. Common among these considered systems, including the standard atomic Au is the formation of their ground state negative ions at the second Ramsauer-Townsend (R-T) minima of their TCSs. Indeed, this is a signature of all the fullerenes and complex atoms considered thus far. Shape resonances, R-T minima and binding energies of the resultant anions are presented. This work was supported by U.S. DOE, Basic Energy Sciences, Office of Energy Research.

Selected bibliography on atomic collisions: Data collections, bibliographies, review articles, books, and papers of particular tutorial value

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

McDaniel, E.W.; Flannery, M.R.; Thomas, E.W.

This bibliography deals mainly with binary and ternary collisions involving electrons, photons, and heavy particles (i.e., atoms, molecules, and ions). The energy range covered for each kind of collision is such that the interactions might be described as electronic, atomic, or chemical--higher-energy collisions involving nuclear forces are not treated. Also covered are particle and photon impact on surfaces, the passage of particles and radiation through bulk matter, and transport phenomena in gases. Practically all of the references cited are data compilations, other bibliographies, review articles, or books. The main objective is to provide easy access to atomic collision data, althoughmore » some references are included principally for their tutorial value.« less

Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition.

PubMed

Paci, Emanuele; Vendruscolo, Michele; Karplus, Martin

2002-12-01

Do Gō-type model potentials provide a valid approach for studying protein folding? They have been widely used for this purpose because of their simplicity and the speed of simulations based on their use. The essential assumption in such models is that only contact interactions existing in the native state determine the energy surface of a polypeptide chain, even for non-native configurations sampled along folding trajectories. Here we use an all-atom molecular mechanics energy function to investigate the adequacy of Gō-type potentials. We show that, although the contact approximation is accurate, non-native contributions to the energy can be significant. The assumed relation between residue-residue interaction energies and the number of contacts between them is found to be only approximate. By contrast, individual residue energies correlate very well with the number of contacts. The results demonstrate that models based on the latter should give meaningful results (e.g., as used to interpret phi values), whereas those that depend on the former are only qualitative, at best.

Low-energy electron holographic imaging of individual tobacco mosaic virions

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

Longchamp, Jean-Nicolas, E-mail: longchamp@physik.uzh.ch; Latychevskaia, Tatiana; Escher, Conrad

2015-09-28

Modern structural biology relies on Nuclear Magnetic Resonance (NMR), X-ray crystallography, and cryo-electron microscopy for gaining information on biomolecules at nanometer, sub-nanometer, or atomic resolution. All these methods, however, require averaging over a vast ensemble of entities, and hence knowledge on the conformational landscape of an individual particle is lost. Unfortunately, there are now strong indications that even X-ray free electron lasers will not be able to image individual molecules but will require nanocrystal samples. Here, we show that non-destructive structural biology of single particles has now become possible by means of low-energy electron holography. As an example, individual tobaccomore » mosaic virions deposited on ultraclean freestanding graphene are imaged at 1 nm resolution revealing structural details arising from the helical arrangement of the outer protein shell of the virus. Since low-energy electron holography is a lens-less technique and since electrons with a deBroglie wavelength of approximately 1 Å do not impose radiation damage to biomolecules, the method has the potential for Angstrom resolution imaging of single biomolecules.« less

Fourier series of atomic radial distribution functions: A molecular fingerprint for machine learning models of quantum chemical properties

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

von Lilienfeld, O. Anatole; Ramakrishnan, Raghunathan; Rupp, Matthias

We introduce a fingerprint representation of molecules based on a Fourier series of atomic radial distribution functions. This fingerprint is unique (except for chirality), continuous, and differentiable with respect to atomic coordinates and nuclear charges. It is invariant with respect to translation, rotation, and nuclear permutation, and requires no preconceived knowledge about chemical bonding, topology, or electronic orbitals. As such, it meets many important criteria for a good molecular representation, suggesting its usefulness for machine learning models of molecular properties trained across chemical compound space. To assess the performance of this new descriptor, we have trained machine learning models ofmore » molecular enthalpies of atomization for training sets with up to 10 k organic molecules, drawn at random from a published set of 134 k organic molecules with an average atomization enthalpy of over 1770 kcal/mol. We validate the descriptor on all remaining molecules of the 134 k set. For a training set of 10 k molecules, the fingerprint descriptor achieves a mean absolute error of 8.0 kcal/mol. This is slightly worse than the performance attained using the Coulomb matrix, another popular alternative, reaching 6.2 kcal/mol for the same training and test sets. (c) 2015 Wiley Periodicals, Inc.« less

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations.

PubMed

Shirai, Hiroki; Ikeda, Kazuyoshi; Yamashita, Kazuo; Tsuchiya, Yuko; Sarmiento, Jamica; Liang, Shide; Morokata, Tatsuaki; Mizuguchi, Kenji; Higo, Junichi; Standley, Daron M; Nakamura, Haruki

2014-08-01

In the second antibody modeling assessment, we used a semiautomated template-based structure modeling approach for 11 blinded antibody variable region (Fv) targets. The structural modeling method involved several steps, including template selection for framework and canonical structures of complementary determining regions (CDRs), homology modeling, energy minimization, and expert inspection. The submitted models for Fv modeling in Stage 1 had the lowest average backbone root mean square deviation (RMSD) (1.06 Å). Comparison to crystal structures showed the most accurate Fv models were generated for 4 out of 11 targets. We found that the successful modeling in Stage 1 mainly was due to expert-guided template selection for CDRs, especially for CDR-H3, based on our previously proposed empirical method (H3-rules) and the use of position specific scoring matrix-based scoring. Loop refinement using fragment assembly and multicanonical molecular dynamics (McMD) was applied to CDR-H3 loop modeling in Stage 2. Fragment assembly and McMD produced putative structural ensembles with low free energy values that were scored based on the OSCAR all-atom force field and conformation density in principal component analysis space, respectively, as well as the degree of consensus between the two sampling methods. The quality of 8 out of 10 targets improved as compared with Stage 1. For 4 out of 10 Stage-2 targets, our method generated top-scoring models with RMSD values of less than 1 Å. In this article, we discuss the strengths and weaknesses of our approach as well as possible directions for improvement to generate better predictions in the future. © 2014 Wiley Periodicals, Inc.

Laplace-transformed atomic orbital-based Møller–Plesset perturbation theory for relativistic two-component Hamiltonians

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

Helmich-Paris, Benjamin, E-mail: b.helmichparis@vu.nl; Visscher, Lucas, E-mail: l.visscher@vu.nl; Repisky, Michal, E-mail: michal.repisky@uit.no

2016-07-07

We present a formulation of Laplace-transformed atomic orbital-based second-order Møller–Plesset perturbation theory (MP2) energies for two-component Hamiltonians in the Kramers-restricted formalism. This low-order scaling technique can be used to enable correlated relativistic calculations for large molecular systems. We show that the working equations to compute the relativistic MP2 energy differ by merely a change of algebra (quaternion instead of real) from their non-relativistic counterparts. With a proof-of-principle implementation we study the effect of the nuclear charge on the magnitude of half-transformed integrals and show that for light elements spin-free and spin-orbit MP2 energies are almost identical. Furthermore, we investigate themore » effect of separation of charge distributions on the Coulomb and exchange energy contributions, which show the same long-range decay with the inter-electronic/atomic distance as for non-relativistic MP2. A linearly scaling implementation is possible if the proper distance behavior is introduced to the quaternion Schwarz-type estimates as for non-relativistic MP2.« less

Influence of bending of monoatomic copper chains with 10 and 22 atoms on their absorbance spectra: TD-DFT calculations

NASA Astrophysics Data System (ADS)

Markin, Alexey V.; Skaptsov, Alexander A.; Markina, Natalia E.

2018-04-01

The aim of the work is the investigation of bending on the properties of hypothetical one-atom-thick copper clusters (CC) (with 10 and 22 atoms). Time-dependent density functional theory with PBE0 functional and lanl2dz basis set were used for all calculations. The bending was performed by changing angle between copper atoms from 180° to 144° and 163.7° (2° step size) for CC with 10 and 22 atoms, correspondingly. The dependences of absorbance spectra in UVvisible-NIR range (400-2000 nm range) and various energetic characteristics (final energy, chemical potential, and binding energy) on bending angle were investigated. Non-bended (linear) clusters were assigned as references. First, absorbance spectra of all CC contain interband transitions (3d->4sp) in UV-visible range (below 600 nm). Linear configuration of CC also contain intensive absorbance band in NIR region (at 900 and 1700 nm for CC with 10 and 22 atoms) which is associated with 4s electron oscillations along clusters (longitudinal transitions). Significant dumping of low energy 4s transitions (HOMO->LUMO) and interband transitions in the range 600‒500 nm was observed during the bending of CC. Obtained results are in agreement with experimental results for 2D copper nanostructures from literature. We explain such influence of bending by formation merging 4s orbitals which form new 4s oscillations in-plane of bending (in the case of ring-like CC - diametral oscillations). An influence of bending on energy, stability, and chemical potential (Fermi level) of CC was also investigated and discussed.

Knowledge Extraction from Atomically Resolved Images.

PubMed

Vlcek, Lukas; Maksov, Artem; Pan, Minghu; Vasudevan, Rama K; Kalinin, Sergei V

2017-10-24

Tremendous strides in experimental capabilities of scanning transmission electron microscopy and scanning tunneling microscopy (STM) over the past 30 years made atomically resolved imaging routine. However, consistent integration and use of atomically resolved data with generative models is unavailable, so information on local thermodynamics and other microscopic driving forces encoded in the observed atomic configurations remains hidden. Here, we present a framework based on statistical distance minimization to consistently utilize the information available from atomic configurations obtained from an atomically resolved image and extract meaningful physical interaction parameters. We illustrate the applicability of the framework on an STM image of a FeSe x Te 1-x superconductor, with the segregation of the chalcogen atoms investigated using a nonideal interacting solid solution model. This universal method makes full use of the microscopic degrees of freedom sampled in an atomically resolved image and can be extended via Bayesian inference toward unbiased model selection with uncertainty quantification.

Critical assessment of Pt surface energy - An atomistic study

NASA Astrophysics Data System (ADS)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

Structural, electronic and vibrational properties of small GaxNy (x+y = 2 5) nanoclusters: a B3LYP-DFT study

NASA Astrophysics Data System (ADS)

Yadav, P. S.; Yadav, R. K.; Agrawal, B. K.

2007-02-01

An ab initio study of the stability, structural and electronic properties has been made for 49 gallium nitride nanoclusters, GaxNy (x+y = 2-5). Among the various configurations corresponding to a fixed x+y = n value, the configuration possessing the maximum value of binding energy (BE) is named as the most stable structure. The vibrational and optical properties have been investigated only for the most stable structures. A B3LYP-DFT/6-311G(3df) method has been employed to optimize the geometries of the nanoclusters fully. The binding energies (BEs), highest-occupied and lowest-unoccupied molecular orbital (HOMO-LUMO) gaps and the bond lengths have been obtained for all the clusters. We have considered the zero-point energy (ZPE) corrections ignored by the earlier workers. The adiabatic and vertical ionization potentials (IPs) and electron affinities (EAs), charge on atoms, dipole moments, vibrational frequencies, infrared intensities (IR Int.), relative infrared intensities (Rel. IR Int.) and Raman scattering activities have been investigated for the most stable structures. The configurations containing the N atoms in majority are seen to be the most stable structures. The strong N-N bond has an important role in stabilizing the clusters. For clusters containing one Ga atom and all the others as N atoms, the BE increases monotonically with the number of the N atoms. The HOMO-LUMO gap and IP fluctuate with the cluster size n, having larger values for the clusters containing odd number of N atoms. On the other hand, the EA decreases with the cluster size up to n = 3, and shows slow fluctuations thereafter for the larger clusters. In general, the adiabatic IP (EA) is smaller (greater) than the vertical IP (EA) because of the lower energies of the most stable ground state of the cationic (anionic) clusters. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every cluster, and may be used to characterize a specific cluster. All the predicted physical quantities are in good agreement with the experimental data wherever available. The growth of these most stable structures should be possible in experiments.

