Quantum Engineering of Strongly Correlated Matter with Ultracold Fermi Gases

DTIC Science & Technology

2013-05-01

aim at realizing model systems of strongly correlated, disordered electrons using ultracold fermionic atoms stored in an optical "crystal". The general...theme is to study high-temperature superfluids, Fermi liquids ("metals") and insulators in the presence of disordered impurities whose influence on...Presidential Early Career Award for Science and Education (PECASE). In this program, we aim at realizing model systems of strongly correlated, disordered

Alkyl hydrogen atom abstraction reactions of the CN radical with ethanol

NASA Astrophysics Data System (ADS)

Athokpam, Bijyalaxmi; Ramesh, Sai G.

2018-04-01

We present a study of the abstraction of alkyl hydrogen atoms from the β and α positions of ethanol by the CN radical in solution using the Empirical Valence Bond (EVB) method. We have built separate 2 × 2 EVB models for the Hβ and Hα reactions, where the atom transfer is parameterized using ab initio calculations. The intra- and intermolecular potentials of the reactant and product molecules were modelled with the General AMBER Force Field, with some modifications. We have carried out the dynamics in water and chloroform, which are solvents of contrasting polarity. We have computed the potential of mean force for both abstractions in each of the solvents. They are found to have a small and early barrier along the reaction coordinate with a large energy release. Analyzing the solvent structure around the reaction system, we have found two solvents to have little effect on either reaction. Simulating the dynamics from the transition state, we also study the fate of the energies in the HCN vibrational modes. The HCN molecule is born vibrationally hot in the CH stretch in both reactions and additionally in the HCN bends for the Hα abstraction reaction. In the early stage of the dynamics, we find that the CN stretch mode gains energy at the expense of the energy in CH stretch mode.

Barrierless growth of precursor-free, ultrafast laser-fragmented noble metal nanoparticles by colloidal atom clusters - A kinetic in situ study.

PubMed

Jendrzej, Sandra; Gökce, Bilal; Amendola, Vincenzo; Barcikowski, Stephan

2016-02-01

Unintended post-synthesis growth of noble metal colloids caused by excess amounts of reactants or highly reactive atom clusters represents a fundamental problem in colloidal chemistry, affecting product stability or purity. Hence, quantified kinetics could allow defining nanoparticle size determination in dependence of the time. Here, we investigate in situ the growth kinetics of ps pulsed laser-fragmented platinum nanoparticles in presence of naked atom clusters in water without any influence of reducing agents or surfactants. The nanoparticle growth is investigated for platinum covering a time scale of minutes to 50days after nanoparticle generation, it is also supplemented by results obtained from gold and palladium. Since a minimum atom cluster concentration is exceeded, a significant growth is determined by time resolved UV/Vis spectroscopy, analytical disc centrifugation, zeta potential measurement and transmission electron microscopy. We suggest a decrease of atom cluster concentration over time, since nanoparticles grow at the expense of atom clusters. The growth mechanism during early phase (<1day) of laser-synthesized colloid is kinetically modeled by rapid barrierless coalescence. The prolonged slow nanoparticle growth is kinetically modeled by a combination of coalescence and Lifshitz-Slyozov-Wagner kinetic for Ostwald ripening, validated experimentally by the temperature dependence of Pt nanoparticle size and growth quenching by Iodide anions. Copyright © 2015. Published by Elsevier Inc.

The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage.

PubMed

Linhananta, Apichart; Boer, Jesse; MacKay, Ian

2005-03-15

The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial alpha-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

The equilibrium properties and folding kinetics of an all-atom Go xAF model of the Trp-cage

NASA Astrophysics Data System (ADS)

Linhananta, Apichart; Boer, Jesse; MacKay, Ian

2005-03-01

The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go ¯ model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial α-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

Modeling and Reality in Early Twentieth-Century Physics

NASA Astrophysics Data System (ADS)

Seth, Suman

2011-04-01

Towards the end of 1913, Arnold Sommerfeld, Professor of theoretical physics at Munich University, sent a letter of congratulations to a young Niels Bohr. The Dane's now-classic trilogy of papers, which coupled Rutherford's conception of the atom with a ``planetary'' configuration of electrons, had just appeared. Sommerfeld saw the calculation of the Rydberg constant as a singular triumph and immediately spotted an opportunity to try to explain the Zeeman effect. Yet he also sounded a note of caution, confessing that he remained ``somewhat skeptical'' of atomic models in general. In this, of course, he was hardly alone. Bohr's atom was a particularly egregious example of a peculiar model, one requiring what even its creator considered ``horrid assumptions.'' Nonetheless, success bred conviction. Expanding upon Bohr's original ideas, Sommerfeld soon produced the so-called ``Bohr-Sommerfeld quantization conditions,'' using them to calculate a myriad of results. Experimental evidence, Sommerfeld argued in 1915, showed that quantised electron-paths ``correspond exactly to reality'' and possess ``real existence.'' This kind of realism would not, of course, last long. In 1925, Werner Heisenberg (earlier a student of Sommerfeld's) made scepticism about the details of the Bohr model into a methodological dictum, one later enshrined in the ``Copenhagen interpretation'' of quantum mechanics. This paper uses Sommerfeld's work from the turn of the twentieth century to the mid-1920s as a window onto a landscape involving multiple contestations over the legitimacy of atomic modelling. The surprise that greeted Heisenberg's and others' phenomenological insistences, we will see, can only be understood with reference to what should be considered a ``realist interlude'' in the history of twentieth century atomic physics, one inspired by the astonishing successes of Rutherford's and Bohr's imaginings.

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

PubMed Central

Rottler, Jörg; Plotkin, Steven S.

2016-01-01

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered. PMID:27898663

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy.

PubMed

Habibi, Mona; Rottler, Jörg; Plotkin, Steven S

2016-11-01

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered.

The role of atomic level steric effects and attractive forces in protein folding.

PubMed

Lammert, Heiko; Wolynes, Peter G; Onuchic, José N

2012-02-01

Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C(β) atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Copyright © 2011 Wiley Periodicals, Inc.

Resonant quantum transitions in trapped antihydrogen atoms.

PubMed

Amole, C; Ashkezari, M D; Baquero-Ruiz, M; Bertsche, W; Bowe, P D; Butler, E; Capra, A; Cesar, C L; Charlton, M; Deller, A; Donnan, P H; Eriksson, S; Fajans, J; Friesen, T; Fujiwara, M C; Gill, D R; Gutierrez, A; Hangst, J S; Hardy, W N; Hayden, M E; Humphries, A J; Isaac, C A; Jonsell, S; Kurchaninov, L; Little, A; Madsen, N; McKenna, J T K; Menary, S; Napoli, S C; Nolan, P; Olchanski, K; Olin, A; Pusa, P; Rasmussen, C Ø; Robicheaux, F; Sarid, E; Shields, C R; Silveira, D M; Stracka, S; So, C; Thompson, R I; van der Werf, D P; Wurtele, J S

2012-03-07

The hydrogen atom is one of the most important and influential model systems in modern physics. Attempts to understand its spectrum are inextricably linked to the early history and development of quantum mechanics. The hydrogen atom's stature lies in its simplicity and in the accuracy with which its spectrum can be measured and compared to theory. Today its spectrum remains a valuable tool for determining the values of fundamental constants and for challenging the limits of modern physics, including the validity of quantum electrodynamics and--by comparison with measurements on its antimatter counterpart, antihydrogen--the validity of CPT (charge conjugation, parity and time reversal) symmetry. Here we report spectroscopy of a pure antimatter atom, demonstrating resonant quantum transitions in antihydrogen. We have manipulated the internal spin state of antihydrogen atoms so as to induce magnetic resonance transitions between hyperfine levels of the positronic ground state. We used resonant microwave radiation to flip the spin of the positron in antihydrogen atoms that were magnetically trapped in the ALPHA apparatus. The spin flip causes trapped anti-atoms to be ejected from the trap. We look for evidence of resonant interaction by comparing the survival rate of trapped atoms irradiated with microwaves on-resonance to that of atoms subjected to microwaves that are off-resonance. In one variant of the experiment, we detect 23 atoms that survive in 110 trapping attempts with microwaves off-resonance (0.21 per attempt), and only two atoms that survive in 103 attempts with microwaves on-resonance (0.02 per attempt). We also describe the direct detection of the annihilation of antihydrogen atoms ejected by the microwaves.

Effects of radiation on the incidence of prostate cancer among Nagasaki atomic bomb survivors.

PubMed

Kondo, Hisayoshi; Soda, Midori; Mine, Mariko; Yokota, Kenichi

2013-10-01

Atomic bomb survivors have been reported to have an increased risk of some cancers, especially leukemia. However, the risk of prostate cancer in atomic bomb survivors is not known to have been examined previously. This study examined the association between atomic bomb radiation and the incidence of prostate cancer among male Nagasaki atomic bomb survivors. The subjects were classified by distance from the hypocenter into a proximal group (<2 km), a distal group (≥2 km), and an early entrance group (those who entered the region <2 km from the hypocenter within 2 weeks after the explosion). Between 1996 and 2009, 631 new cases of prostate cancer were identified among approximately 18 400 male Nagasaki atomic bomb survivors who were alive in 1996. The Cox proportional hazard model was used to estimate the risk of prostate cancer development, with adjustment for age at atomic bomb explosion, attained age, smoking status, and alcohol consumption. Compared with the distal group, the proximal group had significant increased risks of total, localized, and high-grade prostate cancer (relative risk and 95% confidence interval: 1.51 [1.21-1.89]; 1.80 [1.26-2.57]; and 1.88 [1.20-2.94], respectively). This report is the first known to reveal a significant relationship between atomic bomb radiation and prostate cancer. © 2013 Japanese Cancer Association.

Resisting the Bohr Atom: The Early British Opposition

NASA Astrophysics Data System (ADS)

Kragh, Helge

2011-03-01

When Niels Bohr's theory of atomic structure appeared in the summer and fall of 1913, it quickly attracted attention among British physicists. While some of the attention was supportive, others was critical. I consider the opposition to Bohr's theory from 1913 to about 1915, including attempts to construct atomic theories on a classical basis as alternatives to Bohr's. I give particular attention to the astrophysicist John W. Nicholson, who was Bohr's most formidable and persistent opponent in the early years. Although in the long run Nicholson's objections were inconsequential, for a short period of time his atomic theory was considered to be a serious rival to Bohr's. Moreover, Nicholson's theory is of interest in its own right.

Cosmology beyond the Standard Model

NASA Astrophysics Data System (ADS)

Wells, Christopher M.

The Standard Model of Cosmology, like its particle physics counterpart, is incomplete in its present form theoretically and observationally. Additional structure, in the form of an early period of accelerated expansion (inflation), is suggested by the special initial conditions required to produce the visible universe. Furthermore, a wide variety of indirect observations indicate that 80% of the mass in the universe is dark. In this thesis, we construct a class of inflation models free from the usual pathologies. In particular, we build a novel realization of hybrid inflation, in which both the inflaton and waterfall degrees of freedom are moduli of a higher dimensional compactification. Because the inflationary fields are realized as global degrees of freedom in the extra dimension, they are protected from the 4D quantum corrections that would otherwise spoil inflation. Via the Ads/CFT correspondence we can relate our construction to a dual theory of composite inflationary degrees of freedom. We then turn to studying the problem of missing matter in the Standard Cosmology. Despite an abundance of indirect observations of dark matter, direct detection experiments have produced conflicting results which seem to point to a more complicated dark sector. In this thesis, we propose that dark matter be made up primarily of non-relativistic bound states, i.e. dark atoms. We explore the atomic parameter space allowed by the demands that dark matter is predominantly atomic and that the dark atoms and ions satisfy observational bounds on dark matter self-interactions. We then study possible interactions between dark matter and normal matter such that dark atoms scatter inelastically from nuclei in direct detection experiments.

Origins of the high flux hohlraum model

NASA Astrophysics Data System (ADS)

Rosen, M. D.; Hinkel, D. E.; Williams, E. A.; Callahan, D. A.; Town, R. P. J.; Scott, H. A.; Kruer, W. L.; Suter, L. J.

2010-11-01

We review how the ``high flux model'' (HFM) helped clarify the performance of the Autumn 09 National Ignition Campaign (NIC) gas filled/capsule imploding hohlraum energetics campaign. This campaign showed good laser-hohlraum coupling, reasonably high drive, and implosion symmetry control via cross beam transfer. Mysteries that remained included the level and spectrum of the Stimulated Raman light, the tendency towards pancaked implosions, and drive that exceeded (standard model) predictions early in the campaign, and lagged those predictions late in the campaign. The HFM uses a detailed configuration accounting (DCA) atomic physics and a generous flux limiter (f=0.2) both of which contribute to predicting a hohlraum plasma that is cooler than the standard, XSN average atom, f=0.05 model. This cooler plasma proved to be key in solving all of those mysteries. Despite past successes of the HFM in correctly modeling Omega Laser Au sphere data and NIC empty hohlraum drive, the model lacked some credibility for this energetics campaign, because it predicted too much hohlraum drive. Its credibility was then boosted by a re-evaluation of the initially reported SRS levels.

Thermonuclear Propaganda: Presentations of Nuclear Strategy in the Early Atomic Age

DTIC Science & Technology

2014-06-01

comics .17 One scholar of atomic culture noted the ambiguity of the duality of the atomic age as a central tenant to building the “most powerful of all...2004). 18 Ferenc Morton Szasz, Atomic Comics : Cartoonists Confront the Nuclear World (Reno, NV: University of Nevada Press, 2012), 135. 19 Ibid...research.archives.gov/description/36952. 28 Osgood, Total Cold War; Szasz, Atomic Comics ; Zeman and Amundson, Atomic Culture, 3-4. 10 the most modern

Living Colloidal Metal Particles from Solvated Metal Atoms. Clustering of Metal Atoms in Organic Media 15.

DTIC Science & Technology

1986-09-23

alchemists , and over the centuries great medicinal powers were ascribed to gold. And as early as 300 A.D. there are references to the 2 consumption of...gold fluid to prolong life. It is doubtful that this was a colloidal solution of gold since aqua regia 3 was unknown to early Chinese alchemists , and

Time-Resolved Study of Nanomorphology and Nanomechanic Change of Early-Stage Mineralized Electrospun Poly(lactic acid) Fiber by Scanning Electron Microscopy, Raman Spectroscopy and Atomic Force Microscopy

PubMed Central

Wang, Mengmeng; Cai, Yin; Zhao, Bo; Zhu, Peizhi

2017-01-01

In this study, scanning electron microscopy (SEM), Raman spectroscopy and high-resolution atomic force microscopy (AFM) were used to reveal the early-stage change of nanomorphology and nanomechanical properties of poly(lactic acid) (PLA) fibers in a time-resolved manner during the mineralization process. Electrospun PLA nanofibers were soaked in simulated body fluid (SBF) for different periods of time (0, 1, 3, 5, 7 and 21 days) at 10 °C, much lower than the conventional 37 °C, to simulate the slow biomineralization process. Time-resolved Raman spectroscopy analysis can confirm that apatites were deposited on PLA nanofibers after 21 days of mineralization. However, there is no significant signal change among several Raman spectra before 21 days. SEM images can reveal the mineral deposit on PLA nanofibers during the process of mineralization. In this work, for the first time, time-resolved AFM was used to monitor early-stage nanomorphology and nanomechanical changes of PLA nanofibers. The Surface Roughness and Young’s Modulus of the PLA nanofiber quantitatively increased with the time of mineralization. The electrospun PLA nanofibers with delicate porous structure could mimic the extracellular matrix (ECM) and serve as a model to study the early-stage mineralization. Tested by the mode of PLA nanofibers, we demonstrated that AFM technique could be developed as a potential diagnostic tool to monitor the early onset of pathologic mineralization of soft tissues. PMID:28817096

The Saga of Light-Matter Interaction and Magneto-optical Effects Applications to Atomic Magnetometry, Laser-cooled Atoms, Atomic Clocks, Geomagnetism, and Plant Bio-magnetism

NASA Astrophysics Data System (ADS)

Corsini, Eric P.

The quest to expand the limited sensorial domain, in particular to bridge the inability to gauge magnetic fields near and far, has driven the fabrication of remedial tools. The interaction of ferromagnetic material with a magnetic field had been the only available technique to gauge that field for several millennium. The advent of electricity and associated classical phenomena captured in the four Maxwell equations, were a step forward. In the early 1900s, the model of quantum mechanics provided a two-way leap forward. One came from the newly understood interaction of light and matter, and more specifically the three-way coupling of photons, atoms' angular momenta, and magnetic field, which are the foundations of atomic magnetometry. The other came from magnetically sensitive quantum effects in a fabricated energy-ladder form of matter cooled to a temperature below that of the energy steps; these quantum effects gave rise to the superconducting quantum interference device (SQUID). Research using atomic magnetometers and SQUIDs has resulted in thousands of publications, text books, and conferences. The current status in each field is well described in Refs. [48,49,38,42] and all references therein. In this work we develop and investigate techniques and applications pertaining to atomic magnetometry. [Full text: eric.corsini gmail.com].

Prediction of Phase Behavior of Spray-Dried Amorphous Solid Dispersions: Assessment of Thermodynamic Models, Standard Screening Methods and a Novel Atomization Screening Device with Regard to Prediction Accuracy

PubMed Central

Chavez, Pierre-François; Meeus, Joke; Robin, Florent; Schubert, Martin Alexander; Somville, Pascal

2018-01-01

The evaluation of drug–polymer miscibility in the early phase of drug development is essential to ensure successful amorphous solid dispersion (ASD) manufacturing. This work investigates the comparison of thermodynamic models, conventional experimental screening methods (solvent casting, quench cooling), and a novel atomization screening device based on their ability to predict drug–polymer miscibility, solid state properties (Tg value and width), and adequate polymer selection during the development of spray-dried amorphous solid dispersions (SDASDs). Binary ASDs of four drugs and seven polymers were produced at 20:80, 40:60, 60:40, and 80:20 (w/w). Samples were systematically analyzed using modulated differential scanning calorimetry (mDSC) and X-ray powder diffraction (XRPD). Principal component analysis (PCA) was used to qualitatively assess the predictability of screening methods with regards to SDASD development. Poor correlation was found between theoretical models and experimentally-obtained results. Additionally, the limited ability of usual screening methods to predict the miscibility of SDASDs did not guarantee the appropriate selection of lead excipient for the manufacturing of robust SDASDs. Contrary to standard approaches, our novel screening device allowed the selection of optimal polymer and drug loading and established insight into the final properties and performance of SDASDs at an early stage, therefore enabling the optimization of the scaled-up late-stage development. PMID:29518936

Highly ionized atoms in cooling gas. [in model for cooling of hot Galactic corona

NASA Technical Reports Server (NTRS)

Edgar, Richard J.; Chevalier, Roger A.

1986-01-01

The ionization of low density gas cooling from a high temperature was calculated. The evolution during the cooling is assumed to be isochoric, isobaric, or a combination of these cases. The calculations are used to predict the column densities and ultraviolet line luminosities of highly ionized atoms in cooling gas. In a model for cooling of a hot galactic corona, it is shown that the observed value of N(N V) can be produced in the cooling gas, while the predicted value of N(Si IV) falls short of the observed value by a factor of about 5. The same model predicts fluxes of ultraviolet emission lines that are a factor of 10 lower than the claimed detections of Feldman, Bruna, and Henry. Predictions are made for ultraviolet lines in cooling flows in early-type galaxies and clusters of galaxies. It is shown that the column densities of interest vary over a fairly narrow range, while the emission line luminosities are simply proportional to the mass inflow rate.

Molecular vibrational energy flow

NASA Astrophysics Data System (ADS)

Gruebele, M.; Bigwood, R.

This article reviews some recent work in molecular vibrational energy flow (IVR), with emphasis on our own computational and experimental studies. We consider the problem in various representations, and use these to develop a family of simple models which combine specific molecular properties (e.g. size, vibrational frequencies) with statistical properties of the potential energy surface and wavefunctions. This marriage of molecular detail and statistical simplification captures trends of IVR mechanisms and survival probabilities beyond the abilities of purely statistical models or the computational limitations of full ab initio approaches. Of particular interest is IVR in the intermediate time regime, where heavy-atom skeletal modes take over the IVR process from hydrogenic motions even upon X H bond excitation. Experiments and calculations on prototype heavy-atom systems show that intermediate time IVR differs in many aspects from the early stages of hydrogenic mode IVR. As a result, IVR can be coherently frozen, with potential applications to selective chemistry.

Early detection of aging cartilage and osteoarthritis in mice and patient samples using atomic force microscopy

NASA Astrophysics Data System (ADS)

Stolz, Martin; Gottardi, Riccardo; Raiteri, Roberto; Miot, Sylvie; Martin, Ivan; Imer, Raphaël; Staufer, Urs; Raducanu, Aurelia; Düggelin, Marcel; Baschong, Werner; Daniels, A. U.; Friederich, Niklaus F.; Aszodi, Attila; Aebi, Ueli

2009-03-01

The pathological changes in osteoarthritis-a degenerative joint disease prevalent among older people-start at the molecular scale and spread to the higher levels of the architecture of articular cartilage to cause progressive and irreversible structural and functional damage. At present, there are no treatments to cure or attenuate the degradation of cartilage. Early detection and the ability to monitor the progression of osteoarthritis are therefore important for developing effective therapies. Here, we show that indentation-type atomic force microscopy can monitor age-related morphological and biomechanical changes in the hips of normal and osteoarthritic mice. Early damage in the cartilage of osteoarthritic patients undergoing hip or knee replacements could similarly be detected using this method. Changes due to aging and osteoarthritis are clearly depicted at the nanometre scale well before morphological changes can be observed using current diagnostic methods. Indentation-type atomic force microscopy may potentially be developed into a minimally invasive arthroscopic tool to diagnose the early onset of osteoarthritis in situ.

Gating of Connexin Channels by transjunctional-voltage: Conformations and models of open and closed states.

PubMed

Bargiello, Thaddeus A; Oh, Seunghoon; Tang, Qingxiu; Bargiello, Nicholas K; Dowd, Terry L; Kwon, Taekyung

2018-01-01

Voltage is an important physiologic regulator of channels formed by the connexin gene family. Connexins are unique among ion channels in that both plasma membrane inserted hemichannels (undocked hemichannels) and intercellular channels (aggregates of which form gap junctions) have important physiological roles. The hemichannel is the fundamental unit of gap junction voltage-gating. Each hemichannel displays two distinct voltage-gating mechanisms that are primarily sensitive to a voltage gradient formed along the length of the channel pore (the transjunctional voltage) rather than sensitivity to the absolute membrane potential (V m or V i-o ). These transjunctional voltage dependent processes have been termed V j - or fast-gating and loop- or slow-gating. Understanding the mechanism of voltage-gating, defined as the sequence of voltage-driven transitions that connect open and closed states, first and foremost requires atomic resolution models of the end states. Although ion channels formed by connexins were among the first to be characterized structurally by electron microscopy and x-ray diffraction in the early 1980's, subsequent progress has been slow. Much of the current understanding of the structure-function relations of connexin channels is based on two crystal structures of Cx26 gap junction channels. Refinement of crystal structure by all-atom molecular dynamics and incorporation of charge changing protein modifications has resulted in an atomic model of the open state that arguably corresponds to the physiologic open state. Obtaining validated atomic models of voltage-dependent closed states is more challenging, as there are currently no methods to solve protein structure while a stable voltage gradient is applied across the length of an oriented channel. It is widely believed that the best approach to solve the atomic structure of a voltage-gated closed ion channel is to apply different but complementary experimental and computational methods and to use the resulting information to derive a consensus atomic structure that is then subjected to rigorous validation. In this paper, we summarize our efforts to obtain and validate atomic models of the open and voltage-driven closed states of undocked connexin hemichannels. This article is part of a Special Issue entitled: Gap Junction Proteins edited by Jean Claude Herve. Copyright © 2017 Elsevier B.V. All rights reserved.

Atomic Oxygen Interactions With Silicone Contamination on Spacecraft in Low Earth Orbit Studied

NASA Technical Reports Server (NTRS)

Banks, Bruce A.

2001-01-01

Silicones have been widely used on spacecraft as potting compounds, adhesives, seals, gaskets, hydrophobic surfaces, and atomic oxygen protective coatings. Contamination of optical and thermal control surfaces on spacecraft in low Earth orbit (LEO) has been an ever-present problem as a result of the interaction of atomic oxygen with volatile species from silicones and hydrocarbons onboard spacecraft. These interactions can deposit a contaminant that is a risk to spacecraft performance because it can form an optically absorbing film on the surfaces of Sun sensors, star trackers, or optical components or can increase the solar absorptance of thermal control surfaces. The transmittance, absorptance, and reflectance of such contaminant films seem to vary widely from very transparent SiOx films to much more absorbing SiOx-based films that contain hydrocarbons. At the NASA Glenn Research Center, silicone contamination that was oxidized by atomic oxygen has been examined from LEO spacecraft (including the Long Duration Exposure Facility and the Mir space station solar arrays) and from ground laboratory LEO simulations. The findings resulted in the development of predictive models that may help explain the underlying issues and effects. Atomic oxygen interactions with silicone volatiles and mixtures of silicone and hydrocarbon volatiles produce glassy SiOx-based contaminant coatings. The addition of hydrocarbon volatiles in the presence of silicone volatiles appears to cause much more absorbing (and consequently less transmitting) contaminant films than when no hydrocarbon volatiles are present. On the basis of the LDEF and Mir results, conditions of high atomic oxygen flux relative to low contaminant flux appear to result in more transparent contaminant films than do conditions of low atomic oxygen flux with high contaminant flux. Modeling predictions indicate that the deposition of contaminant films early in a LEO flight should depend much more on atomic oxygen flux than it does later in a mission.

Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics.

PubMed

Howard, Rebecca J; Trudell, James R; Harris, R Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.

Compositional Pathways and Capillary Effects during Early-stage Isothermal Precipitation in a Nondilute Ni-Al-Cr Alloy

NASA Technical Reports Server (NTRS)

Sudbrack, Chantal K.; Noebe, Ronald D.; Seidman, David N.

2006-01-01

For a Ni-5.2 Al-14.2 Cr at.% alloy with moderate solute supersaturations, the compositional pathways, as measured with atom-probe tomography, during early to later stage y'(LI2)-precipitation (R = 0.45-10 nm), aged at 873 K, are discussed in light of a multi-component coarsening model. Employing nondilute thermodynamics, detailed model analyses during quasistationary coarsening of the experimental data establish that the y/y' interfacial free-energy is 22- 23+/-7 mJ/sq m. Additionally, solute diffusivities are significantly slower than model estimates. Strong quantitative evidence indicates that an observed y'-supersaturation of Al results from the Gibbs-Thomson effect, providing the first experimental verification of this phenomenon. The Gibbs-Thomson relationship, for a ternary system, as well as differences in measured phase equilibria with CALPHAD assessments, are considered in great detail.

Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

PubMed Central

Trudell, James R.; Harris, R. Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy. PMID:24515646

Partial Characterization of a Novel Amphibian Hemoglobin as a Model for Graduate Student Investigation on Peptide Chemistry, Mass Spectrometry, and Atomic Force Microscopy

ERIC Educational Resources Information Center

Bemquerer, Marcelo P.; Macedo, Jessica K. A.; Ribeiro, Ana Carolina J.; Carvalho, Andrea C.; Silva, Debora O. C.; Braz, Juliana M.; Medeiros, Kelliane A.; Sallet, Lunalva A. P.; Campos, Pollyanna F.; Prates, Maura V.; Silva, Luciano P.

2012-01-01

Graduate students in chemistry, and in biological and biomedical fields must learn the fundamentals and practices of peptide and protein chemistry as early as possible. A project-oriented approach was conducted by first-year M.Sc and Ph.D students in biological sciences. A blind glass slide containing a cellular smear and an aqueous cellular…

Spatial Distributions of Metal Atoms During Carbon SWNTs Formation: Measurements and Modelling

NASA Technical Reports Server (NTRS)

Cau, M.; Dorval, N.; Attal-Tretout, B.; Cochon, J. L.; Loiseau, A.; Farhat, S.; Hinkov, I.; Scott, C. D.

2004-01-01

Experiments and modelling have been undertaken to clarify the role of metal catalysts during single-wall carbon nanotube formation. For instance, we wonder whether the metal catalyst is active as an atom, a cluster, a liquid or solid nanoparticle [1]. A reactor has been developed for synthesis by continuous CO2-laser vaporisation of a carbon-nickel-cobalt target in laminar helium flow. The laser induced fluorescence technique [2] is applied for local probing of gaseous Ni, Co and CZ species throughout the hot carbon flow of the target heated up to 3500 K. A rapid depletion of C2 in contrast to the spatial extent of metal atoms is observed in the plume (Fig. 1). This asserts that C2 condenses earlier than Ni and Co atoms.[3, 4]. The depletion is even faster when catalysts are present. It may indicate that an interaction between metal atoms and carbon dimers takes place in the gas as soon as they are expelled from the target surface. Two methods of modelling are used: a spatially I-D calculation developed originally for the arc process [5], and a zero-D time dependent calculation, solving the chemical kinetics along the streamlines [6]. The latter includes Ni cluster formation. The peak of C2 density is calculated close to the target surface where the temperature is the highest. In the hot region, C; is dominant. As the carbon products move away from the target and mix with the ambient helium, they recombine into larger clusters, as demonstrated by the peak of C5 density around 1 mm. The profile of Ni-atom density compares fairly well with the measured one (Fig. 2). The early increase is due to the drop of temperature, and the final decrease beyond 6 mm results from Ni cluster formation at the eutectic temperature (approx.1600 K).

Atomic hydrogen and diatomic titanium-monoxide molecular spectroscopy in laser-induced plasma

NASA Astrophysics Data System (ADS)

Parigger, Christian G.; Woods, Alexander C.

2017-03-01

This article gives a brief review of experimental studies of hydrogen Balmer series emission spectra. Ongoing research aims to evaluate early plasma evolution following optical breakdown in laboratory air. Of interest is as well laser ablation of metallic titanium and characterization of plasma evolution. Emission of titanium monoxide is discussed together with modeling of diatomic spectra to infer temperature. The behavior of titanium particles in plasma draws research interests ranging from the modeling of stellar atmospheres to the enhancement of thin film production via pulsed laser deposition.

Linking protein structure and dynamics to catalysis: the role of hydrogen tunnelling

PubMed Central

Klinman, Judith P

2006-01-01

Early studies of enzyme-catalysed hydride transfer reactions indicated kinetic anomalies that were initially interpreted in the context of a ‘tunnelling correction’. An alternate model for tunnelling emerged following studies of the hydrogen atom transfer catalysed by the enzyme soybean lipoxygenase. This invokes full tunnelling of all isotopes of hydrogen, with reaction barriers reflecting the heavy atom, environmental reorganization terms. Using the latter approach, we offer an integration of the aggregate data implicating hydrogen tunnelling in enzymes (i.e. deviations from Swain–Schaad relationships and the semi-classical temperature dependence of the hydrogen isotope effect). The impact of site-specific mutations of enzymes plays a critical role in our understanding of the factors that control tunnelling in enzyme reactions. PMID:16873120

"Bohr's Atomic Model."

ERIC Educational Resources Information Center

Willden, Jeff

2001-01-01

"Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…

Classical nucleation theory in the phase-field crystal model

NASA Astrophysics Data System (ADS)

Jreidini, Paul; Kocher, Gabriel; Provatas, Nikolas

2018-04-01

A full understanding of polycrystalline materials requires studying the process of nucleation, a thermally activated phase transition that typically occurs at atomistic scales. The numerical modeling of this process is problematic for traditional numerical techniques: commonly used phase-field methods' resolution does not extend to the atomic scales at which nucleation takes places, while atomistic methods such as molecular dynamics are incapable of scaling to the mesoscale regime where late-stage growth and structure formation takes place following earlier nucleation. Consequently, it is of interest to examine nucleation in the more recently proposed phase-field crystal (PFC) model, which attempts to bridge the atomic and mesoscale regimes in microstructure simulations. In this work, we numerically calculate homogeneous liquid-to-solid nucleation rates and incubation times in the simplest version of the PFC model, for various parameter choices. We show that the model naturally exhibits qualitative agreement with the predictions of classical nucleation theory (CNT) despite a lack of some explicit atomistic features presumed in CNT. We also examine the early appearance of lattice structure in nucleating grains, finding disagreement with some basic assumptions of CNT. We then argue that a quantitatively correct nucleation theory for the PFC model would require extending CNT to a multivariable theory.

Classical nucleation theory in the phase-field crystal model.

PubMed

Jreidini, Paul; Kocher, Gabriel; Provatas, Nikolas

2018-04-01

A full understanding of polycrystalline materials requires studying the process of nucleation, a thermally activated phase transition that typically occurs at atomistic scales. The numerical modeling of this process is problematic for traditional numerical techniques: commonly used phase-field methods' resolution does not extend to the atomic scales at which nucleation takes places, while atomistic methods such as molecular dynamics are incapable of scaling to the mesoscale regime where late-stage growth and structure formation takes place following earlier nucleation. Consequently, it is of interest to examine nucleation in the more recently proposed phase-field crystal (PFC) model, which attempts to bridge the atomic and mesoscale regimes in microstructure simulations. In this work, we numerically calculate homogeneous liquid-to-solid nucleation rates and incubation times in the simplest version of the PFC model, for various parameter choices. We show that the model naturally exhibits qualitative agreement with the predictions of classical nucleation theory (CNT) despite a lack of some explicit atomistic features presumed in CNT. We also examine the early appearance of lattice structure in nucleating grains, finding disagreement with some basic assumptions of CNT. We then argue that a quantitatively correct nucleation theory for the PFC model would require extending CNT to a multivariable theory.

Proton-hydrogen collisions for Rydberg n,l-changing transitions in the early Universe

NASA Astrophysics Data System (ADS)

Vrinceanu, Daniel

2013-05-01

Cosmic Microwave Background (CMB) is a vestige radiation generated during the Recombination era, some 390,000 years after the Big Bang, when the Universe had become transparent for the first time. Initial observations of CMB made by the Wilkinson Microwave Anisotropy Probe (WMAP) led to determining the age of the Universe. The mechanisms that drove the recombination have been discovered by using modeling of the primordial plasma and seeking agreement with the observations. The new Plank Surveyor Instrument launched in 2009 is expected to produce data about the recombination era of an unprecedented accuracy, that require including better information regarding the basic atomic physics processes into the present models. In this talk, I will review the results for various Rydberg atom - charge particle collisions and establish their relative importance during the stages of recombination era, with respect to each other and to radiative processes. Energy changing and angular momentum changing collisions with electrons and ions are considered. This work has been supported by NSF through grants to the Institute for Theoretical Atomic and Molecular Physics at Harvard Smithsonian Center for Astrophysics and to the Center for Research on Complex Networks at Texas Southern University.

THE EFFECTS OF INITIAL ABUNDANCES ON NITROGEN IN PROTOPLANETARY DISKS

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

Schwarz, Kamber R.; Bergin, Edwin A.

2014-12-20

The dominant form of nitrogen provided to most solar system bodies is currently unknown, though available measurements show that the detected nitrogen in solar system rocks and ices is depleted with respect to solar abundances and the interstellar medium. We use a detailed chemical/physical model of the chemical evolution of a protoplanetary disk to explore the evolution and abundance of nitrogen-bearing molecules. Based on this model, we analyze how initial chemical abundances provided as either gas or ice during the early stages of disk formation influence which species become the dominant nitrogen bearers at later stages. We find that amore » disk with the majority of its initial nitrogen in either atomic or molecular nitrogen is later dominated by atomic and molecular nitrogen as well as NH{sub 3} and HCN ices, where the dominant species varies with disk radius. When nitrogen is initially in gaseous ammonia, it later becomes trapped in ammonia ice except in the outer disk where atomic nitrogen dominates. For a disk with the initial nitrogen in the form of ammonia ice, the nitrogen remains trapped in the ice as NH{sub 3} at later stages. The model in which most of the initial nitrogen is placed in atomic N best matches the ammonia abundances observed in comets. Furthermore, the initial state of nitrogen influences the abundance of N{sub 2}H{sup +}, which has been detected in protoplanetary disks. Strong N{sub 2}H{sup +} emission is found to be indicative of an N{sub 2} abundance greater than n{sub N{sub 2}}/n{sub H{sub 2}}>10{sup −6} in addition to tracing the CO snow line. Our models also indicate that NO is potentially detectable, with lower N gas abundances leading to higher NO abundances.« less

Smallest Nanoelectronic with Atomic Devices with Precise Structures

NASA Technical Reports Server (NTRS)

Yamada, Toshishige

2000-01-01

Since its invention in 1948, the transistor has revolutionized our everyday life - transistor radios and TV's appeared in the early 1960s, personal computers came into widespread use in the mid-1980s, and cellular phones, laptops, and palm-sized organizers dominated the 1990s. The electronics revolution is based upon transistor miniaturization; smaller transistors are faster, and denser circuitry has more functionality. Transistors in current generation chips are 0.25 micron or 250 nanometers in size, and the electronics industry has completed development of 0.18 micron transistors which will enter production within the next few years. Industry researchers are now working to reduce transistor size down to 0.13 micron - a thousandth of the width of a human hair. However, studies indicate that the miniaturization of silicon transistors will soon reach its limit. For further progress in microelectronics, scientists have turned to nanotechnology to advance the science. Rather than continuing to miniaturize transistors to a point where they become unreliable, nanotechnology offers the new approach of building devices on the atomic scale [see sidebar]. One vision for the next generation of miniature electronics is atomic chain electronics, where devices are composed of atoms aligned on top of a substrate surface in a regular pattern. The Atomic Chain Electronics Project (ACEP) - part of the Semiconductor Device Modeling and Nanotechnology group, Integrated Product Team at the NAS Facility has been developing the theory of understanding atomic chain devices, and the author's patent for atomic chain electronics is now pending.

On the origin of alkali metals in Europa exosphere

NASA Astrophysics Data System (ADS)

Ozgurel, Ozge; Pauzat, Françoise; Ellinger, Yves; Markovits, Alexis; Mousis, Olivier; LCT, LAM

2016-10-01

At a time when Europa is considered as a plausible habitat for the development of an early form of life, of particular concern is the origin of neutral sodium and potassium atoms already detected in its exosphere (together with magnesium though in smaller abundance), since these atoms are known to be crucial for building the necessary bricks of prebiotic species. However their origin and history are still poorly understood. The most likely sources could be exogenous and result from the contamination produced by Io's intense volcanism and/or by meteoritic bombardment. These sources could also be endogenous if these volatile elements originate directly from Europa's icy mantle. Here we explore the possibility that neutral sodium and potassium atoms were delivered to the satellite's surface via the upwelling of ices formed in contact with the hidden ocean. These metallic elements would have been transferred as ions to the ocean at early epochs after Europa's formation, by direct contact of water with the rocky core. During Europa's subsequent cooling, the icy layers formed at the top of the ocean would have kept trapped the sodium and potassium, allowing their future progression to the surface and final identification in the exosphere of the satellite. To support this scenario, we have used chemistry numerical models based on first principle periodic density functional theory (DFT). These models are shown to be well adapted to the description of compact ice and are capable to describe the trapping and neutralization of the initial ions in the ice matrix. The process is found relevant for all the elements considered, alkali metals like Na and K, as well as for Mg and probably for Ca, their respective abundances depending essentially of their solubility and chemical capabilities to blend with water ices.

Geophysical Plasmas and Atmospheric Modeling.

DTIC Science & Technology

1982-01-01

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

Why Not Start with Quarks? Teachers Investigate a Learning Unit on the Subatomic Structure of Matter with 12-Year-Olds

ERIC Educational Resources Information Center

Wiener, Gerfried J.; Schmeling, Sascha M.; Hopf, Martin

2017-01-01

This paper describes the second in a series of studies exploring the acceptance of the subatomic structure of matter by 12-year-olds. The studies focus on a novel learning unit introducing an atomic model from electrons down to quarks, which is aimed to be used at an early stage in the physics curriculum. Three features are fundamental to the…

Atomic Pioneers, Book 2, From the Mid-19th to the Early 20th Century. A World of the Atom Series Booklet.

ERIC Educational Resources Information Center

Hiebert, Ray; Hiebert, Roselyn

This booklet is concerned with the last half of the 19th and the beginning of the 20th century when a great surge of knowledge vital to atomic science took place, as illustrated by work by Faraday, Mendeleev, Roentgen, Becquerel and the Curies. Each succeeding discovery brought atomic science closer to the great breakthrough that marked the close…

Evolution from Rydberg gas to ultracold plasma in a supersonic atomic beam of Xe

NASA Astrophysics Data System (ADS)

Hung, J.; Sadeghi, H.; Schulz-Weiling, M.; Grant, E. R.

2014-08-01

A Rydberg gas of xenon, entrained in a supersonic atomic beam, evolves slowly to form an ultracold plasma. In the early stages of this evolution, when the free-electron density is low, Rydberg atoms undergo long-range \\ell -mixing collisions, yielding states of high orbital angular momentum. The development of high-\\ell states promotes dipole-dipole interactions that help to drive Penning ionization. The electron density increases until it reaches the threshold for avalanche. Ninety μs after the production of a Rydberg gas with the initial state, {{n}_{0}}{{\\ell }_{0}}=42d, a 432 V cm-1 electrostatic pulse fails to separate charge in the excited volume, an effect which is ascribed to screening by free electrons. Photoexcitation cross sections, observed rates of \\ell -mixing, and a coupled-rate-equation model simulating the onset of the electron-impact avalanche point consistently to an initial Rydberg gas density of 5\\times {{10}^{8}}\\;c{{m}^{-3}}.

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

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

None, None

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

DOE PAGES

None, None

2016-03-22

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Highly ionized atoms in cooling gas

NASA Technical Reports Server (NTRS)

Edgar, R. J.; Chevalier, R. A.

1986-01-01

The ionization of low density gas cooling from a high temperature was calculated. The evolution during the cooling is assumed to be isochoric, isobaric, or a combination of these cases. The calculations are used to predict the column densities and ultraviolet line luminosities of highly ionized atoms in cooling gas. In a model for cooling of a hot galactic corona, it is shown that the observed value of N(N V) can be produced in the cooling gas, while the predicted value of N(Si IV) falls short of the observed value by a factor of about 5. The same model predicts fluxes of ultraviolet emission lines that are a factor of 10 lower than the claimed detections of Feldman, Brune, and Henry. Predictions are made for ultraviolet lines in cooling flows in early-type galaxies and clusters of galaxies. It is shown that the column densities of interest vary over a fairly narrow range, while the emission line luminosities are simply proportional to the mass inflow rate.

Polarized Continuum Radiation from Stellar Atmospheres

NASA Astrophysics Data System (ADS)

Harrington, J. Patrick

2015-10-01

Continuum scattering by free electrons can be significant in early type stars, while in late type stars Rayleigh scattering by hydrogen atoms or molecules may be important. Computer programs used to construct models of stellar atmospheres generally treat the scattering of the continuum radiation as isotropic and unpolarized, but this scattering has a dipole angular dependence and will produce polarization. We review an accurate method for evaluating the polarization and limb darkening of the radiation from model stellar atmospheres. We use this method to obtain results for: (i) Late type stars, based on the MARCS code models (Gustafsson et al. 2008), and (ii) Early type stars, based on the NLTE code TLUSTY (Lanz and Hubeny 2003). These results are tabulated at http://www.astro.umd.edu/~jph/Stellar_Polarization.html. While the net polarization vanishes for an unresolved spherical star, this symmetry is broken by rapid rotation or by the masking of part of the star by a binary companion or during the transit of an exoplanet. We give some numerical results for these last cases.

Alpha phase precipitation from phase-separated beta phase in a model Ti-Mo-Al alloy studied by direct coupling of transmission electron microscopy and atom probe tomography

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

Devaraj, Arun; Nag, Soumya; Banerjee, Rajarshi

2013-10-19

The benefit of direct coupling of APT with TEM dark field imaging to investigate early stages of phase transformation in multicomponent alloys is demonstrated by analyzing alpha phase precipitated in a model Ti-10 at% Mo-10 at% Al alloy during annealing at 400oC. Through such a direct coupling approach a thermodynamically unexpected solute partitioning trend between beta matrix and alpha precipitate is observed in the early stages of precipitation, which is explained based on possible nucleation of alpha phase in the Ti rich (Mo and Al depleted regions) created as a result of phase separation in beta matrix. On further highermore » temperature annealing at 600oC for 1 hour, the alpha precipitates were shown to grow and get enriched in Al and further depleted in Mo reaching the thermodynamic equilibrium.« less

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

Atomic-scale models of early-stage alkali depletion and SiO2-rich gel formation in bioactive glasses.

PubMed

Tilocca, Antonio

2015-01-28

Molecular dynamics simulations of Na(+)/H(+)-exchanged 45S5 Bioglass® models reveal that a large fraction of the hydroxyl groups introduced into the proton-exchanged, hydrated glass structure do not initially form covalent bonds with Si and P network formers but remain free and stabilised by the modifier metal cations, whereas substantial Si-OH and P-OH bonding is observed only at higher Na(+)/H(+) exchange levels. The strong affinity between free OH groups and modifier cations in the highly fragmented 45S5 glass structure appears to represent the main driving force for this effect. This suggests an alternative direct route for the formation of a repolymerised silica-rich gel in the early stages of the bioactive mechanism, not considered before, which does not require sequential repeated breakings of Si-O-Si bonds and silanol condensations.

Coarse-grained Simulations of Conformational Changes in Multidrug Resistance Transporters

NASA Astrophysics Data System (ADS)

Jewel, S. M. Yead; Dutta, Prashanta; Liu, Jin

2016-11-01

The overexpression of multidrug resistance (MDR) systems on the gram negative bacteria causes serious problems for treatment of bacterial infectious diseases. The system effectively pumps the antibiotic drugs out of the bacterial cells. During the pumping process one of the MDR components, AcrB undergoes a series of large-scale conformational changes which are responsible for drug recognition, binding and expelling. All-atom simulations are unable to capture those conformational changes because of computational cost. Here, we implement a hybrid coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid, to investigate the proton-dependent conformational changes of AcrB. The simulation results in early stage ( 100 ns) of proton-dependent conformational changes agree with all-atom simulations, validating the coarse-grained model. The coarse-grained force field allows us to explore the process in microsecond simulations. Starting from the crystal structures of Access(A)/Binding(B)/Extrusion(E) monomers in AcrB, we find that deprotonation of Asp407 and Asp408 in monomer E causes a series of large-scale conformational changes from ABE to AAA in absence of drug molecules, which is consistent with experimental findings. This work is supported by NIH Grant: 1R01GM122081-01.

Atomic-scale simulation of dust grain collisions: Surface chemistry and dissipation beyond existing theory

NASA Astrophysics Data System (ADS)

Quadery, Abrar H.; Doan, Baochi D.; Tucker, William C.; Dove, Adrienne R.; Schelling, Patrick K.

2017-10-01

The early stages of planet formation involve steps where submicron-sized dust particles collide to form aggregates. However, the mechanism through which millimeter-sized particles aggregate to kilometer-sized planetesimals is still not understood. Dust grain collision experiments carried out in the environment of the Earth lead to the prediction of a 'bouncing barrier' at millimeter-sizes. Theoretical models, e.g., Johnson-Kendall-Roberts and Derjaguin-Muller-Toporov theories, lack two key features, namely the chemistry of dust grain surfaces, and a mechanism for atomic-scale dissipation of energy. Moreover, interaction strengths in these models are parameterized based on experiments done in the Earth's environment. To address these issues, we performed atomic-scale simulations of collisions between nonhydroxylated and hydroxylated amorphous silica nanoparticles. We used the ReaxFF approach which enables modeling chemical reactions using an empirical potential. We found that nonhydroxylated nanograins tend to adhere with much higher probability than suggested by existing theories. By contrast, hydroxylated nanograins exhibit a strong tendency to bounce. Also, the interaction between dust grains has the characteristics of a strong chemical force instead of weak van der Waals forces. This suggests that the formation of strong chemical bonds and dissipation via internal atomic vibration may result in aggregation beyond what is expected based on our current understanding. Our results also indicate that experiments should more carefully consider surface conditions to mimic the space environment. We also report results of simulations with molten silica nanoparticles. It is found that molten particles are more likely to adhere due to viscous dissipation, which supports theories that suggest aggregation to kilometer scales might require grains to be in a molten state.

Monte Carlo modeling and meteor showers

NASA Technical Reports Server (NTRS)

Kulikova, N. V.

1987-01-01

Prediction of short lived increases in the cosmic dust influx, the concentration in lower thermosphere of atoms and ions of meteor origin and the determination of the frequency of micrometeor impacts on spacecraft are all of scientific and practical interest and all require adequate models of meteor showers at an early stage of their existence. A Monte Carlo model of meteor matter ejection from a parent body at any point of space was worked out by other researchers. This scheme is described. According to the scheme, the formation of ten well known meteor streams was simulated and the possibility of genetic affinity of each of them with the most probable parent comet was analyzed. Some of the results are presented.

Early Events in Insulin Fibrillization Studied by Time-Lapse Atomic Force Microscopy

PubMed Central

Podestà, Alessandro; Tiana, Guido; Milani, Paolo; Manno, Mauro

2006-01-01

The importance of understanding the mechanism of protein aggregation into insoluble amyloid fibrils lies not only in its medical consequences, but also in its more basic properties of self-organization. The discovery that a large number of uncorrelated proteins can form, under proper conditions, structurally similar fibrils has suggested that the underlying mechanism is a general feature of polypeptide chains. In this work, we address the early events preceding amyloid fibril formation in solutions of zinc-free human insulin incubated at low pH and high temperature. Here, we show by time-lapse atomic force microscopy that a steady-state distribution of protein oligomers with a quasiexponential tail is reached within a few minutes after heating. This metastable phase lasts for a few hours, until fibrillar aggregates are observable. Although for such complex systems different aggregation mechanisms can occur simultaneously, our results indicate that the prefibrillar phase is mainly controlled by a simple coagulation-evaporation kinetic mechanism, in which concentration acts as a critical parameter. These experimental facts, along with the kinetic model used, suggest a critical role for thermal concentration fluctuations in the process of fibril nucleation. PMID:16239333

A computer model for liquid jet atomization in rocket thrust chambers

NASA Astrophysics Data System (ADS)

Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Yang, H. Q.; Ibrahim, E.; Chuech, S.; Przekwas, A. J.

1991-12-01

The process of atomization has been used as an efficient means of burning liquid fuels in rocket engines, gas turbine engines, internal combustion engines, and industrial furnaces. Despite its widespread application, this complex hydrodynamic phenomenon has not been well understood, and predictive models for this process are still in their infancy. The difficulty in simulating the atomization process arises from the relatively large number of parameters that influence it, including the details of the injector geometry, liquid and gas turbulence, and the operating conditions. In this study, numerical models are developed from first principles, to quantify factors influencing atomization. For example, the surface wave dynamics theory is used for modeling the primary atomization and the droplet energy conservation principle is applied for modeling the secondary atomization. The use of empirical correlations has been minimized by shifting the analyses to fundamental levels. During applications of these models, parametric studies are performed to understand and correlate the influence of relevant parameters on the atomization process. The predictions of these models are compared with existing experimental data. The main tasks of this study were the following: development of a primary atomization model; development of a secondary atomization model; development of a model for impinging jets; development of a model for swirling jets; and coupling of the primary atomization model with a CFD code.

Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1992-01-01

The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

The physics and early history of the intergalactic medium

NASA Astrophysics Data System (ADS)

Barkana, Rennan; Loeb, Abraham

2007-04-01

The intergalactic medium—the cosmic gas that fills the great spaces between the galaxies—is affected by processes ranging from quantum fluctuations in the very early Universe to radiative emission from newly formed stars. This gives the intergalactic medium a dual role as a powerful probe both of fundamental physics and of astrophysics. The heading of fundamental physics includes conditions in the very early Universe and cosmological parameters that determine the age of the Universe and its matter content. The astrophysics refers to chapters of the long cosmic history of stars and galaxies that are being revealed through the effects of stellar feedback on the cosmic gas. This review describes the physics of the intergalactic medium, focusing on recent theoretical and observational developments in understanding early cosmic history. In particular, the earliest generation of stars is thought to have transformed the Universe from darkness to light and to have had an enormous impact on the intergalactic medium. Half a million years after the Big Bang the Universe was filled with atomic hydrogen. As gravity pulled gas clouds together, the first stars ignited and their radiation turned the surrounding atoms back into free electrons and ions. From the observed spectral absorption signatures of the gas between us and distant sources, we know that the process of reionization pervaded most of space a billion years after the Big Bang, so that only a small fraction of the primordial hydrogen atoms remained between galaxies. Knowing exactly when and how the reionization process happened is a primary goal of cosmologists, because this would tell us when the early stars and black holes formed and in what kinds of galaxies. The distribution and clustering of these galaxies is particularly interesting since it is driven by primordial density fluctuations in the dark matter. Cosmic reionization is beginning to be understood with the help of theoretical models and computer simulations. Numerical simulations of reionization are computationally challenging, as they require radiative transfer across large cosmological volumes as well as sufficiently high resolution to identify the sources of the ionizing radiation in the infant Universe. Rapid progress in our understanding is expected with additional observational input. A wide variety of instruments currently under design—including large-aperture infrared telescopes on the ground or in space (JWST), and low-frequency radio telescope arrays for the detection of redshifted 21 cm radiation—will probe the first sources of light during an epoch in cosmic history that has been largely unexplored so far. The new observations and the challenges for theoretical models and numerical simulations will motivate intense work in this field over the coming decade.

Drag coefficient Variability and Thermospheric models

NASA Astrophysics Data System (ADS)

Moe, Kenneth

Satellite drag coefficients depend upon a variety of factors: The shape of the satellite, its altitude, the eccentricity of its orbit, the temperature and mean molecular mass of the ambient atmosphere, and the time in the sunspot cycle. At altitudes where the mean free path of the atmospheric molecules is large compared to the dimensions of the satellite, the drag coefficients can be determined from the theory of free-molecule flow. The dependence on altitude is caused by the concentration of atomic oxygen which plays an important role by its ability to adsorb on the satellite surface and thereby affect the energy loss of molecules striking the surface. The eccentricity of the orbit determines the satellite velocity at perigee, and therefore the energy of the incident molecules relative to the energy of adsorption of atomic oxygen atoms on the surface. The temperature of the ambient atmosphere determines the extent to which the random thermal motion of the molecules influences the momentum transfer to the satellite. The time in the sunspot cycle affects the ambient temperature as well as the concentration of atomic oxygen at a particular altitude. Tables and graphs will be used to illustrate the variability of drag coefficients. Before there were any measurements of gas-surface interactions in orbit, Izakov and Cook independently made an excellent estimate that the drag coefficient of satellites of compact shape would be 2.2. That numerical value, independent of altitude, was used by Jacchia to construct his model from the early measurements of satellite drag. Consequently, there is an altitude dependent bias in the model. From the sparce orbital experiments that have been done, we know that the molecules which strike satellite surfaces rebound in a diffuse angular distribution with an energy loss given by the energy accommodation coefficient. As more evidence accumulates on the energy loss, more realistic drag coefficients are being calculated. These improved drag coefficients help evaluate the biases in present models. Moreover, they make possible the derivation of accurate densities from accelerometer measurements.

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

Yong-Ki Kim — His Life and Recent Work

NASA Astrophysics Data System (ADS)

Stone, Philip M.

2007-08-01

Dr. Kim made internationally recognized contributions in many areas of atomic physics research and applications, and was still very active when he was killed in an automobile accident. He joined NIST in 1983 after 17 years at the Argonne National Laboratory following his Ph.D. work at the University of Chicago. Much of his early work at Argonne and especially at NIST was the elucidation and detailed analysis of the structure of highly charged ions. He developed a sophisticated, fully relativistic atomic structure theory that accurately predicts atomic energy levels, transition wavelengths, lifetimes, and transition probabilities for a large number of ions. This information has been vital to model the properties of the hot interior of fusion research plasmas, where atomic ions must be described with relativistic atomic structure calculations. In recent years, Dr. Kim worked on the precise calculation of ionization and excitation cross sections of numerous atoms, ions, and molecules that are important in fusion research and in plasma processing for manufacturing semiconductor chips. Dr. Kim greatly advanced the state-of-the-art of calculations for these cross sections through development and implementation of highly innovative methods, including his Binary-Encounter-Bethe (BEB) theory and a scaled plane wave Born (scaled PWB) theory. His methods, using closed quantum mechanical formulas and no adjustable parameters, avoid tedious large-scale computations with main-frame computers. His calculations closely reproduce the results of benchmark experiments as well as large-scale calculations requiring hours of computer time. This recent work on BEB and scaled PWB is reviewed and examples of its capabilities are shown.

Nuclear energy in the service of biomedicine: the U.S. Atomic Energy Commission's radioisotope program, 1946-1950.

PubMed

Creager, Angela N H

2006-01-01

The widespread adoption of radioisotopes as tools in biomedical research and therapy became one of the major consequences of the "physicists' war" for postwar life science. Scientists in the Manhattan Project, as part of their efforts to advocate for civilian uses of atomic energy after the war, proposed using infrastructure from the wartime bomb project to develop a government-run radioisotope distribution program. After the Atomic Energy Bill was passed and before the Atomic Energy Commission (AEC) was formally established, the Manhattan Project began shipping isotopes from Oak Ridge. Scientists and physicians put these reactor-produced isotopes to many of the same uses that had been pioneered with cyclotron-generated radioisotopes in the 1930s and early 1940s. The majority of early AEC shipments were radioiodine and radiophosphorus, employed to evaluate thyroid function, diagnose medical disorders, and irradiate tumors. Both researchers and politicians lauded radioisotopes publicly for their potential in curing diseases, particularly cancer. However, isotopes proved less successful than anticipated in treating cancer and more successful in medical diagnostics. On the research side, reactor-generated radioisotopes equipped biologists with new tools to trace molecular transformations from metabolic pathways to ecosystems. The U.S. government's production and promotion of isotopes stimulated their consumption by scientists and physicians (both domestic and abroad), such that in the postwar period isotopes became routine elements of laboratory and clinical use. In the early postwar years, radioisotopes signified the government's commitment to harness the atom for peace, particularly through contributions to biology, medicine, and agriculture.

Some Reflections on the Periodic Table and Its Use.

ERIC Educational Resources Information Center

Fernelius, W. Conard

1986-01-01

Discusses early periodic tables; effect on the periodic table of atomic numbers; the periodic table in relation to electron distribution in the atoms of elements; terms and concepts related to the table; and the modern basis of the periodic table. Additional comments about these and other topics are included. (JN)

The Reception of J. H. van't Hoff's Theory of the Asymmetric Carbon Atom

ERIC Educational Resources Information Center

Snelders, H. A. M.

1974-01-01

Discusses Jacobus Henricus van't Hoff's revolutionary theory of the asymmetric carbon atom and its early reception among his contemporaries in the Netherlands. Indicates that the extension of the new idea to practical problems gives the impetus to the development of stereochemistry. (CC)

Early Onset of Ground State Deformation in Neutron Deficient Polonium Isotopes

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

Cocolios, T. E.; Van de Walle, J.; ISOLDE, CERN, CH-1211 Geneva 23

2011-02-04

In-source resonant ionization laser spectroscopy of the even-A polonium isotopes {sup 192-210,216,218}Po has been performed using the 6p{sup 3}7s {sup 5}S{sub 2} to 6p{sup 3}7p {sup 5}P{sub 2} ({lambda}=843.38 nm) transition in the polonium atom (Po-I) at the CERN ISOLDE facility. The comparison of the measured isotope shifts in {sup 200-210}Po with a previous data set allows us to test for the first time recent large-scale atomic calculations that are essential to extract the changes in the mean-square charge radius of the atomic nucleus. When going to lighter masses, a surprisingly large and early departure from sphericity is observed, whichmore » is only partly reproduced by beyond mean field calculations.« less

Partitioning experiments in the laser-heated diamond anvil cell: volatile content in the Earth's core.

PubMed

Jephcoat, Andrew P; Bouhifd, M Ali; Porcelli, Don

2008-11-28

The present state of the Earth evolved from energetic events that were determined early in the history of the Solar System. A key process in reconciling this state and the observable mantle composition with models of the original formation relies on understanding the planetary processing that has taken place over the past 4.5Ga. Planetary size plays a key role and ultimately determines the pressure and temperature conditions at which the materials of the early solar nebular segregated. We summarize recent developments with the laser-heated diamond anvil cell that have made possible extension of the conventional pressure limit for partitioning experiments as well as the study of volatile trace elements. In particular, we discuss liquid-liquid, metal-silicate (M-Sil) partitioning results for several elements in a synthetic chondritic mixture, spanning a wide range of atomic number-helium to iodine. We examine the role of the core as a possible host of both siderophile and trace elements and the implications that early segregation processes at deep magma ocean conditions have for current mantle signatures, both compositional and isotopic. The results provide some of the first experimental evidence that the core is the obvious replacement for the long-sought, deep mantle reservoir. If so, they also indicate the need to understand the detailed nature and scale of core-mantle exchange processes, from atomic to macroscopic, throughout the age of the Earth to the present day.

Building chemistry one atom at a time: An investigation of the effects of two curricula in students' understanding of covalent bonding and atomic size

NASA Astrophysics Data System (ADS)

Bull, Barbara Jeanne

Chemists have to rely on models to aid in the explanation of phenomena they experience. Instruction of atomic theory has been used as the introduction and primary model for many concepts in chemistry. Therefore, it is important for students to have a robust understanding of the different atomic models, their relationships and their limitations. Previous research has shown that students have alternative conceptions concerning their interpretation of atomic models, but there is less exploration into how students apply their understanding of atomic structure to other chemical concepts. Therefore, this research concentrated on the development of three Model Eliciting Activities to investigate the most fundamental topic of the atom and how students applied their atomic model to covalent bonding and atomic size. Along with the investigation into students' use of their atomic models, a comparison was included between a traditional chemistry curriculum using an Atoms First approach and Chemistry, Life, the Universe and Everything (CLUE), a NSF-funded general chemistry curriculum. Treatment and Control groups were employed to determine the effectiveness of the curricula in conveying the relationship between atoms, covalent bonds and atomic size. The CLUE students developed a Cloud representation on the Atomic Model Eliciting Activity and maintained this depiction through the Covalent Bonding Model Eliciting Activity. The traditional students more often illustrated the atom using a Bohr representation and continued to apply the same model to their portrayal of covalent bonding. During the analysis of the Atomic Size Model Eliciting Activity, students had difficulty fully supporting their explanation of the atomic size trend. Utilizing the beSocratic platform, an activity was designed to aid students' construction of explanations using Toulmin's Argumentation Pattern. In order to study the effectiveness of the activity, the students were asked questions relating to a four-week long investigation into the identity of an inorganic salt during their laboratory class. Students who completed the activity exhibited an improvement in their explanation of the identity of their salt's cation. After completing the activity, another question was posed about the identity of their anion. Both groups saw a decrease in the percentage of students who included reasoning in their answer; however, the activity group maintained a significantly higher percentage of responses with a reasoning than the control group.

The Tübingen Model-Atom Database: A Revised Aluminum Model Atom and its Application for the Spectral Analysis of White Dwarfs

NASA Astrophysics Data System (ADS)

Löbling, L.

2017-03-01

Aluminum (Al) nucleosynthesis takes place during the asymptotic-giant-branch (AGB) phase of stellar evolution. Al abundance determinations in hot white dwarf stars provide constraints to understand this process. Precise abundance measurements require advanced non-local thermodynamic stellar-atmosphere models and reliable atomic data. In the framework of the German Astrophysical Virtual Observatory (GAVO), the Tübingen Model-Atom Database (TMAD) contains ready-to- use model atoms for elements from hydrogen to barium. A revised, elaborated Al model atom has recently been added. We present preliminary stellar-atmosphere models and emergent Al line spectra for the hot white dwarfs G191-B2B and RE 0503-289.

Making It Visual: Creating a Model of the Atom

ERIC Educational Resources Information Center

Pringle, Rose M.

2004-01-01

This article describes a lesson in which students construct Bohr's planetary model of the atom. Niels Bohr's atomic model provides a framework for discussing with middle and high school students the historical development of our understanding of the structure of the atom. The model constructed in this activity will enable students to visualize the…

Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

ERIC Educational Resources Information Center

Cipolla, Laura; Ferrari, Lia A.

2016-01-01

A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

"Electronium": A Quantum Atomic Teaching Model.

ERIC Educational Resources Information Center

Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John

2002-01-01

Outlines an alternative atomic model to the probability model, the descriptive quantum atomic model Electronium. Discusses the way in which it is intended to support students in learning quantum-mechanical concepts. (Author/MM)

Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Degroh, Kim K.; Auer, Bruce M.; Gebauer, Linda; Edwards, Jonathan L.

1993-01-01

Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) assists in understanding of the mechanisms involved. Thus the reliability of predicting in-space durability of materials based on ground laboratory testing should be improved. A computational model which simulates atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of an assumed mechanistic behavior of atomic oxygen interaction based on in-space atomic oxygen erosion of unprotected polymers and ground laboratory atomic oxygen interaction with protected polymers, prediction of atomic oxygen interaction with protected polymers on LDEF was accomplished. However, the results of these predictions are not consistent with the observed LDEF results at defect sites in protected polymers. Improved agreement between observed LDEF results and predicted Monte Carlo modeling can be achieved by modifying of the atomic oxygen interactive assumptions used in the model. LDEF atomic oxygen undercutting results, modeling assumptions, and implications are presented.

Geometry-dependent atomic multipole models for the water molecule.

PubMed

Loboda, O; Millot, C

2017-10-28

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Geometry-dependent atomic multipole models for the water molecule

NASA Astrophysics Data System (ADS)

Loboda, O.; Millot, C.

2017-10-01

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Estimating Collisionally-Induced Escape Rates of Light Neutrals from Early Mars

NASA Astrophysics Data System (ADS)

Gacesa, M.; Zahnle, K. J.

2016-12-01

Collisions of atmospheric gases with hot oxygen atoms constitute an important non-thermal mechanism of escape of light atomic and molecular species at Mars. In this study, we present revised theoretical estimates of non-thermal escape rates of neutral O, H, He, and H2 based on recent atmospheric density profiles obtained from the NASA Mars Atmosphere and Volatile Evolution (MAVEN) mission and related theoretical models. As primary sources of hot oxygen, we consider dissociative recombination of O2+ and CO2+ molecular ions. We also consider hot oxygen atoms energized in primary and secondary collisions with energetic neutral atoms (ENAs) produced in charge-exchange of solar wind H+ and He+ ions with atmospheric gases1,2. Scattering of hot oxygen and atmospheric species of interest is modeled using fully-quantum reactive scattering formalism3. This approach allows us to construct distributions of vibrationally and rotationally excited states and predict the products' emission spectra. In addition, we estimate formation rates of excited, translationally hot hydroxyl molecules in the upper atmosphere of Mars. The escape rates are calculated from the kinetic energy distributions of the reaction products using an enhanced 1D model of the atmosphere for a range of orbital and solar parameters. Finally, by considering different scenarios, we estimate the influence of these escape mechanisms on the evolution of Mars's atmosphere throughout previous epochs and their impact on the atmospheric D/H ratio. M.G.'s research was supported by an appointment to the NASA Postdoctoral Program at the NASA Ames Research Center, administered by Universities Space Research Association under contract with NASA. 1N. Lewkow and V. Kharchenko, "Precipitation of Energetic Neutral Atoms and Escape Fluxes induced from the Mars Atmosphere", Astroph. J., 790, 98 (2014) 2M. Gacesa, N. Lewkow, and V. Kharchenko, "Non-thermal production and escape of OH from the upper atmosphere of Mars", arXiv:1607.03602 (2016) 3M. Gacesa and V. Kharchenko, "Non-thermal escape of molecular hydrogen from Mars", Geophys. Res. Lett., 39, L10203 (2012).

Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

NASA Astrophysics Data System (ADS)

Biswal, Debasmita; Kusalik, Peter G.

2017-07-01

Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

Why we should teach the Bohr model and how to teach it effectively

NASA Astrophysics Data System (ADS)

McKagan, S. B.; Perkins, K. K.; Wieman, C. E.

2008-06-01

Some education researchers have claimed that we should not teach the Bohr model of the atom because it inhibits students’ ability to learn the true quantum nature of electrons in atoms. Although the evidence for this claim is weak, many have accepted it. This claim has implications for how to present atoms in classes ranging from elementary school to graduate school. We present results from a study designed to test this claim by developing a curriculum on models of the atom, including the Bohr and Schrödinger models. We examine student descriptions of atoms on final exams in transformed modern physics classes using various versions of this curriculum. We find that if the curriculum does not include sufficient connections between different models, many students still have a Bohr-like view of atoms rather than a more accurate Schrödinger model. However, with an improved curriculum designed to develop model-building skills and with better integration between different models, it is possible to get most students to describe atoms using the Schrödinger model. In comparing our results with previous research, we find that comparing and contrasting different models is a key feature of a curriculum that helps students move beyond the Bohr model and adopt Schrödinger’s view of the atom. We find that understanding the reasons for the development of models is much more difficult for students than understanding the features of the models. We also present interactive computer simulations designed to help students build models of the atom more effectively.

The Temporal Evolution of the Nanostructure of a Model Ni-Al-Cr Superalloy

NASA Technical Reports Server (NTRS)

Sudbrack, Chantal K.; Yoon, Kevin E.; Noebe, Ronald D.; Seidman, David N.

2004-01-01

The early to the later stages of precipitation of ordered gamma'-precipitates (L1(sub 2)) in Ni-5.2 Al-14.2 Cr (at.%) are studied at 873 K. Precipitates with radii as small as 0.45 nm are characterized fully by three-dimensional atom-probe (3DAP) microscopy. Contrary to what is often assumed by theory or in models, the average precipitate composition is shown to evolve with time, such that solute concentrations decrease toward an equilibrium value given by the solvus lines. Power-law time dependencies of the number density, mean radius, and supersaturations of Al and Cr are discussed in light of theoretical predictions for Ostwald ripening.

A History of the Atomic Energy Commission

DOE R&D Accomplishments Database

Buck, Alice L.

1983-07-01

This pamphlet traces the history of the US Atomic Energy Commission's twenty-eight year stewardship of the Nation's nuclear energy program, from the signing of the Atomic Energy Act on August 1, 1946 to the signing of the Energy Reorganization Act on October 11, 1974. The Commission's early concentration on the military atom produced sophisticated nuclear weapons for the Nation's defense and made possible the creation of a fleet of nuclear submarines and surface ships. Extensive research in the nuclear sciences resulted in the widespread application of nuclear technology for scientific, medical and industrial purposes, while the passage of the Atomic Energy Act of 1954 made possible the development of a nuclear industry, and enabled the United States to share the new technology with other nations.

A Market-Basket Approach to Predict the Acute Aquatic Toxicity of Munitions and Energetic Materials.

PubMed

Burgoon, Lyle D

2016-06-01

An ongoing challenge in chemical production, including the production of insensitive munitions and energetics, is the ability to make predictions about potential environmental hazards early in the process. To address this challenge, a quantitative structure activity relationship model was developed to predict acute fathead minnow toxicity of insensitive munitions and energetic materials. Computational predictive toxicology models like this one may be used to identify and prioritize environmentally safer materials early in their development. The developed model is based on the Apriori market-basket/frequent itemset mining approach to identify probabilistic prediction rules using chemical atom-pairs and the lethality data for 57 compounds from a fathead minnow acute toxicity assay. Lethality data were discretized into four categories based on the Globally Harmonized System of Classification and Labelling of Chemicals. Apriori identified toxicophores for categories two and three. The model classified 32 of the 57 compounds correctly, with a fivefold cross-validation classification rate of 74 %. A structure-based surrogate approach classified the remaining 25 chemicals correctly at 48 %. This result is unsurprising as these 25 chemicals were fairly unique within the larger set.

Experimental investigation of early-time diffusion in the quantum kicked rotor using a Bose-Einstein condensate.

PubMed

Duffy, G J; Parkins, S; Müller, T; Sadgrove, M; Leonhardt, R; Wilson, A C

2004-11-01

We report measurements of the early-time momentum diffusion for the atom-optical delta-kicked rotor. In this experiment a Bose-Einstein condensate provides a source of ultracold atoms with an ultranarrow initial momentum distribution, which is then subjected to periodic pulses (or "kicks") using an intense far-detuned optical standing wave. We characterize the effect of varying the effective Planck's constant for the system, while keeping all other parameters fixed. The observed behavior includes both quantum resonances (ballistic energy growth) and antiresonances (re-establishment of the initial state). Our experimental results are compared with theoretical predictions.

An important atomic process in the CVD growth of graphene: Sinking and up-floating of carbon atom on copper surface

NASA Astrophysics Data System (ADS)

Li, Yingfeng; Li, Meicheng; Gu, TianSheng; Bai, Fan; Yu, Yue; Trevor, Mwenya; Yu, Yangxin

2013-11-01

By density functional theory (DFT) calculations, the early stages of the growth of graphene on copper (1 1 1) surface are investigated. At the very first time of graphene growth, the carbon atom sinks into subsurface. As more carbon atoms are adsorbed nearby the site, the sunken carbon atom will spontaneously form a dimer with one of the newly adsorbed carbon atoms, and the formed dimer will up-float on the top of the surface. We emphasize the role of the co-operative relaxation of the co-adsorbed carbon atoms in facilitating the sinking and up-floating of carbon atoms. In detail: when two carbon atoms are co-adsorbed, their co-operative relaxation will result in different carbon-copper interactions for the co-adsorbed carbon atoms. This difference facilitates the sinking of a single carbon atom into the subsurface. As a third carbon atom is co-adsorbed nearby, it draws the sunken carbon atom on top of the surface, forming a dimer. Co-operative relaxations of the surface involving all adsorbed carbon atoms and their copper neighbors facilitate these sinking and up-floating processes. This investigation is helpful for the deeper understanding of graphene synthesis and the choosing of optimal carbon sources or process.

The First Reactor, Understanding the Atom Series.

ERIC Educational Resources Information Center

Allardice, Corbin; And Others

This booklet is one of the "Understanding the Atom" Series. Consisting of three sections, it is an account of the development of the first nuclear reactor by a team of scientists led by Enrico Farmi. The first section briefly reviews the early work on nuclear fission and neutron emission, the impact of Einstein's letter to President Roosevelt, the…

H2-based star formation laws in hierarchical models of galaxy formation

NASA Astrophysics Data System (ADS)

Xie, Lizhi; De Lucia, Gabriella; Hirschmann, Michaela; Fontanot, Fabio; Zoldan, Anna

2017-07-01

We update our recently published model for GAlaxy Evolution and Assembly (GAEA), to include a self-consistent treatment of the partition of cold gas in atomic and molecular hydrogen. Our model provides significant improvements with respect to previous ones used for similar studies. In particular, GAEA (I) includes a sophisticated chemical enrichment scheme accounting for non-instantaneous recycling of gas, metals and energy; (II) reproduces the measured evolution of the galaxy stellar mass function; (III) reasonably reproduces the observed correlation between galaxy stellar mass and gas metallicity at different redshifts. These are important prerequisites for models considering a metallicity-dependent efficiency of molecular gas formation. We also update our model for disc sizes and show that model predictions are in nice agreement with observational estimates for the gas, stellar and star-forming discs at different cosmic epochs. We analyse the influence of different star formation laws including empirical relations based on the hydrostatic pressure of the disc, analytic models and prescriptions derived from detailed hydrodynamical simulations. We find that modifying the star formation law does not affect significantly the global properties of model galaxies, neither their distributions. The only quantity showing significant deviations in different models is the cosmic molecular-to-atomic hydrogen ratio, particularly at high redshift. Unfortunately, however, this quantity also depends strongly on the modelling adopted for additional physical processes. Useful constraints on the physical processes regulating star formation can be obtained focusing on low-mass galaxies and/or at higher redshift. In this case, self-regulation has not yet washed out differences imprinted at early time.

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

1993-01-01

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

Operation of the computer model for microenvironment atomic oxygen exposure

NASA Technical Reports Server (NTRS)

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

1995-01-01

A computer model for microenvironment atomic oxygen exposure has been developed to extend atomic oxygen modeling capability to include shadowing and reflections. The model uses average exposure conditions established by the direct exposure model and extends the application of these conditions to treat surfaces of arbitrary shape and orientation.

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

Risk of myelodysplastic syndromes in people exposed to ionizing radiation: a retrospective cohort study of Nagasaki atomic bomb survivors.

PubMed

Iwanaga, Masako; Hsu, Wan-Ling; Soda, Midori; Takasaki, Yumi; Tawara, Masayuki; Joh, Tatsuro; Amenomori, Tatsuhiko; Yamamura, Masaomi; Yoshida, Yoshiharu; Koba, Takashi; Miyazaki, Yasushi; Matsuo, Tatsuki; Preston, Dale L; Suyama, Akihiko; Kodama, Kazunori; Tomonaga, Masao

2011-02-01

The risk of myelodysplastic syndromes (MDS) has not been fully investigated among people exposed to ionizing radiation. We investigate MDS risk and radiation dose-response in Japanese atomic bomb survivors. We conducted a retrospective cohort study by using two databases of Nagasaki atomic bomb survivors: 64,026 people with known exposure distance in the database of Nagasaki University Atomic-Bomb Disease Institute (ABDI) and 22,245 people with estimated radiation dose in the Radiation Effects Research Foundation Life Span Study (LSS). Patients with MDS diagnosed from 1985 to 2004 were identified by record linkage between the cohorts and the Nagasaki Prefecture Cancer Registry. Cox and Poisson regression models were used to estimate relationships between exposure distance or dose and MDS risk. There were 151 patients with MDS in the ABDI cohort and 47 patients with MDS in the LSS cohort. MDS rate increased inversely with exposure distance, with an excess relative risk (ERR) decay per km of 1.2 (95% CI, 0.4 to 3.0; P < .001) for ABDI. MDS risk also showed a significant linear response to exposure dose level (P < .001) with an ERR per Gy of 4.3 (95% CI, 1.6 to 9.5; P < .001). After adjustment for sex, attained age, and birth year, the MDS risk was significantly greater in those exposed when young. A significant linear radiation dose-response for MDS exists in atomic bomb survivors 40 to 60 years after radiation exposure. Clinicians should perform careful long-term follow-up of irradiated people to detect MDS as early as possible.

Thermospheric density and satellite drag modeling

NASA Astrophysics Data System (ADS)

Mehta, Piyush Mukesh

The United States depends heavily on its space infrastructure for a vast number of commercial and military applications. Space Situational Awareness (SSA) and Threat Assessment require maintaining accurate knowledge of the orbits of resident space objects (RSOs) and the associated uncertainties. Atmospheric drag is the largest source of uncertainty for low-perigee RSOs. The uncertainty stems from inaccurate modeling of neutral atmospheric mass density and inaccurate modeling of the interaction between the atmosphere and the RSO. In order to reduce the uncertainty in drag modeling, both atmospheric density and drag coefficient (CD) models need to be improved. Early atmospheric density models were developed from orbital drag data or observations of a few early compact satellites. To simplify calculations, densities derived from orbit data used a fixed CD value of 2.2 measured in a laboratory using clean surfaces. Measurements from pressure gauges obtained in the early 1990s have confirmed the adsorption of atomic oxygen on satellite surfaces. The varying levels of adsorbed oxygen along with the constantly changing atmospheric conditions cause large variations in CD with altitude and along the orbit of the satellite. Therefore, the use of a fixed CD in early development has resulted in large biases in atmospheric density models. A technique for generating corrections to empirical density models using precision orbit ephemerides (POE) as measurements in an optimal orbit determination process was recently developed. The process generates simultaneous corrections to the atmospheric density and ballistic coefficient (BC) by modeling the corrections as statistical exponentially decaying Gauss-Markov processes. The technique has been successfully implemented in generating density corrections using the CHAMP and GRACE satellites. This work examines the effectiveness, specifically the transfer of density models errors into BC estimates, of the technique using the CHAMP and GRACE satellites. Moving toward accurate atmospheric models and absolute densities requires physics based models for CD. Closed-form solutions of CD have been developed and exist for a handful of simple geometries (flat plate, sphere, and cylinder). However, for complex geometries, the Direct Simulation Monte Carlo (DSMC) method is an important tool for developing CD models. DSMC is computationally intensive and real-time simulations for CD are not feasible. Therefore, parameterized models for CD are required. Modeling CD for an RSO requires knowledge of the gas-surface interaction (GSI) that defines the manner in which the atmospheric particles exchange momentum and energy with the surface. The momentum and energy exchange is further influenced by likely adsorption of atomic oxygen that may partially or completely cover the surface. An important parameter that characterizes the GSI is the energy accommodation coefficient, α. An innovative and state-of-the-art technique of developing parameterized drag coefficient models is presented and validated using the GRACE satellite. The effect of gas-surface interactions on physical drag coefficients is examined. An attempt to reveal the nature of gas-surface interactions at altitudes above 500 km is made using the STELLA satellite. A model that can accurately estimate CD has the potential to: (i) reduce the sources of uncertainty in the drag model, (ii) improve density estimates by resolving time-varying biases and moving toward absolute densities, and (iii) increase data sources for density estimation by allowing for the use of a wide range of RSOs as information sources. Results from this work have the potential to significantly improve the accuracy of conjunction analysis and SSA.

Passive Acoustic Leak Detection for Sodium Cooled Fast Reactors Using Hidden Markov Models

NASA Astrophysics Data System (ADS)

Marklund, A. Riber; Kishore, S.; Prakash, V.; Rajan, K. K.; Michel, F.

2016-06-01

Acoustic leak detection for steam generators of sodium fast reactors have been an active research topic since the early 1970s and several methods have been tested over the years. Inspired by its success in the field of automatic speech recognition, we here apply hidden Markov models (HMM) in combination with Gaussian mixture models (GMM) to the problem. To achieve this, we propose a new feature calculation scheme, based on the temporal evolution of the power spectral density (PSD) of the signal. Using acoustic signals recorded during steam/water injection experiments done at the Indira Gandhi Centre for Atomic Research (IGCAR), the proposed method is tested. We perform parametric studies on the HMM+GMM model size and demonstrate that the proposed method a) performs well without a priori knowledge of injection noise, b) can incorporate several noise models and c) has an output distribution that simplifies false alarm rate control.

Self-consistent assessment of Englert-Schwinger model on atomic properties

NASA Astrophysics Data System (ADS)

Lehtomäki, Jouko; Lopez-Acevedo, Olga

2017-12-01

Our manuscript investigates a self-consistent solution of the statistical atom model proposed by Berthold-Georg Englert and Julian Schwinger (the ES model) and benchmarks it against atomic Kohn-Sham and two orbital-free models of the Thomas-Fermi-Dirac (TFD)-λvW family. Results show that the ES model generally offers the same accuracy as the well-known TFD-1/5 vW model; however, the ES model corrects the failure in the Pauli potential near-nucleus region. We also point to the inability of describing low-Z atoms as the foremost concern in improving the present model.