Interstellar Communication Channel Based on a Biological Universal

NASA Technical Reports Server (NTRS)

Weber, Arthur L.; DeVincenzi, Donald L. (Technical Monitor)

1999-01-01

Cellular biosynthesis starts with sugar substrates and continues energetically downhill to yield amino acid, rapid, and nucleotide products. To understand the energetics of these processes, we calculated the energy for biosynthesis from sugars of E. cali's amino acids, nucleotides, and lipids. We found that the biosynthesis of amino acids and lipids from sugar substrates proceeds by redox disproportionation. of sugar carbon with a favorable energy of about -11 kcal/mole of carbon. Overall, redox disproportion of sugar carbon accounted for 84% and 96% (ATP only 6% and 1%) of the total biosynthetic energy of amino acids and lipids (the major cellular constituents). Next, we calculated for all 48 possible 3-carbon substrates the energy of maximal disproportionation to carbon dioxide and methane. We found no other carbon substrates than matched sugars in biosynthetic energy, efficiency, and simplicity. From this, we concluded that sugars are the optimal biosynthetic substrate. Since this conclusion is based on universal properties of carbon chemistry, other carbon-based life throughout the Universe would also use optimal sugar substrates. Furthermore, this rather obvious universal role of sugars as the optimal biosubstrate would probably be common knowledge of technological civilizations throughout the Universe. Since the elemental building block of all sugars is formaldehyde, the common knowledge that sugars are the universal optimal biosubstrate could reasonably lead to the selection of a line(s) in the microwave spectrum of formaldehyde as a frequency for interstellar communication.

A Structural Model for a Self-Assembled Nanotube Provides Insight into Its Exciton Dynamics

PubMed Central

2016-01-01

The design and synthesis of functional self-assembled nanostructures is frequently an empirical process fraught with critical knowledge gaps about atomic-level structure in these noncovalent systems. Here, we report a structural model for a semiconductor nanotube formed via the self-assembly of naphthalenediimide-lysine (NDI-Lys) building blocks determined using experimental 13C–13C and 13C–15N distance restraints from solid-state nuclear magnetic resonance supplemented by electron microscopy and X-ray powder diffraction data. The structural model reveals a two-dimensional-crystal-like architecture of stacked monolayer rings each containing ∼50 NDI-Lys molecules, with significant π-stacking interactions occurring both within the confines of the ring and along the long axis of the tube. Excited-state delocalization and energy transfer are simulated for the nanotube based on time-dependent density functional theory and an incoherent hopping model. Remarkably, these calculations reveal efficient energy migration from the excitonic bright state, which is in agreement with the rapid energy transfer within NDI-Lys nanotubes observed previously using fluorescence spectroscopy. PMID:26120375

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.

Laboratory astrophysics under the ultraviolet, visible, and gravitational astrophysics research program: Oscillator strengths for ultraviolet atomic transitions

NASA Technical Reports Server (NTRS)

Federman, Steven R.

1992-01-01

The conditions within astrophysical environments can be derived from observational data on atomic and molecular lines. For instance, the density and temperature of the gas are obtained from relative populations among energy levels. Information on populations comes about only when the correspondence between line strength and abundance is well determined. The conversion from line strength to abundance involves knowledge of meanlives and oscillator strengths. For many ultraviolet atomic transitions, unfortunately, the necessary data are either relatively imprecise or not available. Because of the need for more and better atomic oscillator strengths, our program was initiated. Through beam-foil spectroscopy, meanlives of ultraviolet atomic transitions are studied. In this technique, a nearly isotopically pure ion beam of the desired element is accelerated. The beam passes through a thin carbon foil (2 mg/cu cm), where neutralization, ionization, and excitation take place. The dominant process depends on the energy of the beam. Upon exiting the foil, the decay of excited states is monitored via single-photon-counting techniques. The resulting decay curve yields a meanlife. The oscillator strength is easily obtained from the meanlife when no other decay channels are presented. When other channels are present, additional measurements or theoretical calculations are performed in order to extract an oscillator strength. During the past year, three atomic systems have been studied experimentally and/or theoretically; they are Ar, I, Cl I, and N II. The results for the first two are important for studies of interstellar space, while the work on N II bears on processes occurring in planetary atmospheres.

Importance of Unit Cells in Accurate Evaluation of the Characteristics of Graphene

NASA Astrophysics Data System (ADS)

Sabzyan, Hassan; Sadeghpour, Narges

2016-04-01

Effects of the size of the unit cell on energy, atomic charges, and phonon frequencies of graphene at the Γ point of the Brillouin zone are studied in the absence and presence of an electric field using density functional theory (DFT) methods (LDA and DFT-PBE functionals with Goedecker-Teter-Hutter (GTH) and Troullier-Martins (TM) norm-conserving pseudopotentials). Two types of unit cells containing nC=4-28 carbon atoms are considered. Results show that stability of graphene increases with increasing size of the unit cell. Energy, atomic charges, and phonon frequencies all converge above nC=24 for all functional-pseudopotentials used. Except for the LDA-GTH calculations, application of an electric field of 0.4 and 0.9 V/nm strengths does not change the trends with the size of the unit cell but instead slightly decreases the binding energy of graphene. Results of this study show that the choice of unit cell size and type is critical for calculation of reliable characteristics of graphene.

GRID: a high-resolution protein structure refinement algorithm.

PubMed

Chitsaz, Mohsen; Mayo, Stephen L

2013-03-05

The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. Copyright © 2012 Wiley Periodicals, Inc.

D and D Knowledge Management Information Tool - 2012 - 12106

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

Upadhyay, H.; Lagos, L.; Quintero, W.

2012-07-01

Deactivation and decommissioning (D and D) work is a high priority activity across the Department of Energy (DOE) complex. Subject matter specialists (SMS) associated with the different ALARA (As-Low-As-Reasonably-Achievable) Centers, DOE sites, Energy Facility Contractors Group (EFCOG) and the D and D community have gained extensive knowledge and experience over the years in the cleanup of the legacy waste from the Manhattan Project. To prevent the D and D knowledge and expertise from being lost over time from the evolving and aging workforce, DOE and the Applied Research Center (ARC) at Florida International University (FIU) proposed to capture and maintainmore » this valuable information in a universally available and easily usable system. D and D KM-IT provides single point access to all D and D related activities through its knowledge base. It is a community driven system. D and D KM-IT makes D and D knowledge available to the people who need it at the time they need it and in a readily usable format. It uses the World Wide Web as the primary source for content in addition to information collected from subject matter specialists and the D and D community. It brings information in real time through web based custom search processes and its dynamic knowledge repository. Future developments include developing a document library, providing D and D information access on mobile devices for the Technology module and Hotline, and coordinating multiple subject matter specialists to support the Hotline. The goal is to deploy a high-end sophisticated and secured system to serve as a single large knowledge base for all the D and D activities. The system consolidates a large amount of information available on the web and presents it to users in the simplest way possible. (authors)« less

Gamma ray interaction studies of organic nonlinear optical materials in the energy range 122 keV-1330 keV

NASA Astrophysics Data System (ADS)

Awasarmol, V. V.; Gaikwad, D. K.; Raut, S. D.; Pawar, P. P.

The mass attenuation coefficients (μm) for organic nonlinear optical materials measured at 122-1330 keV photon energies were investigated on the basis of mixture rule and compared with obtained values of WinXCOM program. It is observed that there is a good agreement between theoretical and experimental values of the samples. All samples were irradiated with six radioactive sources such as 57Co, 133Ba, 22Na, 137Cs, 54Mn and 60Co using transmission arrangement. Effective atomic and electron numbers or electron densities (Zeff and Neff), molar extinction coefficient (ε), mass energy absorption coefficient (μen/ρ) and effective atomic energy absorption cross section (σa,en) were determined experimentally and theoretically using the obtained μm values for investigated samples and graphs have been plotted. The graph shows that the variation of all samples decreases with increasing photon energy.

σ -SCF: A Direct Energy-targeting Method To Mean-field Excited States

NASA Astrophysics Data System (ADS)

Ye, Hongzhou; Welborn, Matthew; Ricke, Nathan; van Voorhis, Troy

The mean-field solutions of electronic excited states are much less accessible than ground state (e.g. Hartree-Fock) solutions. Energy-based optimization methods for excited states, like Δ-SCF, tend to fall into the lowest solution consistent with a given symmetry - a problem known as ``variational collapse''. In this work, we combine the ideas of direct energy-targeting and variance-based optimization in order to describe excited states at the mean-field level. The resulting method, σ-SCF, has several advantages. First, it allows one to target any desired excited state by specifying a single parameter: a guess of the energy of that state. It can therefore, in principle, find all excited states. Second, it avoids variational collapse by using a variance-based, unconstrained local minimization. As a consequence, all states - ground or excited - are treated on an equal footing. Third, it provides an alternate approach to locate Δ-SCF solutions that are otherwise hardly accessible by the usual non-aufbau configuration initial guess. We present results for this new method for small atoms (He, Be) and molecules (H2, HF). This work was funded by a Grant from NSF (CHE-1464804).

Bose-Einstein Condensate-Hidden Riches for New Forms of Technology and Energy Generation; Potential for Glimpse into Inner Reality

NASA Astrophysics Data System (ADS)

Reed, Don

With the announcement of the recent successful production of a Bose-Einstein condensate (BEC) of photons, a circle has been completed which started in 1925 with the vision of Albert Einstein and Satyendra Nath Bose - a sustained macroscopic condensed state of matter where all atoms are in the same lowest quantum state. The creation of an all-optical BEC, involving a surprisingly straightforward "tabletop" method which bypasses the normally requisite laser/evaporative cooling equipment and ultra-high vacuum chambers necessary for production of the standard delicate atomic BEC, elevates this phenomenon to a new level well beyond its current perception as mere laboratory curiosity. Accordingly, this development certainly heralds eventual incorporation of atomic and photon BECs as standard operating components of energy-efficient mechanical, optical and electrical systems, implying novel ingenious engineering protocols amenable to all the tools of non-linear and quantum optics. Pointing towards such a promising technological future are the suggestion that a photon BEC could serve as a new high-energy ultra-violet (UV) laser photon source, as well as the recent unprecedented implementation of a closed-loop atom circuit (toroidal atomic BEC) demonstrating precise control of superfluid current flow, forecasting the coveted development of an atomic SQUID. Perhaps more significantly, the new highly robust and manageable optical BEC will allow heretofore unfathomable precise probing of the atomic and nano-levels of nature, affording novel high-quality testing procedures of the major foundations of quantum mechanics itself. Such a primary advancement, providing a clearer glimpse into the microscopic realms, may present us as never before with an unprecedented view of the quantum engine that underpins physical reality itself and help place the contextual nature of entanglement and quantum superposition on a firmer foundation. Thus, further progress in achieving mastery over the precise flexible manipulation of BEC states could demonstrate that quantum contextuality might be an unsuspected over-arching archetypal principle in nature, leading to new insight in regards to the interpretation of quantum mechanics as applied to all levels of nature. Moreover, it will be shown that this concealed and hence heretofore unsuspected contextual aspect of natural laws, as exemplified by the dynamics underlying BEC structure, could be brought to bear to account for physical anomalies inexplicable using current paradigms, such as the claimed energy yields from low-energy nuclear reactions (as represented by the so-called process of "cold fusion"), making this phenomenon more tractable and rendered less controversial.

How important is self-consistency for the dDsC density dependent dispersion correction?

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

Brémond, Éric; Corminboeuf, Clémence, E-mail: clemence.corminboeuf@epfl.ch; Golubev, Nikolay

2014-05-14

The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical pointmore » of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation.« less

Density functional theory study of HfCl4, ZrCl4, and Al(CH3)3 decomposition on hydroxylated SiO2: Initial stage of high-k atomic layer deposition

NASA Astrophysics Data System (ADS)

Jeloaica, L.; Estève, A.; Djafari Rouhani, M.; Estève, D.