Self-consistent assessment of Englert-Schwinger model on atomic properties.

PubMed

Lehtomäki, Jouko; Lopez-Acevedo, Olga

2017-12-21

Our manuscript investigates a self-consistent solution of the statistical atom model proposed by Berthold-Georg Englert and Julian Schwinger (the ES model) and benchmarks it against atomic Kohn-Sham and two orbital-free models of the Thomas-Fermi-Dirac (TFD)-λvW family. Results show that the ES model generally offers the same accuracy as the well-known TFD-15vW model; however, the ES model corrects the failure in the Pauli potential near-nucleus region. We also point to the inability of describing low-Z atoms as the foremost concern in improving the present model.

Atomistic Simulation of High-Density Uranium Fuels

DOE PAGES

Garcés, Jorge Eduardo; Bozzolo, Guillermo

2011-01-01

We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS) method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1) the trend indicating formation of interfacial compounds, (2) much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3) Si depletion in the Al matrix, (4) an unexpected interaction between Mo and Simore » which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5) the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.« less

Monte Carlo Computational Modeling of Atomic Oxygen Interactions

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Stueber, Thomas J.; Miller, Sharon K.; De Groh, Kim K.

2017-01-01

Computational modeling of the erosion of polymers caused by atomic oxygen in low Earth orbit (LEO) is useful for determining areas of concern for spacecraft environment durability. Successful modeling requires that the characteristics of the environment such as atomic oxygen energy distribution, flux, and angular distribution be properly represented in the model. Thus whether the atomic oxygen is arriving normal to or inclined to a surface and whether it arrives in a consistent direction or is sweeping across the surface such as in the case of polymeric solar array blankets is important to determine durability. When atomic oxygen impacts a polymer surface it can react removing a certain volume per incident atom (called the erosion yield), recombine, or be ejected as an active oxygen atom to potentially either react with other polymer atoms or exit into space. Scattered atoms can also have a lower energy as a result of partial or total thermal accommodation. Many solutions to polymer durability in LEO involve protective thin films of metal oxides such as SiO2 to prevent atomic oxygen erosion. Such protective films also have their own interaction characteristics. A Monte Carlo computational model has been developed which takes into account the various types of atomic oxygen arrival and how it reacts with a representative polymer (polyimide Kapton H) and how it reacts at defect sites in an oxide protective coating, such as SiO2 on that polymer. Although this model was initially intended to determine atomic oxygen erosion behavior at defect sites for the International Space Station solar arrays, it has been used to predict atomic oxygen erosion or oxidation behavior on many other spacecraft components including erosion of polymeric joints, durability of solar array blanket box covers, and scattering of atomic oxygen into telescopes and microwave cavities where oxidation of critical component surfaces can take place. The computational model is a two dimensional model which has the capability to tune the interactions of how the atomic oxygen reacts, scatters, or recombines on polymer or nonreactive surfaces. In addition to the specification of atomic oxygen arrival details, a total of 15 atomic oxygen interaction parameters have been identified as necessary to properly simulate observed interactions and resulting polymer erosion that have been observed in LEO. The tuning of the Monte Carlo model has been accomplished by adjusting interaction parameters so the erosion patterns produced by the model match those from several actual LEO space experiments. Surface texturing in LEO can also be predicted by the model. Such comparison of space tests with ground laboratory experiments have enabled confidence in ground laboratory lifetime prediction of protected polymers. Results of Monte Carlo tuning, examples of surface texturing and undercutting erosion prediction, and several examples of how the model can be used to predict other LEO and Mars orbital space results are presented.

Atomic Force Microscope

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

Day, R.D.; Russell, P.E.

The Atomic Force Microscope (AFM) is a recently developed instrument that has achieved atomic resolution imaging of both conducting and non- conducting surfaces. Because the AFM is in the early stages of development, and because of the difficulty of building the instrument, it is currently in use in fewer than ten laboratories worldwide. It promises to be a valuable tool for obtaining information about engineering surfaces and aiding the .study of precision fabrication processes. This paper gives an overview of AFM technology and presents plans to build an instrument designed to look at engineering surfaces.

Airplanes, Combat and Maintenance Crews, and Air Bases. The World War II and Early Cold War Architectural Legacy of Holloman Air Force Base (ca. 1942-1962)

DTIC Science & Technology

1998-11-01

to develop and build an atomic bomb. The project was under the direction of physicist J. Robert Oppenheimer , a former student at the Los Alamos Ranch...of AAF Facilities (1942- 1943 ) 39 Victory in Sight and the Atomic Age: Consolidation and Disposition of Facilities ( 1943 - 1945 ) 42 Cold War ( 1945 ...Sight and the Atomic Age ( 1943 - 1945 ) 61 Cold War Inception (July 1945 -January 1953) 63 Nuclear Escalation (January 1953-November 1963) 72 Detente

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

In Situ Atom Probe Deintercalation of Lithium-Manganese-Oxide.

PubMed

Pfeiffer, Björn; Maier, Johannes; Arlt, Jonas; Nowak, Carsten

2017-04-01

Atom probe tomography is routinely used for the characterization of materials microstructures, usually assuming that the microstructure is unaltered by the analysis. When analyzing ionic conductors, however, gradients in the chemical potential and the electric field penetrating dielectric atom probe specimens can cause significant ionic mobility. Although ionic mobility is undesirable when aiming for materials characterization, it offers a strategy to manipulate materials directly in situ in the atom probe. Here, we present experimental results on the analysis of the ionic conductor lithium-manganese-oxide with different atom probe techniques. We demonstrate that, at a temperature of 30 K, characterization of the materials microstructure is possible without measurable Li mobility. Also, we show that at 298 K the material can be deintercalated, in situ in the atom probe, without changing the manganese-oxide host structure. Combining in situ atom probe deintercalation and subsequent conventional characterization, we demonstrate a new methodological approach to study ionic conductors even in early stages of deintercalation.

Quantum crystallographic charge density of urea

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

Wall, Michael E.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Quantum crystallographic charge density of urea

DOE PAGES

Wall, Michael E.

2016-06-08

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Molecular dynamics modeling of bonding two materials by atomic scale friction stir welding

NASA Astrophysics Data System (ADS)

Konovalenko S., Iv.; Konovalenko, Ig. S.; Psakhie, S. G.

2017-12-01

Molecular dynamics model of atomic scale friction stir welding has been developed. Formation of a butt joint between two crystallites was modeled by means of rotating rigid conical tool traveling along the butt joint line. The formed joint had an intermixed atomic structure composed of atoms initially belonged to the opposite mated piece of metal. Heat removal was modeled by adding the extra viscous force to peripheral atomic layers. This technique provides the temperature control in the tool-affected zone during welding. Auxiliary vibration action was added to the rotating tool. The model provides the variation of the tool's angular velocity, amplitude, frequency and direction of the auxiliary vibration action to provide modeling different welding modes.

Nanomechanical clues from morphologically normal cervical squamous cells could improve cervical cancer screening

NASA Astrophysics Data System (ADS)

Geng, Li; Feng, Jiantao; Sun, Quanmei; Liu, Jing; Hua, Wenda; Li, Jing; Ao, Zhuo; You, Ke; Guo, Yanli; Liao, Fulong; Zhang, Youyi; Guo, Hongyan; Han, Jinsong; Xiong, Guangwu; Zhang, Lufang; Han, Dong

2015-09-01

Applying an atomic force microscope, we performed a nanomechanical analysis of morphologically normal cervical squamous cells (MNSCs) which are commonly used in cervical screening. Results showed that nanomechanical parameters of MNSCs correlate well with cervical malignancy, and may have potential in cancer screening to provide early diagnosis.Applying an atomic force microscope, we performed a nanomechanical analysis of morphologically normal cervical squamous cells (MNSCs) which are commonly used in cervical screening. Results showed that nanomechanical parameters of MNSCs correlate well with cervical malignancy, and may have potential in cancer screening to provide early diagnosis. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03662c

Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.

PubMed

Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M

2016-09-21

We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.

Mechanics of Nanostructured Porous Silica Aerogel Resulting from Molecular Dynamics Simulations.

PubMed

Patil, Sandeep P; Rege, Ameya; Sagardas; Itskov, Mikhail; Markert, Bernd

2017-06-08

Silica aerogels are nanostructured, highly porous solids which have, compared to other soft materials, special mechanical properties, such as extremely low densities. In the present work, the mechanical properties of silica aerogels have been studied with molecular dynamics (MD) simulations. The aerogel model of 192 000 atoms was created with different densities by direct expansion of β-cristobalite and subjected to series of thermal treatments. Because of the high number of atoms and improved modeling procedure, the proposed model was more stable and showed significant improvement in the smoothness of the resulting stress-strain curves in comparison to previous models. Resulting Poisson's ratio values for silica aerogels lie between 0.18 and 0.21. The elasticity moduli display a power law dependence on the density, with the exponent estimated to be 3.25 ± 0.1. These results are in excellent agreement with reported experimental as well as computational values. Two different deformation scenarios have been discussed. Under tension, the low-density aerogels were more ductile while the denser ones behaved rather brittle. In the compression simulations of low-density aerogels, deformation occurred without significant increase in stress. However, for high densities, atoms offer a higher resistance to the deformation, resulting in a more stiff response and an early densification. The relationship between different mechanical parameters has been found in the cyclic loading simulations of silica aerogels with different densities. The residual strain grows linearly with the applied strain (≥0.16) and can be approximated by a phenomenological relation ϵ p = 1.09ϵ max - 0.12. The dissipation energy also varies with the compressive strain according to a power law with an exponent of 2.31 ± 0.07. Moreover, the tangent modulus under cyclic loading varies exponentially with the compressive strain. The results of the study pave the way toward multiscale modeling of silica as well as reinforced silica aerogels.

LDEF microenvironments, observed and predicted

NASA Astrophysics Data System (ADS)

Bourassa, R. J.; Pippin, H. G.; Gillis, J. R.

1993-04-01

A computer model for prediction of atomic oxygen exposure of spacecraft in low earth orbit, referred to as the primary atomic oxygen model, was originally described at the First Long Duration Exposure Facility (LDEF) Post-Retrieval Symposium. The primary atomic oxygen model accounts for variations in orbit parameters, the condition of the atmosphere, and for the orientation of exposed surfaces relative to the direction of spacecraft motion. The use of the primary atomic oxygen model to define average atomic oxygen exposure conditions for a spacecraft is discussed and a second microenvironments computer model is described that accounts for shadowing and scattering of atomic oxygen by complex surface protrusions and indentations. Comparisons of observed and predicted erosion of fluorinated ethylene propylene (FEP) thermal control blankets using the models are presented. Experimental and theoretical results are in excellent agreement. Work is in progress to expand modeling capability to include ultraviolet radiation exposure and to obtain more detailed information on reflecting and scattering characteristics of material surfaces.

LDEF microenvironments, observed and predicted

NASA Technical Reports Server (NTRS)

Bourassa, R. J.; Pippin, H. G.; Gillis, J. R.

1993-01-01

A computer model for prediction of atomic oxygen exposure of spacecraft in low earth orbit, referred to as the primary atomic oxygen model, was originally described at the First Long Duration Exposure Facility (LDEF) Post-Retrieval Symposium. The primary atomic oxygen model accounts for variations in orbit parameters, the condition of the atmosphere, and for the orientation of exposed surfaces relative to the direction of spacecraft motion. The use of the primary atomic oxygen model to define average atomic oxygen exposure conditions for a spacecraft is discussed and a second microenvironments computer model is described that accounts for shadowing and scattering of atomic oxygen by complex surface protrusions and indentations. Comparisons of observed and predicted erosion of fluorinated ethylene propylene (FEP) thermal control blankets using the models are presented. Experimental and theoretical results are in excellent agreement. Work is in progress to expand modeling capability to include ultraviolet radiation exposure and to obtain more detailed information on reflecting and scattering characteristics of material surfaces.

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

Three-dimensional time-dependent computer modeling of the electrothermal atomizers for analytical spectrometry

NASA Astrophysics Data System (ADS)

Tsivilskiy, I. V.; Nagulin, K. Yu.; Gilmutdinov, A. Kh.

2016-02-01

A full three-dimensional nonstationary numerical model of graphite electrothermal atomizers of various types is developed. The model is based on solution of a heat equation within solid walls of the atomizer with a radiative heat transfer and numerical solution of a full set of Navier-Stokes equations with an energy equation for a gas. Governing equations for the behavior of a discrete phase, i.e., atomic particles suspended in a gas (including gas-phase processes of evaporation and condensation), are derived from the formal equations molecular kinetics by numerical solution of the Hertz-Langmuir equation. The following atomizers test the model: a Varian standard heated electrothermal vaporizer (ETV), a Perkin Elmer standard THGA transversely heated graphite tube with integrated platform (THGA), and the original double-stage tube-helix atomizer (DSTHA). The experimental verification of computer calculations is carried out by a method of shadow spectral visualization of the spatial distributions of atomic and molecular vapors in an analytical space of an atomizer.

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.

Research on System Coherence Evolution of Different Environmental Models

NASA Astrophysics Data System (ADS)

Zhang, Si-Qi; Lu, Jing-Bin; Li, Hong; Liu, Ji-Ping; Zhang, Xiao-Ru; Liu, Han; Liang, Yu; Ma, Ji; Liu, Xiao-Jing; Wu, Xiang-Yao

2018-04-01

In this paper, we have studied the evolution curve of two-level atomic system that the initial state is excited state. At the different of environmental reservoir models, which include the single Lorentzian, ideal photon band-gap, double Lorentzian and square Lorentzian reservoir, we researched the influence of these environmental reservoir models on the evolution of energy level population. At static no modulation, comparing the four environmental models, the atomic energy level population oscillation of square Lorentzian reservoir model is fastest, and the atomic system decoherence is slowest. Under dynamic modulation, comparing the photon band-gap model with the single Lorentzian reservoir model, no matter what form of dynamic modulation, the time of atoms decay to the ground state is longer for the photonic band-gap model. These conclusions make the idea of using the environmental change to modulate the coherent evolution of atomic system become true.

DR-induced Hot Oxygen and Carbon Coronae of Early Mars

NASA Astrophysics Data System (ADS)

Zhao, J.; Chassefiere, E.; Tian, F.; Chaufray, J. Y.; Leblanc, F.

2017-12-01

The evolution of Martian atmosphere is a key aspect to understand the habitability of Mars in time. The distributions of neutral atoms above the exobase of ancient Mars (corona) is important for understanding the interactions between the corona and the solar wind, which could help improving our understanding of the evolution of Martian atmosphere. In this work, a 3-D Monte Carlo Model is built to simulate Martian corona in different period of Mars history based on thermosphere structure corresponding to 1, 3, 10, and 20 times present solar XUV conditions and dissociative recombination (DR) reaction profiles. DR reactions of O2+, CO2+, and CO+ are considered as the sources of primary O and C. Secondary O and C atoms, which are formed through collisions between primaries and background species. We will discuss the dependence of physical properties of Martian corona as functions of solar XUV flux and DR reactions. We will also discuss the potential importance of CO+ DR as a contributor to Martian corona.

Subcellular boron and fluorine distributions with SIMS ion microscopy in BNCT and cancer research

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

Subhash Chandra

2008-05-30

The development of a secondary ion mass spectrometry (SIMS) based technique of Ion Microscopy in boron neutron capture therapy (BNCT) was the main goal of this project, so that one can study the subcellular location of boron-10 atoms and their partitioning between the normal and cancerous tissue. This information is fundamental for the screening of boronated drugs appropriate for neutron capture therapy of cancer. Our studies at Cornell concentrated mainly on studies of glioblastoma multiforme (GBM). The early years of the grant were dedicated to the development of cryogenic methods and correlative microscopic approaches so that a reliable subcellular analysismore » of boron-10 atoms can be made with SIMS. In later years SIMS was applied to animal models and human tissues of GBM for studying the efficacy of potential boronated agents in BNCT. Under this grant the SIMS program at Cornell attained a new level of excellence and collaborative SIMS studies were published with leading BNCT researchers in the U.S.« less

Footprints of electron correlation in strong-field double ionization of Kr close to the sequential-ionization regime

NASA Astrophysics Data System (ADS)

Li, Xiaokai; Wang, Chuncheng; Yuan, Zongqiang; Ye, Difa; Ma, Pan; Hu, Wenhui; Luo, Sizuo; Fu, Libin; Ding, Dajun

2017-09-01

By combining kinematically complete measurements and a semiclassical Monte Carlo simulation we study the correlated-electron dynamics in the strong-field double ionization of Kr. Interestingly, we find that, as we step into the sequential-ionization regime, there are still signatures of correlation in the two-electron joint momentum spectrum and, more intriguingly, the scaling law of the high-energy tail is completely different from early predictions on the low-Z atom (He). These experimental observations are well reproduced by our generalized semiclassical model adapting a Green-Sellin-Zachor potential. It is revealed that the competition between the screening effect of inner-shell electrons and the Coulomb focusing of nuclei leads to a non-inverse-square central force, which twists the returned electron trajectory at the vicinity of the parent core and thus significantly increases the probability of hard recollisions between two electrons. Our results might have promising applications ranging from accurately retrieving atomic structures to simulating celestial phenomena in the laboratory.

Biospheric-atmospheric coupling on the early Earth

NASA Technical Reports Server (NTRS)

Levine, J. S.

1991-01-01

Theoretical calculations performed with a one-dimensional photochemical model have been performed to assess the biospheric-atmospheric transfer of gases. Ozone reached levels to shield the Earth from biologically lethal solar ultraviolet radiation (220-300 nm) when atmospheric oxygen reached about 1/10 of its present atmospheric level. In the present atmosphere, about 90 percent of atmospheric nitrous oxide is destroyed via solar photolysis in the stratosphere with about 10 percent destroyed via reaction with excited oxygen atoms. The reaction between nitrous oxide and excited oxygen atoms leads to the production of nitric oxide in the stratosphere, which is responsible for about 70 percent of the global destruction of oxygen in the stratosphere. In the oxygen/ozone deficient atmosphere, solar photolysis destroyed about 100 percent of the atmospheric nitrous oxide, relegating the production of nitric oxide via reaction with excited oxygen to zero. Our laboratory and field measurements indicate that atmospheric oxygen promotes the biogenic production of N2O and NO via denitrification and the biogenic production of methane by methanogenesis.

Mathematical Modeling of Resonant Processes in Confined Geometry of Atomic and Atom-Ion Traps

NASA Astrophysics Data System (ADS)

Melezhik, Vladimir S.

2018-02-01

We discuss computational aspects of the developed mathematical models for resonant processes in confined geometry of atomic and atom-ion traps. The main attention is paid to formulation in the nondirect product discrete-variable representation (npDVR) of the multichannel scattering problem with nonseparable angular part in confining traps as the boundary-value problem. Computational efficiency of this approach is demonstrated in application to atomic and atom-ion confinement-induced resonances we predicted recently.

QTAIM charge-charge flux-dipole flux interpretation of electronegativity and potential models of the fluorochloromethane mean dipole moment derivatives.

PubMed

Silva, Arnaldo F; da Silva, João V; Haiduke, R L A; Bruns, Roy E

2011-11-17

Infrared fundamental vibrational intensities and quantum theory atoms in molecules (QTAIM) charge-charge flux-dipole flux (CCFDF) contributions to the polar tensors of the fluorochloromethanes have been calculated at the QCISD/cc-pVTZ level. A root-mean-square error of 20.0 km mol(-1) has been found compared to an experimental error estimate of 14.4 and 21.1 km mol(-1) for MP2/6-311++G(3d,3p) results. The errors in the QCISD polar tensor elements and mean dipole moment derivatives are 0.059 e when compared with the experimental values. Both theoretical levels provide results showing that the dynamical charge and dipole fluxes provide significant contributions to the mean dipole moment derivatives and tend to be of opposite signs canceling one another. Although the experimental mean dipole moment derivative values suggest that all the fluorochloromethane molecules have electronic structures consistent with a simple electronegativity model with transferable atomic charges for their terminal atoms, the QTAIM/CCFDF models confirm this only for the fluoromethanes. Whereas the fluorine atom does not suffer a saturation effect in its capacity to drain electronic charge from carbon atoms that are attached to other fluorine and chlorine atoms, the zero flux electronic charge of the chlorine atom depends on the number and kind of the other substituent atoms. Both the QTAIM carbon charges (r = 0.990) and mean dipole moment derivatives (r = 0.996) are found to obey Siegbahn's potential model for carbon 1s electron ionization energies at the QCISD/cc-pVTZ level. The latter is a consequence of the carbon mean derivatives obeying the electronegativity model and not necessarily to their similarities with atomic charges. Atomic dipole contributions to the neighboring atom electrostatic potentials of the fluorochloromethanes are found to be of comparable size to the atomic charge contributions and increase the accuracy of Siegbahn's model for the QTAIM charge model results. Substitution effects of the hydrogen, fluorine, and chlorine atoms on the charge and dipole flux QTAIM contributions are found to be additive for the mean dipole derivatives of the fluorochloromethanes.

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.

New Measurements of the Cosmic Background Radiation Spectrum

DOE R&D Accomplishments Database

Smoot, G. F.; De Amici, G.; Levin, S.; Witebsky, C.

This pamphlet traces the history of the US Atomic Energy Commission's twenty-eight year stewardship of the Nation's nuclear energy program, from the signing of the Atomic Energy Act on August 1, 1946 to the signing of the Energy Reorganization Act on October 11, 1974. The Commission's early concentration on the military atom produced sophisticated nuclear weapons for the Nation's defense and made possible the creation of a fleet of nuclear submarines and surface ships. Extensive research in the nuclear sciences resulted in the widespread application of nuclear technology for scientific, medical and industrial purposes, while the passage of the Atomic Energy Act of 1954 made possible the development of a nuclear industry, and enabled the United States to share the new technology with other nations.

Quasi-coarse-grained dynamics: modelling of metallic materials at mesoscales

NASA Astrophysics Data System (ADS)

Dongare, Avinash M.

2014-12-01

A computationally efficient modelling method called quasi-coarse-grained dynamics (QCGD) is developed to expand the capabilities of molecular dynamics (MD) simulations to model behaviour of metallic materials at the mesoscales. This mesoscale method is based on solving the equations of motion for a chosen set of representative atoms from an atomistic microstructure and using scaling relationships for the atomic-scale interatomic potentials in MD simulations to define the interactions between representative atoms. The scaling relationships retain the atomic-scale degrees of freedom and therefore energetics of the representative atoms as would be predicted in MD simulations. The total energetics of the system is retained by scaling the energetics and the atomic-scale degrees of freedom of these representative atoms to account for the missing atoms in the microstructure. This scaling of the energetics renders improved time steps for the QCGD simulations. The success of the QCGD method is demonstrated by the prediction of the structural energetics, high-temperature thermodynamics, deformation behaviour of interfaces, phase transformation behaviour, plastic deformation behaviour, heat generation during plastic deformation, as well as the wave propagation behaviour, as would be predicted using MD simulations for a reduced number of representative atoms. The reduced number of atoms and the improved time steps enables the modelling of metallic materials at the mesoscale in extreme environments.

Optical Pattern Formation in Cold Atoms: Explaining the Red-Blue Asymmetry

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie; Gauthier, Daniel

2013-05-01

The study of pattern formation in atomic systems has provided new insight into fundamental many-body physics and low-light-level nonlinear optics. Pattern formation in cold atoms in particular is of great interest in condensed matter physics and quantum information science because atoms undergo self-organization at ultralow input powers. We recently reported the first observation of pattern formation in cold atoms but found that our results were not accurately described by any existing theoretical model of pattern formation. Previous models describing pattern formation in cold atoms predict that pattern formation should occur using both red and blue-detuned pump beams, favoring a lower threshold for blue detunings. This disagrees with our recent work, in which we only observed pattern formation with red-detuned pump beams. Previous models also assume a two-level atom, which cannot account for the cooling processes that arise when beams counterpropagate through a cold atomic vapor. We describe a new model for pattern formation that accounts for Sisyphus cooling in multi-level atoms, which gives rise to a new nonlinearity via spatial organization of the atoms. This spatial organization causes a sharp red-blue detuning asymmetry, which agrees well with our experimental observations. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.

PubMed

Orben, Claudia M; Dittrich, Birger

2014-06-01

For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å(-1). The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å(-1), but requires good low-order data.

Workshop Report on Atomic Bomb Dosimetry--Review of Dose Related Factors for the Evaluation of Exposures to Residual Radiation at Hiroshima and Nagasaki.

PubMed

Kerr, George D; Egbert, Stephen D; Al-Nabulsi, Isaf; Bailiff, Ian K; Beck, Harold L; Belukha, Irina G; Cockayne, John E; Cullings, Harry M; Eckerman, Keith F; Granovskaya, Evgeniya; Grant, Eric J; Hoshi, Masaharu; Kaul, Dean C; Kryuchkov, Victor; Mannis, Daniel; Ohtaki, Megu; Otani, Keiko; Shinkarev, Sergey; Simon, Steven L; Spriggs, Gregory D; Stepanenko, Valeriy F; Stricklin, Daniela; Weiss, Joseph F; Weitz, Ronald L; Woda, Clemens; Worthington, Patricia R; Yamamoto, Keiko; Young, Robert W

2015-12-01

Groups of Japanese and American scientists, supported by international collaborators, have worked for many years to ensure the accuracy of the radiation dosimetry used in studies of health effects in the Japanese atomic bomb survivors. Reliable dosimetric models and systems are especially critical to epidemiologic studies of this population because of their importance in the development of worldwide radiation protection standards. While dosimetry systems, such as Dosimetry System 1986 (DS86) and Dosimetry System 2002 (DS02), have improved, the research groups that developed them were unable to propose or confirm an additional contribution by residual radiation to the survivor's total body dose. In recognition of the need for an up-to-date review of residual radiation exposures in Hiroshima and Nagasaki, a half-day technical session was held for reports on newer studies at the 59 th Annual HPS Meeting in 2014 in Baltimore, MD. A day-and-a-half workshop was also held to provide time for detailed discussion of the newer studies and to evaluate their potential use in clarifying the residual radiation exposure to atomic bomb survivors at Hiroshima and Nagasaki. The process also involved a re-examination of very early surveys of radioisotope emissions from ground surfaces at Hiroshima and Nagasaki and early reports of health effects. New insights were reported on the potential contribution to residual radiation from neutron-activated radionuclides in the airburst's dust stem and pedestal and in unlofted soil, as well as from fission products and weapon debris from the nuclear cloud. However, disparate views remain concerning the actual residual radiation doses received by the atomic bomb survivors at different distances from the hypocenter. The workshop discussion indicated that measurements made using thermal luminescence and optically stimulated luminescence, like earlier measurements, especially in very thin layers of the samples, could be expanded to detect possible radiation exposures to beta particles and to determine their significance plus the extent of the various residual radiation areas at Hiroshima and Nagasaki. Other suggestions for future residual radiation studies are included in this workshop report.

Student perception and conceptual development as represented by student mental models of atomic structure

NASA Astrophysics Data System (ADS)

Park, Eun Jung

The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation

NASA Technical Reports Server (NTRS)

Willey, Ronald J.

1993-01-01

Five kinetic models are compared for their ability to predict recombination coefficients for oxygen and nitrogen atoms over high-temperature reusable surface insulation (HRSI). Four of the models are derived using Rideal-Eley or Langmuir-Hinshelwood catalytic mechanisms to describe the reaction sequence. The fifth model is an empirical expression that offers certain features unattainable through mechanistic description. The results showed that a four-parameter model, with temperature as the only variable, works best with data currently available. The model describes recombination coefficients for oxygen and nitrogen atoms for temperatures from 300 to 1800 K. Kinetic models, with atom concentrations, demonstrate the influence of atom concentration on recombination coefficients. These models can be used for the prediction of heating rates due to catalytic recombination during re-entry or aerobraking maneuvers. The work further demonstrates a requirement for more recombination experiments in the temperature ranges of 300-1000 K, and 1500-1850 K, with deliberate concentration variation to verify model requirements.

The quantum defect: Early history and recent developments

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

Rau, A.R.; Inokuti, M.

1997-03-01

The notion of the quantum defect is important in atomic and molecular spectroscopy and also in unifying spectroscopy with collision theory. In the latter context, the quantum defect may be viewed as an ancestor of the phase shift. However, the origin of the term {open_quotes}quantum defect{close_quotes} does not seem to be explained in standard textbooks. It occurred in a 1921 paper by Schr{umlt o}dinger, preceding quantum mechanics, yet giving the correct meaning as an index of the short-range interactions with the core of an atom. We present the early history of the quantum-defect idea, and sketch its recent developments. {copyright}more » {ital 1997 American Association of Physics Teachers.}« less

Formation of pentacene wetting layer on the SiO2 surface and charge trap in the wetting layer.

PubMed

Kim, Chaeho; Jeon, D

2008-09-01

We studied the early-stage growth of vacuum-evaporated pentacene film on a native SiO(2) surface using atomic force microscopy and in-situ spectroscopic ellipsometry. Pentacene deposition prompted an immediate change in the ellipsometry spectra, but atomic force microscopy images of the early stage films did not show a pentacene-related morphology other than the decrease in the surface roughness. This suggested that a thin pentacene wetting layer was formed by pentacene molecules lying on the surface before the crystalline islands nucleated. Growth simulation based on the in situ spectroscopic ellipsometry spectra supported this conclusion. Scanning capacitance microscopy measurement indicated the existence of trapped charges in the SiO(2) and pentacene wetting layer.

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)

Mg I as a probe of the solar chromosphere - The atomic model

NASA Technical Reports Server (NTRS)

Mauas, Pablo J.; Avrett, Eugene H.; Loeser, Rudolf

1988-01-01

This paper presents a complete atomic model for Mg I line synthesis, where all the atomic parameters are based on recent experimental and theoretical data. It is shown how the computed profiles at 4571 A and 5173 A are influenced by the choice of these parameters and the number of levels included in the model atom. In addition, observed profiles of the 5173 A b2 line and theoretical profiles for comparison (based on a recent atmospheric model for the average quiet sun) are presented.

Photographs and Pamphlet about Nuclear Fallout. The Constitution Community: Postwar United States (1945 to Early 1970s).

ERIC Educational Resources Information Center

Lawlor, John M., Jr.

In August 1945, the United States unleashed an atomic weapon against the Japanese at Hiroshima and Nagasaki and brought an end to World War II. These bombs killed in two ways -- by the blast's magnitude and resulting firestorm, and by nuclear fallout. After the Soviet Union exploded its first atom bomb in 1949, the Cold War waged between the two…

Combating WMD Journal. Issue 4, Fall/Winter 2009

DTIC Science & Technology

2009-01-01

Little Boy " and " Fat Man ". On 6 August 1945 at 08:15...These newer bombs were more powerful and lighter weight compared to the days of Little Boy and Fat Man . Many early bombs are still in service well...Group, released a Mark I atomic bomb called " Little Boy ". This was the first atomic bomb used against the Empire of Japan, the tar- get:

An atomic model for neutral and singly ionized uranium

NASA Technical Reports Server (NTRS)

Maceda, E. L.; Miley, G. H.

1979-01-01

A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.

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.

Atomic bomb: Ultimate faith of diplomacy. Research report, August 1992-April 1993

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

Frank, S.

1993-04-01

This paper examines the development and use of the atomic bombs as the means of achieving a grand strategy formulated by United States President Franklin Roosevelt and British Prime Minister Winston Churchill as early as 1943. This grand strategy consisted of two main goals. First, if necessary, the atomic bombs would be used to end World War II as soon as they were ready. Second, the existence of the atomic bombs would be used as a diplomatic hammer to shape the political landscape of the postwar world - a direct warning to Soviet dictator Joseph Stalin not to attempt tomore » hegemonize Eastern Europe and the Far East. Was the grand strategy successfully accomplished. Could newly sworn President Harry Truman have employed diplomatic means to quickly and successfully end World War II without resorting to the use of the atomic bombs against Japan.« less

The Chocolate Shop and Atomic Orbitals: A New Atomic Model Created by High School Students to Teach Elementary Students

ERIC Educational Resources Information Center

Liguori, Lucia

2014-01-01

Atomic orbital theory is a difficult subject for many high school and beginning undergraduate students, as it includes mathematical concepts not yet covered in the school curriculum. Moreover, it requires certain ability for abstraction and imagination. A new atomic orbital model "the chocolate shop" created "by" students…

Numerical Modeling of Turbulence Effects within an Evaporating Droplet in Atomizing Sprays

NASA Technical Reports Server (NTRS)

Balasubramanyam, M. S.; Chen, C. P.; Trinh, H. P.

2006-01-01

A new approach to account for finite thermal conductivity and turbulence effects within atomizing liquid sprays is presented in this paper. The model is an extension of the T-blob and T-TAB atomization/spray model of Trinh and Chen (2005). This finite conductivity model is based on the two-temperature film theory, where the turbulence characteristics of the droplet are used to estimate the effective thermal diffhsivity within the droplet phase. Both one-way and two-way coupled calculations were performed to investigate the performance of this model. The current evaporation model is incorporated into the T-blob atomization model of Trinh and Chen (2005) and implemented in an existing CFD Eulerian-Lagrangian two-way coupling numerical scheme. Validation studies were carried out by comparing with available evaporating atomization spray experimental data in terms of jet penetration, temperature field, and droplet SMD distribution within the spray. Validation results indicate the superiority of the finite-conductivity model in low speed parallel flow evaporating spray.

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

NASA Astrophysics Data System (ADS)

Chu, Huiying; Peng, Xiangda; Li, Yan; Zhang, Yuebin; Min, Hanyi; Li, Guohui

2018-04-01

A polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values.

Pluto's Extended Atmosphere: New Horizons Alice Lyman-α Imaging

NASA Astrophysics Data System (ADS)

Retherford, Kurt D.; Gladstone, G. Randall; Stern, S. Alan; Weaver, Harold A.; Young, Leslie A.; Ennico, Kimberly A.; Olkin, Cathy B.; Cheng, Andy F.; Greathouse, Thomas K.; Hinson, David P.; Kammer, Joshua A.; Linscott, Ivan R.; Parker, Alex H.; Parker, Joel Wm.; Pryor, Wayne R.; Schindhelm, Eric; Singer, Kelsi N.; Steffl, Andrew J.; Strobel, Darrell F.; Summers, Michael E.; Tsang, Constantine C. C.; Tyler, G. Len; Versteeg, Maarten H.; Woods, William W.; Cunningham, Nathaniel J.; Curdt, Werner

2015-11-01

Pluto's upper atmosphere is expected to extend several planetary radii, proportionally more so than for any planet in our solar system. Atomic hydrogen is readily produced at lower altitudes due to photolysis of methane and transported upward to become an important constituent. The Interplanetary Medium (IPM) provides a natural light source with which to study Pluto's atomic hydrogen atmosphere. While direct solar Lyman-α emissions dominate the signal at 121.6 nm at classical solar system distances, the contribution of diffuse illumination by IPM Lyman-α sky-glow is roughly on par at Pluto (Gladstone et al., Icarus, 2015). Hydrogen atoms in Pluto's upper atmosphere scatter these bright Lyα emission lines, and detailed simulations of the radiative transfer for these photons indicate that Pluto would appear dark against the IPM Lyα background. The Pluto-Alice UV imaging spectrograph on New Horizons conducted several observations of Pluto during the encounter to search for airglow emissions, characterize its UV reflectance spectra, and to measure the radial distribution of IPM Lyα near the disk. Our early results suggest that these model predictions for the darkening of IPM Lyα with decreasing altitude being measureable by Pluto-Alice were correct. We'll report our progress toward extracting H and CH4 density profiles in Pluto's upper atmosphere through comparisons of these data with detailed radiative transfer modeling. These New Horizons findings will have important implications for determining the extent of Pluto's atmosphere and related constraints to high-altitude vertical temperature structure and atmospheric escape.This work was supported by NASA's New Horizons project.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

Resolving the structure of Ti 3C 2T x MXenes through multilevel structural modeling of the atomic pair distribution function

DOE PAGES

Wesolowski, David J.; Wang, Hsiu -Wen; Page, Katharine L.; ...

2015-12-08

MXenes are a recently discovered family of two-dimensional (2D) early transition metal carbides and carbonitrides, which have already shown many attractive properties and great promise in energy storage and many other applications. But, a complex surface chemistry and small coherence length have been obstacles in some applications of MXenes, also limiting the accuracy of predictions of their properties. In this study, we describe and benchmark a novel way of modeling layered materials with real interfaces (diverse surface functional groups and stacking order between the adjacent monolayers) against experimental data. The structures of three kinds of Ti 3C 2T x MXenesmore » (T stands for surface terminating species, including O, OH, and F) produced under different synthesis conditions were resolved for the first time using atomic pair distribution function obtained by high-quality neutron total scattering. We present the true nature of the material can be easily captured with the sensitivity of neutron scattering to the surface species of interest and the detailed “third-generation” structure model. The modeling approach leads to new understanding of MXene structural properties and can replace the currently used idealized models in predictions of a variety of physical, chemical, and functional properties of Ti 3C 2-based MXenes. Moreover, the developed models can be employed to guide the design of new MXene materials with selected surface termination and controlled contact angle, catalytic, optical, electrochemical, and other properties. Finally, we suggest that the multilevel structural modeling should form the basis for a generalized methodology on modeling diffraction and pair distribution function data for 2D and layered materials.« less

Photochemical escape of oxygen from Mars: constraints from MAVEN in situ measurements

NASA Astrophysics Data System (ADS)

Lillis, R. J.; Deighan, J.; Fox, J. L.; Bougher, S. W.; Lee, Y.; Cravens, T.; Rahmati, A.; Mahaffy, P. R.; Andersson, L.; Combi, M. R.; Benna, M.; Jakosky, B. M.; Gröller, H.

2016-12-01

One of the primary goals of the MAVEN mission is to characterize rates of atmospheric escape from Mars at the present epoch and relate those escape rates to solar drivers. Photochemical escape of oxygen is expected to be a significant channel for atmospheric loss, particularly in the early solar system when extreme ultraviolet (EUV) fluxes were much higher. We use near-periapsis (<400 km altitude) data from three instruments. The Langmuir Probe and Waves (LPW) instrument measures electron density and temperature, the Suprathermal And Thermal Ion Composition (STATIC) experiment measures ion temperature and the Neutral Gas and Ion Mass Spectrometer (NGIMS) measures neutral and ion densities. For each profile of in situ measurements, we make a series of calculations, each as a function of altitude. The first uses electron and ion temperatures to calculate the probability distribution for initial energies of hot O atoms. The second calculates the probability that a hot atom born at that altitude will escape. The third takes calculates the production rate of the hot O atoms. We then multiply together the profiles of hot atom production and escape probability to get profiles of the production rate of escaping atoms. We integrate with respect to altitude to give us the escape flux of hot oxygen atoms for that periapsis pass. We will present escape fluxes and derived escape rates from the first Mars year of data collected. Total photochemical loss over time is not very useful to calculate from such escape fluxes derived from current conditions because a thicker atmosphere and much higher solar EUV in the past may change the dynamics of escape dramatically. In the future, we intend to use 3-D Monte Carlo models of global atmospheric escape, in concert with our in situ and remote measurements, to fully characterize photochemical escape under current conditions and carefully extrapolate back in time using further simulations with new boundary conditions.

Retrieval of sodium number density profiles in the mesosphere and lower thermosphere from SCIAMACHY limb emission measurements

NASA Astrophysics Data System (ADS)

Langowski, M. P.; von Savigny, C.; Burrows, J. P.; Rozanov, V. V.; Dunker, T.; Hoppe, U.-P.; Sinnhuber, M.; Aikin, A. C.

2016-01-01

An algorithm has been developed for the retrieval of sodium atom (Na) number density on a latitude and altitude grid from SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) limb measurements of the Na resonance fluorescence. The results are obtained between 50 and 150 km altitude and the resulting global seasonal variations of Na are analyzed. The retrieval approach is adapted from that used for the retrieval of magnesium atom (Mg) and magnesium ion (Mg+) number density profiles recently reported by Langowski et al. (2014). Monthly mean values of Na are presented as a function of altitude and latitude. This data set was retrieved from the 4 years of spectroscopic limb data of the SCIAMACHY mesosphere and lower thermosphere (MLT) measurement mode (mid-2008 to early 2012). The Na layer has a nearly constant peak altitude of 90-93 km for all latitudes and seasons, and has a full width at half maximum of 5-15 km. Small but significant seasonal variations in Na are identified for latitudes less than 40°, where the maximum Na number densities are 3000-4000 atoms cm-3. At middle to high latitudes a clear seasonal variation with a winter maximum of up to 6000 atoms cm-3 is observed. The high latitudes, which are only measured in the summer hemisphere, have lower number densities, with peak densities being approximately 1000 Na atoms cm-3. The full width at half maximum of the peak varies strongly at high latitudes and is 5 km near the polar summer mesopause, while it exceeds 10 km at lower latitudes. In summer the Na atom concentration at high latitudes and at altitudes below 88 km is significantly smaller than that at middle latitudes. The results are compared with other observations and models and there is overall a good agreement with these.

Atomic oxygen in the Martian thermosphere

NASA Technical Reports Server (NTRS)

Stewart, A. I. F.; Alexander, M. J.; Meier, R. R.; Paxton, L. J.; Bougher, S. W.; Fesen, C. G.