2003-07-01

The initial stage of atomic layer deposition of HfO2, ZrO2, and Al2O3 high-k films, i.e., the decomposition of HfCl4, ZrCl4, and Al(CH3)3 precursor molecules on an OH-terminated SiO2 surface, is investigated within density functional theory. The energy barriers are determined using artificial activation of vibrational normal modes. For all precursors, reaction proceeds through the formation of intermediate complexes that have equivalent formation energies (˜-0.45 eV), and results in HCl and CH4 formation with activation energies of 0.88, 0.91, and 1.04 eV for Hf, Zr, and Al based precursors, respectively. The reaction product of Al(CH3)3 decomposition is found to be more stable (by -1.45 eV) than the chemisorbed intermediate complex compared to the endothermic decomposition of HfCl4 and ZrCl4 chemisorbed precursors (0.26 and 0.29 eV, respectively).

Stability, surface features, and atom leaching of palladium nanoparticles: toward prediction of catalytic functionality.

PubMed

Ramezani-Dakhel, Hadi; Mirau, Peter A; Naik, Rajesh R; Knecht, Marc R; Heinz, Hendrik

2013-04-21

Surfactant-stabilized metal nanoparticles have shown promise as catalysts although specific surface features and their influence on catalytic performance have not been well understood. We quantify the thermodynamic stability, the facet composition of the surface, and distinct atom types that affect rates of atom leaching for a series of twenty near-spherical Pd nanoparticles of 1.8 to 3.1 nm size using computational models. Cohesive energies indicate higher stability of certain particles that feature an approximate 60/20/20 ratio of {111}, {100}, and {110} facets while less stable particles exhibit widely variable facet composition. Unique patterns of atom types on the surface cause apparent differences in binding energies and changes in reactivity. Estimates of the relative rate of atom leaching as a function of particle size were obtained by the summation of Boltzmann-weighted binding energies over all surface atoms. Computed leaching rates are in good qualitative correlation with the measured catalytic activity of peptide-stabilized Pd nanoparticles of the same shape and size in Stille coupling reactions. The agreement supports rate-controlling contributions by atom leaching in the presence of reactive substrates. The computational approach provides a pathway to estimate the catalytic activity of metal nanostructures of engineered shape and size, and possible further refinements are described.

Theoretical L-shell Coster-Kronig energies 11 or equal to z or equal to 103

NASA Technical Reports Server (NTRS)

Chen, M. H.; Crasemann, B.; Huang, K. N.; Aoyagi, M.; Mark, H.

1976-01-01

Relativistic relaxed-orbital calculations of L-shell Coster-Kronig transition energies have been performed for all possible transitions in atoms with atomic numbers. Hartree-Fock-Slater wave functions served as zeroth-order eigenfunctions to compute the expectation of the total Hamiltonian. A first-order approximation to the local approximation was thus included. Quantum-electrodynamic corrections were made. Each transition energy was computed as the difference between results of separate self-consistent-field calculations for the initial, singly ionized state and the final two-hole state. The following quantities are listed: total transition energy, 'electric' (Dirac-Hartree-Fock-Slater) contribution, magnetic and retardation contributions, and contributions due to vacuum polarization and self energy.

Photon absorption potential coefficient as a tool for materials engineering

NASA Astrophysics Data System (ADS)

Akande, Raphael Oluwole; Oyewande, Emmanuel Oluwole

2016-09-01

Different atoms achieve ionizations at different energies. Therefore, atoms are characterized by different responses to photon absorption in this study. That means there exists a coefficient for their potential for photon absorption from a photon source. In this study, we consider the manner in which molecular constituents (atoms) absorb photon from a photon source. We observe that there seems to be a common pattern of variation in the absorption of photon among the electrons in all atoms on the periodic table. We assume that the electrons closest to the nucleus (En) and the electrons closest to the outside of the atom (Eo) do not have as much potential for photon absorption as the electrons at the middle of the atom (Em). The explanation we give to this effect is that the En electrons are embedded within the nuclear influence, and similarly, Eo electrons are embedded within the influence of energies outside the atom that there exists a low potential for photon absorption for them. Unlike En and Eo, Em electrons are conditioned, such that there is a quest for balance between being influenced either by the nuclear force or forces external to the atom. Therefore, there exists a higher potential for photon absorption for Em electrons than for En and Eo electrons. The results of our derivations and analysis always produce a bell-shaped curve, instead of an increasing curve as in the ionization energies, for all elements in the periodic table. We obtained a huge data of PAPC for each of the several materials considered. The point at which two or more PAPC values cross one another is termed to be a region of conflicting order of ionization, where all the atoms absorb equal portion of the photon source at the same time. At this point, a greater fraction of the photon source is pumped into the material which could lead to an explosive response from the material. In fact, an unimaginable and unreported phenomenon (in physics) could occur, when two or more PAPCs cross, and the material is able to absorb more than that the photon source could provide, at this point. These resulting effects might be of immense materials engineering applications.

Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals

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

Kroonblawd, Matthew P.; Sewell, Thomas D., E-mail: sewellt@missouri.edu; Maillet, Jean-Bernard, E-mail: jean-bernard.maillet@cea.fr

2016-02-14

In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linearmore » and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.« less

Photodissociation and caging of HBr and HI molecules on the surface of large rare gas clusters.

PubMed

Baumfalk, R; Nahler, N H; Buck, U

2001-01-01

Photodissociation experiments were carried out at a wavelength of 243 nm for single HBr and HI molecules adsorbed on the surface of large Nen, Arn, Krn and Xen clusters. The average size is about = 130; the size ranges = 62-139 for the system HBr-Arn and = 110-830 for HI-Xen were covered. In this way the dependence of the photodissociation dynamics on both the size and the rare gas host cluster was investigated. The main observable is the kinetic energy distribution of the outgoing H atoms. The key results are that we do not find any size dependence for either system but that we observe a strong dependence on the rare gas clusters. All systems exhibit H atoms with no energy loss that indicate direct cage exit and those with nearly zero energy that are an indication of complete caging. The intensity ratio of caged to uncaged H atoms is largest for Nen, decreases with increasing mass of the cage atoms, and is weakest for Xen. On the basis of accompanying calculations this behaviour is attributed to the large amplitude motion of the light H atom. This leads to direct cage exit and penetration of the atom through the cluster with different energy transfer per collision depending on the rare gas atoms. The differences between HBr and HI molecules are attributed to different surface states, a flat and an encapsulated site.

A New Generation of Los Alamos Opacity Tables

DOE PAGES

Colgan, James Patrick; Kilcrease, David Parker; Magee, Jr., Norman H.; ...

2016-01-26

We present a new, publicly available, set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation-of-state (EOS) model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations thatmore » we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.« less

Atomic structure data based on average-atom model for opacity calculations in astrophysical plasmas

NASA Astrophysics Data System (ADS)

Trzhaskovskaya, M. B.; Nikulin, V. K.

2018-03-01

Influence of the plasmas parameters on the electron structure of ions in astrophysical plasmas is studied on the basis of the average-atom model in the local thermodynamic equilibrium approximation. The relativistic Dirac-Slater method is used for the electron density estimation. The emphasis is on the investigation of an impact of the plasmas temperature and density on the ionization stages required for calculations of the plasmas opacities. The level population distributions and level energy spectra are calculated and analyzed for all ions with 6 ≤ Z ≤ 32 occurring in astrophysical plasmas. The plasma temperature range 2 - 200 eV and the density range 2 - 100 mg/cm3 are considered. The validity of the method used is supported by good agreement between our values of ionization stages for a number of ions, from oxygen up to uranium, and results obtained earlier by various methods among which are more complicated procedures.

Hierarchical Architecturing for Layered Thermoelectric Sulfides and Chalcogenides.

PubMed

Jood, Priyanka; Ohta, Michihiro

2015-03-16

Sulfides are promising candidates for environment-friendly and cost-effective thermoelectric materials. In this article, we review the recent progress in all-length-scale hierarchical architecturing for sulfides and chalcogenides, highlighting the key strategies used to enhance their thermoelectric performance. We primarily focus on TiS₂-based layered sulfides, misfit layered sulfides, homologous chalcogenides, accordion-like layered Sn chalcogenides, and thermoelectric minerals. CS₂ sulfurization is an appropriate method for preparing sulfide thermoelectric materials. At the atomic scale, the intercalation of guest atoms/layers into host crystal layers, crystal-structural evolution enabled by the homologous series, and low-energy atomic vibration effectively scatter phonons, resulting in a reduced lattice thermal conductivity. At the nanoscale, stacking faults further reduce the lattice thermal conductivity. At the microscale, the highly oriented microtexture allows high carrier mobility in the in-plane direction, leading to a high thermoelectric power factor.

Hierarchical Architecturing for Layered Thermoelectric Sulfides and Chalcogenides

PubMed Central

Jood, Priyanka; Ohta, Michihiro

2015-01-01

Sulfides are promising candidates for environment-friendly and cost-effective thermoelectric materials. In this article, we review the recent progress in all-length-scale hierarchical architecturing for sulfides and chalcogenides, highlighting the key strategies used to enhance their thermoelectric performance. We primarily focus on TiS2-based layered sulfides, misfit layered sulfides, homologous chalcogenides, accordion-like layered Sn chalcogenides, and thermoelectric minerals. CS2 sulfurization is an appropriate method for preparing sulfide thermoelectric materials. At the atomic scale, the intercalation of guest atoms/layers into host crystal layers, crystal-structural evolution enabled by the homologous series, and low-energy atomic vibration effectively scatter phonons, resulting in a reduced lattice thermal conductivity. At the nanoscale, stacking faults further reduce the lattice thermal conductivity. At the microscale, the highly oriented microtexture allows high carrier mobility in the in-plane direction, leading to a high thermoelectric power factor. PMID:28787992

Comparison of Hyperthermal Ground Laboratory Atomic Oxygen Erosion Yields With Those in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Dill, Grace C.; Loftus, Ryan J.; deGroh, Kim K.; Miller, Sharon K.

2013-01-01

The atomic oxygen erosion yields of 26 materials (all polymers except for pyrolytic graphite) were measured in two directed hyperthermal radio frequency (RF) plasma ashers operating at 30 or 35 kHz with air. The hyperthermal asher results were compared with thermal energy asher results and low Earth orbital (LEO) results from the Materials International Space Station Experiment 2 and 7 (MISSE 2 and 7) flight experiments. The hyperthermal testing was conducted to a significant portion of the atomic oxygen fluence similar polymers were exposed to during the MISSE 2 and 7 missions. Comparison of the hyperthermal asher prediction of LEO erosion yields with thermal energy asher erosion yields indicates that except for the fluorocarbon polymers of PTFE and FEP, the hyperthermal energy ashers are a much more reliable predictor of LEO erosion yield than thermal energy asher testing, by a factor of four.

BepiColombo Serena/ELENA instrument:development and testing

NASA Astrophysics Data System (ADS)

Orsini, S.; De Angelis, E.; Selci, S.; Di Lellis, A. M.:; Leoni, R.; Rispoli, R.; Colasanti, L.; Vertolli, N.; Scheer, J.; Mura, A.; Milillo, A.; Wurz, P.; D'Alessandro, M.; Maschietti, D.; Mattioli, F.; Cibella, S.; Brienza, D.; lo Spazio, Compagnia Generale per

2012-04-01

ELENA is a TOF sensor, based on a novel concept ultra-sonic oscillating shutter (Start section) which is operated at frequencies up to 50 kHz; a MCP detector is used as a Stop section. It is aimed to detect neutral atoms in the range 10 eV - 5 keV, within 70° FOV, perpendicular to the S/C orbital plane. ELENA will monitor the emission of neutral atoms from the whole surface of Mercury thanks to the spacecraft motion. The major scientific objectives are the interaction between the environment and the planet, the global particle loss-rate and the remote sensing of the surface properties. In particular, surface release processes are investigated by identifying particles release from the surface, via solar wind-induced ion sputtering (<1eV - >100 eV) as well as Hydrogen back-scattered at hundreds eV. In particular, the capability to detect non-thermal low energy neutral species is crucial for the sensor ELENA (Emitted Low-Energy Neutral Atoms), part of the package SERENA (Search for Exospheric Refilling and Emitted Natural Abundances) on board the BepiColombo mission to Mercury to be launched in 2014. The instrument is now validated and tested to reach its performances: the up-graded shutter system (Start section) has been operated for the first time with neutral atom beam and tested at high frequency, the Stop section has been calibrated investigating the region of very low energy detection efficiency, the electronics boards and the entire acquisition chain has been appointed and tested with ion beam. The first results of all the ELENA capability will be presented.

The dependence of stress in IBAD films on the ion-irradiation energy and flux

NASA Astrophysics Data System (ADS)

Schweitz, K. O.; Arndt, J.; Bøttiger, J.; Chevallier, J.

1997-05-01

Systematic experimental studies of the stress build-up during e-gun deposition of Ni with simultaneous bombardment by energetic Ar + ions (IBAD) have been carried out. The ion energy E was varied from 60 to 800 eV, and the ratio of the arrival rates of Ni atoms and Ar + ions, {R}/{J}, was varied from 0.5 to 6.4. The Ni-deposition rate was in the range from 0.5 to 2.0 Å/s, with all the depositions carried out near room temperature in a chamber with the base pressure of 5 × 10 -6 Pa. The film stress was measured by use of profilometry and the application of Stoney's equation. The experimental results were compared with predictions of a simple model proposed by Davis. This model assumes that the compressive stress build-up, due to knock-on implantation of film atoms being proportional to E {1}/{2}, is balanced by relaxation by collision-cascade-excited atom migration proportional to E {5}/{3}. To obtain agreement between model and experiment in the investigated ranges of E and {R}/{J}, an additional model parameter had to be added which takes into account that without irradiation, tensile stresses arise.

Low energy electron diffraction and low energy electron microscopy microspot I/V analysis of the (4 x 4)O structure on Ag(111): surface oxide or reconstruction?

PubMed

Reichelt, R; Günther, S; Wintterlin, J; Moritz, W; Aballe, L; Mentes, T O

2007-10-07

A low energy electron diffraction (LEED) I/V analysis was performed of the (4 x 4) oxygen structure on Ag(111). Two data sets were used, one recorded with a conventional LEED system and a second with a low energy electron microscope (LEEM). The data sets agree well with each other, demonstrating that I/V structure analyses can be performed with the same quality with LEEM as with conventional LEED. The structure obtained confirms the recently proposed model that involves a reconstruction of the Ag(111) surface. Previous models based on a thin layer of Ag(2)O that had been accepted for more than 30 years are disproved. The reconstruction model contains two units of six triangularly arranged Ag atoms and a stacking fault in one half of the unit cell. The six O atoms per unit cell occupy sites in the trenches between the Ag(6) triangles. Small lateral displacements of the Ag atoms lift the mirror symmetry of the structure, leading to two nonequivalent groups of O atoms. The atoms of both groups are located approximately 0.5 Angstrom below the top Ag layer, on fourfold positions with respect to the top layer Ag atoms. Ag-O distances between 2.05 and 2.3 Angstrom are found. The oxygen atoms exhibit large static or dynamic displacements of up to 0.3 Angstrom at 300 K.

Do Ag{sub n} (up to n = 8) clusters retain their identity on graphite? Insights from first-principles calculations including dispersion interactions

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

Singh, Akansha; Sen, Prasenjit, E-mail: prasen@hri.res.in; Majumder, Chiranjib

Adsorption of pre-formed Ag{sub n} clusters for n = 1 − 8 on a graphite substrate is studied within the density functional theory employing the vdW-DF2 functional to treat dispersion interactions. Top sites above surface layer carbon atoms turn out to be most favorable for a Ag adatom, in agreement with experimental observations. The same feature is observed for clusters of almost all sizes which have the lowest energies when the Ag atoms are positioned over top sites. Most gas phase isomers retain their structures over the substrate, though a couple of them undergo significant distortions. Energetics of the adsorptionmore » can be understood in terms of a competition between energy cost of disturbing Ag–Ag bonds in the cluster and energy gain from Ag–C interactions at the surface. Ag{sub 3} turns out to be an exceptional candidate in this regard that undergoes significant structural distortion and has only two of the Ag atoms close to surface C atoms in its lowest energy structure.« less

Extension of coarse-grained UNRES force field to treat carbon nanotubes.

PubMed

Sieradzan, Adam K; Mozolewska, Magdalena A

2018-04-26

Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3-4 order of magnitude larger timescale than using regular all-atom force fields. Graphical abstract Bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ.

Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

PubMed

A Rohrdanz, Mary; Zheng, Wenwei; Lambeth, Bradley; Vreede, Jocelyne; Clementi, Cecilia

2014-10-01

The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

PubMed

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

Evolution in time of an N-atom system. II. Calculation of the eigenstates

NASA Astrophysics Data System (ADS)

Rudolph, Terry; Yavin, Itay; Freedhoff, Helen

2004-01-01

We calculate the energy eigenvalues and eigenstates corresponding to coherent single and multiple excitations of a number of different arrays of N identical two-level atoms (TLA’s) or qubits, including polygons, “diamond” structures, polygon multilayers, icosahedra, and dodecahedra. We assume only that the coupling occurs via an exchange interaction which depends on the separation between the atoms. We include the interactions between all pairs of atoms, and our results are valid for arbitrary separations relative to the radiation wavelength.

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms.

PubMed

Sulimov, Alexey V; Zheltkov, Dmitry A; Oferkin, Igor V; Kutov, Danil C; Katkova, Ekaterina V; Tyrtyshnikov, Eugene E; Sulimov, Vladimir B

2017-01-01

We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.

FROM THE HISTORY OF PHYSICS: The development of the first Soviet atomic bomb

NASA Astrophysics Data System (ADS)

Goncharov, German A.; Ryabev, Lev D.

2001-01-01

In the late 1930s and early 1940s, two remarkable physical phenomena — the fission of heavy nuclei and the chain fission reaction — were discovered, implying that a new powerful source of energy (nuclear fission energy) might become a practical possibility for mankind. At that time, however, the political situation in the world made the development of the atomic bomb the main objective of nuclear energy research in the countries involved. The first atomic bombs, notoriously used in the war against Japan, were produced by the United States of America only six and a half years after the discovery of fission. Four years later, the first Soviet atomic bomb was tested. This was a major step toward the establishment of nuclear parity which led to stability and global peace and thus greatly influenced the destiny of human kind. Based on documentary materials covering the period from 1939 to 1949, this paper traces the origin and evolution of the physical ideas behind the first Soviet atomic bomb and discusses the most important events associated with the project.

Electronic conductance of a poly(p-phenylene)-like nanowire in the presence of thermal atomic vibrations

NASA Astrophysics Data System (ADS)

Shariati, Ashrafalsadat; Rabani, Hassan; Mardaani, Mohammad

2017-10-01

We present a theoretical method based on Green’s function technique and tight-binding approach as well as harmonic approximation in order to calculate the coherent electronic conductance of an extended poly(p-phenylene) oligomer in the presence of thermal atomic vibrations. We study two proposed mass-spring models for atomic vibrations: one, including rigid benzene rings connected to each other by vibrating bonds; and in another, the bonds along the oligomer vibrate even in the benzene rings. The electron-phonon (e-ph) interaction influences the electron hopping energies linearly with respect to atomic displacements. The model shows that the conductance spectra exhibit some new energy gaps in the presence of e-ph interaction even at zero temperature. The conductance is more affected by e-ph interaction when the atomic vibrations are supposed to be present in the benzene rings. At the edges of the band energy and central gap, the phonon-assisted phenomena can be observed. Generally, the increasing e-ph interaction strength as well as temperature destroys the electronic conductance especially in the resonance region.

Mass energy-absorption coefficients and average atomic energy-absorption cross-sections for amino acids in the energy range 0.122-1.330 MeV

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

More, Chaitali V., E-mail: chaitalimore89@gmail.com; Lokhande, Rajkumar M.; Pawar, Pravina P., E-mail: pravinapawar4@gmail.com

Mass attenuation coefficients of amino acids such as n-acetyl-l-tryptophan, n-acetyl-l-tyrosine and d-tryptophan were measured in the energy range 0.122-1.330 MeV. NaI (Tl) scintillation detection system was used to detect gamma rays with a resolution of 8.2% at 0.662 MeV. The measured attenuation coefficient values were then used to determine the mass energy-absorption coefficients (σ{sub a,en}) and average atomic energy-absorption cross sections (μ{sub en}/ρ) of the amino acids. Theoretical values were calculated based on XCOM data. Theoretical and experimental values are found to be in good agreement.

Network Computing Infrastructure to Share Tools and Data in Global Nuclear Energy Partnership

NASA Astrophysics Data System (ADS)

Kim, Guehee; Suzuki, Yoshio; Teshima, Naoya

CCSE/JAEA (Center for Computational Science and e-Systems/Japan Atomic Energy Agency) integrated a prototype system of a network computing infrastructure for sharing tools and data to support the U.S. and Japan collaboration in GNEP (Global Nuclear Energy Partnership). We focused on three technical issues to apply our information process infrastructure, which are accessibility, security, and usability. In designing the prototype system, we integrated and improved both network and Web technologies. For the accessibility issue, we adopted SSL-VPN (Security Socket Layer-Virtual Private Network) technology for the access beyond firewalls. For the security issue, we developed an authentication gateway based on the PKI (Public Key Infrastructure) authentication mechanism to strengthen the security. Also, we set fine access control policy to shared tools and data and used shared key based encryption method to protect tools and data against leakage to third parties. For the usability issue, we chose Web browsers as user interface and developed Web application to provide functions to support sharing tools and data. By using WebDAV (Web-based Distributed Authoring and Versioning) function, users can manipulate shared tools and data through the Windows-like folder environment. We implemented the prototype system in Grid infrastructure for atomic energy research: AEGIS (Atomic Energy Grid Infrastructure) developed by CCSE/JAEA. The prototype system was applied for the trial use in the first period of GNEP.

Structure and vibrational spectra of low-energy silicon clusters

NASA Astrophysics Data System (ADS)

Sieck, A.; Porezag, D.; Frauenheim, Th.; Pederson, M. R.; Jackson, K.

1997-12-01

We have identified low-energy structures of silicon clusters with 9 to 14 atoms using a nonorthogonal tight-binding method (TB) based on density-functional theory (DF). We have further investigated the resulting structures with an accurate all-electron first-principles technique. The results for cohesive energies, cluster geometries, and highest occupied to lowest unoccupied molecular orbital (HOMO-LUMO) gaps show an overall good agreement between DF-TB and self-consistent-field (SCF) DF theory. For Si9 and Si14, we have found equilibrium structures, whereas for Si11, Si12, and Si13, we present clusters with energies close to that of the corresponding ground-state structure recently proposed in the literature. The bonding scheme of clusters in this size range is different from the bulk tetrahedral symmetry. The most stable structures, characterized by low energies and large HOMO-LUMO gaps, have similar common subunits. To aid in their experimental identification, we have computed the full vibrational spectra of the structures, along with the Raman activities, IR intensities, and static polarizabilities, using SCF-DF theory within the local-density approximation (LDA). This method has already been successfully applied to the determination of Raman and IR spectra of silicon clusters with 3-8, 10, 13, 20, and 21 atoms.

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

PubMed Central

Allen, Lucy R.; Krivov, Sergei V.; Paci, Emanuele

2009-01-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical λ-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins. PMID:19593364

Analysis of the free-energy surface of proteins from reversible folding simulations.

PubMed

Allen, Lucy R; Krivov, Sergei V; Paci, Emanuele

2009-07-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

10 CFR 810.15 - Violations.

Code of Federal Regulations, 2012 CFR

2012-01-01

... ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.15 Violations. (a) The Atomic Energy Act... person from violating any provision of the Atomic Energy Act or its implementing regulations. (2) Any... Atomic Energy Act may be fined up to $10,000 or imprisoned up to 10 years, or both. If the offense is...