1992-01-01

The Mariner 9 Ultraviolet Spectrometer (UVS) made extensive observations of air-glow emissions from the thermosphere of Mars throughout the nominal mission (November 1971 - February 1972), during late summer in the southern hemisphere. Limb and disc measurements of the 130 nm triplet emission from thermospheric atomic oxygen were modelled by Strickland et al. Recently, the thermospheric general circulation models (TGCMs) developed for the Earth and Venus have been applied to Mars; we refer to it as the MTGCM. Our analysis shows that the oxygen mixing ratio is the fundamental unknown controlling the 130 nm brightness. Our radiative transport calculation shows that the emergent intensity at 130 nm is not very sensitive to variations in thermospheric temperature. The pattern of diurnal variation derived from our analysis is roughly the same as Strickland et al. although with somewhat lower values for the O mixing ratio. The main reasons for this difference are the more important role played by the photoelectron source in our model, and the somewhat larger 130 nm solar flux; thus, we require less oxygen to match the observed brightnesses. Strickland et al. also found that the OI 130 nm emission on Mars is correlated with solar activity. We find that the correlation is virtually non-existent during the early orbits when the planet was covered with a thick global dust storm, but later orbits, during the clearing of the storm, show a persistent correlation.

Is It Time to Retire the Hybrid Atomic Orbital?

ERIC Educational Resources Information Center

Grushow, Alexander

2011-01-01

A rationale for the removal of the hybrid atomic orbital from the chemistry curriculum is examined. Although the hybrid atomic orbital model does not accurately predict spectroscopic energies, many chemical educators continue to use and teach the model despite the confusion it can cause for students. Three arguments for retaining the model in the…

Adiabatic quantum computation with neutral atoms via the Rydberg blockade

NASA Astrophysics Data System (ADS)

Goyal, Krittika; Deutsch, Ivan

2011-05-01

We study a trapped-neutral-atom implementation of the adiabatic model of quantum computation whereby the Hamiltonian of a set of interacting qubits is changed adiabatically so that its ground state evolves to the desired output of the algorithm. We employ the ``Rydberg blockade interaction,'' which previously has been used to implement two-qubit entangling gates in the quantum circuit model. Here it is employed via off-resonant virtual dressing of the excited levels, so that atoms always remain in the ground state. The resulting dressed-Rydberg interaction is insensitive to the distance between the atoms within a certain blockade radius, making this process robust to temperature and vibrational fluctuations. Single qubit interactions are implemented with global microwaves and atoms are locally addressed with light shifts. With these ingredients, we study a protocol to implement the two-qubit Quadratic Unconstrained Binary Optimization (QUBO) problem. We model atom trapping, addressing, coherent evolution, and decoherence. We also explore collective control of the many-atom system and generalize the QUBO problem to multiple qubits. We study a trapped-neutral-atom implementation of the adiabatic model of quantum computation whereby the Hamiltonian of a set of interacting qubits is changed adiabatically so that its ground state evolves to the desired output of the algorithm. We employ the ``Rydberg blockade interaction,'' which previously has been used to implement two-qubit entangling gates in the quantum circuit model. Here it is employed via off-resonant virtual dressing of the excited levels, so that atoms always remain in the ground state. The resulting dressed-Rydberg interaction is insensitive to the distance between the atoms within a certain blockade radius, making this process robust to temperature and vibrational fluctuations. Single qubit interactions are implemented with global microwaves and atoms are locally addressed with light shifts. With these ingredients, we study a protocol to implement the two-qubit Quadratic Unconstrained Binary Optimization (QUBO) problem. We model atom trapping, addressing, coherent evolution, and decoherence. We also explore collective control of the many-atom system and generalize the QUBO problem to multiple qubits. We acknowledge funding from the AQUARIUS project, Sandia National Laboratories

Modeling Solar Atmospheric Phenomena with AtomDB and PyAtomDB

NASA Astrophysics Data System (ADS)

Dupont, Marcus; Foster, Adam

2018-01-01

Taking advantage of the modeling tools made available by PyAtomDB (Foster 2015), we evaluated the impact of changing atomic data on solar phenomena, in particular their effects on models of coronal mass ejections (CME). Intitially, we perform modifications to the canonical SunNEI code (Murphy et al. 2011) in order to include non-equilibrium ionization (NEI) processes that occur in the CME modeled in SunNEI. The methods used involve the consideration of radiaitive cooling as well as ion balance calculations. These calculations were subsequently implemented within the SunNEI simulation. The insertion of aforementioned processes and parameter customizaton produced quite similar results of the original except for the case of iron. These differences were traced to inconsistencies in the recombination rates for Argon-like iron ions between the CHIANTI and AtomDB databases, even though they in theory use the same data. The key finding was that theoretical models are greatly impacted by the relative atomic database update cycles.Following the SunNEI comparison, we then use the AtomDB database to model the time depedencies of intensity flux spikes produced by a coronal shock wave (Ma et al. 2011). We produced a theretical representation for an ionizing plasma that interpolated over the intensity in four Astronomical Imaging Assembly (AIA) filters. Specifically, the 171 A (Fe IX) ,193 A (Fe XII, FeXXIV),211 A (Fe XIV),and 335 A (Fe XVI) wavelengths in order to assess the comparative spectral emissions between AtomDB and the observed data. The results of the theoretical model, in principle, shine light on both the equilibrium conditions before the shock and the non-equilibrium response to the shock front, as well as discrepancies introduced by changing the atomic data.

Atom counting in HAADF STEM using a statistical model-based approach: methodology, possibilities, and inherent limitations.

PubMed

De Backer, A; Martinez, G T; Rosenauer, A; Van Aert, S

2013-11-01

In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration. © 2013 Elsevier B.V. All rights reserved.

Dynamics of atom-field entanglement for Tavis-Cummings models

NASA Astrophysics Data System (ADS)

Bashkirov, Eugene K.

2018-04-01

An exact solution of the problem of two-atom one- and two-mode Jaynes-Cummings model with intensity- dependent coupling is presented. Asymptotic solutions for system state vectors are obtained in the approximation of large initial coherent fields. The atom-field entanglement is investigated on the basis of the reduced atomic entropy dynamics. The possibility of the system being initially in a pure disentangled state to revive into this state during the evolution process for both models is shown. Conditions and times of disentanglement are derived.

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

PubMed

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

Molecular processes in astrophysics: Calculations of hydrogen + hydrogen gas excitation, de-excitation, and cooling

NASA Astrophysics Data System (ADS)

Kelley, Matthew Thomas

The implications of H+H2 cooling in astrophysics is important to several applications. One of the most significant and pure applications is its role in cooling in the early universe. Other applications would include molecular dynamics in nebulae and their collapse into stars and astrophysical shocks. Shortly after the big bang, the universe was a hot primordial gas of photons, electrons, and nuclei among other ingredients. By far the most dominant nuclei in the early universe was hydrogen. In fact, in the early universe the matter density was 90 percent hydrogen and only 10 percent helium with small amounts of lithium and deuterium. In order for structure to form in the universe, this primordial gas must form atoms and cool. One of the significant cooling mechanisms is the collision of neutral atomic hydrogen with a neutral diatomic hydrogen molecule. This work performs calculations to determine collisional cooling rates of hydrogen using two potential surfaces.

Multiscale simulations of the early stages of the growth of graphene on copper

NASA Astrophysics Data System (ADS)

Gaillard, P.; Chanier, T.; Henrard, L.; Moskovkin, P.; Lucas, S.

2015-07-01

We have performed multiscale simulations of the growth of graphene on defect-free copper (111) in order to model the nucleation and growth of graphene flakes during chemical vapour deposition and potentially guide future experimental work. Basic activation energies for atomic surface diffusion were determined by ab initio calculations. Larger scale growth was obtained within a kinetic Monte Carlo approach (KMC) with parameters based on the ab initio results. The KMC approach counts the first and second neighbours to determine the probability of surface diffusion. We report qualitative results on the size and shape of the graphene islands as a function of deposition flux. The dominance of graphene zigzag edges for low deposition flux, also observed experimentally, is explained by its larger dynamical stability that the present model fully reproduced.

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.

Nagaoka's atomic model and hyperfine interactions.

PubMed

Inamura, Takashi T

2016-01-01

The prevailing view of Nagaoka's "Saturnian" atom is so misleading that today many people have an erroneous picture of Nagaoka's vision. They believe it to be a system involving a 'giant core' with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka's model is exactly the same as Rutherford's. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure.

Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I.

NASA Technical Reports Server (NTRS)

Bautista, M. A.; Fivet, V.; Quinet, P.; Dunn, J.; Gull, T. R.; Kallman, T. R.; Mendoza, C.

2013-01-01

We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data.We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of Oiii and Fe ii and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe ii]. Key words: atomic data - atomic processes - line: formation - methods: data analysis - molecular data - molecular processes - techniques: spectroscopic

A three-level atomicity model for decentralized workflow management systems

NASA Astrophysics Data System (ADS)

Ben-Shaul, Israel Z.; Heineman, George T.

1996-12-01

A workflow management system (WFMS) employs a workflow manager (WM) to execute and automate the various activities within a workflow. To protect the consistency of data, the WM encapsulates each activity with a transaction; a transaction manager (TM) then guarantees the atomicity of activities. Since workflows often group several activities together, the TM is responsible for guaranteeing the atomicity of these units. There are scalability issues, however, with centralized WFMSs. Decentralized WFMSs provide an architecture for multiple autonomous WFMSs to interoperate, thus accommodating multiple workflows and geographically-dispersed teams. When atomic units are composed of activities spread across multiple WFMSs, however, there is a conflict between global atomicity and local autonomy of each WFMS. This paper describes a decentralized atomicity model that enables workflow administrators to specify the scope of multi-site atomicity based upon the desired semantics of multi-site tasks in the decentralized WFMS. We describe an architecture that realizes our model and execution paradigm.

Length and Dimensional Measurements at NIST

PubMed Central

Swyt, Dennis A.

2001-01-01

This paper discusses the past, present, and future of length and dimensional measurements at NIST. It covers the evolution of the SI unit of length through its three definitions and the evolution of NBS-NIST dimensional measurement from early linescales and gage blocks to a future of atom-based dimensional standards. Current capabilities include dimensional measurements over a range of fourteen orders of magnitude. Uncertainties of measurements on different types of material artifacts range down to 7×10−8 m at 1 m and 8 picometers (pm) at 300 pm. Current work deals with a broad range of areas of dimensional metrology. These include: large-scale coordinate systems; complex form; microform; surface finish; two-dimensional grids; optical, scanning-electron, atomic-force, and scanning-tunneling microscopies; atomic-scale displacement; and atom-based artifacts. PMID:27500015

Optical Pattern Formation in Spatially Bunched Atoms: A Self-Consistent Model and Experiment

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie L.; Gauthier, Daniel J.

2014-05-01

The nonlinear optics and optomechanical physics communities use different theoretical models to describe how optical fields interact with a sample of atoms. There does not yet exist a model that is valid for finite atomic temperatures but that also produces the zero temperature results that are generally assumed in optomechanical systems. We present a self-consistent model that is valid for all atomic temperatures and accounts for the back-action of the atoms on the optical fields. Our model provides new insights into the competing effects of the bunching-induced nonlinearity and the saturable nonlinearity. We show that it is crucial to keep the fifth and seventh-order nonlinearities that arise when there exists atomic bunching, even at very low optical field intensities. We go on to apply this model to the results of our experimental system where we observe spontaneous, multimode, transverse optical pattern formation at ultra-low light levels. We show that our model accurately predicts our experimentally observed threshold for optical pattern formation, which is the lowest threshold ever reported for pattern formation. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

Polarization Bremsstrahlung: what is it and why haven't we seen it?

NASA Astrophysics Data System (ADS)

Quarles, C. A.

1997-10-01

Normal bremsstrahlung (NB) is the radiation by a charged particle when deflected in the Coulomb field of a target atom. This process has been studied in some detail since identification of the continuous x-ray spectrum early in this century. Since the early 1980's it has been possible, mainly due to the work of R. H. Pratt and co-workers, to obtain good theoretical predictions for NB for a wide range of incident electron energies and target atomic numbers. In the early 1980's, a second, distinct and competing process which has come to be called polarization bremsstrahlung (PB) was proposed by M. Ya. Amusia and others. PB is the radiation by a polarizable target due to the changing dipole moment induced by the passing charged projectile. It was argued that in some cases, especially for photon energies near the target atom absorption edges, PB would dominate over NB. Only recently, however, with the calculations of A. Korol and his co-workers has it been possible to consider what PB may look like over the whole range of the photon spectrum observed in a typical bremsstrahlung experiment. This paper will discuss, from the point of view of an experimentalist, what is involved in looking for the PB effect, why perhaps it has not been convincingly detected in bremsstrahlung experiments to date, and what the prospects are for its future observation.

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

Kaplan, David E.; Krnjaic, Gordan Z.; Rehermann, Keith R.

We present a simple UV completion of Atomic Dark Matter (aDM) in which heavy right-handed neutrinos decay to induce both dark and lepton number densities. This model addresses several outstanding cosmological problems: the matter/anti-matter asymmetry, the dark matter abundance, the number of light degrees of freedom in the early universe, and the smoothing of small-scale structure. Additionally, this realization of aDM may reconcile the CoGeNT excess with recently published null results and predicts a signal in the CRESST Oxygen band. We also find that, due to unscreened long-range interactions, the residual un recombined dark ions settle into a diffuse isothermalmore » halo.« less

Atomic-level study of a thickness-dependent phase change in gold thin films heated by an ultrafast laser.

PubMed

Gan, Yong; Shi, Jixiang; Jiang, Shan

2012-08-20

An ultrafast laser-induced phase change in gold thin films with different thicknesses has been simulated by the method of coupling the two-temperature model and the molecular dynamics, including transient optical properties. Numerical results show that the decrease of film thickness leads to faster melting in the early nonequilibrium time and a larger melting depth. Moreover, earlier occurrence and a higher rate of resolidification are observed for the thicker film. Further analysis reveals that the mechanism for the thickness-dependent phase change in the films is the fast electron thermal conduction in the nonequilibrium state.

An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

PubMed

Wang, Zhao; Hryc, Corey F; Bammes, Benjamin; Afonine, Pavel V; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F; Adams, Paul D; Chiu, Wah

2014-09-04

Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

Rotational excitation of hydrogen molecules by collisions with hydrogen atoms. [interstellar gas energetics

NASA Technical Reports Server (NTRS)

Green, S.; Truhlar, D. G.

1979-01-01

Rate constants for rotational excitation of hydrogen molecules by collisions with hydrogen atoms have been obtained from quantum-mechanical calculations for kinetic temperatures between 100 and 5000 K. These calculations involve the rigid-rotator approximation, but other possible sources of error should be small. The calculations indicate that the early values of Nishimura are larger than accurate rigid-rotator values by about a factor of 20 or more.

On the treatment of ℓ-changing proton-hydrogen Rydberg atom collisions

NASA Astrophysics Data System (ADS)

Vrinceanu, D.; Onofrio, R.; Sadeghpour, H. R.

2017-11-01

Energy-conserving, angular momentum changing collisions between protons and highly excited Rydberg hydrogen atoms are important for precise understanding of atomic recombination at the photon decoupling era and the elemental abundance after primordial nucleosynthesis. Early approaches to ℓ-changing collisions used perturbation theory only for dipole-allowed (Δℓ = ±1) transitions. An exact non-perturbative quantum mechanical treatment is possible, but it comes at a computational cost for highly excited Rydberg states. In this paper, we show how to obtain a semiclassical limit that is accurate and simple, and develop further physical insights afforded by the non-perturbative quantum mechanical treatment.

Passive acoustic leak detection for sodium cooled fast reactors using hidden Markov models

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

Riber Marklund, A.; Kishore, S.; Prakash, V.

2015-07-01

Acoustic leak detection for steam generators of sodium fast reactors have been an active research topic since the early 1970's and several methods have been tested over the years. Inspired by its success in the field of automatic speech recognition, we here apply hidden Markov models (HMM) in combination with Gaussian mixture models (GMM) to the problem. To achieve this, we propose a new feature calculation scheme, based on the temporal evolution of the power spectral density (PSD) of the signal. Using acoustic signals recorded during steam/water injection experiments done at the Indira Gandhi Centre for Atomic Research (IGCAR), themore » proposed method is tested. We perform parametric studies on the HMM+GMM model size and demonstrate that the proposed method a) performs well without a priori knowledge of injection noise, b) can incorporate several noise models and c) has an output distribution that simplifies false alarm rate control. (authors)« less

Modelling of c-C2H4O Formation on Grain-Surfaces

NASA Astrophysics Data System (ADS)

Occhiogrosso, Angela; Viti, S.; Ward, M. D.; Price, S. D.

2013-01-01

Ethylene oxide (c-C2H4O) is a ring-shaped organic compound that may lead to the synthesis of amino acids and the early metabolic pathways in the interstellar medium (ISM) (Cleaves 2003; Miller & Schlesinger 1993). This molecule has been detected towards several high-mass star forming regions (Ikeda et al. 2001) but to date, its observational abundances cannot be reproduced by chemical models. We include new experimental results in the UCL_CHEM chemical model with the aim of reproducing the abundances of ethylene oxide across high-mass sources. In particular, we focused on the solid state reaction investigated by Ward & Price (2011). By comparing our theoretical column densities with those from the observations we found that the reaction between atomic oxygen and ethylene on grains is a viable route of formation for ethylene oxide (Occhiogrosso et al., accepted by MNRAS).

Fast Three-Dimensional Method of Modeling Atomic Oxygen Undercutting of Protected Polymers

NASA Technical Reports Server (NTRS)

Snyder, Aaron; Banks, Bruce A.

2002-01-01

A method is presented to model atomic oxygen erosion of protected polymers in low Earth orbit (LEO). Undercutting of protected polymers by atomic oxygen occurs in LEO due to the presence of scratch, crack or pin-window defects in the protective coatings. As a means of providing a better understanding of undercutting processes, a fast method of modeling atomic-oxygen undercutting of protected polymers has been developed. Current simulation methods often rely on computationally expensive ray-tracing procedures to track the surface-to-surface movement of individual "atoms." The method introduced in this paper replaces slow individual particle approaches by substituting a model that utilizes both a geometric configuration-factor technique, which governs the diffuse transport of atoms between surfaces, and an efficient telescoping series algorithm, which rapidly integrates the cumulative effects stemming from the numerous atomic oxygen events occurring at the surfaces of an undercut cavity. This new method facilitates the systematic study of three-dimensional undercutting by allowing rapid simulations to be made over a wide range of erosion parameters.

Atomic Data Needs for X-ray Astronomy

NASA Technical Reports Server (NTRS)

Bautista, Manuel A. (Editor); Kallman, Timothy R. (Editor); Pradhan, Anil K. (Editor)

2000-01-01

This publication contains written versions of most of the invited talks presented at the workshop on "Atomic Data Needs for X-ray Astronomy," which was held at NASA's Goddard Space Flight Center on December 16-17, 1999. The workshop was divided into five major areas: Observational Spectroscopy, Theoretical Calculations of Atomic Data, Laboratory Measurements of Atomic Parameters, Spectra Modeling, and Atomic Databases. These proceedings are expected to be of interest to producers and users of atomic data. Moreover, the contributions presented here have been written in a way that can be used by a general audience of scientists and graduate students in X-ray astronomy, modelling, and in computational and experimental atomic physics.

The unfolding mechanism of monomeric mutant SOD1 by simulated force spectroscopy.

PubMed

Habibi, Mona; Rottler, Jörg; Plotkin, Steven S

2017-11-01

Mechanical unfolding of mutated apo, disulfide-reduced, monomeric superoxide dismutase 1 protein (SOD1) has been simulated via force spectroscopy techniques, using both an all-atom (AA), explicit solvent model and a coarse-grained heavy-atom Gō (HA-Gō) model. The HA-Gō model was implemented at two different pulling speeds for comparison. The most-common sequence of unfolding in the AA model agrees well with the most-common unfolding sequence of the HA-Gō model, when the same normalized pulling rate was used. Clustering of partially-native structures as the protein unfolds shows that the AA and HA-Gō models both exhibit a dominant pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches after the protein is about half-unfolded. The force-extension curve exhibits multiple force drops, which are concomitant with jumps in the local interaction potential energy between specific β-strands in the protein. These sudden jumps in the potential energy coincide with the dissociation of specific pairs of β-strands, and thus intermediate unfolding events. The most common sequence of β-strand dissociation in the unfolding pathway of the AA model is β-strands 5, 4, 8, 7, 1, 2, then finally β-strands 3 and 6. The observation that β-strand 5 is among the first to unfold here, but the last to unfold in simulations of loop-truncated SOD1, could imply the existence of an evolutionary compensation mechanism, which would stabilize β-strands flanking long loops against their entropic penalty by strengthening intramolecular interactions. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Mixing of gaseous reactants in chemical generation of atomic iodine for COIL: two-dimensional study

NASA Astrophysics Data System (ADS)

Jirasek, Vit; Spalek, Otomar; Kodymova, Jarmila; Censky, Miroslav

2003-11-01

Two-dimensional CFD model was applied for the study of mixing and reaction between gaseous chlorine dioxide and nitrogen monoxide diluted with nitrogen during atomic iodine generation. The influence of molecular diffusion on the production of atomic chlorine as a precursor of atomic iodine was predominantly studied. The results were compared with one-dimensional modeling of the system.

Early Impairment of Lung Mechanics in a Murine Model of Marfan Syndrome

PubMed Central

Uriarte, Juan J.; Meirelles, Thayna; Gorbenko del Blanco, Darya; Nonaka, Paula N.; Campillo, Noelia; Sarri, Elisabet; Navajas, Daniel; Egea, Gustavo; Farré, Ramon

2016-01-01

Early morbidity and mortality in patients with Marfan syndrome (MFS) -a connective tissue disease caused by mutations in fibrillin-1 gene- are mainly caused by aorta aneurysm and rupture. However, the increase in the life expectancy of MFS patients recently achieved by reparatory surgery promotes clinical manifestations in other organs. Although some studies have reported respiratory alterations in MFS, our knowledge of how this connective tissue disease modifies lung mechanics is scarce. Hence, we assessed whether the stiffness of the whole lung and of its extracellular matrix (ECM) is affected in a well-characterized MFS mouse model (FBN1C1039G/+). The stiffness of the whole lung and of its ECM were measured by conventional mechanical ventilation and atomic force microscopy, respectively. We studied 5-week and 9-month old mice, whose ages are representative of early and late stages of the disease. At both ages, the lungs of MFS mice were significantly more compliant than in wild type (WT) mice. By contrast, no significant differences were found in local lung ECM stiffness. Moreover, histopathological lung evaluation showed a clear emphysematous-like pattern in MFS mice since alveolar space enlargement was significantly increased compared with WT mice. These data suggest that the mechanism explaining the increased lung compliance in MFS is not a direct consequence of reduced ECM stiffness, but an emphysema-like alteration in the 3D structural organization of the lung. Since lung alterations in MFS are almost fully manifested at an early age, it is suggested that respiratory monitoring could provide early biomarkers for diagnosis and/or follow-up of patients with the Marfan syndrome. PMID:27003297

PROGEN: An automated modelling algorithm for the generation of complete protein structures from the α-carbon atomic coordinates

NASA Astrophysics Data System (ADS)

Mandal, Chhabinath; Linthicum, D. Scott

1993-04-01

A modelling algorithm (PROGEN) for the generation of complete protein atomic coordinates from only the α-carbon coordinates is described. PROGEN utilizes an optimal geometry parameter (OGP) database for the positioning of atoms for each amino acid of the polypeptide model. The OGP database was established by examining the statistical correlations between 23 different intra-peptide and inter-peptide geometric parameters relative to the α-carbon distances for each amino acid in a library of 19 known proteins from the Brookhaven Protein Database (BPDB). The OGP files for specific amino acids and peptides were used to generate the atomic positions, with respect to α-carbons, for main-chain and side-chain atoms in the modelled structure. Refinement of the initial model was accomplished using energy minimization (EM) and molecular dynamics techniques. PROGEN was tested using 60 known proteins in the BPDB, representing a wide spectrum of primary and secondary structures. Comparison between PROGEN models and BPDB crystal reference structures gave r.m.s.d. values for peptide main-chain atoms between 0.29 and 0.76 Å, with a grand average of 0.53 Å for all 60 models. The r.m.s.d. for all non-hydrogen atoms ranged between 1.44 and 1.93 Å for the 60 polypeptide models. PROGEN was also able to make the correct assignment of cis- or trans-proline configurations in the protein structures examined. PROGEN offers a fully automatic building and refinement procedure and requires no special or specific structural considerations for the protein to be modelled.

Simulating Cosmic Reionization and Its Observable Consequences

NASA Astrophysics Data System (ADS)

Shapiro, Paul

2017-01-01

I summarize recent progress in modelling the epoch of reionization by large- scale simulations of cosmic structure formation, radiative transfer and their interplay, which trace the ionization fronts that swept across the IGM, to predict observable signatures. Reionization by starlight from early galaxies affected their evolution, impacting reionization, itself, and imprinting the galaxies with a memory of reionization. Star formation suppression, e.g., may explain the observed underabundance of Local Group dwarfs relative to N-body predictions for Cold Dark Matter. I describe CoDa (''Cosmic Dawn''), the first fully-coupled radiation-hydrodynamical simulation of reionization and galaxy formation in the Local Universe, in a volume large enough to model reionization globally but with enough resolving power to follow all the atomic-cooling galactic halos in that volume. A 90 Mpc box was simulated from a constrained realization of primordial fluctuations, chosen to reproduce present-day features of the Local Group, including the Milky Way and M31, and the local universe beyond, including the Virgo cluster. The new RAMSES-CUDATON hybrid CPU-GPU code took 11 days to perform this simulation on the Titan supercomputer at Oak Ridge National Laboratory, with 4096-cubed N-body particles for the dark matter and 4096-cubed cells for the atomic gas and ionizing radiation.

CH4 dissociation in the early stage of graphene growth on Fe-Cu(100) surface: Theoretical insights

NASA Astrophysics Data System (ADS)

Tian, Baoyang; Liu, Tianhui; Yang, YanYan; Li, Kai; Wu, Zhijian; Wang, Ying

2018-01-01

The mechanism of CH4 dissociation and carbon nucleation process on the Fe doped Cu(100) surface were investigated systematically by using the density functional theory (DFT) calculations and microkinetic model. The activity of the Cu(100) surface was improved by the doped Fe atom and the atomic Fe on the Fe-Cu(100) surface was the reaction center due to the synergistic effect. In the dissociation process of CH4, CH3 → CH2 + H was regarded as the rate-determining step. The results obtained from the microkinetic model showed that the coverage of CHx(x = 1-3) was gradually decreased with the temperature increasing and CH3 was always the major intermediate at the broad range of the temperature (from 1035 to 1080 °C) and the ratio of H2/CH4 (from 0 to 5). It is also found that the reaction rates were increased with the temperature increasing. However, the reaction rates were reduced (or increased) at the range of H2/CH4 = 0-0.2 (or H2/CH4 > 0.2). It is noted that controlling the H2 partial pressure was an effective method to regulate the major intermediates and reaction rates of CH4 dissociation and further influence the growing process of graphene.

Effect of secondary electron emission on subnanosecond breakdown in high-voltage pulse discharge

NASA Astrophysics Data System (ADS)

Schweigert, I. V.; Alexandrov, A. L.; Gugin, P.; Lavrukhin, M.; Bokhan, P. A.; Zakrevsky, Dm E.

2017-11-01

The subnanosecond breakdown in open discharge may be applied for producing superfast high power switches. Such fast breakdown in high-voltage pulse discharge in helium was explored both in experiment and in kinetic simulations. The kinetic model of electron avalanche development was developed using PIC-MCC technique. The model simulates motion of electrons, ions and fast helium atoms, appearing due to ions scattering. It was shown that the mechanism responsible for ultra-fast breakdown development is the electron emission from cathode. The photoemission and emission by ions or fast atoms impact is the main reason of current growth at the early stage of breakdown, but at the final stage, when the voltage on discharge gap drops, the secondary electron emission (SEE) is responsible for subnanosecond time scale of current growth. It was also found that the characteristic time of the current growth τS depends on the SEE yield of the cathode material. Three types of cathode material (titanium, SiC, and CuAlMg-alloy) were tested. It is shown that in discharge with SiC and CuAlMg-alloy cathodes (which have enhanced SEE) the current can increase with a subnanosecond characteristic time as small as τS = 0.4 ns, for the pulse voltage amplitude of 5- 12 kV..

Nagaoka’s atomic model and hyperfine interactions

PubMed Central

INAMURA, Takashi T.

2016-01-01

The prevailing view of Nagaoka’s “Saturnian” atom is so misleading that today many people have an erroneous picture of Nagaoka’s vision. They believe it to be a system involving a ‘giant core’ with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka’s model is exactly the same as Rutherford’s. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure. PMID:27063182

Multipartite quantum correlations among atoms in QED cavities

NASA Astrophysics Data System (ADS)

Batle, J.; Farouk, A.; Tarawneh, O.; Abdalla, S.

2018-02-01

We study the nonlocality dynamics for two models of atoms in cavity quantum electrodynamics (QED); the first model contains atoms in a single cavity undergoing nearest-neighbor interactions with no initial correlation, and the second contains atoms confined in n different and noninteracting cavities, all of which were initially prepared in a maximally correlated state of n qubits corresponding to the atomic degrees of freedom. The nonlocality evolution of the states in the second model shows that the corresponding maximal violation of a multipartite Bell inequality exhibits revivals at precise times, defining, nonlocality sudden deaths and nonlocality sudden rebirths, in analogy with entanglement. These quantum correlations are provided analytically for the second model to make the study more thorough. Differences in the first model regarding whether the array of atoms inside the cavity is arranged in a periodic or open fashion are crucial to the generation or redistribution of quantum correlations. This contribution paves the way to using the nonlocality multipartite correlation measure for describing the collective complex behavior displayed by slightly interacting cavity QED arrays.

Constructing Molecular Models with Low-Cost Toy Beads

ERIC Educational Resources Information Center

Ng, Pun-hon; Wong, Siu-ling; Mak, Se-yuen

2012-01-01

In teaching the science of the nano world, ball-and-stick molecular models are frequently used as 3D representations of molecules. Unlike a chemical formula, a molecular model allows us to visualise the 3D shape of the molecule and the relative positions of its atoms, the bonds between atoms and why a pair of mirror isomers with the same atoms,…

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

PubMed

Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

2013-04-01

When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantitative composition determination at the atomic level using model-based high-angle annular dark field scanning transmission electron microscopy.

PubMed

Martinez, G T; Rosenauer, A; De Backer, A; Verbeeck, J; Van Aert, S

2014-02-01

High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed. © 2013 Published by Elsevier B.V. All rights reserved.

Polder maps: Improving OMIT maps by excluding bulk solvent

DOE PAGES

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; ...

2017-02-01

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factorsmore » and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

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.

Atomic data and spectral modeling constraints from high-resolution X-ray observations of the Perseus cluster with Hitomi

NASA Astrophysics Data System (ADS)

Hitomi Collaboration; Aharonian, Felix; Akamatsu, Hiroki; Akimoto, Fumie; Allen, Steven W.; Angelini, Lorella; Audard, Marc; Awaki, Hisamitsu; Axelsson, Magnus; Bamba, Aya; Bautz, Marshall W.; Blandford, Roger; Brenneman, Laura W.; Brown, Gregory V.; Bulbul, Esra; Cackett, Edward M.; Chernyakova, Maria; Chiao, Meng P.; Coppi, Paolo S.; Costantini, Elisa; de Plaa, Jelle; de Vries, Cor P.; den Herder, Jan-Willem; Done, Chris; Dotani, Tadayasu; Ebisawa, Ken; Eckart, Megan E.; Enoto, Teruaki; Ezoe, Yuichiro; Fabian, Andrew C.; Ferrigno, Carlo; Foster, Adam R.; Fujimoto, Ryuichi; Fukazawa, Yasushi; Furuzawa, Akihiro; Galeazzi, Massimiliano; Gallo, Luigi C.; Gandhi, Poshak; Giustini, Margherita; Goldwurm, Andrea; Gu, Liyi; Guainazzi, Matteo; Haba, Yoshito; Hagino, Kouichi; Hamaguchi, Kenji; Harrus, Ilana M.; Hatsukade, Isamu; Hayashi, Katsuhiro; Hayashi, Takayuki; Hayashida, Kiyoshi; Hell, Natalie; Hiraga, Junko S.; Hornschemeier, Ann; Hoshino, Akio; Hughes, John P.; Ichinohe, Yuto; Iizuka, Ryo; Inoue, Hajime; Inoue, Yoshiyuki; Ishida, Manabu; Ishikawa, Kumi; Ishisaki, Yoshitaka; Iwai, Masachika; Kaastra, Jelle; Kallman, Tim; Kamae, Tsuneyoshi; Kataoka, Jun; Katsuda, Satoru; Kawai, Nobuyuki; Kelley, Richard L.; Kilbourne, Caroline A.; Kitaguchi, Takao; Kitamoto, Shunji; Kitayama, Tetsu; Kohmura, Takayoshi; Kokubun, Motohide; Koyama, Katsuji; Koyama, Shu; Kretschmar, Peter; Krimm, Hans A.; Kubota, Aya; Kunieda, Hideyo; Laurent, Philippe; Lee, Shiu-Hang; Leutenegger, Maurice A.; Limousin, Olivier; Loewenstein, Michael; Long, Knox S.; Lumb, David; Madejski, Greg; Maeda, Yoshitomo; Maier, Daniel; Makishima, Kazuo; Markevitch, Maxim; Matsumoto, Hironori; Matsushita, Kyoko; McCammon, Dan; McNamara, Brian R.; Mehdipour, Missagh; Miller, Eric D.; Miller, Jon M.; Mineshige, Shin; Mitsuda, Kazuhisa; Mitsuishi, Ikuyuki; Miyazawa, Takuya; Mizuno, Tsunefumi; Mori, Hideyuki; Mori, Koji; Mukai, Koji; Murakami, Hiroshi; Mushotzky, Richard F.; Nakagawa, Takao; Nakajima, Hiroshi; Nakamori, Takeshi; Nakashima, Shinya; Nakazawa, Kazuhiro; Nobukawa, Kumiko K.; Nobukawa, Masayoshi; Noda, Hirofumi; Odaka, Hirokazu; Ohashi, Takaya; Ohno, Masanori; Okajima, Takashi; Ota, Naomi; Ozaki, Masanobu; Paerels, Frits; Paltani, Stéphane; Petre, Robert; Pinto, Ciro; Porter, Frederick S.; Pottschmidt, Katja; Reynolds, Christopher S.; Safi-Harb, Samar; Saito, Shinya; Sakai, Kazuhiro; Sasaki, Toru; Sato, Goro; Sato, Kosuke; Sato, Rie; Sawada, Makoto; Schartel, Norbert; Serlemtsos, Peter J.; Seta, Hiromi; Shidatsu, Megumi; Simionescu, Aurora; Smith, Randall K.; Soong, Yang; Stawarz, Łukasz; Sugawara, Yasuharu; Sugita, Satoshi; Szymkowiak, Andrew; Tajima, Hiroyasu; Takahashi, Hiromitsu; Takahashi, Tadayuki; Takeda, Shin'ichiro; Takei, Yoh; Tamagawa, Toru; Tamura, Takayuki; Tanaka, Takaaki; Tanaka, Yasuo; Tanaka, Yasuyuki T.; Tashiro, Makoto S.; Tawara, Yuzuru; Terada, Yukikatsu; Terashima, Yuichi; Tombesi, Francesco; Tomida, Hiroshi; Tsuboi, Yohko; Tsujimoto, Masahiro; Tsunemi, Hiroshi; Tsuru, Takeshi Go; Uchida, Hiroyuki; Uchiyama, Hideki; Uchiyama, Yasunobu; Ueda, Shutaro; Ueda, Yoshihiro; Uno, Shin'ichiro; Urry, C. Megan; Ursino, Eugenio; Watanabe, Shin; Werner, Norbert; Wilkins, Dan R.; Williams, Brian J.; Yamada, Shinya; Yamaguchi, Hiroya; Yamaoka, Kazutaka; Yamasaki, Noriko Y.; Yamauchi, Makoto; Yamauchi, Shigeo; Yaqoob, Tahir; Yatsu, Yoichi; Yonetoku, Daisuke; Zhuravleva, Irina; Zoghbi, Abderahmen; Raassen, A. J. J.

2018-03-01

The Hitomi Soft X-ray Spectrometer spectrum of the Perseus cluster, with ˜5 eV resolution in the 2-9 keV band, offers an unprecedented benchmark of the atomic modeling and database for hot collisional plasmas. It reveals both successes and challenges of the current atomic data and models. The latest versions of AtomDB/APEC (3.0.8), SPEX (3.03.00), and CHIANTI (8.0) all provide reasonable fits to the broad-band spectrum, and are in close agreement on best-fit temperature, emission measure, and abundances of a few elements such as Ni. For the Fe abundance, the APEC and SPEX measurements differ by 16%, which is 17 times higher than the statistical uncertainty. This is mostly attributed to the differences in adopted collisional excitation and dielectronic recombination rates of the strongest emission lines. We further investigate and compare the sensitivity of the derived physical parameters to the astrophysical source modeling and instrumental effects. The Hitomi results show that accurate atomic data and models are as important as the astrophysical modeling and instrumental calibration aspects. Substantial updates of atomic databases and targeted laboratory measurements are needed to get the current data and models ready for the data from the next Hitomi-level mission.

Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model.

PubMed

Woo Kim, Hyun; Rhee, Young Min

2012-07-30

Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. Copyright © 2012 Wiley Periodicals, Inc.

Challenging the Science Curriculum Paradigm: Teaching Primary Children Atomic-Molecular Theory

NASA Astrophysics Data System (ADS)

Haeusler, Carole; Donovan, Jennifer

2017-11-01

Solutions to global issues demand the involvement of scientists, yet concern exists about retention rates in science as students pass through school into University. Young children are curious about science, yet are considered incapable of grappling with abstract and microscopic concepts such as atoms, sub-atomic particles, molecules and DNA. School curricula for primary (elementary) aged children reflect this by their limitation to examining only what phenomena are without providing any explanatory frameworks for how or why they occur. This research challenges the assumption that atomic-molecular theory is too difficult for young children, examining new ways of introducing atomic theory to 9 year olds and seeks to verify their efficacy in producing genuine learning in the participants. Early results in three cases in different schools indicate these novel methods fostered further interest in science, allowed diverse children to engage and learn aspects of atomic theory, and satisfied the children's desire for intellectual challenge. Learning exceeded expectations as demonstrated in the post-interview findings. Learning was also remarkably robust, as demonstrated in two schools 8 weeks after the intervention and, in one school, 1 year after their first exposure to ideas about atoms, elements and molecules.

Modeling of Turbulence Effects on Liquid Jet Atomization and Breakup

NASA Technical Reports Server (NTRS)

Trinh, Huu; Chen, C. P.

2004-01-01

Recent experimental investigations and physical modeling studies have indicated that turbulence behaviors within a liquid jet have considerable effects on the atomization process. For certain flow regimes, it has been observed that the liquid jet surface is highly turbulent. This turbulence characteristic plays a key role on the breakup of the liquid jet near to the injector exit. Other experiments also showed that the breakup length of the liquid core is sharply shortened as the liquid jet is changed from the laminar to the turbulent flow conditions. In the numerical and physical modeling arena, most of commonly used atomization models do not include the turbulence effect. Limited attempts have been made in modeling the turbulence phenomena on the liquid jet disintegration. The subject correlation and models treat the turbulence either as an only source or a primary driver in the breakup process. This study aims to model the turbulence effect in the atomization process of a cylindrical liquid jet. In the course of this study, two widely used models, Reitz's primary atomization (blob) and Taylor-Analogy-Break (TAB) secondary droplet breakup by O Rourke et al. are examined. Additional terms are derived and implemented appropriately into these two models to account for the turbulence effect on the atomization process. Since this enhancement effort is based on a framework of the two existing atomization models, it is appropriate to denote the two present models as T-blob and T-TAB for the primary and secondary atomization predictions, respectively. In the primary breakup model, the level of the turbulence effect on the liquid breakup depends on the characteristic time scales and the initial flow conditions. This treatment offers a balance of contributions of individual physical phenomena on the liquid breakup process. For the secondary breakup, an addition turbulence force acted on parent drops is modeled and integrated into the TAB governing equation. The drop size formed from this breakup regime is estimated based on the energy balance before and after the breakup occurrence. The turbulence energy is also considered in this process.

Rydberg interaction induced enhanced excitation in thermal atomic vapor.

PubMed

Kara, Dushmanta; Bhowmick, Arup; Mohapatra, Ashok K

2018-03-27

We present the experimental demonstration of interaction induced enhancement in Rydberg excitation or Rydberg anti-blockade in thermal atomic vapor. We have used optical heterodyne detection technique to measure Rydberg population due to two-photon excitation to the Rydberg state. The anti-blockade peak which doesn't satisfy the two-photon resonant condition is observed along with the usual two-photon resonant peak which can't be explained using the model with non-interacting three-level atomic system. A model involving two interacting atoms is formulated for thermal atomic vapor using the dressed states of three-level atomic system to explain the experimental observations. A non-linear dependence of vapor density is observed for the anti-blockade peak which also increases with increase in principal quantum number of the Rydberg state. A good agreement is found between the experimental observations and the proposed interacting model. Our result implies possible applications towards quantum logic gates using Rydberg anti-blockade in thermal atomic vapor.