10 CFR 810.15 - Violations.

Code of Federal Regulations, 2014 CFR

2014-01-01

... ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.15 Violations. (a) The Atomic Energy Act... person from violating any provision of the Atomic Energy Act or its implementing regulations. (2) Any... Atomic Energy Act may be fined up to $10,000 or imprisoned up to 10 years, or both. If the offense is...

10 CFR 810.15 - Violations.

Code of Federal Regulations, 2013 CFR

2013-01-01

... ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.15 Violations. (a) The Atomic Energy Act... person from violating any provision of the Atomic Energy Act or its implementing regulations. (2) Any... Atomic Energy Act may be fined up to $10,000 or imprisoned up to 10 years, or both. If the offense is...

10 CFR 810.15 - Violations.

Code of Federal Regulations, 2011 CFR

2011-01-01

... ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.15 Violations. (a) The Atomic Energy Act... person from violating any provision of the Atomic Energy Act or its implementing regulations. (2) Any... Atomic Energy Act may be fined up to $10,000 or imprisoned up to 10 years, or both. If the offense is...

10 CFR 810.15 - Violations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.15 Violations. (a) The Atomic Energy Act... person from violating any provision of the Atomic Energy Act or its implementing regulations. (2) Any... Atomic Energy Act may be fined up to $10,000 or imprisoned up to 10 years, or both. If the offense is...

Comparison of Atomic Oxygen Erosion Yields of Materials at Various Energy and Impact Angles

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Waters, Deborah L.; Thorson, Stephen D.; deGroh, Kim, K.; Snyder, Aaron; Miller, Sharon

2006-01-01

The atomic oxygen erosion yields of various materials, measured in volume of material oxidized per incident atomic oxygen atom, are compared to the commonly accepted standard of Kapton H (DuPont) polyimide. The ratios of the erosion yield of Kapton H to the erosion yield of various materials are not consistent at different atomic oxygen energies. Although it is most convenient to use isotropic thermal energy RF plasma ashers to assess atomic oxygen durability, the results can be misleading because the relative erosion rates at thermal energies are not necessarily the same as low Earth orbital (LEO) energies of approx.4.5 eV. An experimental investigation of the relative atomic oxygen erosion yields of a wide variety of polymers and carbon was conducted using isotropic thermal energy (approx.0.1 eV) and hyperthermal energy (approx.70 eV) atomic oxygen using an RF plasma asher and an end Hall ion source. For hyperthermal energies, the atomic oxygen erosion yields relative to normal incident Kapton H were compared for sweeping atomic oxygen arrival with that of normal incidence arrival. The results of isotropic thermal energy, normal incident, and sweeping incident atomic oxygen are also compared with measured or projected LEO values.

De-Excitation of High-Rydberg Antihydrogen in a Strongly Magnetized Pure Positron Plasma

NASA Astrophysics Data System (ADS)

Bass, E. M.

2005-10-01

The rate at which highly excited atoms relax to deeper binding is found with classical theories and simulations. This rate relates to antihydrogen formation experiments where such atoms are formed in pure-positron, Penning trap plasmas.ootnotetextG.Gabrielse, N.S. Bowden, P. Oxley, et al., Phys. Rev. Lett. 89, 213401 (2002); M. Amoretti, C. Amsler, G. Bonomi, et al., Nature (London) 419, 456 (2002). The analysis concerns atoms that have passed the kinetic bottleneck at binding energy ɛ 4kT.ootnotetextM.E. Glinsky and T.M. O'Neil, Phys. Fluids B 3, 1279 (1991). Energy loss caused by collisions between atoms and plasma positrons is calculated in two ways: For close collisions, a molecular dynamics simulation gives the energy loss; for large-impact parameter collisions, theoretical expressions based on Fokker-Planck theory are employed.ootnotetextEric M. Bass and Daniel H.E. Dubin, Phys. Plasmas 11, 1240 (2004). For a finite magnetic field, the energy loss rate scales as 1/ɛ, just as for infinite field,^2 but with a larger coefficient. A statistical description of energy loss by radiation and Stark mixing will also be discussed.

Finding concealed high atomic numbered materials hidden in cargo containers using dual-energy high-energy x-rays from a linear accelerator with the unique signature from photofission

NASA Astrophysics Data System (ADS)

Clayton, James E.; Bjorkholm, Paul

2006-05-01

The Dual Energy X-ray technique employs two X-ray projection images of an object with X-ray energy spectra at a low X-ray energy and a high X-ray energy. The two energies are both high enough to penetrate all cargoes. The endpoint energies for low and high will be approximately 5-6 MeV and 8-9.5 MeV respectively. These energies are chosen such that pair production is the dominant energy loss mechanism for the high energy mode. By defining the ratio of the transmitted X-ray photon R = T high/T low it can be shown that there is a difference in the ratio that will permit the detection of materials that are significantly higher in atomic number than the low to mid atomic numbered elements that normally appear in the stream of commerce. This difference can be used to assist in the automatic detection of high atomic numbered materials. These materials might be a WMD or dirty bomb. When coupled with detectors that can observe the delayed signature of photon induced fission a confirmation of a WMD may be made. The use of the delayed photons and neutrons from Photofission can confirm the presence of Special Nuclear Materials (SNM). The energy required to induce fission in SNM by a photon is approximately 6 MeV with the maximum fission production rate from X-ray photons in the energy range of 12-15 MeV.

Interfacial Structure and Chemistry of GaN on Ge(111)

NASA Astrophysics Data System (ADS)

Zhang, Siyuan; Zhang, Yucheng; Cui, Ying; Freysoldt, Christoph; Neugebauer, Jörg; Lieten, Ruben R.; Barnard, Jonathan S.; Humphreys, Colin J.

2013-12-01

The interface of GaN grown on Ge(111) by plasma-assisted molecular beam epitaxy is resolved by aberration corrected scanning transmission electron microscopy. A novel interfacial structure with a 5∶4 closely spaced atomic bilayer is observed that explains why the interface is flat, crystalline, and free of GeNx. Density functional theory based total energy calculations show that the interface bilayer contains Ge and Ga atoms, with no N atoms. The 5∶4 bilayer at the interface has a lower energy than a direct stacking of GaN on Ge(111) and enables the 5∶4 lattice-matching growth of GaN.

The Pt site reactivity of the molecular graphs of Au6Pt isomers

NASA Astrophysics Data System (ADS)

Xu, Tianlv; Jenkins, Samantha; Xiao, Chen-Xia; Maza, Julio R.; Kirk, Steven R.

2013-12-01

Within the framework of the theory of atoms in molecules (QTAIM), in an exploratory study we propose a new measure of site reactivity equivalent to the atomic coordination number based purely on the electronic structure. It was found that the number of ring critical points (NNRCPs) positioned on the boundary of the atomic basin of the dopant (Pt) nucleus correlated very well with the relative zero point energy (ZPE) corrected energies. A weaker condition (i.e. than the number of associated bond paths) for the association of the dopant Pt nucleus with the Au6Pt molecular graph is found for NNRCP = 0.

Atomically thick bismuth selenide freestanding single layers achieving enhanced thermoelectric energy harvesting.

PubMed

Sun, Yongfu; Cheng, Hao; Gao, Shan; Liu, Qinghua; Sun, Zhihu; Xiao, Chong; Wu, Changzheng; Wei, Shiqiang; Xie, Yi

2012-12-19

Thermoelectric materials can realize significant energy savings by generating electricity from untapped waste heat. However, the coupling of the thermoelectric parameters unfortunately limits their efficiency and practical applications. Here, a single-layer-based (SLB) composite fabricated from atomically thick single layers was proposed to optimize the thermoelectric parameters fully. Freestanding five-atom-thick Bi(2)Se(3) single layers were first synthesized via a scalable interaction/exfoliation strategy. As revealed by X-ray absorption fine structure spectroscopy and first-principles calculations, surface distortion gives them excellent structural stability and a much increased density of states, resulting in a 2-fold higher electrical conductivity relative to the bulk material. Also, the surface disorder and numerous interfaces in the Bi(2)Se(3) SLB composite allow for effective phonon scattering and decreased thermal conductivity, while the 2D electron gas and energy filtering effect increase the Seebeck coefficient, resulting in an 8-fold higher figure of merit (ZT) relative to the bulk material. This work develops a facile strategy for synthesizing atomically thick single layers and demonstrates their superior ability to optimize the thermoelectric energy harvesting.

An accurate empirical method to predict the adsorption strength for π-orbital contained molecules on two dimensional materials.

PubMed

Li, Hongping; Wang, Changwei; Xun, Suhang; He, Jing; Jiang, Wei; Zhang, Ming; Zhu, Wenshuai; Li, Huaming

2018-06-01

To obtain the adsorption strength is the key point for materials design and parameters optimization in chemical engineering. Here we report a simple but accuracy method to estimate the adsorptive energies by counting the number of π-orbital involved atoms based on theoretical computations for hexagonal boron nitride (h-BN) and graphene. Computational results by density function theory (DFT) as well as spin-component scaled second-order Møller-Plesset perturbation theory (SCS-MP2) both confirm that the adsorptive energies correlate well with the number of π-orbital involved atoms for π-orbital contained molecules. The selected molecules (adsorbates) are commonly used in chemical industry, which contains C, N, S, O atoms. The predicted results for the proposed formulas agree well with the current and previous DFT calculated values both on h-BN and graphene surfaces. Further, it can be also used to predict the adsorptive energies for small π-orbital contained molecules on BN and carbon nanotubes. The interaction type for these adsorptions is typical π-π interaction. Further investigations show that the physical origin of these interactions source from the polar interactions between the adsorbents and adsorbates. Hence, for separation or removal of aromatic molecules, how to modify the aromaticity and polarity of both adsorbents and adsorbates will be the key points for experiments. Copyright © 2018 Elsevier Inc. All rights reserved.

Middle school students' beliefs about matter

NASA Astrophysics Data System (ADS)

Nakhleh, Mary B.; Samarapungavan, Ala; Saglam, Yilmaz

2005-05-01

The objective of this study was to examine middle school students' developing understanding of the nature of matter and to compare middle school students' ideas to those of elementary schools students, as was done by Nakhleh and Samarapungavan [J Res Sci Teach 36(7):777-805, 1999]. Nine middle school students were interviewed using a scripted, semistructured interview. The interview probed students' understanding of the composition and particulate (atomic/molecular) structure of a variety of material substances; the relationship between particulate structure and macroscopic properties such as fluidity and malleability; as well as understanding of processes such as phase transition and dissolving. The results indicate that most of the middle school students interviewed knew that matter was composed of atoms and molecules and some of them were able to use this knowledge to explain some processes such as phase transitions of water. In contrast, almost no elementary students knew that matter was composed of atoms and molecules. However, the middle school students were unable to consistently explain material properties or processes based on their knowledge of material composition. In contrast to elementary school students, who had scientifically inaccurate but relatively consistent (macrocontinuous or macroparticulate) knowledge frameworks, the middle school students could not be classified as having consistent knowledge frameworks because their ideas were very fragmented. The fragmentation of middle school students' ideas about matter probably reflects the difficulty of assimilating the microscopic level scientific knowledge acquired through formal instruction into students' initial macroscopic knowledge frameworks.

Nuclear-size correction to the Lamb shift of one-electron atoms

NASA Astrophysics Data System (ADS)

Yerokhin, Vladimir A.

2011-01-01

The nuclear-size effect on the one-loop self-energy and vacuum polarization is evaluated for the 1s, 2s, 3s, 2p1/2, and 2p3/2 states of hydrogen-like ions. The calculation is performed to all orders in the nuclear binding strength parameter Zα. Detailed comparison is made with previous all-order calculations and calculations based on the expansion in the parameter Zα. Extrapolation of the all-order numerical results obtained toward Z=1 provides results for the radiative nuclear-size effect on the hydrogen Lamb shift.