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

DOE PAGES

Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

2018-06-08

TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B 24 , 63–76]. The results of a TLS refinement are T , L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both proceduresmore » are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.« less

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

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

Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B 24 , 63–76]. The results of a TLS refinement are T , L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both proceduresmore » are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.« less

Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

PubMed

Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

2015-12-28

Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

A Comparison between Elementary School Students' Mental Models and Visualizations in Textbooks for the Concept of Atom

ERIC Educational Resources Information Center

Polat-Yaseen, Zeynep

2012-01-01

This study was designed for two major goals, which are to describe students' mental models about atom concept from 6th to 8th grade and to compare students' mental models with visual representations of atom in textbooks. Qualitative and quantitative data were collected with 4 open-ended questions including drawings which were quantified using the…

Optical-bistability-enabled control of resonant light transmission for an atom-cavity system

NASA Astrophysics Data System (ADS)

Sawant, Rahul; Rangwala, S. A.

2016-02-01

The control of light transmission through a standing-wave Fabry-Pérot cavity containing atoms is theoretically and numerically investigated, when the cavity mode beam and an intersecting control beam are both close to specific atomic resonances. A four-level atomic system is considered and its interaction with the cavity mode is studied by solving for the cavity field and atomic state populations. The conditions for optical bistability of the atom-cavity system are obtained. The response of the intracavity intensity to an intersecting beam on atomic resonance is understood in the presence of stationary atoms (closed system) and nonstatic atoms (open system) in the cavity. The nonstatic system of atoms is modelled by adjusting the atomic state populations to represent the exchange of atoms in the cavity mode, which corresponds to a thermal environment where atoms are moving in and out of the cavity mode volume. The control behavior with three- and two-level atomic systems is also studied, and the rich physics arising out of these systems for closed and open atomic systems is discussed. The solutions to the models are used to interpret the steady-state and transient behavior observed by Sharma et al. [Phys. Rev. A 91, 043824 (2015)], 10.1103/PhysRevA.91.043824.

Optimal control of complex atomic quantum systems

PubMed Central

van Frank, S.; Bonneau, M.; Schmiedmayer, J.; Hild, S.; Gross, C.; Cheneau, M.; Bloch, I.; Pichler, T.; Negretti, A.; Calarco, T.; Montangero, S.

2016-01-01

Quantum technologies will ultimately require manipulating many-body quantum systems with high precision. Cold atom experiments represent a stepping stone in that direction: a high degree of control has been achieved on systems of increasing complexity. However, this control is still sub-optimal. In many scenarios, achieving a fast transformation is crucial to fight against decoherence and imperfection effects. Optimal control theory is believed to be the ideal candidate to bridge the gap between early stage proof-of-principle demonstrations and experimental protocols suitable for practical applications. Indeed, it can engineer protocols at the quantum speed limit – the fastest achievable timescale of the transformation. Here, we demonstrate such potential by computing theoretically and verifying experimentally the optimal transformations in two very different interacting systems: the coherent manipulation of motional states of an atomic Bose-Einstein condensate and the crossing of a quantum phase transition in small systems of cold atoms in optical lattices. We also show that such processes are robust with respect to perturbations, including temperature and atom number fluctuations. PMID:27725688

Optimal control of complex atomic quantum systems.

PubMed

van Frank, S; Bonneau, M; Schmiedmayer, J; Hild, S; Gross, C; Cheneau, M; Bloch, I; Pichler, T; Negretti, A; Calarco, T; Montangero, S

2016-10-11

Quantum technologies will ultimately require manipulating many-body quantum systems with high precision. Cold atom experiments represent a stepping stone in that direction: a high degree of control has been achieved on systems of increasing complexity. However, this control is still sub-optimal. In many scenarios, achieving a fast transformation is crucial to fight against decoherence and imperfection effects. Optimal control theory is believed to be the ideal candidate to bridge the gap between early stage proof-of-principle demonstrations and experimental protocols suitable for practical applications. Indeed, it can engineer protocols at the quantum speed limit - the fastest achievable timescale of the transformation. Here, we demonstrate such potential by computing theoretically and verifying experimentally the optimal transformations in two very different interacting systems: the coherent manipulation of motional states of an atomic Bose-Einstein condensate and the crossing of a quantum phase transition in small systems of cold atoms in optical lattices. We also show that such processes are robust with respect to perturbations, including temperature and atom number fluctuations.

Atmospheric Mining in the Outer Solar System: Outer Planet Orbital Transfer and Lander Analyses

NASA Technical Reports Server (NTRS)

Palaszewski, Bryan

2016-01-01

High energy propellants for human lunar missions are analyzed, focusing on very advanced ozone and atomic hydrogen. One of the most advanced launch vehicle propulsion systems, such as the Space Shuttle Main Engine (SSME), used hydrogen and oxygen and had a delivered specific impulse of 453 seconds. In the early days of the space program, other propellants (or so called metapropellants) were suggested, including atomic hydrogen and liquid ozone. Theoretical and experimental studies of atomic hydrogen and ozone were conducted beginning in the late 1940s. This propellant research may have provided screenwriters with the idea of an atomic hydrogen-ozone rocket engine in the 1950 movie, Rocketship X-M. This paper presents analyses showing that an atomic hydrogen-ozone rocket engine could produce a specific impulse over a wide range of specific impulse values reaching as high as 1,600 seconds. A series of single stage and multistage rocket vehicle analyses were conducted to find the minimum specific impulse needed to conduct high energy round trip lunar missions.

Propulsion Estimates for High Energy Lunar Missions Using Future Propellants

NASA Technical Reports Server (NTRS)

Palaszewski, Bryan A.; Bennett, Gary L.

2016-01-01

High energy propellants for human lunar missions are analyzed, focusing on very advanced ozone and atomic hydrogen. One of the most advanced launch vehicle propulsion systems, such as the Space Shuttle Main Engine (SSME), used hydrogen and oxygen and had a delivered specific impulse of 453 seconds. In the early days of the space program, other propellants (or so called metapropellants) were suggested, including atomic hydrogen and liquid ozone. Theoretical and experimental studies of atomic hydrogen and ozone were conducted beginning in the late 1940s. This propellant research may have provided screenwriters with the idea of an atomic hydrogen-ozone rocket engine in the 1950 movie, Rocketship X-M. This paper presents analyses showing that an atomic hydrogen-ozone rocket engine could produce a specific impulse over a wide range of specific impulse values reaching as high as 1,600 s. A series of single stage and multistage rocket vehicle analyses were conducted to find the minimum specific impulse needed to conduct high energy round trip lunar missions.

Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule

NASA Astrophysics Data System (ADS)

Takahashi, Takuya; Sugiura, Junnnosuke; Nagayama, Kuniaki

2002-05-01

To investigate the role hydration plays in the electrostatic interactions of proteins, the time-averaged electrostatic potential of the B1 domain of protein G in an aqueous solution was calculated with full atomic molecular dynamics simulations that explicitly considers every atom (i.e., an all atom model). This all atom calculated potential was compared with the potential obtained from an electrostatic continuum model calculation. In both cases, the charge-screening effect was fairly well formulated with an effective relative dielectric constant which increased linearly with increasing charge-charge distance. This simulated linear dependence agrees with the experimentally determined linear relation proposed by Pickersgill. Cut-off approximations for Coulomb interactions failed to reproduce this linear relation. Correlation between the all atom model and the continuum models was found to be better than the respective correlation calculated for linear fitting to the two models. This confirms that the continuum model is better at treating the complicated shapes of protein conformations than the simple linear fitting empirical model. We have tried a sigmoid fitting empirical model in addition to the linear one. When weights of all data were treated equally, the sigmoid model, which requires two fitting parameters, fits results of both the all atom and the continuum models less accurately than the linear model which requires only one fitting parameter. When potential values are chosen as weighting factors, the fitting error of the sigmoid model became smaller, and the slope of both linear fitting curves became smaller. This suggests the screening effect of an aqueous medium within a short range, where potential values are relatively large, is smaller than that expected from the linear fitting curve whose slope is almost 4. To investigate the linear increase of the effective relative dielectric constant, the Poisson equation of a low-dielectric sphere in a high-dielectric medium was solved and charges distributed near the molecular surface were indicated as leading to the apparent linearity.

Project Physics Tests 5, Models of the Atom.

ERIC Educational Resources Information Center

Harvard Univ., Cambridge, MA. Harvard Project Physics.

Test items relating to Project Physics Unit 5 are presented in this booklet. Included are 70 multiple-choice and 23 problem-and-essay questions. Concepts of atomic model are examined on aspects of relativistic corrections, electron emission, photoelectric effects, Compton effect, quantum theories, electrolysis experiments, atomic number and mass,…

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Atom-atom inelastic collisions and three-body atomic recombination in weakly ionized argon plasmas

NASA Technical Reports Server (NTRS)

Braun, C. G.; Kunc, J. A.

1989-01-01

A stationary collisional-radiative model including both inelastic electron-atom and atom-atom collisions is used to examine nonequilibrium weakly ionized argon plasmas with atomic densities 10 to the 16th to 10 to the 20th/cu cm, temperatures below 6000 K, and with different degrees of radiation trapping. It is shown that three-body atomic recombination becomes important at high particle densities. Comparison is made between the present approach and Thomson's theory for atomic recombination.

Factors that drive peptide assembly and fibril formation: experimental and theoretical analysis of Sup35 NNQQNY mutants.

PubMed

Do, Thanh D; Economou, Nicholas J; LaPointe, Nichole E; Kincannon, William M; Bleiholder, Christian; Feinstein, Stuart C; Teplow, David B; Buratto, Steven K; Bowers, Michael T

2013-07-18

Residue mutations have substantial effects on aggregation kinetics and propensities of amyloid peptides and their aggregate morphologies. Such effects are attributed to conformational transitions accessed by various types of oligomers such as steric zipper or single β-sheet. We have studied the aggregation propensities of six NNQQNY mutants: NVVVVY, NNVVNV, NNVVNY, VIQVVY, NVVQIY, and NVQVVY in water using a combination of ion-mobility mass spectrometry, transmission electron microscopy, atomic force microscopy, and all-atom molecular dynamics simulations. Our data show a strong correlation between the tendency to form early β-sheet oligomers and the subsequent aggregation propensity. Our molecular dynamics simulations indicate that the stability of a steric zipper structure can enhance the propensity for fibril formation. Such stability can be attained by either hydrophobic interactions in the mutant peptide or polar side-chain interdigitations in the wild-type peptide. The overall results display only modest agreement with the aggregation propensity prediction methods such as PASTA, Zyggregator, and RosettaProfile, suggesting the need for better parametrization and model peptides for these algorithms.

The grave is wide: the Hibakusha of Hiroshima and Nagasaki and the legacy of the Atomic Bomb Casualty Commission and the Radiation Effects Research Foundation.

PubMed

O'Malley, Gerald F

2016-07-01

Following the atomic bomb attacks on Japan in 1945, scientists from the United States and Japan joined together to study the Hibakusha - the bomb affected people in what was advertised as a bipartisan and cooperative effort. In reality, despite the best efforts of some very dedicated and earnest scientists, the early years of the collaboration were characterized by political friction, censorship, controversy, tension, hostility, and racism. The 70-year history, scientific output and cultural impact of the Atomic Bomb Casualty Commission and the Radiation Effects Research Foundation are described in the context of the development of Occupied Japan.

Theoretical modeling of the catch-slip bond transition in biological adhesion

NASA Astrophysics Data System (ADS)

Gunnerson, Kim; Pereverzev, Yuriy; Prezhdo, Oleg

2006-05-01

The mechanism by which leukocytes leave the blood stream and enter inflamed tissue is called extravasation. This process is facilitated by the ability of selectin proteins, produced by the endothelial cells of blood vessels, to form transient bonds with the leukocytes. In the case of P-selectin, the protein bonds with P-selectin glycoprotein ligands (PSGL-1) produced by the leukocyte. Recent atomic force microscopy and flow chamber analyses of the binding of P-selectin to PSGL-1 provide evidence for an unusual biphasic catch-bond/slip-bond behavior in response to the strength of exerted force. This biphasic process is not well-understood. There are several theoretical models for describing this phenomenon. These models use different profiles for potential energy landscapes and how they change under forces. We are exploring these changes using molecular dynamics. We will present a simple theoretical model as well as share some of our early MD results for describing this phenomenon.

Enhancing light-atom interactions via atomic bunching

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie L.; Gauthier, Daniel J.

2014-07-01

There is a broad interest in enhancing the strength of light-atom interactions to the point where injecting a single photon induces a nonlinear material response. Here we show theoretically that sub-Doppler-cooled two-level atoms that are spatially organized by weak optical fields give rise to a nonlinear material response that is greatly enhanced beyond that attainable in a homogeneous gas. Specifically, in the regime where the intensity of the applied optical fields is much less than the off-resonance saturation intensity, we show that the third-order nonlinear susceptibility scales inversely with atomic temperature and, due to this scaling, can be two orders of magnitude larger than that of a homogeneous gas for typical experimental parameters. As a result, we predict that spatially bunched two-level atoms can exhibit single-photon nonlinearities. Our model is valid for all regimes of atomic bunching and simultaneously accounts for the backaction of the atoms on the optical fields. Our results agree with previous theoretical and experimental results for light-atom interactions that have considered only limited regimes of atomic bunching. For lattice beams tuned to the low-frequency side of the atomic transition, we find that the nonlinearity transitions from a self-focusing type to a self-defocusing type at a critical intensity. We also show that higher than third-order nonlinear optical susceptibilities are significant in the regime where the dipole potential energy is on the order of the atomic thermal energy. We therefore find that it is crucial to retain high-order nonlinearities to accurately predict interactions of laser fields with spatially organized ultracold atoms. The model presented here is a foundation for modeling low-light-level nonlinear optical processes for ultracold atoms in optical lattices.

Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Degroh, Kim K.; Sechkar, Edward A.

1992-01-01

Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) will assist in understanding the mechanisms involved, and will lead to improved reliability in predicting in-space durability of materials based on ground laboratory testing. A computational simulation of atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of assumed mechanistic behavior of atomic oxygen and results of both ground laboratory and LDEF data, a predictive Monte Carlo model was developed which simulates the oxidation processes that occur on polymers with applied protective coatings that have defects. The use of high atomic oxygen fluence-directed ram LDEF results has enabled mechanistic implications to be made by adjusting Monte Carlo modeling assumptions to match observed results based on scanning electron microscopy. Modeling assumptions, implications, and predictions are presented, along with comparison of observed ground laboratory and LDEF results.

A Nonlinear Model for Fuel Atomization in Spray Combustion

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Coherent scattering of near-resonant light by a dense, microscopic cloud of cold two-level atoms: Experiment versus theory

NASA Astrophysics Data System (ADS)

Jennewein, Stephan; Brossard, Ludovic; Sortais, Yvan R. P.; Browaeys, Antoine; Cheinet, Patrick; Robert, Jacques; Pillet, Pierre

2018-05-01

We measure the coherent scattering of low-intensity, near-resonant light by a cloud of laser-cooled two-level rubidium atoms with a size comparable to the wavelength of light. We isolate a two-level atomic structure by applying a 300-G magnetic field. We measure both the temporal and the steady-state coherent optical response of the cloud for various detunings of the laser and for atom numbers ranging from 5 to 100. We compare our results to a microscopic coupled-dipole model and to a multimode, paraxial Maxwell-Bloch model. In the low-intensity regime, both models are in excellent agreement, thus validating the Maxwell-Bloch model. Comparing to the data, the models are found in very good agreement for relatively low densities (n /k3≲0.1 ), while significant deviations start to occur at higher density. This disagreement indicates that light scattering in dense, cold atomic ensembles is still not quantitatively understood, even in pristine experimental conditions.

Efficient Nonlinear Atomization Model for Thin 3D Free Liquid Films

NASA Astrophysics Data System (ADS)

Mehring, Carsten

2007-03-01

Reviewed is a nonlinear reduced-dimension thin-film model developed by the author and aimed at the prediction of spray formation from thin films such as those found in gas-turbine engines (e.g., prefilming air-blast atomizers), heavy-fuel-oil burners (e.g., rotary-cup atomizers) and in the paint industry (e.g., flat-fan atomizers). Various implementations of the model focusing on different model-aspects, i.e., effect of film geometry, surface tension, liquid viscosity, coupling with surrounding gas-phase flow, influence of long-range intermolecular forces during film rupture are reviewed together with a validation of the nonlinear wave propagation characteristics predicted by the model for inviscid planar films using a two-dimensional vortex- method. An extension and generalization of the current nonlinear film model for implementation into a commercial flow- solver is outlined.

Atomic and molecular_diagnostics of the interstellar medium

NASA Astrophysics Data System (ADS)

Roueff, E.

1987-08-01

Ever since molecular species have been discovered in space in the 30's and early 40's by the optical identification of CH, CH+ and CN in absorption towards nearby hot stars, the question of molecule formation has accompanied the observational efforts. The purpose of this paper is to point out presently existing observational constraints and the limits they may cast on our knowledge of the interstellar medium. The need for reliable atomic and molecular data will be emphasized with some specific examples.

Non-thermal hydrogen atoms in the terrestrial upper thermosphere.

PubMed

Qin, Jianqi; Waldrop, Lara

2016-12-06

Model predictions of the distribution and dynamical transport of hydrogen atoms in the terrestrial atmosphere have long-standing discrepancies with ultraviolet remote sensing measurements, indicating likely deficiencies in conventional theories regarding this crucial atmospheric constituent. Here we report the existence of non-thermal hydrogen atoms that are much hotter than the ambient oxygen atoms in the upper thermosphere. Analysis of satellite measurements indicates that the upper thermospheric hydrogen temperature, more precisely the mean kinetic energy of the atomic hydrogen population, increases significantly with declining solar activity, contrary to contemporary understanding of thermospheric behaviour. The existence of hot hydrogen atoms in the upper thermosphere, which is the key to reconciling model predictions and observations, is likely a consequence of low atomic oxygen density leading to incomplete collisional thermalization of the hydrogen population following its kinetic energization through interactions with hot atomic or ionized constituents in the ionosphere, plasmasphere or magnetosphere.

Non-thermal hydrogen atoms in the terrestrial upper thermosphere

PubMed Central

Qin, Jianqi; Waldrop, Lara

2016-01-01

Model predictions of the distribution and dynamical transport of hydrogen atoms in the terrestrial atmosphere have long-standing discrepancies with ultraviolet remote sensing measurements, indicating likely deficiencies in conventional theories regarding this crucial atmospheric constituent. Here we report the existence of non-thermal hydrogen atoms that are much hotter than the ambient oxygen atoms in the upper thermosphere. Analysis of satellite measurements indicates that the upper thermospheric hydrogen temperature, more precisely the mean kinetic energy of the atomic hydrogen population, increases significantly with declining solar activity, contrary to contemporary understanding of thermospheric behaviour. The existence of hot hydrogen atoms in the upper thermosphere, which is the key to reconciling model predictions and observations, is likely a consequence of low atomic oxygen density leading to incomplete collisional thermalization of the hydrogen population following its kinetic energization through interactions with hot atomic or ionized constituents in the ionosphere, plasmasphere or magnetosphere. PMID:27922018

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

PubMed

DiMaio, F; Chiu, W

2016-01-01

Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

Physically representative atomistic modeling of atomic-scale friction

NASA Astrophysics Data System (ADS)

Dong, Yalin

Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

Hirshfeld atom refinement for modelling strong hydrogen bonds.

PubMed

Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

2014-09-01

High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations

NASA Astrophysics Data System (ADS)

Meng, Qingyong; Meyer, Hans-Dieter

2015-10-01

Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.

Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations

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

Meng, Qingyong, E-mail: mengqingyong@dicp.ac.cn; Meyer, Hans-Dieter, E-mail: hans-dieter.meyer@pci.uni-heidelberg.de

2015-10-28

Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in themore » present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.« less

The Quantum Atomic Model "Electronium": A Successful Teaching Tool.

ERIC Educational Resources Information Center

Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John

2002-01-01

Focuses on the quantum atomic model Electronium. Outlines the Bremen teaching approach in which this model is used, and analyzes the learning of two students as they progress through the teaching unit. (Author/MM)

Continuous measurement of an atomic current

NASA Astrophysics Data System (ADS)

Laflamme, C.; Yang, D.; Zoller, P.

2017-04-01

We are interested in dynamics of quantum many-body systems under continuous observation, and its physical realizations involving cold atoms in lattices. In the present work we focus on continuous measurement of atomic currents in lattice models, including the Hubbard model. We describe a Cavity QED setup, where measurement of a homodyne current provides a faithful representation of the atomic current as a function of time. We employ the quantum optical description in terms of a diffusive stochastic Schrödinger equation to follow the time evolution of the atomic system conditional to observing a given homodyne current trajectory, thus accounting for the competition between the Hamiltonian evolution and measurement back action. As an illustration, we discuss minimal models of atomic dynamics and continuous current measurement on rings with synthetic gauge fields, involving both real space and synthetic dimension lattices (represented by internal atomic states). Finally, by "not reading" the current measurements the time evolution of the atomic system is governed by a master equation, where—depending on the microscopic details of our CQED setups—we effectively engineer a current coupling of our system to a quantum reservoir. This provides interesting scenarios of dissipative dynamics generating "dark" pure quantum many-body states.

Circuit QED with qutrits: Coupling three or more atoms via virtual-photon exchange

NASA Astrophysics Data System (ADS)

Zhao, Peng; Tan, Xinsheng; Yu, Haifeng; Zhu, Shi-Liang; Yu, Yang

2017-10-01

We present a model to describe a generic circuit QED system which consists of multiple artificial three-level atoms, namely, qutrits, strongly coupled to a cavity mode. When the state transition of the atoms disobeys the selection rules the process that does not conserve the number of excitations can happen determinatively. Therefore, we can realize coherent exchange interaction among three or more atoms mediated by the exchange of virtual photons. In addition, we generalize the one-cavity-mode mediated interactions to the multicavity situation, providing a method to entangle atoms located in different cavities. Using experimentally feasible parameters, we investigate the dynamics of the model including three cyclic-transition three-level atoms, for which the two lowest energy levels can be treated as qubits. Hence, we have found that two qubits can jointly exchange excitation with one qubit in a coherent and reversible way. In the whole process, the population in the third level of atoms is negligible and the cavity photon number is far smaller than 1. Our model provides a feasible scheme to couple multiple distant atoms together, which may find applications in quantum information processing.

Edge enhanced growth induced shape transition in the formation of GaN nanowall network

NASA Astrophysics Data System (ADS)

Nayak, Sanjay; Kumar, Rajendra; Shivaprasad, S. M.

2018-01-01

We address the mechanism of early stages of growth and shape transition of the unique nanowall network (NwN) of GaN by experimentally monitoring its morphological evolution and complementing it by first-principles calculations. Using atomic force and scanning electron microscopy, we observe the formation of oval shaped islands at very early stages of the growth which later transformed into tetrahedron shaped (3 faced pyramid) islands. These tetrahedron shaped islands further grow anisotropically along their edges of the (20 2 ¯ 1) facets to form the wall-like structure as the growth proceeds. The mechanism of this crystal growth is discussed in light of surface free energies of the different surfaces, adsorption energy, and diffusion barrier of Ga ad-atoms on the (20 2 ¯ 1) facets. By first-principles calculations, we find that the diffusion barrier of ad-atoms reduces with decreasing width of facets and is responsible for the anisotropic growth leading to the formation of NwN. This study suggests that formation of NwN is an archetype example of structure dependent attachment kinetic instability induced shape transition in thin film growth.

Prevalence of monoclonal gammopathy of undetermined significance in Asia: a viewpoint from nagasaki atomic bomb survivors.

PubMed

Iwanaga, Masako; Tomonaga, Masao

2014-02-01

Exposure to ionizing radiation is a known environmental risk factor for a variety of cancers including hematological malignancies, such as leukemia, myelodysplastic syndromes, and multiple myeloma. Therefore, for Hiroshima and Nagasaki atomic bomb survivors (surviving victims who were exposed to ionizing radiation emitted from the nuclear weapons), several cancer-screening tests have been provided annually, with government support, to detect the early stage of malignancies. An M-protein screening test has been used to detect multiple myeloma at an early stage among atomic bomb survivors. In the screening process, a number of patients with monoclonal gammopathy of undetermined significance (MGUS), in addition to multiple myeloma, have been identified. In 2009 and 2011, we reported the age- and sex-specific prevalence of MGUS between 1988 and 2004 and the possible role of radiation exposure in the development of MGUS using the screening data of more than 1000 patients with MGUS among approximately 52,000 Nagasaki atomic bomb survivors. The findings included: (1) a significant lower overall prevalence (2.1%) than that observed in Caucasian or African-origin populations; (2) a significantly higher prevalence in men than in women; (3) an age-related increase in the prevalence; (4) a significantly higher prevalence in people exposed to higher radiation doses only among those exposed at age 20 years or younger; and (5) a lower frequency of immunoglobulin M MGUS in Japanese patients than in patients in Western countries. The large study of MGUS among Nagasaki atomic bomb survivors has provided important findings for the etiology of MGUS, including a possible role of radiation exposure on the cause of MGUS and an ethnicity-related difference in the characteristics of MGUS. Copyright © 2014 Elsevier Inc. All rights reserved.

Metastability of the atomic structures of size-selected gold nanoparticles

NASA Astrophysics Data System (ADS)

Wells, Dawn M.; Rossi, Giulia; Ferrando, Riccardo; Palmer, Richard E.

2015-04-01

All nanostructures are metastable - but some are more metastable than others. Here we employ aberration-corrected electron microscopy and atomistic computer simulations to demonstrate the hierarchy of metastability in deposited, size-selected gold nanoparticles (clusters), an archetypal class of nanomaterials well known for the catalytic activity which only appears on the nanometer-scale. We show that the atomic structures presented by ``magic number'' Au561, Au742 and Au923 clusters are ``locked''. They are in fact determined by the solidification which occurs from the liquid state early in their growth (by assembly from atoms in the gas phase) followed by template growth. It is quite likely that transitions from a locked, metastable configuration to a more stable (but still metastable) structure, as observed here under the electron beam, will occur during catalytic reactions, for example.All nanostructures are metastable - but some are more metastable than others. Here we employ aberration-corrected electron microscopy and atomistic computer simulations to demonstrate the hierarchy of metastability in deposited, size-selected gold nanoparticles (clusters), an archetypal class of nanomaterials well known for the catalytic activity which only appears on the nanometer-scale. We show that the atomic structures presented by ``magic number'' Au561, Au742 and Au923 clusters are ``locked''. They are in fact determined by the solidification which occurs from the liquid state early in their growth (by assembly from atoms in the gas phase) followed by template growth. It is quite likely that transitions from a locked, metastable configuration to a more stable (but still metastable) structure, as observed here under the electron beam, will occur during catalytic reactions, for example. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05811a

OH and halogen atom influence on the variability of non-methane hydrocarbons in the Antarctic Boundary Layer

NASA Astrophysics Data System (ADS)

Read, Katie A.; Lewis, Alastair C.; Salmon, Rhian A.; Jones, Anna E.; Bauguitte, Stéphane

2007-02-01

Measurements of C2-C8 non-methane hydrocarbons (NMHCs) have been made in situ at Halley Base, Antarctica (75°35'S, 26°19'W) from February 2004 to February 2005 as part of the Chemistry of the Antarctic Boundary Layer and the Interface with Snow (CHABLIS) experiment. The data show long- and short-term variabilities in NMHCs controlled by the seasonal and geographic dependence of emissions and variation in atmospheric removal rates and pathways. Ethane, propane, iso-butane, n-butane and acetylene abundances followed a general OH-dependent sinusoidal seasonal cycle. The yearly averages were 186, 31, 3.2, 4.9 and 19 pptV, respectively, lower than those which were reported in some previous studies. Superimposed on a seasonal cycle was shorter-term variability that could be attributed to both synoptic airmass variability and localized loss processes due to other radical species. Hydrocarbon variability during periods of hour-to-day-long surface O3 depletion in late winter/early spring indicated active halogen atom chemistry estimated to be in the range 1.7 × 103-3.4 × 104 atom cm-3 for Cl and 4.8 × 106-9.6 × 107 atom cm-3 for Br. Longer-term negative deviations from sinusoidal behaviour in the late August were indicative of NMHC reaction with a persistent [Cl] of 2.3 × 103 atom cm-3. Maximum ethene and propene of 157 and 179 pptV, respectively, were observed in the late February/early March, consistent with increased oceanic biogenic emissions; however, their presence was significant year-round (June-August concentrations of 17.1 +/- 18.3 and 7.9 +/- 20.0 pptV, respectively).

Precisely detecting atomic position of atomic intensity images.

PubMed

Wang, Zhijun; Guo, Yaolin; Tang, Sai; Li, Junjie; Wang, Jincheng; Zhou, Yaohe

2015-03-01

We proposed a quantitative method to detect atomic position in atomic intensity images from experiments such as high-resolution transmission electron microscopy, atomic force microscopy, and simulation such as phase field crystal modeling. The evaluation of detection accuracy proves the excellent performance of the method. This method provides a chance to precisely determine atomic interactions based on the detected atomic positions from the atomic intensity image, and hence to investigate the related physical, chemical and electrical properties. Copyright © 2014 Elsevier B.V. All rights reserved.

Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Miller, Sharon K.

2004-01-01

Atomic oxygen is one of the predominant constituents of Earth's upper atmosphere. It is created by the photodissociation of molecular oxygen (O2) into single O atoms by ultraviolet radiation. It is chemically very reactive because a single O atom readily combines with another O atom or with other atoms or molecules that can form a stable oxide. The effects of atomic oxygen on the external surfaces of spacecraft in low Earth orbit can have dire consequences for spacecraft life, and this is a well-known and much studied problem. Much less information is known about the effects of atomic oxygen on the internal surfaces of spacecraft. This degradation can occur when openings in components of the spacecraft exterior exist that allow the entry of atomic oxygen into regions that may not have direct atomic oxygen attack but rather scattered attack. Openings can exist because of spacecraft venting, microwave cavities, and apertures for Earth viewing, Sun sensors, or star trackers. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft were simulated at the NASA Glenn Research Center by using Monte Carlo computational techniques. A two-dimensional model was used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of the distance into a parallel-walled cavity. The model allows the atomic oxygen arrival direction, the Maxwell Boltzman temperature, and the ram energy to be varied along with the interaction parameters of the degree of recombination upon impact with polymer or nonreactive surfaces, the initial reaction probability, the reaction probability dependence upon energy and angle of attack, degree of specularity of scattering of reactive and nonreactive surfaces, and the degree of thermal accommodation upon impact with reactive and non-reactive surfaces to be varied to allow the model to produce atomic oxygen erosion geometries that replicate actual experimental results from space. The degree of erosion of various interior locations was compared with the erosion that would occur external to the spacecraft. Results of one cavity model indicate that, at depths into a two-dimensional cavity that are equal to 10 cavity widths, the erosion on the walls of the cavity is less than that on the top surface by over 2 orders of magnitude. Wall erosion near the surface of a cavity depends on which wall is receiving direct atomic oxygen attack. However, deep in the cavity little difference is present. Testing of various cavity models such as these gives spacecraft designers an indication of the level of threat to sensitive interior surfaces for different geometries. Even though the Monte Carlo model is two-dimensional, it can be used to provide qualitative information about spacecraft openings that are three-dimensional by offering reasonable insight as to the nature of the attenuation of damage that occurs within a spacecraft in low Earth orbit. As shown, there is more erosion on the side seeing direct atomic oxygen attack until a depth of approximately 5 times the width of the opening, where the erosion is the same on both sides.

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

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

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

2009-08-07

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

Modeling Strongly Correlated Fermi Systems Using Ultra-Cold Atoms

DTIC Science & Technology

2008-06-28

the two-dimensional Hubbard model on a square lattice ( a model which is purported to describe the high-temperature superconducting cuprates...beams and (2) stroboscopically alternating the beams very rapidly (~100 kHz) such that the beams were never on simultaneously ( the atoms experience a ...gases relies on (1) using a large-volume, magnetic trap to compress the atomic gas to a volume that can be captured by an optical trap

Dynamics of entanglement of a three-level atom in motion interacting with two coupled modes including parametric down conversion

NASA Astrophysics Data System (ADS)

Faghihi, M. J.; Tavassoly, M. K.; Hatami, M.

In this paper, a model by which we study the interaction between a motional three-level atom and two-mode field injected simultaneously in a bichromatic cavity is considered; the three-level atom is assumed to be in a Λ-type configuration. As a result, the atom-field and the field-field interaction (parametric down conversion) will be appeared. It is shown that, by applying a canonical transformation, the introduced model can be reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions, which may be prepared for the atom and the field, the time evolution of state vector of the entire system is analytically evaluated. Then, the dynamics of atom by considering ‘atomic population inversion’ and two different measures of entanglement, i.e., ‘von Neumann entropy’ and ‘idempotency defect’ is discussed, in detail. It is deduced from the numerical results that, the duration and the maximum amount of the considered physical quantities can be suitably tuned by selecting the proper field-mode structure parameter p and the detuning parameters.

Hot Canyon

ScienceCinema

None

2018-05-07

This historical film footage, originally produced in the early 1950s as part of a series by WOI-TV, shows atomic research at Ames Laboratory. The work was conducted in a special area of the Laboratory known as the "Hot Canyon".

Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities.

PubMed

Smalø, Hans S; Astrand, Per-Olof; Jensen, Lasse

2009-07-28

The electronegativity equalization model (EEM) has been combined with a point-dipole interaction model to obtain a molecular mechanics model consisting of atomic charges, atomic dipole moments, and two-atom relay tensors to describe molecular dipole moments and molecular dipole-dipole polarizabilities. The EEM has been phrased as an atom-atom charge-transfer model allowing for a modification of the charge-transfer terms to avoid that the polarizability approaches infinity for two particles at infinite distance and for long chains. In the present work, these shortcomings have been resolved by adding an energy term for transporting charges through individual atoms. A Gaussian distribution is adopted for the atomic charge distributions, resulting in a damping of the electrostatic interactions at short distances. Assuming that an interatomic exchange term may be described as the overlap between two electronic charge distributions, the EEM has also been extended by a short-range exchange term. The result is a molecular mechanics model where the difference of charge transfer in insulating and metallic systems is modeled regarding the difference in bond length between different types of system. For example, the model is capable of modeling charge transfer in both alkanes and alkenes with alternating double bonds with the same set of carbon parameters only relying on the difference in bond length between carbon sigma- and pi-bonds. Analytical results have been obtained for the polarizability of a long linear chain. These results show that the model is capable of describing the polarizability scaling both linearly and nonlinearly with the size of the system. Similarly, a linear chain with an end atom with a high electronegativity has been analyzed analytically. The dipole moment of this model system can either be independent of the length or increase linearly with the length of the chain. In addition, the model has been parametrized for alkane and alkene chains with data from density functional theory calculations, where the polarizability behaves differently with the chain length. For the molecular dipole moment, the same two systems have been studied with an aldehyde end group. Both the molecular polarizability and the dipole moment are well described as a function of the chain length for both alkane and alkene chains demonstrating the power of the presented model.

Proposed reference models for atomic oxygen in the terrestrial atmosphere

NASA Technical Reports Server (NTRS)

Llewellyn, E. J.; Mcdade, I. C.; Lockerbie, M. D.

1989-01-01

A provisional Atomic Oxygen Reference model was derived from average monthly ozone profiles and the MSIS-86 reference model atmosphere. The concentrations are presented in tabular form for the altitude range 40 to 130 km.

The ratio of molecular to atomic gas in spiral galaxies as a function of morphological type

NASA Technical Reports Server (NTRS)

Knezek, Patricia M.; Young, Judith S.

1990-01-01

In order to gain an understanding of the global processes which influence cloud and star formation in disk galaxies, it is necessary to determine the relative amounts of atomic, molecular, and ionized gas both as a function of position in galaxies and from galaxy to galaxy. With observations of the CO distributions in over 200 galaxies now completed as part of the Five College Radio Astronomy Observatory (FCRAO) Extragalactic CO Survey (Young et al. 1989), researchers are finally in a position to determine the type dependence of the molecular content of spiral galaxies, along with the ratio of molecular to atomic gas as a function of type. Do late type spirals really have more gas than early types when the molecular gas content is included. Researchers conclude that there is more than an order of magnitude decrease in the ratio of molecular to atomic gas mass as a function of morphological type from Sa-Sd; an average Sa galaxy has more molecular than atomic gas, and an average Sc has less. Therefore, the total interstellar gas mass to blue luminosity ratio, M sub gas/L sub B, increases by less than a factor of two as a function of type from Sa-Sd. The dominant effect found is that the phase of the gas in the cool interstellar medium (ISM) varies along the Hubble sequence. Researchers suggest that the more massive and centrally concentrated galaxies are able to achieve a molecular-dominated ISM through the collection of more gas in the potential. That gas may then form molecular clouds when a critical density is exceeded. The picture which these observations support is one in which the conversion of atomic gas to molecular gas is a global process which depends on large scale dynamics (cf Wyse 1986). Among interacting and merging systems, researchers find considerable scatter in the M(H2)/M(HI) ratio, with the mean ratio similar to that in the early type galaxies. The high global ratio of molecular to atomic gas could result from the removal of HI gas, the enhanced conversion of HI into H2, or both.

Internal Energy Transfer and Dissociation Model Development using Accelerated First-Principles Simulations of Hypersonic Flow Features

DTIC Science & Technology

2013-07-11

in Fig. 3) is simulated. Each atom interacts with its neighboring atoms through a potential energy surface (PES), such as the simple Lennard - Jones ... Lennard -­‐ Jones  (LJ)   potential  energy  surface  (PES)  dictating  atomic  interaction  forces. The main point of this section is to...the potential energy surface (PES) that governs individual atomic interaction forces. In contrast to existing rotational energy models, we found

The Kelvin-Thomson Atom. Part 2: The Many-Electron Atoms

ERIC Educational Resources Information Center

Walton, Alan J.

1977-01-01

Presents part two of a two-part article describing the Kelvin-Thomson atom. This part discusses the arrangement of electrons within the atom and examines some of the properties predicted for elements in the Kelvin-Thomson model. (SL)

Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness

ERIC Educational Resources Information Center

Park, Eun Jung; Light, Gregory

2009-01-01

Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…

Diffraction peak profiles of surface relaxed spherical nanocrystals

NASA Astrophysics Data System (ADS)

Perez-Demydenko, C.; Scardi, P.

2017-09-01

A model is proposed for surface relaxation of spherical nanocrystals. Besides reproducing the primary effect of changing the average unit cell parameter, the model accounts for the inhomogeneous atomic displacement caused by surface relaxation and its effect on the diffraction line profiles. Based on three parameters with clear physical meanings - extension of the sub-coordination effect, maximum radial displacement due to sub-coordination, and effective hydrostatic pressure - the model also considers elastic anisotropy and provides parametric expressions of the diffraction line profiles directly applicable in data analysis. The model was tested on spherical nanocrystals of several fcc metals, matching atomic positions with those provided by Molecular Dynamics (MD) simulations based on embedded atom potentials. Agreement was also verified between powder diffraction patterns generated by the Debye scattering equation, using atomic positions from MD and the proposed model.

New Experiment to Measure the Electron Electric Dipole Moment

NASA Technical Reports Server (NTRS)

Kittle, Melanie

2003-01-01

An electron can possess an electric dipole moment (edm) only if time reversal symmetry (T) is violated. No edm of any particle has yet been discovered. CP-violation, equivalent to T-violation by the CPT theorem, does occur in Kaon decays and can be accounted for by the standard model. However, this mechanism leads to an electron edm d(sub e) of the order of 10(exp -38) e cm, whereas the current experimental bound on d(sub e) is about 10(exp -27) e cm. However, well-motivated extensions of the standard model such as supersymmetric theories do predict that de could be as large as the current bound. In addition, CP violation in the early universe is required to explain the preponderance of matter over anti-matter, but the exact mechanism of this CP violation is unclear. For these reasons, we are undertaking a new experimental program to determine de to an improved accuracy of 10(exp -29) e cm. Our experiment will use laser-cooled, trapped Cesium atoms to measure the atomic edm d(sub Cs) that occurs if d(sub e) is not zero. In order to do this, we will measure the energy splitting between the atoms spin states in parallel electric and magnetic fields. The signature of an edm would be a linear dependence of the splitting on the electric field E due to the interaction - d(sub Cs) dot E. Our measurement will be much more sensitive than previous measurements because atoms can be stored in the trap for tens of seconds, allowing for much narrower Zeeman resonance linewidths. Also, our method eliminates the most important systematic errors, proportional to atomic velocity, which have limited previous experiments. In this presentation, we will describe the design of our new apparatus, which is presently under construction. An important feature of our experimental apparatus is that magnetic field noise will be suppressed to a very low value of the order of 1 fT/(Hz)1/2. This requires careful attention to the Johnson noise currents in the chamber, which have not been important in previous experiments. In addition we will present estimates of the limits of the various errors that we expect for our experiment.

Subnanosecond breakdown development in high-voltage pulse discharge: Effect of secondary electron emission

NASA Astrophysics Data System (ADS)

Alexandrov, A. L.; Schweigert, I. V.; Zakrevskiy, Dm. E.; Bokhan, P. A.; Gugin, P.; Lavrukhin, M.

2017-10-01

A subnanosecond breakdown in high-voltage pulse discharge may be a key tool for superfast commutation of high power devices. The breakdown in high-voltage open discharge at mid-high pressure in helium was studied in experiment and in kinetic simulations. The kinetic model of electron avalanche development was constructed, based on PIC-MCC simulations, including dynamics of electrons, ions and fast helium atoms, produced by ions scattering. Special attention was paid to electron emission processes from cathode, such as: photoemission by Doppler-shifted resonant photons, produced in excitation processes involving fast atoms; electron emission by ions and fast atoms bombardment of cathode; the secondary electron emission (SEE) by hot electrons from bulk plasma. The simulations show that the fast atoms accumulation is the main reason of emission growth at the early stage of breakdown, but at the final stage, when the voltage on plasma gap diminishes, namely the SEE is responsible for subnanosecond rate of current growth. It was shown that the characteristic time of the current growth can be controlled by the SEE yield. The influence of SEE yield for three types of cathode material (titanium, SiC, and CuAlMg-alloy) was tested. By changing the pulse voltage amplitude and gas pressure, the area of existence of subnanosecond breakdown is identified. It is shown that in discharge with SiC and CuAlMg-alloy cathodes (which have enhanced SEE) the current can increase with a subnanosecond characteristic time value as small as τs = 0.4 ns, for the pulse voltage amplitude of 5÷12 kV. An increase of gas pressure from 15 Torr to 30 Torr essentially decreases the time of of current front growth, whereas the pulse voltage variation weakly affects the results.