Can the electronegativity equalization method predict spectroscopic properties?

PubMed

Verstraelen, T; Bultinck, P

2015-02-05

The electronegativity equalization method is classically used as a method allowing the fast generation of atomic charges using a set of calibrated parameters and provided knowledge of the molecular structure. Recently, it has started being used for the calculation of other reactivity descriptors and for the development of polarizable and reactive force fields. For such applications, it is of interest to know whether the method, through the inclusion of the molecular geometry in the Taylor expansion of the energy, would also allow sufficiently accurate predictions of spectroscopic data. In this work, relevant quantities for IR spectroscopy are considered, namely the dipole derivatives and the Cartesian Hessian. Despite careful calibration of parameters for this specific task, it is shown that the current models yield insufficiently accurate results. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of Various Material Properties on the Adhesive Stage of Fretting

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1974-01-01

Various properties of metals and alloys were studied with respect to their effect on the initial stage of the fretting process, namely adhesion. Crystallographic orientation, crystal structure, interfacial binding energies of dissimiliar metal, segregation of alloy constituents and the nature and structure of surface films were found to influence adhesion. High atomic density, low surface energy grain orientations exhibited lower adhesion than other orientations. Knowledge of interfacial surface binding energies assists in predicting adhesive transfer and wear. Selective surface segregation of alloy constituents accomplishes both a reduction in adhesion and improved surface oxidation characteristics. Equivalent surface coverages of various adsorbed species indicate that some are markedly more effective in inhibiting adhesion than others.

Photofragment slice imaging studies of pyrrole and the Xe…pyrrole cluster

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

Rubio-Lago, L.; Zaouris, D.; Sakellariou, Y.

The photolysis of pyrrole has been studied in a molecular beam at wavelengths 250 nm, 240 nm and 193.3 nm, using 2 different carrier gases, He and Xe. A broad bimodal distribution of H atom fragment velocities has been observed at all wavelengths. Near threshold at both 240 and 250 nm, , sharp features have been observed in the fast part of the H-atom distribution. Under appropriate molecular beam conditions, these sharp features and the photolysis of pyrrole at both 240 and 250 nm disappear when using Xe as opposed to He as the carrier gas. We attribute this phenomenonmore » to cluster formation between Xe and pyrrole, and this assumption is supported by observation of resonance enhanced multiphoton ionization spectra for the (Xe…pyrrole) cluster followed by photofragmentation of the nascent cation cluster. Ab initio calculations are performed to support the experimental data. Part of this work is supported by the transfer of knowledge program SOUTHERN DYNAMICS MTKD-CT-2004-014306. The experimental work was performed at the Ultraviolet Laser Facility operating at IESL-FORTH and has been supported in part by the European Commission through the Research Infrastructures activity of FP6 (“Laserlab- Europe” RII3-CT-2003-506350). We also wish to thank the graduate program Applied Molecular Spectroscopy (EPEAEK). Part of this work was supported by the Division of Chemical Sciences, Geosciences and Biosciences, Office of Basic Energy Sciences, US Department of Energy with Battelle Memorial Institute, which operates the Pacific Northwest National Laboratory. Computer resources were provided by the Office of Science, US Department of Energy.« less

Spontaneous sulfur dioxide activation by Group V metal (V, Nb, Ta) atoms in excess argon at cryogenic temperatures.

PubMed

Liu, Xing; Wang, Xuefeng; Wang, Qiang; Andrews, Lester

2013-06-28

Reactions of laser-ablated V, Nb and Ta atoms with SO2 in excess argon during condensation gave new absorptions in the M=O stretching region, which were assigned to metal sulfide oxides SMO2 and anions SMO2(-) (M = V, Nb, Ta). The metal oxide complex OV(η(2)-SO) was also identified through the V=O and the characteristic side-on coordinated S-O stretching modes. The assignments of major vibrational modes were confirmed by appropriate S(18)O2 and (34)SO2 isotopic shifts, and density functional frequency calculations. DFT calculations were employed to study the behavior of reactions of Group V bare metal atoms with SO2, and a representative profile was derived which not only showed the preferred coordinating fashion of metal atoms but also tracked the path of S-O bond activation. The η(2)-O,O' bridge coordinated complexes are preferred with energy decreases of ca. 50 kcal mol(-1) for all three metals, which facilitate the activation of two S-O bonds in succession and finally direct the reaction to the most stable molecules SMO2 (M = V, Nb, Ta) along the potential energy surface (PES). Finally the SMO2 molecules capture electrons to give anions SMO2(-) with about 3.6 eV electron affinities based on DFT calculations.

Machine learning-based screening of complex molecules for polymer solar cells

NASA Astrophysics Data System (ADS)

Jørgensen, Peter Bjørn; Mesta, Murat; Shil, Suranjan; García Lastra, Juan Maria; Jacobsen, Karsten Wedel; Thygesen, Kristian Sommer; Schmidt, Mikkel N.

2018-06-01

Polymer solar cells admit numerous potential advantages including low energy payback time and scalable high-speed manufacturing, but the power conversion efficiency is currently lower than for their inorganic counterparts. In a Phenyl-C_61-Butyric-Acid-Methyl-Ester (PCBM)-based blended polymer solar cell, the optical gap of the polymer and the energetic alignment of the lowest unoccupied molecular orbital (LUMO) of the polymer and the PCBM are crucial for the device efficiency. Searching for new and better materials for polymer solar cells is a computationally costly affair using density functional theory (DFT) calculations. In this work, we propose a screening procedure using a simple string representation for a promising class of donor-acceptor polymers in conjunction with a grammar variational autoencoder. The model is trained on a dataset of 3989 monomers obtained from DFT calculations and is able to predict LUMO and the lowest optical transition energy for unseen molecules with mean absolute errors of 43 and 74 meV, respectively, without knowledge of the atomic positions. We demonstrate the merit of the model for generating new molecules with the desired LUMO and optical gap energies which increases the chance of finding suitable polymers by more than a factor of five in comparison to the randomised search used in gathering the training set.

Second-order relativistic corrections for the S(L=0) states in one- and two-electron atomic systems

NASA Astrophysics Data System (ADS)

Frolov, A. M.; Mitelut, C. C.; Zhong, Z.

2005-01-01

An analytical approach is developed to compute the first- (similar to alpha(2)) and second-order (similar to alpha(4)) relativistic corrections in one- and two-electron atomic systems. The approach is based on the reduction of all operators to divergent (singular) and nondivergent (regular) parts. Then, we show that all the divergent parts from the differentmatrix elements cancel each other. The remaining expression contains only regular operators and its expectation value can be easily computed. Analysis of the S(L = 0) states in such systems is of specific interest since the corresponding operators for these states contain a large number of singularities. For one-electron systems the computed relativistic corrections coincide exactly with the appropriate result that follows from the Taylor expansion of the relativistic (i.e., Dirac) energy. We also discuss an alternative approach that allows one to cancel all singularities by using the so-called operator-compensation technique. This second approach is found to be very effective in applications of more complex systems, such as helium-like atoms and ions, H-2(+)-like ions, and some exotic three-body systems.

Correlation consistent basis sets for actinides. I. The Th and U atoms.

PubMed

Peterson, Kirk A

2015-02-21

New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc - pV nZ - PP and cc - pV nZ - DK3, as well as outer-core correlation (valence + 5s5p5d), cc - pwCV nZ - PP and cc - pwCV nZ - DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Both series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThFn (n = 2 - 4), ThO2, and UFn (n = 4 - 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF4, ThF3, ThF2, and ThO2 are all within their experimental uncertainties. Bond dissociation energies of ThF4 and ThF3, as well as UF6 and UF5, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF4 and ThO2. The DKH3 atomization energy of ThO2 was calculated to be smaller than the DKH2 value by ∼1 kcal/mol.

Probability Distribution of Dose and Dose-Rate Effectiveness Factor for use in Estimating Risks of Solid Cancers From Exposure to Low-Let Radiation.

PubMed

Kocher, David C; Apostoaei, A Iulian; Hoffman, F Owen; Trabalka, John R

2018-06-01

This paper presents an analysis to develop a subjective state-of-knowledge probability distribution of a dose and dose-rate effectiveness factor for use in estimating risks of solid cancers from exposure to low linear energy transfer radiation (photons or electrons) whenever linear dose responses from acute and chronic exposure are assumed. A dose and dose-rate effectiveness factor represents an assumption that the risk of a solid cancer per Gy at low acute doses or low dose rates of low linear energy transfer radiation, RL, differs from the risk per Gy at higher acute doses, RH; RL is estimated as RH divided by a dose and dose-rate effectiveness factor, where RH is estimated from analyses of dose responses in Japanese atomic-bomb survivors. A probability distribution to represent uncertainty in a dose and dose-rate effectiveness factor for solid cancers was developed from analyses of epidemiologic data on risks of incidence or mortality from all solid cancers as a group or all cancers excluding leukemias, including (1) analyses of possible nonlinearities in dose responses in atomic-bomb survivors, which give estimates of a low-dose effectiveness factor, and (2) comparisons of risks in radiation workers or members of the public from chronic exposure to low linear energy transfer radiation at low dose rates with risks in atomic-bomb survivors, which give estimates of a dose-rate effectiveness factor. Probability distributions of uncertain low-dose effectiveness factors and dose-rate effectiveness factors for solid cancer incidence and mortality were combined using assumptions about the relative weight that should be assigned to each estimate to represent its relevance to estimation of a dose and dose-rate effectiveness factor. The probability distribution of a dose and dose-rate effectiveness factor for solid cancers developed in this study has a median (50th percentile) and 90% subjective confidence interval of 1.3 (0.47, 3.6). The harmonic mean is 1.1, which implies that the arithmetic mean of an uncertain estimate of the risk of a solid cancer per Gy at low acute doses or low dose rates of low linear energy transfer radiation is only about 10% less than the mean risk per Gy at higher acute doses. Data were also evaluated to define a low acute dose or low dose rate of low linear energy transfer radiation, i.e., a dose or dose rate below which a dose and dose-rate effectiveness factor should be applied in estimating risks of solid cancers.

Atom Resonance Lines for Modeling Atmosphere: Studies of Pressure-Broadening of Alkali Atom Resonance Lines for Modeling Atmospheres of Extrasolar Giant Planets and Brown Dwarfs

NASA Technical Reports Server (NTRS)

Hasan, Hashima (Technical Monitor); Kirby, K.; Babb, J.; Yoshino, K.

2005-01-01

We report on progress made in a joint program of theoretical and experimental research to study the line-broadening of alkali atom resonance lines due to collisions with species such as helium and molecular hydrogen. Accurate knowledge of the line profiles of Na and K as a function of temperature and pressure will allow such lines to serve as valuable diagnostics of the atmospheres of brown dwarfs and extra-solar giant planets. A new experimental apparatus has been designed, built and tested over the past year, and we are poised to begin collecting data on the first system of interest, the potassium resonance lines perturbed by collisions with helium. On the theoretical front, calculations of line-broadening due to sodium collisions with helium are nearly complete, using accurate molecular potential energy curves and transition moments just recently computed for this system. In addition we have completed calculations of the three relevant potential energy curves and associated transition moments for K - He, using the MOLPRO quantum chemistry codes. Currently, calculations of the potential surfaces describing K-H2 are in progress.

Disorders of metal metabolism

PubMed Central

Ferreira, Carlos R.; Gahl, William A.

2017-01-01

Trace elements are chemical elements needed in minute amounts for normal physiology. Some of the physiologically relevant trace elements include iodine, copper, iron, manganese, zinc, selenium, cobalt and molybdenum. Of these, some are metals, and in particular, transition metals. The different electron shells of an atom carry different energy levels, with those closest to the nucleus being lowest in energy. The number of electrons in the outermost shell determines the reactivity of such an atom. The electron shells are divided in sub-shells, and in particular the third shell has s, p and d sub-shells. Transition metals are strictly defined as elements whose atom has an incomplete d sub-shell. This incomplete d sub-shell makes them prone to chemical reactions, particularly redox reactions. Transition metals of biologic importance include copper, iron, manganese, cobalt and molybdenum. Zinc is not a transition metal, since it has a complete d sub-shell. Selenium, on the other hand, is strictly speaking a nonmetal, although given its chemical properties between those of metals and nonmetals, it is sometimes considered a metalloid. In this review, we summarize the current knowledge on the inborn errors of metal and metalloid metabolism. PMID:29354481

Influence of spokes on the ionized metal flux fraction in chromium high power impulse magnetron sputtering

NASA Astrophysics Data System (ADS)

Biskup, B.; Maszl, C.; Breilmann, W.; Held, J.; Böke, M.; Benedikt, J.; von Keudell, A.

2018-03-01

High power impulse magnetron sputtering (HiPIMS) discharges are an excellent tool for deposition of thin films with superior properties. By adjusting the plasma parameters, an energetic metal and reactive species growth flux can be controlled. This control requires, however, a quantitative knowledge of the ion-to-neutral ratio in the growth flux and of the ion energy distribution function to optimize the deposited energy per incorporated atom in the film. This quantification is performed by combining two diagnostics, a quartz crystal microbalance (QCM) combined with an ion-repelling grid system (IReGS) to discriminate ions versus neutrals and a HIDEN EQP plasma monitor to measure the ion energy distribution function (IEDF). This approach yields the ionized metal flux fraction (IMFF) as the ionization degree in the growth flux. This is correlated to the plasma performance recorded by time resolved ICCD camera measurements, which allow to identify the formation of pronounced ionization zones, so called spokes, in the HiPIMS plasma. Thereby an automatic technique was developed to identify the spoke mode number. The data indicates two distinct regimes with respect to spoke formation that occur with increasing peak power, a stochastic regime with no spokes at low peak powers followed by a regime with distinct spokes at varying mode numbers at higher peak powers. The IMFF increases with increasing peak power reaching values of almost 80% at very high peak powers. The transition in between the two regimes coincides with a pronounced change in the IMFF. This change indicates that the formation of spokes apparently counteracts the return effect in HiPIMS. Based on the IMFF and the mean energy of the ions, the energy per deposited atom together with the overall energy flux onto the substrate is calculated. This allows us to determine an optimum for the peak power density around 0.5 kW cm-2 for chromium HiPIMS.

Is there a Stobbs factor in atomic-resolution STEM-EELS mapping?

PubMed

Xin, Huolin L; Dwyer, Christian; Muller, David A

2014-04-01

Recent work has convincingly argued that the Stobbs factor-disagreement in contrast between simulated and experimental atomic-resolution images-in ADF-STEM imaging can be accounted for by including the incoherent source size in simulation. However, less progress has been made for atomic-resolution STEM-EELS mapping. Here we have performed carefully calibrated EELS mapping experiments of a [101] DyScO3 single-crystal specimen, allowing atomic-resolution EELS signals to be extracted on an absolute scale for a large range of thicknesses. By simultaneously recording the elastic signal, also on an absolute scale, and using it to characterize the source size, sample thickness and inelastic mean free path, we eliminate all free parameters in the simulation of the core-loss signals. Coupled with double channeling simulations that incorporate both core-loss inelastic scattering and dynamical elastic and thermal diffuse scattering, the present work enables a close scrutiny of the scattering physics in the inelastic channel. We found that by taking into account the effective source distribution determined from the ADF images, both the absolute signal and the contrast in atomic-resolution Dy-M5 maps can be closely reproduced by the double-channeling simulations. At lower energy losses, discrepancies are present in the Sc-L2,3 and Dy-N4,5 maps due to the energy-dependent spatial distribution of the background spectrum, core-hole effects, and omitted complexities in the final states. This work has demonstrated the possibility of using quantitative STEM-EELS for element-specific column-by-column atom counting at higher energy losses and for atomic-like final states, and has elucidated several possible improvements for future theoretical work. Copyright © 2014 Elsevier B.V. All rights reserved.

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

2008-06-01

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A˚ Cα RMSD away from the experimentally determined structure.

Lithium-decorated oxidized graphyne for hydrogen storage by first principles study

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

Yan, Zeyu; Wang, Lang; Cheng, Julong

2014-11-07

The geometric stability and hydrogen storage capacity of Li decorated oxidized γ-graphyne are studied based on the first-principles calculations. It is found that oxygen atoms trend to bond with acetylenic carbons and form C=O double bonds on both sides of graphyne. The binding energy of single Li atom on oxidized graphyne is 3.29 eV, owning to the strong interaction between Li atom and O atom. Meanwhile, the dispersion of Li is stable even under a relatively high density. One attached Li atom can at least adsorb six hydrogen molecules around. Benefitting from the porous structure of graphyne and the high attachedmore » Li density, a maximum hydrogen storage density 12.03 wt. % is achieved with four Li atoms in graphyne cell. The corresponding average binding energy is 0.24 eV/H{sub 2}, which is suitable for reversible storage. These results indicate that Li decorated graphyne can serve as a promising hydrogen storage material.« less

Extended wave-packet model to calculate energy-loss moments of protons in matter

NASA Astrophysics Data System (ADS)

Archubi, C. D.; Arista, N. R.

2017-12-01

In this work we introduce modifications to the wave-packet method proposed by Kaneko to calculate the energy-loss moments of a projectile traversing a target which is represented in terms of Gaussian functions for the momentum distributions of electrons in the atomic shells. These modifications are introduced using the Levine and Louie technique to take into account the energy gaps corresponding to the different atomic levels of the target. We use the extended wave-packet model to evaluate the stopping power, the energy straggling, the inverse mean free path, and the ionization cross sections for protons in several targets, obtaining good agreements for all these quantities on an extensive energy range that covers low-, intermediate-, and high-energy regions. The extended wave-packet model proposed here provides a method to calculate in a very straightforward way all the significant terms of the inelastic interaction of light ions with any element of the periodic table.

Laser theory with finite atom-field interacting time

NASA Astrophysics Data System (ADS)

Yu, Deshui; Chen, Jingbiao

2008-07-01

We investigate the influence of atomic transit time τ on the laser linewidth by the quantum Langevin approach. With comparing the bandwidths of cavity mode κ , atomic polarization γab , and atomic transit broadening τ-1 , we study the laser linewidth in different limits. We also discuss the spectrum of fluctuations of output field and the influence of pumping statistics on the output field.The influence of atomic transit time τ on laser field has not been carefully discussed before, to our knowledge. In particular, a laser operating in the region of γab≪τ-1≪κ/2 appears not to have been analyzed in previous laser theories. Our work could be a useful complementarity to laser theory. It is also an important theoretical foundation for the recently proposed active optical atomic clock based on bad-cavity laser mechanism.

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

PubMed Central

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2014-01-01

Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

General Atomics Sciences Education Foundation Outreach Programs

NASA Astrophysics Data System (ADS)

Winter, Patricia S.

1997-11-01

Scientific literacy for all students is a national goal. The General Atomics (GA) Foundation Outreach Program is committed to playing a major role in enhancing pre-college education in science, engineering and new technologies. GA has received wide recognition for its Sciences Education Program, a volunteer effort of GA employees and San Diego science teachers. GA teacher/scientist teams have developed inquiry-based education modules and associated workshops based on areas of core competency at GA: Fusion -- Energy of the Stars; Explorations in Materials Science; Portrait of an Atom; DNA Technology. [http://www.sci-ed-ga.org]. Workshops [teachers receive printed materials and laboratory kits for ``hands-on" modules] have been presented for 700+ teachers from 200+ area schools. Additional workshops include: University of Denver for Denver Public Schools; National Educators Workshop; Standard Experiments in Engineering Materials; Update '96 in Los Alamos; Newspapers in Education Workshop (LA Times); American Chemical Society Regional/National meetings, and California Science Teachers Association Conference. Other outreach includes High School Science Day, school partnerships, teacher and student mentoring and the San Diego Science Alliance [http://www.sdsa.org].

The study of the plasmon modes of square atomic clusters based on the eigen-oscillation equation of charge under the free-electron gas model

NASA Astrophysics Data System (ADS)

Xue, Hong-Jie; Wu, Reng-Lai; Hu, Cheng-Xi; Zhang, Ming

2018-04-01

In atomic clusters, plasmon modes are generally gained by the resonant responses for external fields. However, these resonant methods still carry some defects: some plasmon modes may not have been found as that may not have been excited by the external fields. Recently, by employing the extended Hubbard model to describe electron systems of atomic clusters, we have presented the eigen-oscillation equation of charge to study plasmon modes. In this work, based on the free-electron gas model, we further explore the eigen-equation method. Under different external electric fields, some of the plasmon mode spectrums with obvious differences are found, which display the defects of the resonant methods. All the plasmon modes obtained by the resonant methods are predicted by the eigen-equation method. This effectively shows that the eigen-equation method is feasible and reliable in the process of finding plasmon. In addition, various kinds of plasmons are displayed by charge distributions, and the evolution features of plasmon with system parameters are gained by the energy absorption spectrum.

Comparison of Martian meteorites with earth composition: Study of effective atomic numbers in the energy range 1 keV-100 GeV

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

Ün, Adem, E-mail: ademun25@yahoo.com; Han, İbrahim, E-mail: ibrahimhan25@hotmail.com; Ün, Mümine, E-mail: mun@agri.edu.tr

2016-04-18

Effective atomic (Z{sub eff}) and electron numbers (N{sub eff}) for 24 Martian meteorites have been determined in the energy range from 1 keV to 100 GeV and also for sixteen significant energies of commonly used radioactive sources. The values of Z{sub eff} and N{sub eff} for all sample were obtained from the DirectZeff program. The obtained results for Martian meteorites have been compared with the results for Earth composition and similarities or differences also evaluated.

Trampoline motions in Xe-graphite(0 0 0 1) surface scattering

NASA Astrophysics Data System (ADS)

Watanabe, Yoshimasa; Yamaguchi, Hiroki; Hashinokuchi, Michihiro; Sawabe, Kyoichi; Maruyama, Shigeo; Matsumoto, Yoichiro; Shobatake, Kosuke

2005-09-01

We have investigated Xe scattering from the graphite(0 0 0 1) surface at hyperthermal incident energies using a molecular beam-surface scattering technique and molecular dynamics simulations. For all incident conditions, the incident Xe atom conserves the momentum parallel to the surface and loses approximately 80% of the normal incident energy. The weak interlayer potential of graphite disperses the deformation over the wide range of a graphene sheet. The dynamic corrugation induced by the collision is smooth even at hyperthermal incident energy; the graphene sheet moves like a trampoline net and the Xe atom like a trampoliner.

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.

78 FR 64414 - Assistance to Foreign Atomic Energy Activities

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-29

... DEPARTMENT OF ENERGY 10 CFR Part 810 RIN 1994-AA02 Assistance to Foreign Atomic Energy Activities... Assistance to Foreign Atomic Energy Activities since 1986. The NOPR reflected a need to make the regulations... concerning Assistance to Foreign Atomic Energy Activities since 1986. (76 FR 55278) The NOPR reflected a need...

Fragmentation of ionized doped helium nanodroplets: theoretical evidence for a dopant ejection mechanism.