Extreme Adiabatic Expansion in Micro-gravity: Modeling for the Cold Atomic Laboratory

NASA Astrophysics Data System (ADS)

Sackett, C. A.; Lam, T. C.; Stickney, J. C.; Burke, J. H.

2017-12-01

The upcoming Cold Atom Laboratory mission for the International Space Station will allow the investigation of ultracold gases in a microgravity environment. Cold atomic samples will be produced using evaporative cooling in a magnetic chip trap. We investigate here the possibility to release atoms from the trap via adiabatic expansion. We discuss both general considerations and a detailed model of the planned apparatus. We find that it should be possible to reduce the mean trap confinement frequency to about 0.2 Hz, which will correspond to a three-dimensional sample temperature of about 150 pK and a mean atom velocity of 0.1 mm/s.

Effect of dispersion forces on squeezing with Rydberg atoms

NASA Technical Reports Server (NTRS)

Ng, S. K.; Muhamad, M. R.; Wahiddin, M. R. B.

1994-01-01

We report exact results concerning the effect of dipole-dipole interaction (dispersion forces) on dynamic and steady-state characteristics of squeezing in the emitted fluorescent field from two identical coherently driven two-level atoms. The atomic system is subjected to three different damping baths in particular the normal vacuum, a broad band thermal field and a broad band squeezed vacuum. The atomic model is the Dicke model, hence possible experiments are most likely to agree with theory when performed on systems of Rydberg atoms making microwave transitions. The presence of dipole-dipole interaction can enhance squeezing for realizable values of the various parameters involved.

Extreme Adiabatic Expansion in Micro-gravity: Modeling for the Cold Atomic Laboratory

NASA Astrophysics Data System (ADS)

Sackett, C. A.; Lam, T. C.; Stickney, J. C.; Burke, J. H.

2018-05-01

The upcoming Cold Atom Laboratory mission for the International Space Station will allow the investigation of ultracold gases in a microgravity environment. Cold atomic samples will be produced using evaporative cooling in a magnetic chip trap. We investigate here the possibility to release atoms from the trap via adiabatic expansion. We discuss both general considerations and a detailed model of the planned apparatus. We find that it should be possible to reduce the mean trap confinement frequency to about 0.2 Hz, which will correspond to a three-dimensional sample temperature of about 150 pK and a mean atom velocity of 0.1 mm/s.

The Atmospheric Tomography Mission (ATom): Comparing the Chemical Climatology of Reactive Species and Air Parcels from Measurements and Global Models

NASA Astrophysics Data System (ADS)

Prather, M. J.; Flynn, C.; Wennberg, P. O.; Kim, M. J.; Ryerson, T. B.; Hanisco, T. F.; Diskin, G. S.; Daube, B. C.; Commane, R.; McKain, K.; Apel, E. C.; Blake, N. J.; Blake, D. R.; Elkins, J. W.; Hall, S.; Steenrod, S.; Strahan, S. E.; Lamarque, J. F.; Fiore, A. M.; Horowitz, L. W.; Murray, L. T.; Mao, J.; Shindell, D. T.; Wofsy, S. C.

2017-12-01

The NASA Atmospheric Tomography Mission (ATom) is building a photochemical climatology of the remote troposphere based on objective sampling and profiling transects over the Pacific and Atlantic Oceans. These statistics provide direct tests of chemistry-climate models. The choice of species focuses on those controlling primary reactivity (a.k.a. oxidative state) of the troposphere, specifically chemical tendencies of O3 and CH4. These key species include, inter alia, O3, CH4, CO, C2H6, other alkanes, alkenes, aromatics, NOx, HNO3, HO2NO2, PAN, other organic nitrates, H2O, HCHO, H2O2, CH3OOH. Three of the four ATom deployments are now complete, and data from the first two (ATom-1 & -2) have been released as of this talk (see espoarchive.nasa.gov/archive/browse/atom). The statistical distributions of key species are presented as 1D and 2D probability densities (PDs) and we focus here on the tropical and mid-latitude regions of the Pacific during ATom-1 (Aug) and -2 (Feb). PDs are computed from ATom observations and 6 global chemistry models over the tropospheric depth (0-12 km) and longitudinal extent of the observations. All data are weighted to achieve equal mass-weighting by latitude regimes to account for spatial sampling biases. The models are used to calculate the reactivity in each ATom air parcel. Reweighting parcels with loss of CH4 or production of O3, for example, allows us to identify which air parcels are most influential, including assessment of the importance of fine pollution layers in the most remote troposphere. Another photochemical climatology developed from ATom, and used to test models, includes the effect of clouds on photolysis rates. The PDs and reactivity-weighted PDs reveal important seasonal differences and similarities between the two campaigns and also show which species may be most important in controlling reactivities. They clearly identify some very specific failings in the modeled climatologies and help us evaluate the chemical importance of fine-scale laminae with distinct chemical composition that are beyond model simulations.

Detailed low-energy electron diffraction analysis of the (4×4) surface structure of C60 on Cu(111): Seven-atom-vacancy reconstruction

NASA Astrophysics Data System (ADS)

Xu, Geng; Shi, Xing-Qiang; Zhang, R. Q.; Pai, Woei Wu; Jeng, H. T.; Van Hove, M. A.

2012-08-01

A detailed and exhaustive structural analysis by low-energy electron diffraction (LEED) is reported for the C60-induced reconstruction of Cu(111), in the system Cu(111) + (4 × 4)-C60. A wide LEED energy range allows enhanced sensitivity to the crucial C60-metal interface that is buried below the 7-Å-thick molecular layer. The analysis clearly favors a seven-Cu-atom vacancy model (with Pendry R-factor Rp = 0.376) over a one-Cu-atom vacancy model (Rp = 0.608) and over nonreconstructed models (Rp = 0.671 for atop site and Rp = 0.536 for hcp site). The seven-Cu-atom vacancy forms a (4 × 4) lattice of bowl-like holes. In each hole, a C60 molecule can nestle by forming strong bonds (shorter than 2.30 Å) between 15 C atoms of the molecule and 12 Cu atoms of the outermost and second Cu layers.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

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.

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

PubMed Central

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

The Challenges of Plasma Modeling: Current Status and Future Plans

NASA Astrophysics Data System (ADS)

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

2010-12-01

Successfully modeling X-ray emission from astrophysical plasmas requires a wide range of atomic data to be rapidly accessible by modeling codes, enabling calculation of synthetic spectra for fitting with observations. Over many years the astrophysical databases have roughly kept pace with the advances in detector and spectrometer technology. We outline here the basic atomic processes contributing to the emission from different types of plasmas and briefly touch on the difference between the methods used to calculate this data. We then discuss in more detail the different issues addressed by atomic databases in regards to what data to store and how to make it accessible. Finally, the question of the effect of uncertainties in atomic data is explored, as a reminder to observers that atomic data is not known to infinite precision, and should not be treated as such.

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.

Effect of atomic disorder on the magnetic phase separation.

PubMed

Groshev, A G; Arzhnikov, A K

2018-05-10

The effect of disorder on the magnetic phase separation between the antiferromagnetic and incommensurate helical [Formula: see text] and [Formula: see text] phases is investigated. The study is based on the quasi-two-dimensional single-band Hubbard model in the presence of atomic disorder (the [Formula: see text] Anderson-Hubbard model). A model of binary alloy disorder is considered, in which the disorder is determined by the difference in energy between the host and impurity atomic levels at a fixed impurity concentration. The problem is solved within the theory of functional integration in static approximation. Magnetic phase diagrams are obtained as functions of the temperature, the number of electrons and impurity concentration with allowance for phase separation. It is shown that for the model parameters chosen, the disorder caused by impurities whose atomic-level energy is greater than that of the host atomic levels, leads to qualitative changes in the phase diagram of the impurity-free system. In the opposite case, only quantitative changes occur. The peculiarities of the effect of disorder on the phase separation regions of the quasi-two-dimensional Hubbard model are discussed.

Effect of atomic disorder on the magnetic phase separation

NASA Astrophysics Data System (ADS)

Groshev, A. G.; Arzhnikov, A. K.

2018-05-01

The effect of disorder on the magnetic phase separation between the antiferromagnetic and incommensurate helical and phases is investigated. The study is based on the quasi-two-dimensional single-band Hubbard model in the presence of atomic disorder (the Anderson–Hubbard model). A model of binary alloy disorder is considered, in which the disorder is determined by the difference in energy between the host and impurity atomic levels at a fixed impurity concentration. The problem is solved within the theory of functional integration in static approximation. Magnetic phase diagrams are obtained as functions of the temperature, the number of electrons and impurity concentration with allowance for phase separation. It is shown that for the model parameters chosen, the disorder caused by impurities whose atomic-level energy is greater than that of the host atomic levels, leads to qualitative changes in the phase diagram of the impurity-free system. In the opposite case, only quantitative changes occur. The peculiarities of the effect of disorder on the phase separation regions of the quasi-two-dimensional Hubbard model are discussed.

Ultracold few fermionic atoms in needle-shaped double wells: spin chains and resonating spin clusters from microscopic Hamiltonians emulated via antiferromagnetic Heisenberg and t-J models

NASA Astrophysics Data System (ADS)

Yannouleas, Constantine; Brandt, Benedikt B.; Landman, Uzi

2016-07-01

Advances with trapped ultracold atoms intensified interest in simulating complex physical phenomena, including quantum magnetism and transitions from itinerant to non-itinerant behavior. Here we show formation of antiferromagnetic ground states of few ultracold fermionic atoms in single and double well (DW) traps, through microscopic Hamiltonian exact diagonalization for two DW arrangements: (i) two linearly oriented one-dimensional, 1D, wells, and (ii) two coupled parallel wells, forming a trap of two-dimensional, 2D, nature. The spectra and spin-resolved conditional probabilities reveal for both cases, under strong repulsion, atomic spatial localization at extemporaneously created sites, forming quantum molecular magnetic structures with non-itinerant character. These findings usher future theoretical and experimental explorations into the highly correlated behavior of ultracold strongly repelling fermionic atoms in higher dimensions, beyond the fermionization physics that is strictly applicable only in the 1D case. The results for four atoms are well described with finite Heisenberg spin-chain and cluster models. The numerical simulations of three fermionic atoms in symmetric DWs reveal the emergent appearance of coupled resonating 2D Heisenberg clusters, whose emulation requires the use of a t-J-like model, akin to that used in investigations of high T c superconductivity. The highly entangled states discovered in the microscopic and model calculations of controllably detuned, asymmetric, DWs suggest three-cold-atom DW quantum computing qubits.

Endo-Fullerene and Doped Diamond Nanocrystallite Based Models of Qubits for Solid-State Quantum Computers

NASA Technical Reports Server (NTRS)

Park, Seongjun; Srivastava, Deepak; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

Models of encapsulated 1/2 nuclear spin H-1 and P-31 atoms in fullerene and diamond nanocrystallite, respectively, are proposed and examined with ab-initio local density functional method for possible applications as single quantum bits (qubits) in solid-state quantum computers. A H-1 atom encapsulated in a fully deuterated fullerene, C(sub 20)D(sub 20), forms the first model system and ab-initio calculation shows that H-1 atom is stable in atomic state at the center of the fullerene with a barrier of about 1 eV to escape. A P-31 atom positioned at the center of a diamond nanocrystallite is the second model system, and 3 1P atom is found to be stable at the substitutional site relative to interstitial sites by 15 eV, Vacancy formation energy is 6 eV in diamond so that substitutional P-31 atom will be stable against diffusion during the formation mechanisms within the nanocrystallite. The coupling between the nuclear spin and weakly bound (valance) donor electron coupling in both systems is found to be suitable for single qubit applications, where as the spatial distributions of (valance) donor electron wave functions are found to be preferentially spread along certain lattice directions facilitating two or more qubit applications. The feasibility of the fabrication pathways for both model solid-state qubit systems within practical quantum computers is discussed with in the context of our proposed solid-state qubits.

Advanced Kr Atomic Structure and Ionization Kinetics for Pinches on ZR

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

PubMed

Ionescu, Crina-Maria; Geidl, Stanislav; Svobodová Vařeková, Radka; Koča, Jaroslav

2013-10-28

We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; Giese, Timothy J.; York, Darrin M.

2015-12-01

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom's local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion and dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the SN2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.

On the road to metallic nanoparticles by rational design: bridging the gap between atomic-level theoretical modeling and reality by total scattering experiments

NASA Astrophysics Data System (ADS)

Prasai, Binay; Wilson, A. R.; Wiley, B. J.; Ren, Y.; Petkov, Valeri

2015-10-01

The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au100-xPdx (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when ``tuned up'' against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design.The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au100-xPdx (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when ``tuned up'' against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modelling methodology. See DOI: 10.1039/c5nr04678e

Dynamical Evolution of Properties for Atom and Field in the Process of Two-Photon Absorption and Emission Between Atomic Levels

NASA Astrophysics Data System (ADS)

Wang, Jian-ming; Xu, Xue-xiang

2018-04-01

Using dressed state method, we cleverly solve the dynamics of atom-field interaction in the process of two-photon absorption and emission between atomic levels. Here we suppose that the atom is initially in the ground state and the optical field is initially in Fock state, coherent state or thermal state, respectively. The properties of the atom, including the population in excited state and ground state, the atom inversion, and the properties for optical field, including the photon number distribution, the mean photon number, the second-order correlation function and the Wigner function, are discussed in detail. We derive their analytical expressions and then make numerical analysis for them. In contrast with Jaynes-Cummings model, some similar results, such as quantum Rabi oscillation, revival and collapse, are also exhibit in our considered model. Besides, some novel nonclassical states are generated.

Interplay of weak interactions in the atom-by-atom condensation of xenon within quantum boxes

PubMed Central

Nowakowska, Sylwia; Wäckerlin, Aneliia; Kawai, Shigeki; Ivas, Toni; Nowakowski, Jan; Fatayer, Shadi; Wäckerlin, Christian; Nijs, Thomas; Meyer, Ernst; Björk, Jonas; Stöhr, Meike; Gade, Lutz H.; Jung, Thomas A.

2015-01-01

Condensation processes are of key importance in nature and play a fundamental role in chemistry and physics. Owing to size effects at the nanoscale, it is conceptually desired to experimentally probe the dependence of condensate structure on the number of constituents one by one. Here we present an approach to study a condensation process atom-by-atom with the scanning tunnelling microscope, which provides a direct real-space access with atomic precision to the aggregates formed in atomically defined ‘quantum boxes’. Our analysis reveals the subtle interplay of competing directional and nondirectional interactions in the emergence of structure and provides unprecedented input for the structural comparison with quantum mechanical models. This approach focuses on—but is not limited to—the model case of xenon condensation and goes significantly beyond the well-established statistical size analysis of clusters in atomic or molecular beams by mass spectrometry. PMID:25608225

Improving atomic displacement and replacement calculations with physically realistic damage models

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

Nordlund, Kai; Zinkle, Steven J.; Sand, Andrea E.

Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor ofmore » 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.« less

Improving atomic displacement and replacement calculations with physically realistic damage models

DOE PAGES

Nordlund, Kai; Zinkle, Steven J.; Sand, Andrea E.; ...

2018-03-14

Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor ofmore » 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.« less

Improving atomic displacement and replacement calculations with physically realistic damage models.

PubMed

Nordlund, Kai; Zinkle, Steven J; Sand, Andrea E; Granberg, Fredric; Averback, Robert S; Stoller, Roger; Suzudo, Tomoaki; Malerba, Lorenzo; Banhart, Florian; Weber, William J; Willaime, Francois; Dudarev, Sergei L; Simeone, David

2018-03-14

Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor of 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.

Isotropic Inelastic Collisions in a Multiterm Atom with Hyperfine Structure

NASA Astrophysics Data System (ADS)

Belluzzi, Luca; Landi Degl'Innocenti, Egidio; Trujillo Bueno, Javier

2015-10-01

A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron-atom interaction is described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D1 and D2 lines is presented.

AtomPy: an open atomic-data curation environment

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

PubMed

Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

2015-02-02

Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Why We Should Teach the Bohr Model and How to Teach it Effectively

ERIC Educational Resources Information Center

McKagan, S. B.; Perkins, K. K.; Wieman, C. E.

2008-01-01

Some education researchers have claimed that we should not teach the Bohr model of the atom because it inhibits students' ability to learn the true quantum nature of electrons in atoms. Although the evidence for this claim is weak, many have accepted it. This claim has implications for how to present atoms in classes ranging from elementary school…

Evolutionary Optimization of a Charge Transfer Ionic Potential Model for Ta/Ta-Oxide Heterointerfaces

DOE PAGES

Sasikumar, Kiran; Narayanan, Badri; Cherukara, Mathew; ...

2017-03-19

Heterostructures of tantalum and its oxide are of tremendous technological interest for a myriad of technological applications, including electronics, thermal management, catalysis and biochemistry. In particular, local oxygen stoichiometry variation in TaO x memristors comprising of thermodynamically stable metallic (Ta) and insulating oxide (Ta 2O 5) have been shown to result in fast switching on the subnanosecond timescale over a billion cycles. This rapid switching opens up the potential for advanced functional platforms such as stateful logic operations and neuromorphic computation. Despite its broad importance, an atomistic scale understanding of oxygen stoichiometry variation across Ta/TaO x heterointerfaces, such as duringmore » early stages of oxidation and oxide growth, is not well understood. This is mainly due to the lack of a unified interatomic potential model for tantalum oxides that can accurately describe metallic (Ta), ionic (TaO x) as well as mixed (Ta/TaO x interfaces) bonding environments simultaneously. To address this challenge, we introduce a Charge Transfer Ionic Potential (CTIP) model for Ta/Ta-oxide system by training against lattice parameters, cohesive energies, equations of state (EOS), elastic properties, and surface energies of the various experimentally observed Ta 2O 5 polymorphs (hexagonal, orthorhombic and monoclinic) obtained from density functional theory (DFT) calculations. The best CTIP parameters are determined by employing a global optimization scheme driven by genetic algorithms followed by local Simplex optimization. Our newly developed CTIP potential accurately predicts structure, thermodynamics, energetic ordering of polymorphs, as well as elastic and surface properties of both Ta and Ta 2O 5, in excellent agreement with DFT calculations and experiments. We employ our newly parameterized CTIP potential to investigate the early stages of oxidation and atomic scale mechanisms associated with oxide growth on Ta surface at various temperatures. Furthermore, the CTIP potential developed in this work is an invaluable tool to investigate atomic-scale mechanisms and transport phenomena underlying the response of Ta/TaO x interfaces to external stimuli (e.g, temperature, pressure, strain, electric field etc.), as well as other interesting dynamical phenomena including the physics of switching dynamics in TaO x based memristors and neuromorphic devices.« less

Effects of the local structure dependence of evaporation fields on field evaporation behavior

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

Yao, Lan; Marquis, Emmanuelle A., E-mail: emarq@umich.edu; Withrow, Travis

2015-12-14

Accurate three dimensional reconstructions of atomic positions and full quantification of the information contained in atom probe microscopy data rely on understanding the physical processes taking place during field evaporation of atoms from needle-shaped specimens. However, the modeling framework for atom probe microscopy has only limited quantitative justification. Building on the continuum field models previously developed, we introduce a more physical approach with the selection of evaporation events based on density functional theory calculations. This model reproduces key features observed experimentally in terms of sequence of evaporation, evaporation maps, and depth resolution, and provides insights into the physical limit formore » spatial resolution.« less

MAVEN in situ measurements of photochemical escape of oxygen from Mars

NASA Astrophysics Data System (ADS)

Lillis, Robert; Deighan, Justin; Fox, Jane; Bougher, Stephen; Lee, Yuni; Cravens, Thomas; Rahmati, Ali; Mahaffy, Paul; Benna, Mehdi; Groller, Hannes; Jakosky, Bruce

2016-04-01

One of the primary goals of the MAVEN mission is to characterize rates of atmospheric escape from Mars at the present epoch and relate those escape rates to solar drivers. One of the known escape processes is photochemical escape, where a) an exothermic chemical reaction in the atmosphere results in an upward-traveling neutral particle whose velocity exceeds planetary escape velocity and b) the particle is not prevented from escaping through subsequent collisions. At Mars, photochemical escape of oxygen is expected to be a significant channel for atmospheric escape, particularly in the early solar system when extreme ultraviolet (EUV) fluxes were much higher. Thus characterizing this escape process and its variability with solar drivers is central to understanding the role escape to space has played in Mars' climate evolution. We use near-periapsis (<400 km altitude) data from three MAVEN instruments: the Langmuir Probe and Waves (LPW) instrument measures electron density and temperature, the Suprathermal And Thermal Ion Composition (STATIC) experiment measures ion temperature and the Neutral Gas and Ion Mass Spectrometer (NGIMS) measures neutral and ion densities. For each profile of in situ measurements, we make several calculations, each as a function of altitude. The first uses electron and temperatures and simulates the dissociative recombination of both O2+ and CO2+ to calculate the probability distribution for the initial energies of the resulting hot oxygen atoms. The second is a Monte Carlo hot atom transport model that takes that distribution of initial O energies and the measured neutral density profiles and calculates the probability that a hot atom born at that altitude will escape. The third takes the measured electron and ion densities and electron temperatures and calculates the production rate of hot O atoms. We then multiply together the profiles of hot atom production and escape probability to get profiles of the production rate of escaping atoms. We integrate with respect to altitude to give us the escape flux of hot oxygen atoms for that periapsis pass. We have sufficient coverage in solar zenith angle (SZA) to estimate total escape rates for two intervals with the obvious assumption that escape rates are the same at all points with the same SZA. We estimate total escape rates of 3.5-5.8 x 1025 s-1 for Ls = 289° to 319° and 1.6-2.6 x 1025 s-1 for Ls = 326° to 348°. The latter is the most directly comparable to previous model-based estimates and is roughly in line with several of them. Total photochemical loss over Mars history is not very useful to calculate from such escape fluxes derived over a limited area and under limited conditions. A thicker atmosphere and much higher solar EUV in the past may change the dynamics of escape dramatically. In the future, we intend to use 3-D Monte Carlo models of global atmospheric escape, in concert with our in situ and remote measurements, to fully characterize photochemical escape under current conditions and carefully extrapolate back in time using further simulations with new boundary conditions.

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

DOE PAGES

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

2016-08-31

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

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.

Entanglement evaluation with atomic Fisher information

NASA Astrophysics Data System (ADS)

Obada, A.-S. F.; Abdel-Khalek, S.

2010-02-01

In this paper, the concept of atomic Fisher information (AFI) is introduced. The marginal distributions of the AFI are defined. This quantity is used as a parameter of entanglement and compared with linear and atomic Wehrl entropies of the two-level atom. The evolution of the atomic Fisher information and atomic Wehrl entropy for only the pure state (or dissipation-free) of the Jaynes-Cummings model is analyzed. We demonstrate the connections between these measures.

Experimental Criticality Benchmarks for SNAP 10A/2 Reactor Cores

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

Krass, A.W.

2005-12-19

This report describes computational benchmark models for nuclear criticality derived from descriptions of the Systems for Nuclear Auxiliary Power (SNAP) Critical Assembly (SCA)-4B experimental criticality program conducted by Atomics International during the early 1960's. The selected experimental configurations consist of fueled SNAP 10A/2-type reactor cores subject to varied conditions of water immersion and reflection under experimental control to measure neutron multiplication. SNAP 10A/2-type reactor cores are compact volumes fueled and moderated with the hydride of highly enriched uranium-zirconium alloy. Specifications for the materials and geometry needed to describe a given experimental configuration for a model using MCNP5 are provided. Themore » material and geometry specifications are adequate to permit user development of input for alternative nuclear safety codes, such as KENO. A total of 73 distinct experimental configurations are described.« less

Tracking the Growth Transitions of A Solvent-Charged Model Globular Protein

NASA Astrophysics Data System (ADS)

Babcock, Jeremiah; Friday, Jacob; Brancaleon, Lorenzo

2011-03-01

Biophysical studies have shown that solutes like proteins undergo aggregation through specific pathways that often lead to long polymeric structures called fibrils. The knowledge of the size of early-stage protein aggregates (oligomers) has an important bearing on the elucidation of the dynamics of the process of protein unit combinations. In this study, bovine serum albumin, a well-characterized model protein known to polymerize in alkaline and acidic conditions in the normal (N) to basic (B) or (N) to (E) transition, was incubated at pH 9.0 and pH 3.1 for longer than eight days. Particle growth in solution was monitored by absorption, fluorescence and circular dichroism spectroscopy and concurrently measured by atomic force microscopy (AFM) methods to yield BSA oligomer size distributions. Results show that the BSA aggregation pathway is concentration-dependent and rapidly forms spherical aggregates, which preferentially come together to form flexible polymers.

Atomic Precision Plasma Processing - Modeling Investigations

NASA Astrophysics Data System (ADS)

Rauf, Shahid

2016-09-01

Sub-nanometer precision is increasingly being required of many critical plasma processes in the semiconductor industry. Some of these critical processes include atomic layer etch and plasma enhanced atomic layer deposition. Accurate control over ion energy and ion / radical composition is needed during plasma processing to meet the demanding atomic-precision requirements. While improvements in mainstream inductively and capacitively coupled plasmas can help achieve some of these goals, newer plasma technologies can expand the breadth of problems addressable by plasma processing. Computational modeling is used to examine issues relevant to atomic precision plasma processing in this paper. First, a molecular dynamics model is used to investigate atomic layer etch of Si and SiO2 in Cl2 and fluorocarbon plasmas. Both planar surfaces and nanoscale structures are considered. It is shown that accurate control of ion energy in the sub-50 eV range is necessary for atomic scale precision. In particular, if the ion energy is greater than 10 eV during plasma processing, several atomic layers get damaged near the surface. Low electron temperature (Te) plasmas are particularly attractive for atomic precision plasma processing due to their low plasma potential. One of the most attractive options in this regard is energetic-electron beam generated plasma, where Te <0.5 eV has been achieved in plasmas of molecular gases. These low Te plasmas are computationally examined in this paper using a hybrid fluid-kinetic model. It is shown that such plasmas not only allow for sub-5 eV ion energies, but also enable wider range of ion / radical composition. Coauthors: Jun-Chieh Wang, Jason Kenney, Ankur Agarwal, Leonid Dorf, and Ken Collins.

Researcher Poses with a Nuclear Rocket Model

NASA Image and Video Library

1961-11-21

A researcher at the NASA Lewis Research Center with slide ruler poses with models of the earth and a nuclear-propelled rocket. The Nuclear Engine for Rocket Vehicle Applications (NERVA) was a joint NASA and Atomic Energy Commission (AEC) endeavor to develop a nuclear-powered rocket for both long-range missions to Mars and as a possible upper-stage for the Apollo Program. The early portion of the program consisted of basic reactor and fuel system research. This was followed by a series of Kiwi reactors built to test nuclear rocket principles in a non-flying nuclear engine. The next phase, NERVA, would create an entire flyable engine. The AEC was responsible for designing the nuclear reactor and overall engine. NASA Lewis was responsible for developing the liquid-hydrogen fuel system. The nuclear rocket model in this photograph includes a reactor at the far right with a hydrogen propellant tank and large radiator below. The payload or crew would be at the far left, distanced from the reactor.

Theoretical modeling of laser-induced plasmas using the ATOMIC code

NASA Astrophysics Data System (ADS)

Colgan, James; Johns, Heather; Kilcrease, David; Judge, Elizabeth; Barefield, James, II; Clegg, Samuel; Hartig, Kyle

2014-10-01

We report on efforts to model the emission spectra generated from laser-induced breakdown spectroscopy (LIBS). LIBS is a popular and powerful method of quickly and accurately characterizing unknown samples in a remote manner. In particular, LIBS is utilized by the ChemCam instrument on the Mars Science Laboratory. We model the LIBS plasma using the Los Alamos suite of atomic physics codes. Since LIBS plasmas generally have temperatures of somewhere between 3000 K and 12000 K, the emission spectra typically result from the neutral and singly ionized stages of the target atoms. We use the Los Alamos atomic structure and collision codes to generate sets of atomic data and use the plasma kinetics code ATOMIC to perform LTE or non-LTE calculations that generate level populations and an emission spectrum for the element of interest. In this presentation we compare the emission spectrum from ATOMIC with an Fe LIBS laboratory-generated plasma as well as spectra from the ChemCam instrument. We also discuss various physics aspects of the modeling of LIBS plasmas that are necessary for accurate characterization of the plasma, such as multi-element target composition effects, radiation transport effects, and accurate line shape treatments. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.

Six decades of atomic collisions in solids

NASA Astrophysics Data System (ADS)

Sigmund, Peter

2017-09-01

In response to an invitation by the organizers of the 27th international conference on atomic collisions in solids, a brief survey is presented, starting from the roots of the field in the 1950s and 1960s, of some major discoveries, longstanding problems, surprising findings and memorable controversies in topics covered by the conference. Considering the breadth of the field, the selection of topics is necessarily subjective, but with the emphasis on channeling, stopping and sputtering, three topical areas are discussed which have been active from the early 1960s until now.

Optical trapping and manipulation of neutral particles using lasers

PubMed Central

Ashkin, Arthur

1997-01-01

The techniques of optical trapping and manipulation of neutral particles by lasers provide unique means to control the dynamics of small particles. These new experimental methods have played a revolutionary role in areas of the physical and biological sciences. This paper reviews the early developments in the field leading to the demonstration of cooling and trapping of neutral atoms in atomic physics and to the first use of optical tweezers traps in biology. Some further major achievements of these rapidly developing methods also are considered. PMID:9144154

Nanostructures nucleation in carbon-metal gaseous phase: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Galiullina, G. M.; Orekhov, N. D.; Stegailov, V. V.

2018-01-01

We perform nonequilibrium molecular dynamics simulation of carbon nanoclusters nucleation and early stages of growth from the gaseous phase. We analyze the catalytic effect of iron atoms on the nucleation kinetics and structure of the resultant nanoparticles. Reactive Force Field (ReaxFF) is used in the simulations for the description of bond formation and dissociation during the nucleation process at the nanoscale. The catalytic effect of iron reveals itself even on nanosecond simulation times: iron atoms accelerate the process of clustering but result in less graphitized carbon structures.

Cluster adsorption on amorphous and crystalline surfaces - A molecular dynamics study of model Pt on Cu and model Pd on Pt

NASA Technical Reports Server (NTRS)

Garofalini, S. H.; Halicioglu, T.; Pound, G. M.

1981-01-01

Molecular dynamics was used to study the structure, dispersion and short-time behavior of ten-atom clusters adsorbed onto amorphous and crystalline substrates, in which the cluster atoms differed from the substrate atoms. Two adatom-substrate model systems were chosen; one, in which the interaction energy between adatom pairs was greater than that between substrate pairs, and the other, in which the reverse was true. At relatively low temperature ranges, increased dispersion of cluster atoms occurred: (a) on the amorphous substrate as compared to the FCC(100) surface, (b) with increasing reduced temperature, and (c) with adatom-substrate interaction energy stronger than adatom-adatom interaction. Two-dimensional clusters (rafts) on the FCC(100) surface displayed migration of edge atoms only, indicating a mechanism for the cluster rotation and shape changes found in experimental studies.

Quantitative Subsurface Atomic Structure Fingerprint for 2D Materials and Heterostructures by First-Principles-Calibrated Contact-Resonance Atomic Force Microscopy.

PubMed

Tu, Qing; Lange, Björn; Parlak, Zehra; Lopes, Joao Marcelo J; Blum, Volker; Zauscher, Stefan

2016-07-26

Interfaces and subsurface layers are critical for the performance of devices made of 2D materials and heterostructures. Facile, nondestructive, and quantitative ways to characterize the structure of atomically thin, layered materials are thus essential to ensure control of the resultant properties. Here, we show that contact-resonance atomic force microscopy-which is exquisitely sensitive to stiffness changes that arise from even a single atomic layer of a van der Waals-adhered material-is a powerful experimental tool to address this challenge. A combined density functional theory and continuum modeling approach is introduced that yields sub-surface-sensitive, nanomechanical fingerprints associated with specific, well-defined structure models of individual surface domains. Where such models are known, this information can be correlated with experimentally obtained contact-resonance frequency maps to reveal the (sub)surface structure of different domains on the sample.

ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.

PubMed

Park, Jungkap; Saitou, Kazuhiro

2014-09-18

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures. In this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named "rotamer-dependent atomic statistical potential" (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality. A new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.

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

Ünlü, Hilmi, E-mail: hunlu@itu.edu.tr

We propose a non-orthogonal sp{sup 3} hybrid bond orbital model to determine the electronic properties of semiconductor heterostructures. The model considers the non-orthogonality of sp{sup 3} hybrid states of nearest neighboring adjacent atoms using the intra-atomic Coulomb interactions corrected Hartree-Fock atomic energies and metallic contribution to calculate the valence band width energies of group IV elemental and group III-V and II-VI compound semiconductors without any adjustable parameter.

Students' Mental Models of Atomic Spectra

ERIC Educational Resources Information Center

Körhasan, Nilüfer Didis; Wang, Lu

2016-01-01

Mental modeling, which is a theory about knowledge organization, has been recently studied by science educators to examine students' understanding of scientific concepts. This qualitative study investigates undergraduate students' mental models of atomic spectra. Nine second-year physics students, who have already taken the basic chemistry and…

2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching.

PubMed

Matsumoto, Atsushi; Miyazaki, Naoyuki; Takagi, Junichi; Iwasaki, Kenji

2017-03-23

In this study, we develop an approach termed "2D hybrid analysis" for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

Herschel GASPS spectral observations of T Tauri stars in Taurus. Unraveling far-infrared line emission from jets and discs

NASA Astrophysics Data System (ADS)

Alonso-Martínez, M.; Riviere-Marichalar, P.; Meeus, G.; Kamp, I.; Fang, M.; Podio, L.; Dent, W. R. F.; Eiroa, C.

2017-07-01

Context. At early stages of stellar evolution young stars show powerful jets and/or outflows that interact with protoplanetary discs and their surroundings. Despite the scarce knowledge about the interaction of jets and/or outflows with discs, spectroscopic studies based on Herschel and ISO data suggests that gas shocked by jets and/or outflows can be traced by far-IR (FIR) emission in certain sources. Aims: We want to provide a consistent catalogue of selected atomic ([OI] and [CII]) and molecular (CO, H2O, and OH) line fluxes observed in the FIR, separate and characterize the contribution from the jet and the disc to the observed line emission, and place the observations in an evolutionary picture. Methods: The atomic and molecular FIR (60-190 μm) line emission of protoplanetary discs around 76 T Tauri stars located in Taurus are analysed. The observations were carried out within the Herschel key programme Gas in Protoplanetary Systems (GASPS). The spectra were obtained with the Photodetector Array Camera and Spectrometer (PACS). The sample is first divided in outflow and non-outflow sources according to literature tabulations. With the aid of archival stellar/disc and jet/outflow tracers and model predictions (PDRs and shocks), correlations are explored to constrain the physical mechanisms behind the observed line emission. Results: Outflow sources exhibit brighter atomic and molecular emission lines and higher detection rates than non-outflow sources. The line detection fractions decrease with SED evolutionary status (from Class I to Class III). We find correlations between [OI] 63.18 μm and [OI] 6300 Å, o-H2O 78.74 μm, CO 144.78 μm, OH 79.12+79.18 μm, and the continuum flux at 24 μm. The atomic line ratios can be explain either by fast (Vshock > 50 km s-1) dissociative J-shocks at low densities (n 103 cm-3) occurring along the jet and/or PDR emission (G0 > 102, n 103-106 cm-3). To account for the [CII] absolute fluxes, PDR emission or UV irradiation of shocks is needed. In comparison, the molecular emission is more compact and the line ratios are better explained with slow (Vshock < 40 km s-1) C-type shocks with high pre-shock densities (104-106 cm-3), with the exception of OH lines, that are better described by J-type shocks. Disc models alone fail to reproduce the observed molecular line fluxes, but a contribution to the line fluxes from UV-illuminated discs and/or outflow cavities is expected. Far-IR lines dominate disc cooling at early stages and weaken as the star+disc system evolves from Class I to Class III, with an increasing relative disc contribution to the line fluxes. Conclusions: Models which take into account jets, discs, and their mutual interaction are needed to disentangle the different components and study their evolution. The much higher detection rate of emission lines in outflow sources and the compatibility of line ratios with shock model predictions supports the idea of a dominant contribution from the jet/outflow to the line emission, in particular at earlier stages of the stellar evolution as the brightness of FIR lines depends in large part on the specific evolutionary stage. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins

PubMed Central

Guttman, Miklos; Weinkam, Patrick; Sali, Andrej; Lee, Kelly K.

2013-01-01

Summary The flexible and heterogeneous nature of carbohydrate chains often renders glycoproteins refractory to traditional structure determination methods. Small Angle X-ray scattering (SAXS) can be a useful tool for obtaining structural information of these systems. All-atom modeling of glycoproteins with flexible glycan chains was applied to interpret the solution SAXS data for a set of glycoproteins. For simpler systems (single glycan, with a well defined protein structure), all-atom modeling generates models in excellent agreement with the scattering pattern, and reveals the approximate spatial occupancy of the glycan chain in solution. For more complex systems (several glycan chains, or unknown protein substructure), the approach can still provide insightful models, though the orientations of glycans become poorly determined. Ab initio shape reconstructions appear to capture the global morphology of glycoproteins, but in most cases offer little information about glycan spatial occupancy. The all-atom modeling methodology is available as a webserver at http://modbase.compbio.ucsf.edu/allosmod-foxs. PMID:23473666

An atomic and molecular fluid model for efficient edge-plasma transport simulations at high densities

NASA Astrophysics Data System (ADS)

Rognlien, Thomas; Rensink, Marvin

2016-10-01

Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.

Modelling the atomic structure of Al92U8 metallic glass.

PubMed

Michalik, S; Bednarcik, J; Jóvári, P; Honkimäki, V; Webb, A; Franz, H; Fazakas, E; Varga, L K

2010-10-13

The local atomic structure of the glassy Al(92)U(8) alloy was modelled by the reverse Monte Carlo (RMC) method, fitting x-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) signals. The final structural model was analysed by means of partial pair correlation functions, coordination number distributions and Voronoi tessellation. In our study we found that the most probable atomic separations between Al-Al and U-Al pairs in the glassy Al(92)U(8) alloy are 2.7 Å and 3.1 Å with coordination numbers 11.7 and 17.1, respectively. The Voronoi analysis did not support evidence of the existence of well-defined building blocks directly embedded in the amorphous matrix. The dense-random-packing model seems to be adequate for describing the connection between solvent and solute atoms.

A comprehensive Two-Fluid Model for Cavitation and Primary Atomization Modelling of liquid jets - Application to a large marine Diesel injector

NASA Astrophysics Data System (ADS)

Habchi, Chawki; Bohbot, Julien; Schmid, Andreas; Herrmann, Kai

2015-12-01

In this paper, a comprehensive two-fluid model is suggested in order to compute the in-nozzle cavitating flow and the primary atomization of liquid jets, simultaneously. This model has been applied to the computation of a typical large marine Diesel injector. The numerical results have shown a strong correlation between the in-nozzle cavitating flow and the ensuing spray orientation and atomization. Indeed, the results have confirmed the existence of an off-axis liquid core. This asymmetry is likely to be at the origin of the spray deviation observed experimentally. In addition, the primary atomization begins very close to the orifice exit as in the experiments, and the smallest droplets are generated due to cavitation pocket shape oscillations located at the same side, inside the orifice.

Tensor algebra-based geometric methodology to codify central chirality on organic molecules.

PubMed

García-Jacas, C R; Marrero-Ponce, Y; Hernández-Ortega, T; Martinez-Mayorga, K; Cabrera-Leyva, L; Ledesma-Romero, J C; Aguilera-Fernández, I; Rodríguez-León, A R

2017-06-01

A novel mathematical procedure to codify chiral features of organic molecules in the QuBiLS-MIDAS framework is introduced. This procedure constitutes a generalization to that commonly used to date, where the values 1 and -1 (correction factor) are employed to weight the molecular vectors when each atom is labelled as R (rectus) or S (sinister) according to the Cahn-Ingold-Prelog rules. Therefore, values in the range [Formula: see text] with steps equal to 0.25 may be accounted for. The atoms labelled R or S can have negative and positive values assigned (e.g. -3 for an R atom and 1 for an S atom, or vice versa), opposed values (e.g. -3 for an R atom and 3 for an S atom, or vice versa), positive values (e.g. 3 for an R atom and 1 for an S atom) or negative values (e.g. -3 for an R atom and -1 for an S atom). These proposed Chiral QuBiLS-MIDAS 3D-MDs are real numbers, non-symmetric and reduced to 'classical' (non-chiral) QuBiLS-MIDAS 3D-MDs when symmetry is not codified (correction factor equal to zero). In this report, only the factors with opposed values were considered with the purpose of demonstrating the feasibility of this proposal. From QSAR modelling carried out on four chemical datasets (Cramer's steroids, fenoterol stereoisomer derivatives, N-alkylated 3-(3-hydroxyphenyl)-piperidines, and perindoprilat stereoisomers), it was demonstrated that the use of several correction factors contributes to the building of models with greater robustness and predictive ability than those reported in the literature, as well as with respect to the models exclusively developed with QuBiLS-MIDAS 3D-MDs based on the factor 1 | -1. In conclusion, it can be stated that this novel strategy constitutes a suitable alternative to computed chirality-based descriptors, contributing to the development of good models to predict properties depending on symmetry.