PubMed

Bonhommeau, D; Lewerenz, M; Halberstadt, N

2008-02-07

We report a theoretical study of the effect induced by a helium nanodroplet environment on the fragmentation dynamics of a dopant. The dopant is an ionized neon cluster Ne(n) (+) (n=4-6) surrounded by a helium nanodroplet composed of 100 atoms. A newly designed mixed quantum/classical approach is used to take into account both the large helium cluster zero-point energy due to the light mass of the helium atoms and all the nonadiabatic couplings between the Ne(n) (+) potential-energy surfaces. The results reveal that the intermediate ionic dopant can be ejected from the droplet, possibly with some helium atoms still attached, thereby reducing the cooling power of the droplet. Energy relaxation by helium atom evaporation and dissociation, the other mechanism which has been used in most interpretations of doped helium cluster dynamics, also exhibits new features. The kinetic energy distribution of the neutral monomer fragments can be fitted to the sum of two Boltzmann distributions, one with a low kinetic energy and the other with a higher kinetic energy. This indicates that cooling by helium atom evaporation is more efficient than was believed so far, as suggested by recent experiments. The results also reveal the predominance of Ne(2) (+) and He(q)Ne(2) (+) fragments and the absence of bare Ne(+) fragments, in agreement with available experimental data (obtained for larger helium nanodroplets). Moreover, the abundance in fragments with a trimeric neon core is found to increase with the increase in dopant size. Most of the fragmentation is achieved within 10 ps and the only subsequent dynamical process is the relaxation of hot intermediate He(q)Ne(2) (+) species to Ne(2) (+) by helium atom evaporation. The dependence of the ionic fragment distribution on the parent ion electronic state reached by ionization is also investigated. It reveals that He(q)Ne(+) fragments are produced only from the highest electronic state, whereas He(q)Ne(2) (+) fragments originate from all the electronic states. Surprisingly, the highest electronic states also lead to fragments that still contain the original ionic dopant species. A mechanism is conjectured to explain this fragmentation inhibition.

Single d-metal atoms on F(s) and F(s+) defects of MgO(001): a theoretical study across the periodic table.

PubMed

Neyman, Konstantin M; Inntam, Chan; Matveev, Alexei V; Nasluzov, Vladimir A; Rösch, Notker

2005-08-24

Single d-metal atoms on oxygen defects F(s) and F(s+) of the MgO(001) surface were studied theoretically. We employed an accurate density functional method combined with cluster models, embedded in an elastic polarizable environment, and we applied two gradient-corrected exchange-correlation functionals. In this way, we quantified how 17 metal atoms from groups 6-11 of the periodic table (Cu, Ag, Au; Ni, Pd, Pt; Co, Rh, Ir; Fe, Ru, Os; Mn, Re; and Cr, Mo, W) interact with terrace sites of MgO. We found bonding with F(s) and F(s+) defects to be in general stronger than that with O2- sites, except for Mn-, Re-, and Fe/F(s) complexes. In M/F(s) systems, electron density is accumulated on the metal center in a notable fashion. The binding energy on both kinds of O defects increases from 3d- to 4d- to 5d-atoms of a given group, at variance with the binding energy trend established earlier for the M/O2- complexes, 4d < 3d < 5d. Regarding the evolution of the binding energy along a period, group 7 atoms are slightly destabilized compared to their group 6 congeners in both the F(s) and F(s+) complexes; for later transition elements, the binding energy increases gradually up to group 10 and finally decreases again in group 11, most strongly on the F(s) site. This trend is governed by the negative charge on the adsorbed atoms. We discuss implications for an experimental detection of metal atoms on oxide supports based on computed core-level energies.

Atomic Data for the CHIANTI Database

NASA Technical Reports Server (NTRS)

Bhatia, Anand K.; Landi, E.

2012-01-01

The CHIANTI spectral code consists of an atomic database and a suite of computer programs to calculate the optically thin spectrum of astrophysical objects and to carry out spectroscopic plasma diagnostics. The database includes atomic energy levels, wavelengths, radiative transition rates, collisional excitation, ionization and recombination rate coefficients, as well as data to calculate free-free, free-bound and two-photon continuum emission. In recent years, we have been pursuing a program to calculate atomic data for ions whose lines have been observed in astrophysical spectra but have been neglected in the literature, and to provide CHIANTI with all the data necessary to predict line intensities. There are two types of such ions: those for which calculations are available for low-energy configurations but not for high-energy configurations (i.e., C-like, N-like, O-like systems), and ions that have never or only seldom been studied. This poster will summarize the current status of this project and indicate the future activities .

Hydrogen atom addition to the surface of graphene nanoflakes: A density functional theory study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto

2017-02-01

Polycyclic aromatic hydrocarbons (PAHs) provide a 2-dimensional (2D) reaction surface in 3-dimensional (3D) interstellar space and have been utilized as a model of graphene surfaces. In the present study, the reaction of PAHs with atomic hydrogen was investigated by means of density functional theory (DFT) to systematically elucidate the binding nature of atomic hydrogen to graphene nanoflakes. PAHs with n = 4-37 were chosen, where n indicates the number of benzene rings. Activation energies of hydrogen addition to the graphene surface were calculated to be 5.2-7.0 kcal/mol at the CAM-B3LYP/6-311G(d,p) level, which is almost constant for all PAHs. The binding energies of hydrogen atom were slightly dependent on the size (n): 14.8-28.5 kcal/mol. The absorption spectra showed that a long tail is generated at the low-energy region after hydrogen addition to the graphene surface. The electronic states of hydrogenated graphenes were discussed on the basis of theoretical results.

VoroMQA: Assessment of protein structure quality using interatomic contact areas.

PubMed

Olechnovič, Kliment; Venclovas, Česlovas

2017-06-01

In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge-based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue-residue or atom-atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation-based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single-model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa. Proteins 2017; 85:1131-1145. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

ISPE: A knowledge-based system for fluidization studies. 1990 Annual report

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

Reddy, S.

1991-01-01

Chemical engineers use mathematical simulators to design, model, optimize and refine various engineering plants/processes. This procedure requires the following steps: (1) preparation of an input data file according to the format required by the target simulator; (2) excecuting the simulation; and (3) analyzing the results of the simulation to determine if all ``specified goals`` are satisfied. If the goals are not met, the input data file must be modified and the simulation repeated. This multistep process is continued until satisfactory results are obtained. This research was undertaken to develop a knowledge based system, IPSE (Intelligent Process Simulation Environment), that canmore » enhance the productivity of chemical engineers/modelers by serving as an intelligent assistant to perform a variety tasks related to process simulation. ASPEN, a widely used simulator by the US Department of Energy (DOE) at Morgantown Energy Technology Center (METC) was selected as the target process simulator in the project. IPSE, written in the C language, was developed using a number of knowledge-based programming paradigms: object-oriented knowledge representation that uses inheritance and methods, rulebased inferencing (includes processing and propagation of probabilistic information) and data-driven programming using demons. It was implemented using the knowledge based environment LASER. The relationship of IPSE with the user, ASPEN, LASER and the C language is shown in Figure 1.« less

10 CFR 810.2 - Scope.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Scope. 810.2 Section 810.2 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.2 Scope. 10 CFR part 810: (a) Applies to all persons subject to the jurisdiction of the United States who engage directly or indirectly in the production of...

10 CFR 810.2 - Scope.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Scope. 810.2 Section 810.2 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.2 Scope. 10 CFR part 810: (a) Applies to all persons subject to the jurisdiction of the United States who engage directly or indirectly in the production of...

10 CFR 810.2 - Scope.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Scope. 810.2 Section 810.2 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.2 Scope. 10 CFR part 810: (a) Applies to all persons subject to the jurisdiction of the United States who engage directly or indirectly in the production of...

10 CFR 810.2 - Scope.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Scope. 810.2 Section 810.2 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.2 Scope. 10 CFR part 810: (a) Applies to all persons subject to the jurisdiction of the United States who engage directly or indirectly in the production of...

10 CFR 810.2 - Scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Scope. 810.2 Section 810.2 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.2 Scope. 10 CFR part 810: (a) Applies to all persons subject to the jurisdiction of the United States who engage directly or indirectly in the production of...

Low-loss electron energy loss spectroscopy: An atomic-resolution complement to optical spectroscopies and application to graphene

DOE PAGES

Kapetanakis, Myron; Zhou, Wu; Oxley, Mark P.; ...

2015-09-25

Photon-based spectroscopies have played a central role in exploring the electronic properties of crystalline solids and thin films. They are a powerful tool for probing the electronic properties of nanostructures, but they are limited by lack of spatial resolution. On the other hand, electron-based spectroscopies, e.g., electron energy loss spectroscopy (EELS), are now capable of subangstrom spatial resolution. Core-loss EELS, a spatially resolved analog of x-ray absorption, has been used extensively in the study of inhomogeneous complex systems. In this paper, we demonstrate that low-loss EELS in an aberration-corrected scanning transmission electron microscope, which probes low-energy excitations, combined with amore » theoretical framework for simulating and analyzing the spectra, is a powerful tool to probe low-energy electron excitations with atomic-scale resolution. The theoretical component of the method combines density functional theory–based calculations of the excitations with dynamical scattering theory for the electron beam. We apply the method to monolayer graphene in order to demonstrate that atomic-scale contrast is inherent in low-loss EELS even in a perfectly periodic structure. The method is a complement to optical spectroscopy as it probes transitions entailing momentum transfer. The theoretical analysis identifies the spatial and orbital origins of excitations, holding the promise of ultimately becoming a powerful probe of the structure and electronic properties of individual point and extended defects in both crystals and inhomogeneous complex nanostructures. The method can be extended to probe magnetic and vibrational properties with atomic resolution.« less

TheoReTS - An information system for theoretical spectra based on variational predictions from molecular potential energy and dipole moment surfaces

NASA Astrophysics Data System (ADS)

Rey, Michaël; Nikitin, Andrei V.; Babikov, Yurii L.; Tyuterev, Vladimir G.

2016-09-01

Knowledge of intensities of rovibrational transitions of various molecules and theirs isotopic species in wide spectral and temperature ranges is essential for the modeling of optical properties of planetary atmospheres, brown dwarfs and for other astrophysical applications. TheoReTS ("Theoretical Reims-Tomsk Spectral data") is an Internet accessible information system devoted to ab initio based rotationally resolved spectra predictions for some relevant molecular species. All data were generated from potential energy and dipole moment surfaces computed via high-level electronic structure calculations using variational methods for vibration-rotation energy levels and transitions. When available, empirical corrections to band centers were applied, all line intensities remaining purely ab initio. The current TheoReTS implementation contains information on four-to-six atomic molecules, including phosphine, methane, ethylene, silane, methyl-fluoride, and their isotopic species 13CH4 , 12CH3D , 12CH2D2 , 12CD4 , 13C2H4, … . Predicted hot methane line lists up to T = 2000 K are included. The information system provides the associated software for spectra simulation including absorption coefficient, absorption and emission cross-sections, transmittance and radiance. The simulations allow Lorentz, Gauss and Voight line shapes. Rectangular, triangular, Lorentzian, Gaussian, sinc and sinc squared apparatus function can be used with user-defined specifications for broadening parameters and spectral resolution. All information is organized as a relational database with the user-friendly graphical interface according to Model-View-Controller architectural tools. The full-featured web application is written on PHP using Yii framework and C++ software modules. In case of very large high-temperature line lists, a data compression is implemented for fast interactive spectra simulations of a quasi-continual absorption due to big line density. Applications for the TheoReTS may include: education/training in molecular absorption/emission, radiative and non-LTE processes, spectroscopic applications, opacity calculations for planetary and astrophysical applications. The system is freely accessible via internet on the two mirror sites: in Reims, France

Partially ionized hydrogen plasma in strong magnetic fields.

PubMed

Potekhin, A Y; Chabrier, G; Shibanov, Y A

1999-08-01

We study the thermodynamic properties of a partially ionized hydrogen plasma in strong magnetic fields, B approximately 10(12)-10(13) G, typical of neutron stars. The properties of the plasma depend significantly on the quantum-mechanical sizes and binding energies of the atoms, which are strongly modified by thermal motion across the field. We use new fitting formulas for the atomic binding energies and sizes, based on accurate numerical calculations and valid for any state of motion of the atom. In particular, we take into account decentered atomic states, neglected in previous studies of thermodynamics of magnetized plasmas. We also employ analytic fits for the thermodynamic functions of nonideal fully ionized electron-ion Coulomb plasmas. This enables us to construct an analytic model of the free energy. An ionization equilibrium equation is derived, taking into account the strong magnetic field effects and the nonideality effects. This equation is solved by an iteration technique. Ionization degrees, occupancies, and the equation of state are calculated.