The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

PubMed

Noel, Jeffrey K; Whitford, Paul C; Onuchic, José N

2012-07-26

Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called "Shadow". The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.

Students' use of atomic and molecular models in learning chemistry

NASA Astrophysics Data System (ADS)

O'Connor, Eileen Ann

1997-09-01

The objective of this study was to investigate the development of introductory college chemistry students' use of atomic and molecular models to explain physical and chemical phenomena. The study was conducted during the first semester of the course at a University and College II. Public institution (Carnegie Commission of Higher Education, 1973). Students' use of models was observed during one-on-one interviews conducted over the course of the semester. The approach to introductory chemistry emphasized models. Students were exposed to over two-hundred and fifty atomic and molecular models during lectures, were assigned text readings that used over a thousand models, and worked interactively with dozens of models on the computer. These models illustrated various features of the spatial organization of valence electrons and nuclei in atoms and molecules. Despite extensive exposure to models in lectures, in textbook, and in computer-based activities, the students in the study based their explanation in large part on a simple Bohr model (electrons arranged in concentric circles around the nuclei)--a model that had not been introduced in the course. Students used visual information from their models to construct their explanation, while overlooking inter-atomic and intra-molecular forces which are not represented explicitly in the models. In addition, students often explained phenomena by adding separate information about the topic without either integrating or logically relating this information into a cohesive explanation. The results of the study demonstrate that despite the extensive use of models in chemistry instruction, students do not necessarily apply them appropriately in explaining chemical and physical phenomena. The results of this study suggest that for the power of models as aids to learning to be more fully realized, chemistry professors must give more attention to the selection, use, integration, and limitations of models in their instruction.

A non-LTE study of silicon line formation in early-type main-sequence atmospheres.

NASA Technical Reports Server (NTRS)

Kamp, L. W.

1973-01-01

We have computed populations of 16 levels of Si III-V and radiation fields in all connecting transitions; in particular the first six Si III triplet levels, including the 4553 line, and the first six Si IV levels including 4089. The computations were done for four non-LTE H-He model atmospheres, provided by Auer and Mihalas. Estimates of corresponding MK types are B1.5 V, B0.5 V, O9 V, and O6. Solutions were obtained by iterating the linearized equations of radiative transfer and statistical equilibrium, except that for less important lines an approximate equivalent two-level atom treatment was used. Continuous opacities of C, N, O, and Ne were included. All abundances were solar values.

Advertising the atom: federal promotion of nuclear power, 1953-1984

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

Smith, M.

The public relations strategies of the Atomic Energy Commission (AEC) and the nuclear power industry reveal both public and official perceptions of nuclear power and the social uses of technology in general during the first 15 years after passage of the Atomic Energy Act of 1954. The relation between nuclear promotion and regulation also helps explain the environmental crisis of the 1969-1984 years. Project Plowshare coincides roughly with the early promotional years, and provides a case study of the relation of regulatory standards to promotion in AEC policymaking. The author examines the environmentalists challenge to nuclear power that emerged inmore » 1969 alongside government and industry response. He concludes with an assessment of the present state of federal nuclear power policy and of the nuclear power industry.« less

Atomic level structural modulation during the structural relaxation and its effect on magnetic properties of Fe81Si4B10P4Cu1 nanocrystalline alloy

NASA Astrophysics Data System (ADS)

Cao, C. C.; Zhu, L.; Meng, Y.; Zhai, X. B.; Wang, Y. G.

2018-06-01

The evolution of local structure and defects in the Fe81Si4B10P4Cu1 amorphous alloy during the structural relaxation has been investigated by Mössbauer spectroscopy, positron annihilation lifetime spectroscopy and transmission electron microscopy to explore their effects on magnetic properties of the nanocrystalline. The atomic rearrangements at the early stage of the structural relaxation cause the density increase of the amorphous matrix, but the subsequent atomic rearrangements contribute to the transformation of Fe3B-like atomic arrangements to FeB-like ones with the temperature increasing. As the structural relaxation processes, the released Fe atoms both from Fe3B- and Fe3P-like atomic arrangements result in the formation of new Fe clusters and the increase of Fe-Fe coordination number in the existing Fe clusters and the nucleation sites for α-Fe gradually increase, both of which promote the crystallization. However, the homogeneity of amorphous matrix will be finally destroyed under excessive relaxation temperature, which coarsens nanograins during the crystallization instead. Therefore, soft magnetic properties of the Fe81Si4B10P4Cu1 nanocrystalline alloy can be improved by pre-annealing the amorphous precursor at an appropriate temperature due to the atomic level structural optimization.

Lifecycle of laser-produced air sparks

DOE PAGES

Harilal, S. S.; Brumfield, B. E.; Phillips, M. C.

2015-06-03

Here, we investigated the lifecycle of laser-generated air sparks or plasmas using multiple plasma diagnostic tools. The sparks were generated by focusing the fundamental radiation from an Nd:YAG laser in air, and studies included early and late time spark dynamics, decoupling of the shock wave from the plasma core, emission from the spark kernel, cold gas excitation by UV radiation, shock waves produced by the air spark, and the spark's final decay and turbulence formation. The shadowgraphic and self-emission images showed similar spark morphology at earlier and late times of its lifecycle; however, significant differences are seen in the midlifemore » images. Spectroscopic studies in the visible region showed intense blackbody-type radiation at early times followed by clearly resolved ionic, atomic, and molecular emission. The detected spectrum at late times clearly contained emission from both CN and N 2 +. Additional spectral features have been identified at late times due to emission from O and N atoms, indicating some degree of molecular dissociation and excitation. Detailed spatially and temporally resolved emission analysis provides insight about various physical mechanisms leading to molecular and atomic emission by air sparks, including spark plasma excitation, heating of cold air by UV radiation emitted by the spark, and shock-heating.« less

Lifecycle of laser-produced air sparks

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

Harilal, S. S., E-mail: hari@pnnl.gov; Brumfield, B. E.; Phillips, M. C.

2015-06-15

We investigated the lifecycle of laser-generated air sparks or plasmas using multiple plasma diagnostic tools. The sparks were generated by focusing the fundamental radiation from an Nd:YAG laser in air, and studies included early and late time spark dynamics, decoupling of the shock wave from the plasma core, emission from the spark kernel, cold gas excitation by UV radiation, shock waves produced by the air spark, and the spark's final decay and turbulence formation. The shadowgraphic and self-emission images showed similar spark morphology at earlier and late times of its lifecycle; however, significant differences are seen in the midlife images.more » Spectroscopic studies in the visible region showed intense blackbody-type radiation at early times followed by clearly resolved ionic, atomic, and molecular emission. The detected spectrum at late times clearly contained emission from both CN and N{sub 2}{sup +}. Additional spectral features have been identified at late times due to emission from O and N atoms, indicating some degree of molecular dissociation and excitation. Detailed spatially and temporally resolved emission analysis provides insight about various physical mechanisms leading to molecular and atomic emission by air sparks, including spark plasma excitation, heating of cold air by UV radiation emitted by the spark, and shock-heating.« less

DFT Modeling of Cross-Linked Polyethylene: Role of Gold Atoms and Dispersion Interactions.

PubMed

Blaško, Martin; Mach, Pavel; Antušek, Andrej; Urban, Miroslav

2018-02-08

Using DFT modeling, we analyze the concerted action of gold atoms and dispersion interactions in cross-linked polyethylene. Our model consists of two oligomer chains (PEn) with 7, 11, 15, 19, or 23 carbon atoms in each oligomer cross-linked with one to three Au atoms through C-Au-C bonds. In structures with a single gold atom the C-Au-C bond is located in the central position of the oligomer. Binding energies (BEs) with respect to two oligomer radical fragments and Au are as high as 362-489 kJ/mol depending on the length of the oligomer chain. When the dispersion contribution in PEn-Au-PEn oligomers is omitted, BE is almost independent of the number of carbon atoms, lying between 293 and 296 kJ/mol. The dispersion energy contributions to BEs in PEn-Au-PEn rise nearly linearly with the number of carbon atoms in the PEn chain. The carbon-carbon distance in the C-Au-C moiety is around 4.1 Å, similar to the bond distance between saturated closed shell chains in the polyethylene crystal. BEs of pure saturated closed shell PEn-PEn oligomers are 51-187 kJ/mol. Both Au atoms and dispersion interactions contribute considerably to the creation of nearly parallel chains of oligomers with reasonably high binding energies.

Two-level structural sparsity regularization for identifying lattices and defects in noisy images

DOE PAGES

Li, Xin; Belianinov, Alex; Dyck, Ondrej E.; ...

2018-03-09

Here, this paper presents a regularized regression model with a two-level structural sparsity penalty applied to locate individual atoms in a noisy scanning transmission electron microscopy image (STEM). In crystals, the locations of atoms is symmetric, condensed into a few lattice groups. Therefore, by identifying the underlying lattice in a given image, individual atoms can be accurately located. We propose to formulate the identification of the lattice groups as a sparse group selection problem. Furthermore, real atomic scale images contain defects and vacancies, so atomic identification based solely on a lattice group may result in false positives and false negatives.more » To minimize error, model includes an individual sparsity regularization in addition to the group sparsity for a within-group selection, which results in a regression model with a two-level sparsity regularization. We propose a modification of the group orthogonal matching pursuit (gOMP) algorithm with a thresholding step to solve the atom finding problem. The convergence and statistical analyses of the proposed algorithm are presented. The proposed algorithm is also evaluated through numerical experiments with simulated images. The applicability of the algorithm on determination of atom structures and identification of imaging distortions and atomic defects was demonstrated using three real STEM images. In conclusion, we believe this is an important step toward automatic phase identification and assignment with the advent of genomic databases for materials.« less

Two-level structural sparsity regularization for identifying lattices and defects in noisy images

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

Li, Xin; Belianinov, Alex; Dyck, Ondrej E.

Here, this paper presents a regularized regression model with a two-level structural sparsity penalty applied to locate individual atoms in a noisy scanning transmission electron microscopy image (STEM). In crystals, the locations of atoms is symmetric, condensed into a few lattice groups. Therefore, by identifying the underlying lattice in a given image, individual atoms can be accurately located. We propose to formulate the identification of the lattice groups as a sparse group selection problem. Furthermore, real atomic scale images contain defects and vacancies, so atomic identification based solely on a lattice group may result in false positives and false negatives.more » To minimize error, model includes an individual sparsity regularization in addition to the group sparsity for a within-group selection, which results in a regression model with a two-level sparsity regularization. We propose a modification of the group orthogonal matching pursuit (gOMP) algorithm with a thresholding step to solve the atom finding problem. The convergence and statistical analyses of the proposed algorithm are presented. The proposed algorithm is also evaluated through numerical experiments with simulated images. The applicability of the algorithm on determination of atom structures and identification of imaging distortions and atomic defects was demonstrated using three real STEM images. In conclusion, we believe this is an important step toward automatic phase identification and assignment with the advent of genomic databases for materials.« less

ISOTROPIC INELASTIC COLLISIONS IN A MULTITERM ATOM WITH HYPERFINE STRUCTURE

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

Belluzzi, Luca; Landi Degl’Innocenti, Egidio; Bueno, Javier Trujillo

2015-10-10

A correct modeling of the scattering polarization profiles observed in some spectral lines of diagnostic interest, the sodium doublet being one of the most important examples, requires taking hyperfine structure (HFS) and quantum interference between different J-levels into account. An atomic model suitable for taking these physical ingredients into account is the so-called multiterm atom with HFS. In this work, we introduce and study the transfer and relaxation rates due to isotropic inelastic collisions with electrons, which enter the statistical equilibrium equations (SEE) for the atomic density matrix of this atomic model. Under the hypothesis that the electron–atom interaction ismore » described by a dipolar operator, we provide useful relations between the rates describing the transfer and relaxation of quantum interference between different levels (whose numerical values are in most cases unknown) and the usual rates for the atomic level populations, for which experimental data and/or approximate theoretical expressions are generally available. For the particular case of a two-term atom with HFS, we present an analytical solution of the SEE for the spherical statistical tensors of the upper term, including both radiative and collisional processes, and we derive the expression of the emission coefficient in the four Stokes parameters. Finally, an illustrative application to the Na i D{sub 1} and D{sub 2} lines is presented.« less

A Rutherford Scattering Simulation with Microcomputer Graphics.

ERIC Educational Resources Information Center

Calle, Carlos I.; Wright, Lavonia F.

1989-01-01

Lists a program for a simulation of Rutherford's gold foil experiment in BASIC for both Apple II and IBM compatible computers. Compares Rutherford's model of the atom with Thompson's plum pudding model of the atom. (MVL)

The Particle Adventure | What is fundamental? | Fundamental

Science.gov Websites

? The modern atom model The scale of the atom What are we looking for? The standard model The standard Major accelerators The event Detectors Detector shapes Modern detectors Typical detector components

The Particle Adventure | Accelerators and Particle Detectors

Science.gov Websites

? The modern atom model The scale of the atom What are we looking for? The standard model The standard Major accelerators The event Detectors Detector shapes Modern detectors Typical detector components

Accurate atom-mapping computation for biochemical reactions.

PubMed

Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

2012-11-26

The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

The Lesson of Hiroshima and Nagasaki--Part I: The Past.

ERIC Educational Resources Information Center

Kauffman, George B.

1985-01-01

Examines scientific discoveries which underlie the atomic bomb and its technological development in the United States during World War II. Changing views, super-weapon development, early American efforts, production/dropping the bombs, and the Oppenheimer case are considered. (DH)

Historiography for Educational Leadership in Mathematics: Content Analysis of a 1904 K-8 Mathematics Series and the Early 20th Century Context of Its Use

ERIC Educational Resources Information Center

Goodwin, Diana

2012-01-01

Math education is as important today as it was 100 years ago when the early 20th century was transforming from the old world into an era of factories, airplanes, atomic energy, and medical breakthroughs. Educational leaders of the era were wrestling with how long children should stay in school, meeting the diverse needs of an influx of immigrants,…

On the temperature dependence of H-U{sub iso} in the riding hydrogen model

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

Lübben, Jens; Volkmann, Christian; Grabowsky, Simon

The temperature dependence of hydrogen U{sub iso} and parent U{sub eq} in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K. The temperature dependence of H-U{sub iso} in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-U{sub iso} below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for thismore » study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.« less

Kinetic Energy Distribution of D(2p) Atoms From Analysis of the D Lyman-a Line Profile

NASA Technical Reports Server (NTRS)

Ciocca, Marco; Ajello, Joseph M.; Liu, Xianming; Maki, Justin

1997-01-01

The absolute cross sections of the line center (slow atoms) and wings (fast atoms) and total emission line profile were measured from threshold to 400 eV. Analytical model coeffiecients are given for the energy dependence of the measured slow atom cross section.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

PubMed

Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

Secondary Interstellar Oxygen in the Heliosphere: Numerical Modeling and Comparison with IBEX-Lo Data

NASA Astrophysics Data System (ADS)

Baliukin, I. I.; Izmodenov, V. V.; Möbius, E.; Alexashov, D. B.; Katushkina, O. A.; Kucharek, H.

2017-12-01

Quantitative analysis of the interstellar heavy (oxygen and neon) atom fluxes obtained by the Interstellar Boundary Explorer (IBEX) suggests the existence of the secondary interstellar oxygen component. This component is formed near the heliopause due to charge exchange of interstellar oxygen ions with hydrogen atoms, as was predicted theoretically. A detailed quantitative analysis of the fluxes of interstellar heavy atoms is only possible with a model that takes into account both the filtration of primary and the production of secondary interstellar oxygen in the boundary region of the heliosphere as well as a detailed simulation of the motion of interstellar atoms inside the heliosphere. This simulation must take into account photoionization, charge exchange with the protons of the solar wind and solar gravitational attraction. This paper presents the results of modeling interstellar oxygen and neon atoms through the heliospheric interface and inside the heliosphere based on a three-dimensional kinetic-MHD model of the solar wind interaction with the local interstellar medium and a comparison of these results with the data obtained on the IBEX spacecraft.

Quantum-mechanical elaboration for the description of low- and high-order harmonics generated by extended gas media: prospects to the efficiency enhancement in spatially modulated media

NASA Astrophysics Data System (ADS)

Stremoukhov, Sergey Yu; Andreev, Anatoly V.

2018-03-01

A simple model fully matching the description of the low- and high-order harmonic generation in extended media interacting with multicolor laser fields is proposed. The extended atomic media is modeled by a 1D chain of atoms, the number of atoms and the distance between them depend on the pressure of the gas and the length of the gas cell. The response of the individual atoms is calculated accurately in the frame of the non-perturbative theory where the driving field for each atom is calculated with account of dispersion properties of any multicolor field component. In spite of the simplicity of the proposed model it provides the detailed description of behaviour of harmonic spectra under variation of the gas pressure and medium length, it also predicts a scaling law for harmonic generation (an invariant). To demonstrate the wide range of applications of the model we have simulated the results of recent experiments dealing with spatially modulated media and obtained good coincidence between the numerical results and the experimental ones.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

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

Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it; Jackson, Bret; Hughes, Keith H.

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theorymore » for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.« less

On the effect of irradiation-induced resolution in modelling fission gas release in UO2 LWR fuel

NASA Astrophysics Data System (ADS)

Lösönen, Pekka

2017-12-01

Irradiation resolution of gas atoms and vacancies from intra- and intergranular bubbles in sintered UO2 fuel was studied by comparing macroscopic models with a more mechanistic approach. The applied macroscopic models imply the resolution rate of gas atoms to be proportional to gas concentration in intragranular bubbles and at grain boundary (including intergranular bubbles). A relation was established between the macroscopic models and a single encounter of an energetic fission fragment with a bubble. The effect of bubble size on resolution was quantified. The number of resoluted gas atoms per encounter of a fission fragment per bubble was of the same order of magnitude for intra- and intergranular bubbles. However, the resulting macroscopic resolution rate of gas atoms was about two orders of magnitude larger from intragranular bubbles. The number of vacancies resoluted from a grain face bubble by a passing fission fragment was calculated. The obtained correlations for resolution of gas atoms from intragranular bubbles and grain boundaries and for resolution of vacancies from grain face bubbles were used to demonstrate the effect of irradiation resolution on fission gas release.

Testing the Agreement/Tense Omission Model: Why the Data on Children's Use of Non-Nominative 3psg Subjects Count against the ATOM

ERIC Educational Resources Information Center

Pine, Julian M.; Rowland, Caroline F.; Lieven, Elena V. M.; Theakston, Anna L.

2005-01-01

One of the most influential recent accounts of pronoun case-marking errors in young children's speech is Schutze & Wexler's (1996) Agreement/Tense Omission Model (ATOM). The ATOM predicts that the rate of agreeing verbs with non-nominative subjects will be so low that such errors can be reasonably disregarded as noise in the data. The present…

The role of ion exchange in the passivation of In(Zn)P nanocrystals with ZnS

PubMed Central

Cho, Deok-Yong; Xi, Lifei; Boothroyd, Chris; Kardynal, Beata; Lam, Yeng Ming

2016-01-01

We have investigated the chemical state of In(Zn)P/ZnS core/shell nanocrystals (NCs) for color conversion applications using hard X-ray absorption spectroscopy (XAS) and photoluminescence excitation (PLE). Analyses of the edge energies as well as the X-ray absorption fine structure (XAFS) reveal that the Zn2+ ions from ZnS remain in the shell while the S2− ions penetrate into the core at an early stage of the ZnS deposition. It is further demonstrated that for short growth times, the ZnS shell coverage on the core was incomplete, whereas the coverage improved gradually as the shell deposition time increased. Together with evidence from PLE spectra, where there is a strong indication of the presence of P vacancies, this suggests that the core-shell interface in the In(Zn)P/ZnS NCs are subject to substantial atomic exchanges and detailed models for the shell structure beyond simple layer coverage are needed. This substantial atomic exchange is very likely to be the reason for the improved photoluminescence behavior of the core-shell particles compare to In(Zn)P-only NCs as S can passivate the NCs surfaces. PMID:26972936

Charge Exchange Contribution to the Decay of the Ring Current, Measured by Energetic Neutral Atoms (ENAs)

NASA Technical Reports Server (NTRS)

Jorgensen, A. M.; Henderson, M. G.; Roelof, E. C.; Reeves, G. D.; Spence, H. E.

2001-01-01

In this paper we calculate the contribution of charge exchange to the decay of the ring current. Past works have suggested that charge exchange of ring current protons is primarily responsible for the decay of the ring current during the late recovery phase, but there is still much debate about the fast decay of the early recovery phase. We use energetic neutral atom (ENA) measurements from Polar to calculate the total ENA energy escape. To get the total ENA escape we apply a forward modeling technique, and to estimate the total ring current energy escape we use the Dessler-Parker-Sckopke relationship. We find that during the late recovery phase of the March 10, 1998 storm ENAs with energies greater than 17.5 keV can account for 75% of the estimated energy loss from the ring current. During the fast recovery the measured ENAs can only account for a small portion of the total energy loss. We also find that the lifetime of the trapped ions is significantly shorter during the fast recovery phase than during the late recovery phase, suggesting that different processes are operating during the two phases.

Elementary surface processes during reactive magnetron sputtering of chromium

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

Monje, Sascha; Corbella, Carles, E-mail: carles.corbella@rub.de; Keudell, Achim von

2015-10-07

The elementary surface processes occurring on chromium targets exposed to reactive plasmas have been mimicked in beam experiments by using quantified fluxes of Ar ions (400–800 eV) and oxygen atoms and molecules. For this, quartz crystal microbalances were previously coated with Cr thin films by means of high-power pulsed magnetron sputtering. The measured growth and etching rates were fitted by flux balance equations, which provided sputter yields of around 0.05 for the compound phase and a sticking coefficient of O{sub 2} of 0.38 on the bare Cr surface. Further fitted parameters were the oxygen implantation efficiency and the density of oxidationmore » sites at the surface. The increase in site density with a factor 4 at early phases of reactive sputtering is identified as a relevant mechanism of Cr oxidation. This ion-enhanced oxygen uptake can be attributed to Cr surface roughening and knock-on implantation of oxygen atoms deeper into the target. This work, besides providing fundamental data to control oxidation state of Cr targets, shows that the extended Berg's model constitutes a robust set of rate equations suitable to describe reactive magnetron sputtering of metals.« less

Accurate model annotation of a near-atomic resolution cryo-EM map

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

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structuralmore » features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.« less

Accurate model annotation of a near-atomic resolution cryo-EM map.

PubMed

Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah

2017-03-21

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

Accurate model annotation of a near-atomic resolution cryo-EM map

PubMed Central

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D.; King, Jonathan A.; Schmid, Michael F.; Chiu, Wah

2017-01-01

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages. PMID:28270620

Accurate model annotation of a near-atomic resolution cryo-EM map

DOE PAGES

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; ...

2017-03-07

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structuralmore » features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.« less

FAST TRACK COMMUNICATION: Generalized geometrical model for photoionization of polarized atoms: II. Magnetic dichroism in the 3p photoemission from the K 3p64s 2S1/2 ground state

NASA Astrophysics Data System (ADS)

Grum-Grzhimailo, A. N.; Cubaynes, D.; Heinecke, E.; Hoffmann, P.; Zimmermann, P.; Meyer, M.

2010-10-01

The generalized geometrical model for photoionization from polarized atoms is extended to include mixing of configurations in the initial atomic and/or the final photoion states. The theoretical results for angle-resolved linear and circular magnetic dichroism are in good agreement with new high-resolution photoelectron data for 3p-1 photoionization of potassium atoms polarized in the K 3p64s 2S1/2 ground state by laser optical pumping.

Demonstration of the Jaynes-Cummings ladder with Rydberg-dressed atoms

DOE PAGES

Lee, Jongmin; Martin, Michael J.; Jau, Yuan-Yu; ...

2017-04-06

Here, we observe the nonlinearity of the Jaynes-Cummings (JC) ladder in the Autler-Townes spectroscopy of the hyperfine ground states for a Rydberg-dressed two-atom system. The role of the two-level system in the JC model is played by the presence or absence of a collective Rydberg excitation, and the bosonic mode manifests as the number n of single-atom spin flips, symmetrically distributed between the atoms. We also measure the normal-mode splitting and √ n nonlinearity as a function of detuning and Rabi frequency, thereby experimentally establishing the isomorphism with the JC model.

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

Pang, Yuan-Ping, E-mail: pang@mayo.edu

Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its nativemore » conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.« less

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

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

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

2017-01-01

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

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.

Comet Hyakutake C/1996 B2

NASA Technical Reports Server (NTRS)

1998-01-01

These are two images of the inner coma of Comet Hyakutake made on April 3 and 4, 1996, using the NASA Hubble Space Telescope Wide Field Planetary Camera 2 (WFPC2). The first one, shown in red, was taken through a narrow-band red filter that shows only sunlight scattered by dust particles in the inner coma of the comet. The second one, shown in blue was taken with an ultraviolet 'Woods' filter image that shows the distribution of scattered ultraviolet radiation from hydrogen atoms in the inner coma. The coma is the head or dusty-gas atmosphere of a comet. The square field of view is 14,000 km on a side and the sun is toward the upper right corner of the image. Hydrogen atoms represent the most abundant gas in the whole coma of the comet. They are produced when solar ultraviolet light breaks up molecules of water, the major constituent of the nucleus of the comet. These images were taken as part of an observing program to study water photochemistry in comets. Measurements of hydrogen (H) and hydroxyl (OH) in the coma (or atmosphere) of Comet Hyakutake were also made using the Goddard High Resolution Spectrograph (GHRS) and the Faint Object Spectrograph (FOS). A self-consistent analysis of all the data shows that the water production rate of the comet was between 7 and 8 tons per second on the April 3 and 4. A theoretical model was used in the analysis which accounts for the detailed physics and chemistry of the photochemical destruction of the water, the production of the H and OH, and their expansion in the coma (or atmosphere) of the comet. The model matched the velocity measurements of hydrogen atoms made using the high spectral resolution capabilities of the GHRS instrument. The importance of such a detailed model is that is permits the accurate calculation of the production rate of water from observations of H and OH.

The inner yellow region near the center of the red dust image is dominated by the contribution from the dust which shows sunward directed spiral jets toward the upper right, and the thin straight particle trail pointing toward the lower left. The trail was a permanent feature of the comet around the time of its close approach to the Earth in late March and early April. Also barely visible just beyond the lower left end of the trail are two of the many condensations which were seen to travel slowly down the tail are believed to be clumps of material released from the nucleus.

The inner white region of the blue image appears to show that the hydrogen atoms like the dust might be preferentially ejected toward the sunward or day side of the nucleus. However, this is not true. The asymmetric ultraviolet radiation pattern is produced by a roughly spherical distribution of hydrogen atoms because they are so efficient at scattering the incoming solar ultraviolet light. The atoms on the sunward side actually shadow the atoms on the tailward or night side of the coma. The same detailed model analysis of the coma which explains the expansion of the hydrogen atoms in the coma also explains the appearance of the image.

The team was lead by Michael Combi, The University of Michigan, and included Michael Brown, California Institute of Technology, Paul Feldman, Johns Hopkins University, H. Uwe Keller of the Max Planck Institute, Lindau, Robert Meier of the Naval Research Laboratory, and William Smyth of Atmospheric and Environmental Research, Inc.

The Wide Field/Planetary Camera 2 was developed by the Jet Propulsion Laboratory and managed by the Goddard Spaced Flight Center for NASA's Office of Space Science.

This image and other images and data received from the Hubble Space Telescope are posted on the World Wide Web on the Space Telescope Science Institute home page at URL http://oposite.stsci.edu/pubinfo/

These are two images of the inner coma of Comet Hyakutake

NASA Technical Reports Server (NTRS)

2002-01-01

These are two images of the inner coma of Comet Hyakutake made on April 3 and 4, 1996, using the NASA Hubble Space Telescope Wide Field Planetary Camera 2 (WFPC2). The first one, shown in red, was taken through a narrow-band red filter that shows only sunlight scattered by dust particles in the inner coma of the comet. The second one, shown in blue was taken with an ultraviolet 'Woods' filter image that shows the distribution of scattered ultraviolet radiation from hydrogen atoms in the inner coma. The coma is the head or dusty-gas atmosphere of a comet. The square field of view is 14,000 km on a side and the sun is toward the upper right corner of the image. Hydrogen atoms represent the most abundant gas in the whole coma of the comet. They are produced when solar ultraviolet light breaks up molecules of water, the major constitutent of the nucleus of the comet. These images were taken as part of an observing program to study water photochemistry in comets. Measurements of hydrogen (H) and hydroxyl (OH) in the coma (or atmosphere) of Comet Hyakutake were also made using the Goddard High Resolution Spectrograph (GHRS) and the Faint Object Spectrograph (FOS). A self-consistent analysis of all the data shows that the water production rate of the comet was between 7 and 8 tons per second on the April 3 and 4. A theoretical model was used in the analysis which accounts for the detailed physics and chemistry of the photochemical destruction of the water, the production of the H and OH, and their expansion in the coma (or atmosphere) of the comet. The model matched the velocity measurements of hydrogen atoms made using the high spectral resolution capabilities of the GHRS instrument. The importance of such a detailed model is that is permits the accurate calculation of the production rate of water from observations of H and OH. The inner yellow region near the center of the red dust image is dominated by the contribution from the dust which shows sunward directed spiral jets toward the upper right, and the thin straight particle trail pointing toward the lower left. The trail was a permanent feature of the comet around the time of its close approach to the earth in late March and early April. Also barely visible just beyond the lower left end of the trail are two of the many condensations which were seen to travel slowly down the tail are are believed to be clumps of material released from the nucleus. The inner white region of the blue image appears to show that the hydrogen atoms like the dust might be preferentially ejected toward the sunward or day side of the nucleus. However, this is not true. The asymmetric ultraviolet radiation pattern is produced by a roughly spherical distribution of hydrogen atoms because they are so efficient at scattering the incoming solar ultraviolet light. The atoms on the sunward side actually shadow the atoms on the tailward or night side of the coma. The same detailed model analysis of the coma which explains the expansion of the hydrogen atoms in the coma also explains the appearance of the image. The team was lead by Michael Combi, The University of Michigan, and included Michael Brown, California Institute of Technology, Paul Feldman, Johns Hopkins University, H. Uwe Keller of the Max Planck Institute, Lindau, Robert Meier of the Naval Research Laboratory, and William Smyth of Atmospheric and Environmental Research, Inc. Credit: M.R. Combi (The University of Michigan)

Atomic disorder, phase transformation, and phase restoration in Co3Sn2

NASA Astrophysics Data System (ADS)

di, L. M.; Zhou, G. F.; Bakker, H.

1993-03-01

The behavior of the intermetallic compound Co3Sn2 upon ball milling was studied by x-ray diffraction, high-field-magnetization measurements, and subsequently by differential scanning calorimetry. It turns out that starting from the stoichiometric-ordered compound, mechanical attrition of Co3Sn2 generates atomic disorder in the early stage of milling. The nonequilibrium phase transformation from the low-temperature phase with orthorhombic structure to the high-temperature phase with a hexagonal structure was observed in the intermediate stage of milling. It was accompanied by the creation of increasing atomic disorder. After long milling periods, the phase transformation was completed and the atomic disordering became saturated. All the physical parameters measured in the present work remained constant during this period. The above outcome was confirmed by comparison with the high-temperature phase thermally induced by quenching. The good agreement of the results obtained by different techniques proves that the ball milling generates well-defined metastable states in Co3Sn2.

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.

On the road to metallic nanoparticles by rational design: bridging the gap between atomic-level theoretical modeling and reality by total scattering experiments.

PubMed

Prasai, Binay; Wilson, A R; Wiley, B J; Ren, Y; Petkov, Valeri

2015-11-14

The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au(100-x)Pd(x) (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when "tuned up" against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design.

Texturing Carbon-carbon Composite Radiator Surfaces Utilizing Atomic Oxygen

NASA Technical Reports Server (NTRS)

Raack, Taylor

2004-01-01

Future space nuclear power systems will require radiator technology to dissipate excess heat created by a nuclear reactor. Large radiator fins with circulating coolant are in development for this purpose and an investigation of how to make them most efficient is underway. Maximizing the surface area while minimizing the mass of such radiator fins is critical for obtaining the highest efficiency in dissipating heat. Processes to develop surface roughness are under investigation to maximize the effective surface area of a radiator fin. Surface roughness is created through several methods including oxidation and texturing. The effects of atomic oxygen impingement on carbon-carbon surfaces are currently being investigated for texturing a radiator surface. Early studies of atomic oxygen impingement in low Earth orbit indicate significant texturing due to ram atomic oxygen. The surface morphology of the affected surfaces shows many microscopic cones and valleys which have been experimentally shown to increase radiation emittance. Further study of this morphology proceeded in the Long Duration Exposure Facility (LDEF). Atomic oxygen experiments on the LDEF successfully duplicated the results obtained from materials in spaceflight by subjecting samples to 4.5 eV atomic oxygen from a fixed ram angle. These experiments replicated the conical valley morphology that was seen on samples subjected to low Earth orbit.

Non-LTE line formation for N: Abundances and stellar parameters. Model atom and first results on BA-type stars

NASA Astrophysics Data System (ADS)

Przybilla, N.; Butler, K.

2001-12-01

A comprehensive model atom for non-LTE line formation calculations for neutral and singly-ionized nitrogen is presented. Highly accurate radiative and collisional atomic data are incorporated, recently determined for astrophysical and fusion research using the R-matrix method in the close-coupling approximation. As a test and first application of the model, nitrogen abundances are determined on the basis of line-blanketed LTE model atmospheres for five stars, the main sequence object Vega (A0 V) and the supergiants eta Leo (A0 Ib), HD 111613 (A2 Iabe), HD 92207 (A0 Iae) and beta Ori (B8 Iae), using high S/N and high-resolution spectra at visual and near-IR wavelengths. The computed non-LTE line profiles fit the observations excellently for a given nitrogen abundance in each object. Moreover, the ionization equilibrium of \\ion{N}{i/ii} proves to be a sensitive temperature indicator for late B-type and early A-type supergiants - even at low metallicities - due to the apparent nitrogen overabundance in these objects. All supergiants within our sample show an enrichment of nitrogen on the order of ~ 0.3-0.6 dex, indicating the mixing of CN-cycled material into atmospheric layers, with the sum of the CNO abundances staying close to solar. This finding is in accordance with recent stellar evolution models accounting for mass-loss and rotation. For Vega, an underabundance of nitrogen by 0.25 dex is found, in good agreement with the similar underabundance of other light elements. The dependence of the non-LTE effects on the atmospheric parameters is discussed with special emphasis on the supergiants where a strong radiation field at low particle densities favours deviations from LTE. Non-LTE effects systematically strengthen the \\ion{N}{i/ii} lines. For some N I lines in supergiants non-LTE abundance corrections in excess of 1 dex are found and they react sensitively to modifications of the collisional excitation data. The influence of microturbulence on the statistical-equilibrium calculations is also investigated: the line-strengths of the strong N I features show some sensitivity due to modifications of the line-formation depths and the departure coefficients, while the - in this parameter range - weak N Ii lines remain unaffected. Based on observations collected at the European Southern Observatory, Chile (ESO Ndeg 62.H-0176).

Metal powder production by gas atomization

NASA Technical Reports Server (NTRS)

Ting, E. Y.; Grant, N. J.

1986-01-01

The confined liquid, gas-atomization process was investigated. Results from a two-dimensional water model showed the importance of atomization pressure, as well as delivery tube and atomizer design. The atomization process at the tip of the delivery tube was photographed. Results from the atomization of a modified 7075 aluminum alloy yielded up to 60 wt pct. powders that were finer than 45 microns in diameter. Two different atomizer designs were evaluated. The amount of fine powders produced was correlated to a calculated gas-power term. An optimal gas-power value existed for maximized fine powder production. Atomization at gas-power greater than or less than this optimal value produced coarser powders.

Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

NASA Technical Reports Server (NTRS)

Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

1997-01-01

The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.

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

PubMed

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

2015-07-21

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

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

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

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

2015-07-21

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

A predictive structural model for bulk metallic glasses

PubMed Central

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

2015-01-01

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

Fast-responding property of electromagnetically induced transparency in Rydberg atoms

NASA Astrophysics Data System (ADS)

Zhang, Qi; Bai, Zhengyang; Huang, Guoxiang

2018-04-01

We investigate the transient optical response property of an electromagnetically induced transparency (EIT) in a cold Rydberg atomic gas. We show that both the transient behavior and the steady-state EIT spectrum of the system depend strongly on Rydberg interaction. Especially, the response speed of the Rydberg-EIT can be five times faster (and even higher) than the conventional EIT without the Rydberg interaction. For comparison, two different theoretical approaches (i.e., two-atom model and many-atom model) are considered, revealing that Rydberg blockade effect plays a significant role for increasing the response speed of the Rydberg-EIT. The fast-responding Rydberg-EIT by using the strong, tunable Rydberg interaction uncovered here is not only helpful for enhancing the understanding of the many-body dynamics of Rydberg atoms but also useful for practical applications in quantum information processing by using Rydberg atoms.

Atomic charges of sulfur in ionic liquids: experiments and calculations.

PubMed

Fogarty, Richard M; Rowe, Rebecca; Matthews, Richard P; Clough, Matthew T; Ashworth, Claire R; Brandt, Agnieszka; Corbett, Paul J; Palgrave, Robert G; Smith, Emily F; Bourne, Richard A; Chamberlain, Thomas W; Thompson, Paul B J; Hunt, Patricia A; Lovelock, Kevin R J

2017-12-14

Experimental near edge X-ray absorption fine structure (NEXAFS) spectra, X-ray photoelectron (XP) spectra and Auger electron spectra are reported for sulfur in ionic liquids (ILs) with a range of chemical structures. These values provide experimental measures of the atomic charge in each IL and enable the evaluation of the suitability of NEXAFS spectroscopy and XPS for probing the relative atomic charge of sulfur. In addition, we use Auger electron spectroscopy to show that when XPS binding energies differ by less than 0.5 eV, conclusions on atomic charge should be treated with caution. Our experimental data provides a benchmark for calculations of the atomic charge of sulfur obtained using different methods. Atomic charges were computed for lone ions and ion pairs, both in the gas phase (GP) and in a solvation model (SMD), with a wide range of ion pair conformers considered. Three methods were used to compute the atomic charges: charges from the electrostatic potential using a grid based method (ChelpG), natural bond orbital (NBO) population analysis and Bader's atoms in molecules (AIM) approach. By comparing the experimental and calculated measures of the atomic charge of sulfur, we provide an order for the sulfur atoms, ranging from the most negative to the most positive atomic charge. Furthermore, we show that both ChelpG and NBO are reasonable methods for calculating the atomic charge of sulfur in ILs, based on the agreement with both the XPS and NEXAFS spectroscopy results. However, the atomic charges of sulfur derived from ChelpG are found to display significant, non-physical conformational dependence. Only small differences in individual atomic charge of sulfur were observed between lone ion (GP) and ion pair IL(SMD) model systems, indicating that ion-ion interactions do not strongly influence individual atomic charges.

Building a pseudo-atomic model of the anaphase-promoting complex.

PubMed

Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; da Fonseca, Paula C A; Barford, David

2013-11-01

The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14-15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.

Atomic density functional and diagram of structures in the phase field crystal model

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

Ankudinov, V. E., E-mail: vladimir@ankudinov.org; Galenko, P. K.; Kropotin, N. V.

2016-02-15

The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindricalmore » tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.« less

Determination of early warning signs for photocatalytic degradation of titanium white oil paints by means of surface analysis

NASA Astrophysics Data System (ADS)

van Driel, B. A.; Wezendonk, T. A.; van den Berg, K. J.; Kooyman, P. J.; Gascon, J.; Dik, J.

2017-02-01

Titanium white (TiO2) has been widely used as a pigment in the 20th century. However, its most photocatalytic form (anatase) can cause severe degradation of the oil paint in which it is contained. UV light initiates TiO2-photocatalyzed processes in the paint film, degrading the oil binder into volatile components resulting in chalking of the paint. This will eventually lead to severe changes in the appearance of a painting. To date, limited examples of degraded works of art containing titanium white are known due to the relatively short existence of the paintings in question and the slow progress of the degradation process. However, UV light will inevitably cause degradation of paint in works of art containing photocatalytic titanium white. In this work, a method to detect early warning signs of photocatalytic degradation of unvarnished oil paint is proposed, using atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). Consequently, a four-stage degradation model was developed through in-depth study of TiO2-containing paint films in various stages of degradation. The XPS surface analysis proved very valuable for detecting early warning signs of paint degradation, whereas the AFM results provide additional confirmation and are in good agreement with bulk gloss reduction.

Measurements and kinetic modeling of atomic species in fuel-oxidizer mixtures excited by a repetitive nanosecond pulse discharge

NASA Astrophysics Data System (ADS)

Winters, C.; Eckert, Z.; Yin, Z.; Frederickson, K.; Adamovich, I. V.

2018-01-01

This work presents the results of number density measurements of metastable Ar atoms and ground state H atoms in diluted mixtures of H2 and O2 with Ar, as well as ground state O atoms in diluted H2-O2-Ar, CH4-O2-Ar, C3H8-O2-Ar, and C2H4-O2-Ar mixtures excited by a repetitive nanosecond pulse discharge. The measurements have been made in a nanosecond pulse, double dielectric barrier discharge plasma sustained in a flow reactor between two plane electrodes encapsulated within dielectric material, at an initial temperature of 500 K and pressures ranging from 300 Torr to 700 Torr. Metastable Ar atom number density distribution in the afterglow is measured by tunable diode laser absorption spectroscopy, and used to characterize plasma uniformity. Temperature rise in the reacting flow is measured by Rayleigh scattering. H atom and O atom number densities are measured by two-photon absorption laser induced fluorescence. The results are compared with kinetic model predictions, showing good agreement, with the exception of extremely lean mixtures. O atoms and H atoms in the plasma are produced mainly during quenching of electronically excited Ar atoms generated by electron impact. In H2-Ar and O2-Ar mixtures, the atoms decay by three-body recombination. In H2-O2-Ar, CH4-O2-Ar, and C3H8-O2-Ar mixtures, O atoms decay in a reaction with OH, generated during H atom reaction with HO2, with the latter produced by three-body H atom recombination with O2. The net process of O atom decay is O  +  H  →  OH, such that the decay rate is controlled by the amount of H atoms produced in the discharge. In extra lean mixtures of propane and ethylene with O2-Ar the model underpredicts the O atom decay rate. At these conditions, when fuel is completely oxidized by the end of the discharge burst, the net process of O atom decay, O  +  O  →  O2, becomes nearly independent of H atom number density. Lack of agreement with the data at these conditions is likely due to diffusion of H atoms from the partially oxidized regions near the side walls of the reactor into the plasma. Although significant fractions of hydrogen and hydrocarbon fuels are oxidized by O atoms produced in the plasma, chain branching remains a minor effect at these relatively low temperature conditions.

Deciphering chemical order/disorder and material properties at the single-atom level.

PubMed

Yang, Yongsoo; Chen, Chien-Chun; Scott, M C; Ophus, Colin; Xu, Rui; Pryor, Alan; Wu, Li; Sun, Fan; Theis, Wolfgang; Zhou, Jihan; Eisenbach, Markus; Kent, Paul R C; Sabirianov, Renat F; Zeng, Hao; Ercius, Peter; Miao, Jianwei

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

Experimental Preparation and Measurement of Quantum States of Motion of a Trapped Atom

DTIC Science & Technology

1997-01-01

trapped atom are quantum harmonic oscillators, their couplings to internal atomic levels (described by the Jaynes - Cummings model (JCM) [ l , 21) are... wave approximation in a frame rotating with WO, where hwo is the energy difference of the two internal levels, the interaction of the classical laser... Jaynes - Cummings model , the system is suited to realizing many proposals originally introduced in the realm of quantum optics and cavity quantum

Modeling of Elastic Collisions between High Energy and Slow Neutral Atoms

DTIC Science & Technology

2015-07-01

cylindrical test cell, and the currents on the four different electrodes-Inner Cylinder , Exit Plate, Back Aperture, and Collector Plat~were measured...Inner Cylinder electrode. Nevertheless, the neutral atom current to the Inner Cylinder electrode predicted by the VHS model is comparable to the...Figure 9. Normalized curre nt at the Inner Cylinder e lectrode. the point of collision. T he discrepancy in the Exit Plate neutral atom current is due to

A model of optical trapping cold atoms using a metallic nano wire with surface plasmon effect

NASA Astrophysics Data System (ADS)

Thi Phuong Lan, Nguyen; Thi Nga, Do; Viet, Nguyen Ai

2016-06-01

In this work, we construct a new model of optical trapping cold atoms with a metallic nano wire by using surface plasmon effect generated by strong field of laser beams. Using the skin effect, we send a strong oscillated electromagnetic filed through the surface of a metallic nano wire. The local field generated by evanescent effect creates an effective attractive potential near the surface of metallic nano wires. The consideration of some possible boundary and frequency conditions might lead to non-trivial bound state solution for a cold atom. We discus also the case of the laser reflection optical trap with shell-core design, and compare our model with another recent schemes of cold atom optical traps using optical fibers and carbon nanotubes.

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE PAGES

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

2015-09-03

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

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

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

PubMed Central

Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.

2016-01-01

A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

10Be measured in a GRIP snow pit and modeled using the ECHAM5-HAM general circulation model

NASA Astrophysics Data System (ADS)

Heikkilä, U.; Beer, J.; Jouzel, J.; Feichter, J.; Kubik, P.

2008-03-01

10Be measured in a Greenland Ice Core Project (GRIP) snow pit (1986-1990) with a seasonal resolution is compared with the ECHAM5-HAM GCM run. The mean modeled 10Be concentration in ice (1.0.104 atoms/g) agrees well with the measured value (1.2.104 atoms/g). The measured 10Be deposition flux (88 atoms/m2/s) also agrees well with the modeled flux (69 atoms/m2/s) and the measured precipitation rate (0.67 mm/day) agrees with the modeled rate (0.61 mm/day). The mean surface temperature of -31°C estimated from δ 18O is lower than the temperature measured at a near-by weather station (-29°C) and the modeled temperature (-26°C). During the 5-year period the concentrations and deposition fluxes, both measured and modeled, show a decreasing trend consistent with the increase in the solar activity. The variability of the measured and modeled concentrations and deposition fluxes is very similar suggesting that the variability is linked to a variability in production rather than the local meteorology.

Ionization equilibrium at the transition from valence-band to acceptor-band migration of holes in boron-doped diamond

NASA Astrophysics Data System (ADS)

Poklonski, N. A.; Vyrko, S. A.; Poklonskaya, O. N.; Kovalev, A. I.; Zabrodskii, A. G.

2016-06-01

A quasi-classical model of ionization equilibrium in the p-type diamond between hydrogen-like acceptors (boron atoms which substitute carbon atoms in the crystal lattice) and holes in the valence band (v-band) is proposed. The model is applicable on the insulator side of the insulator-metal concentration phase transition (Mott transition) in p-Dia:B crystals. The densities of the spatial distributions of impurity atoms (acceptors and donors) and of holes in the crystal are considered to be Poissonian, and the fluctuations of their electrostatic potential energy are considered to be Gaussian. The model accounts for the decrease in thermal ionization energy of boron atoms with increasing concentration, as well as for electrostatic fluctuations due to the Coulomb interaction limited to two nearest point charges (impurity ions and holes). The mobility edge of holes in the v-band is assumed to be equal to the sum of the threshold energy for diffusion percolation and the exchange energy of the holes. On the basis of the virial theorem, the temperature Tj is determined, in the vicinity of which the dc band-like conductivity of holes in the v-band is approximately equal to the hopping conductivity of holes via the boron atoms. For compensation ratio (hydrogen-like donor to acceptor concentration ratio) K ≈ 0.15 and temperature Tj, the concentration of "free" holes in the v-band and their jumping (turbulent) drift mobility are calculated. Dependence of the differential energy of thermal ionization of boron atoms (at the temperature 3Tj/2) as a function of their concentration N is calculated. The estimates of the extrapolated into the temperature region close to Tj hopping drift mobility of holes hopping from the boron atoms in the charge states (0) to the boron atoms in the charge states (-1) are given. Calculations based on the model show good agreement with electrical conductivity and Hall effect measurements for p-type diamond with boron atom concentrations in the range from 3 × 1017 to 3 × 1020 cm-3, i.e., up to the Mott transition. The model uses no fitting parameters.

Modeling of Turbulence Effect on Liquid Jet Atomization

NASA Technical Reports Server (NTRS)

Trinh, H. P.

2007-01-01

Recent studies indicate that turbulence behaviors within a liquid jet have considerable effect on the atomization process. Such turbulent flow phenomena are encountered in most practical applications of common liquid spray devices. This research aims to model the effects of turbulence occurring inside a cylindrical liquid jet to its atomization process. The two widely used atomization models Kelvin-Helmholtz (KH) instability of Reitz and the Taylor analogy breakup (TAB) of O'Rourke and Amsden portraying primary liquid jet disintegration and secondary droplet breakup, respectively, are examined. Additional terms are formulated and appropriately implemented into these two models to account for the turbulence effect. Results for the flow conditions examined in this study indicate that the turbulence terms are significant in comparison with other terms in the models. In the primary breakup regime, the turbulent liquid jet tends to break up into large drops while its intact core is slightly shorter than those without turbulence. In contrast, the secondary droplet breakup with the inside liquid turbulence consideration produces smaller drops. Computational results indicate that the proposed models provide predictions that agree reasonably well with available measured data.

On the Treatment of l-changing Proton-hydrogen Rydberg Atom Collisions

NASA Astrophysics Data System (ADS)

Vrinceanu, Daniel; Onofrio, Roberto; Sadeghpour, Hossein

2018-01-01

Energy-conserving, angular momentum-changing collisions between protons and highly excited Rydberg hydrogen atoms are important for precise understanding of the primordial recombination cascade, and the elemental abundance.Early approaches to l-changing collisions used perturbation theory for only dipole-allowed (Δl = ±1) transitions. An exact non-perturbative quantum mechanical treatment is possible, but it comes at computational cost for highly excited Rydberg states. In this note we show how to obtain a semi-classical limit that is accurate and simple, and develop further physical insights afforded by the non-perturbative quantum mechanical treatment.

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

Bhattacharya, Arunodaya; Meslin, Estelle; Henry, Jean

Effect of helium on void swelling was studied in high-purity α-iron, irradiated using energetic self-ions to 157 displacements per atom (dpa) at 773 K, with and without helium co-implantation up to 17 atomic parts-per-million (appm) He/dpa. Helium is known to enhance cavity formation in metals in irradiation environments, leading to early void swelling onset. In this study, microstructure characterization by transmission electron microscopy revealed compelling evidence of dramatic swelling reduction by helium co-implantation, achieved primarily by cavity size reduction. In conclusion, a comprehensive understanding of helium induced cavity microstructure development is discussed using sink strength ratios of dislocations and cavities.

Early stages of collapsing pentacene crystal by Au

NASA Astrophysics Data System (ADS)

Ihm, Kyuwook; Chung, Sukmin; Kang, Tai-Hee; Cheong, Sang-Wook

2008-10-01

The characteristic feature of metal contacts with gold on organics is deterioration of the organic crystals during the contact formation. The unveiled key challenge is to probe dynamic details of the microscopic evolution of the organic crystal when the atomic Au is introduced. Here, we report how the collapse of the pentacene crystal is initiated even by a few Au atoms. Our results indicate that the gentle decoupling of intra and intermolecular π-π interactions causes the localization of the lowest unoccupied molecular orbital as well as the removal of cohesive forces between molecules, leading to the subsequent crystal collapse.

Understanding the atomic-level Green-Kubo stress correlation function for a liquid through phonons in a model crystal

NASA Astrophysics Data System (ADS)

Levashov, V. A.

2014-11-01

In order to gain insight into the connection between the vibrational dynamics and the atomic-level Green-Kubo stress correlation function in liquids, we consider this connection in a model crystal instead. Of course, vibrational dynamics in liquids and crystals are quite different and it is not expected that the results obtained on a model crystal should be valid for liquids. However, these considerations provide a benchmark to which the results of the previous molecular dynamics simulations can be compared. Thus, assuming that vibrations are plane waves, we derive analytical expressions for the atomic-level stress correlation functions in the classical limit and analyze them. These results provide, in particular, a recipe for analysis of the atomic-level stress correlation functions in Fourier space and extraction of the wave-vector and frequency-dependent information. We also evaluate the energies of the atomic-level stresses. The energies obtained are significantly smaller than the energies previously determined in molecular dynamics simulations of several model liquids. This result suggests that the average energies of the atomic-level stresses in liquids and glasses are largely determined by the structural disorder. We discuss this result in the context of equipartition of the atomic-level stress energies. Analysis of the previously published data suggests that it is possible to speak about configurational and vibrational contributions to the average energies of the atomic-level stresses in a glass state. However, this separation in a liquid state is problematic. We also introduce and briefly consider the atomic-level transverse current correlation function. Finally, we address the broadening of the peaks in the pair distribution function with increase of distance. We find that the peaks' broadening (by ≈40 % ) occurs due to the transverse vibrational modes, while contribution from the longitudinal modes does not change with distance.

AtomDB: Expanding an Accessible and Accurate Atomic Database for X-ray Astronomy

NASA Astrophysics Data System (ADS)

Smith, Randall

Since its inception in 2001, the AtomDB has become the standard repository of accurate and accessible atomic data for the X-ray astrophysics community, including laboratory astrophysicists, observers, and modelers. Modern calculations of collisional excitation rates now exist - and are in AtomDB - for all abundant ions in a hot plasma. AtomDB has expanded beyond providing just a collisional model, and now also contains photoionization data from XSTAR as well as a charge exchange model, amongst others. However, building and maintaining an accurate and complete database that can fully exploit the diagnostic potential of high-resolution X-ray spectra requires further work. The Hitomi results, sadly limited as they were, demonstrated the urgent need for the best possible wavelength and rate data, not merely for the strongest lines but for the diagnostic features that may have 1% or less of the flux of the strong lines. In particular, incorporation of weak but powerfully diagnostic satellite lines will be crucial to understanding the spectra expected from upcoming deep observations with Chandra and XMM-Newton, as well as the XARM and Athena satellites. Beyond incorporating this new data, a number of groups, both experimental and theoretical, have begun to produce data with errors and/or sensitivity estimates. We plan to use this to create statistically meaningful spectral errors on collisional plasmas, providing practical uncertainties together with model spectra. We propose to continue to (1) engage the X-ray astrophysics community regarding their issues and needs, notably by a critical comparison with other related databases and tools, (2) enhance AtomDB to incorporate a large number of satellite lines as well as updated wavelengths with error estimates, (3) continue to update the AtomDB with the latest calculations and laboratory measurements, in particular velocity-dependent charge exchange rates, and (4) enhance existing tools, and create new ones as needed to increase the functionality of, and access to, AtomDB.

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

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

Atomic oxygen interaction at defect sights in protective coatings on polymers flown on LDEF

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Degroh, Kim K.; Auer, Bruce M.; Gebauer, Linda; Lamoreaux, Cynthia

1993-01-01

Although the Long Duration Exposure Facility (LDEF) has exposed materials with a fixed orientation relative to the ambient low-Earth-orbital environment, arrival of atomic oxygen is angularly distributed as a result of the atomic oxygen's high temperature Maxwellian velocity distribution and the LDEF's orbital inclination. Thus, atomic oxygen entering defects in protective coatings on polymeric surfaces can cause wider undercut cavities than the size of the defect in the protective coating. Because only a small fraction of atomic oxygen reacts upon first impact with most polymeric materials, secondary reactions with lower energy thermally accommodated atomic oxygen can occur. The secondary reactions of scattered and/or thermally accommodated atomic oxygen also contribute to widening the undercut cavity beneath the protective coating defect. As the undercut cavity enlarges, exposing more polymer, the probability of atomic oxygen reacting with underlying polymeric material increases because of multiple opportunities for reaction. Thus, the effective atomic oxygen erosion yield for atoms entering defects increases above that of the unprotected material. Based on the results of analytical modeling and computational modeling, aluminized Kapton multilayer insulation exposed to atomic oxygen on row 9 lost the entire externally exposed layer of polyimide Kapton, yet based on the results of this investigation, the bottom surface aluminum film must have remained in place, but crazed. Atomic oxygen undercutting at defect sites in protective coatings on graphite epoxy composites indicates that between 40 to 100 percent of the atomic oxygen thermally accommodates upon impact, and that the reaction probability of thermally accommodated atomic oxygen may range from 7.7 x 10(exp -6) to 2.1 x 10(exp -3), depending upon the degree of thermal accommodation upon each impact.

Atom optics in the time domain

NASA Astrophysics Data System (ADS)

Arndt, M.; Szriftgiser, P.; Dalibard, J.; Steane, A. M.

1996-05-01

Atom-optics experiments are presented using a time-modulated evanescent light wave as an atomic mirror in the trampoline configuration, i.e., perpendicular to the direction of the atomic free fall. This modulated mirror is used to accelerate cesium atoms, to focus their trajectories, and to apply a ``multiple lens'' to separately focus different velocity classes of atoms originating from a point source. We form images of a simple two-slit object to show the resolution of the device. The experiments are modelled by a general treatment analogous to classical ray optics.

Structure and conformational dynamics of scaffolded DNA origami nanoparticles

DTIC Science & Technology

2017-05-08

all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conforma... finite element (FE) modeling approach CanDo is also routinely used to predict the 3D equilibrium conformation of programmed DNA assemblies based on a...model with both experimental cryo-electron microscopy (cryo-EM) data and all-atom modeling. MATERIALS AND METHODS Lattice-free finite element model

Atomic and molecular supernovae

NASA Technical Reports Server (NTRS)

Liu, Weihong

1997-01-01

Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

AtomicJ: An open source software for analysis of force curves

NASA Astrophysics Data System (ADS)

Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

2014-06-01

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

DIFFRACTION FROM MODEL CRYSTALS

USDA-ARS?s Scientific Manuscript database

Although calculating X-ray diffraction patterns from atomic coordinates of a crystal structure is a widely available capability, calculation from non-periodic arrays of atoms has not been widely applied to cellulose. Non-periodic arrays result from modeling studies that, even though started with at...

Treatment of atomic and molecular line blanketing by opacity sampling. [atmospheric optics - stellar atmospheres

NASA Technical Reports Server (NTRS)

Johnson, H. R.; Krupp, B. M.

1975-01-01

An opacity sampling (OS) technique for treating the radiative opacity of large numbers of atomic and molecular lines in cool stellar atmospheres is presented. Tests were conducted and results show that the structure of atmospheric models is accurately fixed by the use of 1000 frequency points, and 500 frequency points is often adequate. The effects of atomic and molecular lines are separately studied. A test model computed by using the OS method agrees very well with a model having identical atmospheric parameters computed by the giant line (opacity distribution function) method.

The Pharmacokinetics of Atomized Lidocaine Administered via the Trachea: A Randomized Trial.

PubMed

Takaenoki, Yumiko; Masui, Kenichi; Oda, Yutaka; Kazama, Tomiei

2016-07-01

Under emergent conditions, endotracheal drug administration may be an effective method of delivering emergency drugs. A common technique is to administer these drugs using a nonatomized spray. Atomized drug delivery may be an attractive alternative to nonatomized delivery because atomized particles are small, cover a large surface area, and may better adhere to endotracheal membrane resulting in more effective drug absorption. In this study, we compared the pharmacokinetic profile of lidocaine administered into the trachea using an atomized or a nonatomized technique. Twenty patients were anesthetized using propofol and remifentanil. Ten minutes after rocuronium was administered, patients received 4% lidocaine (2 mg/kg) intratracheally over 2 seconds before tracheal intubation. Ten patients received atomized lidocaine using a mucosal atomization device, and the other 10 patients received nonatomized lidocaine using a traditional spray tube. Arterial lidocaine plasma concentrations were measured before; at 1, 3, 5, 7, 10, 15, 20, 30, 45, and 60 minutes; and then every 60 minutes after the administration of lidocaine until the end of the operation. We developed a pharmacokinetic model to examine whether bioavailability or absorption rate was different between atomized versus nonatomized lidocaine administration. The total body clearance was fixed at a published value to determine the bioavailability. Peak plasma concentrations were larger using the mucosal atomization device (median [range]: 1.9 [1.4-3.2] μg/mL) than the spray tube (1.1 [0.6-2.0] μg/mL; P = 0.0021). Our pharmacokinetic model estimated a difference of bioavailability between the atomized and the nonatomized lidocaine (0.801 and 0.559 respectively, P = 0.0005), whereas our model estimated no difference in the absorption rate constant (0.00688/min). Our results suggest that when using atomized delivery of lidocaine, less drug is required to achieve a near equivalent plasma lidocaine concentration. Atomized drug administration may be a more efficient method for endotracheal drug administration.

Fluorescent Fe K Emission from High Density Accretion Disks

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Garcia, Javier; Kallman, Timothy R.; Palmeri, Patrick; Deprince, Jerome; Quinet, Pascal

2018-06-01

Iron K-shell lines emitted by gas closely orbiting black holes are observed to be grossly broadened and skewed by Doppler effects and gravitational redshift. Accordingly, models for line profiles are widely used to measure the spin (i.e., the angular momentum) of astrophysical black holes. The accuracy of these spin estimates is called into question because fitting the data requires very high iron abundances, several times the solar value. Meanwhile, no plausible physical explanation has been proffered for why these black hole systems should be so iron rich. The most likely explanation for the super-solar iron abundances is a deficiency in the models, and the leading candidate cause is that current models are inapplicable at densities above 1018 cm-3. We study the effects of high densities on the atomic parameters and on the spectral models for iron ions. At high densities, Debye plasma can affect the effective atomic potential of the ions, leading to observable changes in energy levels and atomic rates with respect to the low density case. High densities also have the effec of lowering energy the atomic continuum and reducing the recombination rate coefficients. On the spectral modeling side, high densities drive level populations toward a Boltzman distribution and very large numbers of excited atomic levels, typically accounted for in theoretical spectral models, may contribute to the K-shell spectrum.

Study of crystallization mechanisms of Fe nanoparticle

NASA Astrophysics Data System (ADS)

Kien, P. H.; Trang, G. T. T.; Hung, P. K.

2017-06-01

In this paper, the nanoparticle (NP) Fe was investigated by means of molecular dynamics simulation. The crystallization mechanism was studied through the time evolution of crystal cluster and potential energies of different atom types. The simulation shows that the NP was crystallized into bcc crystal structure when it was annealed at 900 K for long times. At early stage of the annealing, small nuclei form in different places of NP and dissolve for short times. After long times some nuclei form and gather nearby which create the stable clusters in the core of NP. After that the crystal clusters grow in the direction to cover the core and then to spread into the surface of NP. Analyzing the energies of different type atoms, we found that the crystal growth is originated from specific atomic arrangement in the boundary region of crystal clusters.

Optimization of Simplex Atomizer Inlet Port Configuration through Computational Fluid Dynamics and Experimental Study for Aero-Gas Turbine Applications

NASA Astrophysics Data System (ADS)

Marudhappan, Raja; Chandrasekhar, Udayagiri; Hemachandra Reddy, Koni

2017-10-01

The design of plain orifice simplex atomizer for use in the annular combustion system of 1100 kW turbo shaft engine is optimized. The discrete flow field of jet fuel inside the swirl chamber of the atomizer and up to 1.0 mm downstream of the atomizer exit are simulated using commercial Computational Fluid Dynamics (CFD) software. The Euler-Euler multiphase model is used to solve two sets of momentum equations for liquid and gaseous phases and the volume fraction of each phase is tracked throughout the computational domain. The atomizer design is optimized after performing several 2D axis symmetric analyses with swirl and the optimized inlet port design parameters are used for 3D simulation. The Volume Of Fluid (VOF) multiphase model is used in the simulation. The orifice exit diameter is 0.6 mm. The atomizer is fabricated with the optimized geometric parameters. The performance of the atomizer is tested in the laboratory. The experimental observations are compared with the results obtained from 2D and 3D CFD simulations. The simulated velocity components, pressure field, streamlines and air core dynamics along the atomizer axis are compared to previous research works and found satisfactory. The work has led to a novel approach in the design of pressure swirl atomizer.

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

PubMed

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

2017-06-13

We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

Alices in a nuclear Wonderland

NASA Astrophysics Data System (ADS)

Brown, Kate

2014-02-01

Denise Kiernan's The Girls of Atomic City tells the story of a dozen women who left rural America in the early 1940s and tumbled suddenly, like Alice down the rabbit hole, into the nascent US military-industrial complex, with all its regulations, factory discipline, dangers and surveillance.

Quantum Optics Models of EIT Noise and Power Broadening

NASA Astrophysics Data System (ADS)

Snider, Chad; Crescimanno, Michael; O'Leary, Shannon

2011-04-01

When two coherent beams of light interact with an atom they tend to drive the atom to a non-absorbing state through a process called Electromagnetically Induced Transparency (EIT). If the light's frequency dithers, the atom's state stochastically moves in and out of this non-absorbing state. We describe a simple quantum optics model of this process that captures the essential experimentally observed statistical features of this EIT noise, with a particular emphasis on understanding power broadening.

A combined Eulerian-volume of fraction-Lagrangian method for atomization simulation

NASA Technical Reports Server (NTRS)

Seung, S. P.; Chen, C. P.; Ziebarth, John P.

1994-01-01

The tracking of free surfaces between liquid and gas phases and analysis of the interfacial phenomena between the two during the atomization and breakup process of a liquid fuel jet is modeled. Numerical modeling of liquid-jet atomization requires the resolution of different conservation equations. Detailed formulation and validation are presented for the confined dam broken problem, the water surface problem, the single droplet problem, a jet breakup problem, and the liquid column instability problem.

The Pre-Service Science Teachers' Mental Models for Concept of Atoms and Learning Difficulties

ERIC Educational Resources Information Center

Kiray, Seyit Ahmet

2016-01-01

The purpose of this study is to reveal the pre-service science teachers' difficulties about the concept of atoms. The data was collected from two different sources: The Draw an Atom Test (DAAT) and face-to-face interviews. Draw an atom test (DAAT) were administered to the 142 science teacher candidates. To elaborate the results, the researcher…

Analysis of spatial correlations in a model two-dimensional liquid through eigenvalues and eigenvectors of atomic-level stress matrices.

PubMed

Levashov, V A; Stepanov, M G

2016-01-01

Considerations of local atomic-level stresses associated with each atom represent a particular approach to address structures of disordered materials at the atomic level. We studied structural correlations in a two-dimensional model liquid using molecular dynamics simulations in the following way. We diagonalized the atomic-level stress tensor of every atom and investigated correlations between the eigenvalues and orientations of the eigenvectors of different atoms as a function of distance between them. It is demonstrated that the suggested approach can be used to characterize structural correlations in disordered materials. In particular, we found that changes in the stress correlation functions on decrease of temperature are the most pronounced for the pairs of atoms with separation distance that corresponds to the first minimum in the pair density function. We also show that the angular dependencies of the stress correlation functions previously reported by Wu et al. [Phys. Rev. E 91, 032301 (2015)10.1103/PhysRevE.91.032301] do not represent the anisotropic Eshelby's stress fields, as it is suggested, but originate in the rotational properties of the stress tensors.

A constructive model potential method for atomic interactions

NASA Technical Reports Server (NTRS)

Bottcher, C.; Dalgarno, A.

1974-01-01

A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.

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.

Impact-parameter dependence of the energy loss of fast molecular clusters in hydrogen

NASA Astrophysics Data System (ADS)

Fadanelli, R. C.; Grande, P. L.; Schiwietz, G.

2008-03-01

The electronic energy loss of molecular clusters as a function of impact parameter is far less understood than atomic energy losses. For instance, there are no analytical expressions for the energy loss as a function of impact parameter for cluster ions. In this work, we describe two procedures to evaluate the combined energy loss of molecules: Ab initio calculations within the semiclassical approximation and the coupled-channels method using atomic orbitals; and simplified models for the electronic cluster energy loss as a function of the impact parameter, namely the molecular perturbative convolution approximation (MPCA, an extension of the corresponding atomic model PCA) and the molecular unitary convolution approximation (MUCA, a molecular extension of the previous unitary convolution approximation UCA). In this work, an improved ansatz for MPCA is proposed, extending its validity for very compact clusters. For the simplified models, the physical inputs are the oscillators strengths of the target atoms and the target-electron density. The results from these models applied to an atomic hydrogen target yield remarkable agreement with their corresponding ab initio counterparts for different angles between cluster axis and velocity direction at specific energies of 150 and 300 keV/u.

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

Studying the Consistency between and within the Student Mental Models for Atomic Structure

ERIC Educational Resources Information Center

Zarkadis, Nikolaos; Papageorgiou, George; Stamovlasis, Dimitrios

2017-01-01

Science education research has revealed a number of student mental models for atomic structure, among which, the one based on Bohr's model seems to be the most dominant. The aim of the current study is to investigate the coherence of these models when students apply them for the explanation of a variety of situations. For this purpose, a set of…

Metallic glass alloys of Zr, Ti, Cu and Ni

DOEpatents

Lin, X.; Peker, A.; Johnson, W.L.

1997-04-08

At least quaternary alloys form metallic glass upon cooling below the glass transition temperature at a rate less than 10{sup 3} K/s. Such alloys comprise titanium from 19 to 41 atomic percent, an early transition metal (ETM) from 4 to 21 atomic percent and copper plus a late transition metal (LTM) from 49 to 64 atomic percent. The ETM comprises zirconium and/or hafnium. The LTM comprises cobalt and/or nickel. The composition is further constrained such that the product of the copper plus LTM times the atomic proportion of LTM relative to the copper is from 2 to 14. The atomic percentage of ETM is less than 10 when the atomic percentage of titanium is as high as 41, and may be as large as 21 when the atomic percentage of titanium is as low as 24. Furthermore, when the total of copper and LTM are low, the amount of LTM present must be further limited. Another group of glass forming alloys has the formula (ETM{sub 1{minus}x}Ti{sub x}){sub a} Cu{sub b} (Ni{sub 1{minus}y}Co{sub y}){sub c} wherein x is from 0.1 to 0.3, y{center_dot}c is from 0 to 18, a is from 47 to 67, b is from 8 to 42, and c is from 4 to 37. This definition of the alloys has additional constraints on the range of copper content, b. 2 figs.

Metallic glass alloys of Zr, Ti, Cu and Ni

DOEpatents

Lin, Xianghong; Peker, Atakan; Johnson, William L.

1997-01-01

At least quaternary alloys form metallic glass upon cooling below the glass transition temperature at a rate less than 10.sup.3 K/s. Such alloys comprise titanium from 19 to 41 atomic percent, an early transition metal (ETM) from 4 to 21 atomic percent and copper plus a late transition metal (LTM) from 49 to 64 atomic percent. The ETM comprises zirconium and/or hafnium. The LTM comprises cobalt and/or nickel. The composition is further constrained such that the product of the copper plus LTM times the atomic proportion of LTM relative to the copper is from 2 to 14. The atomic percentage of ETM is less than 10 when the atomic percentage of titanium is as high as 41, and may be as large as 21 when the atomic percentage of titanium is as low as 24. Furthermore, when the total of copper and LTM are low, the amount of LTM present must be further limited. Another group of glass forming alloys has the formula (ETM.sub.1-x Ti.sub.x).sub.a Cu.sub.b (Ni.sub.1-y Co.sub.y).sub.c wherein x is from 0.1 to 0.3, y.cndot.c is from 0 to 18, a is from 47 to 67, b is from 8 to 42, and c is from 4 to 37. This definition of the alloys has additional constraints on the range of copper content, b.

New insights on the collisional escape of light neutrals from Mars

NASA Astrophysics Data System (ADS)

Gacesa, Marko; Zahnle, Kevin

2017-04-01

Photodissociative recombination (PDR) of atmospheric molecules on Mars is a major mechanism of production of hot (suprathermal) atoms with sufficient kinetic energy to either directly escape to space or to eject other atmospheric species. This collisional ejection mechanism is important for evaluating the escape rates of all light neutrals that are too heavy to escape via Jeans escape. In particular, it plays a role in estimating the total volume of escaped water constituents (i.e., O and H) from Mars, as well as influences evolution of the atmospheric [D]/[H] ratio1. We present revised estimates of total collisional escape rates of neutral light elements including H, He, and H2, based on recent (years 2015-2016) atmospheric density profiles obtained from the NASA Mars Atmosphere and Volatile Evolution (MAVEN) mission. We also estimate the contribution to the collisional escape from Energetic Neutral Atoms (ENAs) produced in charge-exchange of solar wind H+ and He+ ions with atmospheric gases2,3. Scattering of hot oxygen and atmospheric species of interest is modeled using fully-quantum reactive scattering formalism1,3. The escape rates are evaluated using a 1D model of the atmosphere supplemented with MAVEN measurements of the neutrals. Finally, new estimates of contributions of these non-thermal mechanisms to the estimated PDR escape rates from young Mars4 are presented. [1] M. Gacesa and V. Kharchenko, "Non-thermal escape of molecular hydrogen from Mars", Geophys. Res. Lett., 39, L10203 (2012). [2] N. Lewkow and V. Kharchenko, "Precipitation of Energetic Neutral Atoms and Escape Fluxes induced from the Mars Atmosphere", Astroph. J., 790, 98 (2014). [3] M. Gacesa, N. Lewkow, and V. Kharchenko, "Non-thermal production and escape of OH from the upper atmosphere of Mars", Icarus 284, 90 (2017). [4] J. Zhao, F. Tian, Y. Ni, and X. Huang, "DR-induced escape of O and C from early Mars", Icarus 284, 305 (2017).

Five-Year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Data Processing, Sky Maps, and Basic Results

NASA Technical Reports Server (NTRS)

Weiland, J.L.; Hill, R.S.; Odegard, 3.; Larson, D.; Bennett, C.L.; Dunkley, J.; Jarosik, N.; Page, L.; Spergel, D.N.; Halpern, M.;

Biophysical properties of normal and diseased renal glomeruli.

PubMed

Wyss, Hans M; Henderson, Joel M; Byfield, Fitzroy J; Bruggeman, Leslie A; Ding, Yaxian; Huang, Chunfa; Suh, Jung Hee; Franke, Thomas; Mele, Elisa; Pollak, Martin R; Miner, Jeffrey H; Janmey, Paul A; Weitz, David A; Miller, R Tyler

2011-03-01

The mechanical properties of tissues and cells including renal glomeruli are important determinants of their differentiated state, function, and responses to injury but are not well characterized or understood. Understanding glomerular mechanics is important for understanding renal diseases attributable to abnormal expression or assembly of structural proteins and abnormal hemodynamics. We use atomic force microscopy (AFM) and a new technique, capillary micromechanics, to measure the elastic properties of rat glomeruli. The Young's modulus of glomeruli was 2,500 Pa, and it was reduced to 1,100 Pa by cytochalasin and latunculin, and to 1,400 Pa by blebbistatin. Cytochalasin or latrunculin reduced the F/G actin ratios of glomeruli but did not disrupt their architecture. To assess glomerular biomechanics in disease, we measured the Young's moduli of glomeruli from two mouse models of primary glomerular disease, Col4a3(-/-) mice (Alport model) and Tg26(HIV/nl) mice (HIV-associated nephropathy model), at stages where glomerular injury was minimal by histopathology. Col4a3(-/-) mice express abnormal glomerular basement membrane proteins, and Tg26(HIV/nl) mouse podocytes have multiple abnormalities in morphology, adhesion, and cytoskeletal structure. In both models, the Young's modulus of the glomeruli was reduced by 30%. We find that glomeruli have specific and quantifiable biomechanical properties that are dependent on the state of the actin cytoskeleton and nonmuscle myosins. These properties may be altered early in disease and represent an important early component of disease. This increased deformability of glomeruli could directly contribute to disease by permitting increased distension with hemodynamic force or represent a mechanically inhospitable environment for glomerular cells.

Kinetics of Fast Atoms in the Terrestrial Atmosphere

NASA Technical Reports Server (NTRS)

Kharchenko, Vasili A.; Dalgarno, A.; Mellott, Mary (Technical Monitor)

2002-01-01

This report summarizes our investigations performed under NASA Grant NAG5-8058. The three-year research supported by the Geospace Sciences SR&T program (Ionospheric, Thermospheric, and Mesospheric Physics) has been designed to investigate fluxes of energetic oxygen and nitrogen atoms in the terrestrial thermosphere. Fast atoms are produced due to absorption of the solar radiation and due to coupling between the ionosphere and the neutral thermospheric gas. We have investigated the impact of hot oxygen and nitrogen atoms on the thermal balance, chemistry and radiation properties of the terrestrial thermosphere. Our calculations have been focused on the accurate quantitative description of the thermalization of O and N energetic atoms in collisions with atom and molecules of the ambient neutral gas. Upward fluxes of oxygen and nitrogen atoms, the rate of atmospheric heating by hot oxygen atoms, and the energy input into translational and rotational-vibrational degrees of atmospheric molecules have been evaluated. Altitude profiles of hot oxygen and nitrogen atoms have been analyzed and compared with available observational data. Energetic oxygen atoms in the terrestrial atmosphere have been investigated for decades, but insufficient information on the kinetics of fast atmospheric atoms has been a main obstacle for the interpretation of observational data and modeling of the hot geocorona. The recent development of accurate computational methods of the collisional kinetics is seen as an important step in the quantitative description of hot atoms in the thermosphere. Modeling of relaxation processes in the terrestrial atmosphere has incorporated data of recent observations, and theoretical predictions have been tested by new laboratory measurements.

Influence of inelastic Rydberg atom-atom collisional process on kinetic and optical properties of low-temperature laboratory and astrophysical plasmas

NASA Astrophysics Data System (ADS)

Klyucharev, A. N.; Bezuglov, N. N.; Mihajlov, A. A.; Ignjatović, Lj M.

2010-11-01

Elementary processes in plasma phenomena traditionally attract physicist's attention. The channel of charged-particle formation in Rydberg atom-atom thermal and sub-thermal collisions (the low temperature plasmas conditions) leads to creation of the molecular ions - associative ionization (AI). atomic ions - Penning-like ionization (PI) and the pair of the negative and positive ions. In our universe the chemical composition of the primordial gas consists mainly of Hydrogen and Helium (H, H-, H+, H2, He,He+). Hydrogen-like alkali-metal Lithium (Li, Li+,Li-) and combinations (HeH+, LiH-, LiH+). There is a wide range of plasma parameters in which the Rydberg atoms of the elements mentioned above make the dominant contribution to ionization and that process may be regarded as a prototype of the elementary process of light excitation energy transformation into electric one. The latest stochastic version of chemi-ionisation (AI+PI) on Rydberg atom-atom collisions extends the treatment of the "dipole resonant" model by taking into account redistribution of population over a range of Rydberg states prior to ionization. This redistribution is modelled as diffusion within the frame of stochastic dynamic of the Rydberg electron in the Rydberg energy spectrum. This may lead to anomalies of Rydberg atom spectra. Another result obtained in recent time is understanding that experimental results on chemi-ionization relate to the group of mixed Rydberg atom closed to the primary selected one. The Rydberg atoms ionisation theory today makes a valuable contribution in the deterministic and stochastic approaches correlation in atomic physic.

Effects of cavity-cavity interaction on the entanglement dynamics of a generalized double Jaynes-Cummings model

NASA Astrophysics Data System (ADS)

Pandit, Mahasweta; Das, Sreetama; Singha Roy, Sudipto; Shekhar Dhar, Himadri; Sen, Ujjwal

2018-02-01

We consider a generalized double Jaynes-Cummings model consisting of two isolated two-level atoms, each contained in a lossless cavity that interact with each other through a controlled photon-hopping mechanism. We analytically show that at low values of such a mediated cavity-cavity interaction, the temporal evolution of entanglement between the atoms, under the effects of cavity perturbation, exhibits the well-known phenomenon of entanglement sudden death (ESD). Interestingly, for moderately large interaction values, a complete preclusion of ESD is achieved, irrespective of its value in the initial atomic state. Our results provide a model to sustain entanglement between two atomic qubits, under the adverse effect of cavity induced perturbation, by introducing a non-intrusive inter-cavity photon exchange that can be physically realized through cavity-QED setups in contemporary experiments.

Treatment of atomic and molecular line blanketing by opacity sampling

NASA Technical Reports Server (NTRS)

Johnson, H. R.; Krupp, B. M.

1976-01-01

A sampling technique for treating the radiative opacity of large numbers of atomic and molecular lines in cool stellar atmospheres is subjected to several tests. In this opacity sampling (OS) technique, the global opacity is sampled at only a selected set of frequencies, and at each of these frequencies the total monochromatic opacity is obtained by summing the contribution of every relevant atomic and molecular line. In accord with previous results, we find that the structure of atmospheric models is accurately fixed by the use of 1000 frequency points, and 100 frequency points are adequate for many purposes. The effects of atomic and molecular lines are separately studied. A test model computed using the OS method agrees very well with a model having identical atmospheric parameters, but computed with the giant line (opacity distribution function) method.

Stochastic models for atomic clocks

NASA Technical Reports Server (NTRS)

Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.

1983-01-01

For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.

Spectral asymmetry of atoms in the van der Waals potential of an optical nanofiber

NASA Astrophysics Data System (ADS)

Patterson, B. D.; Solano, P.; Julienne, P. S.; Orozco, L. A.; Rolston, S. L.

2018-03-01

We measure the modification of the transmission spectra of cold 87Rb atoms in the proximity of an optical nanofiber (ONF). Van der Waals interactions between the atoms an the ONF surface decrease the resonance frequency of atoms closer to the surface. An asymmetric spectra of the atoms holds information of their spatial distribution around the ONF. We use a far-detuned laser beam coupled to the ONF to thermally excite atoms at the ONF surface. We study the change of transmission spectrum of these atoms as a function of heating laser power. A semiclassical phenomenological model for the thermal excitation of atoms in the atom-surface van der Waals bound states is in good agreement with the measurements. This result suggests that van der Waals potentials could be used to trap and probe atoms at few nanometers from a dielectric surface, a key tool for hybrid photonic-atomic quantum systems.

Temporal Evolution of the Nanostructure and Phase Compositions in a Model Ni-Al-Cr Alloy

NASA Technical Reports Server (NTRS)

Sudbrack, Chantal K.; Yoon, Kevin E.; Seidman, David N.; Seidman, David N.

2006-01-01

In a Ni-5.2 Al-14.2 Cr at.% alloy with moderate solute supersaturations and a very small gamma/gamma prime lattice parameter misfit, the nanostructural and compositional pathways during gamma prime(L12) precipitation at 873 K are investigated using atom-probe tomography, conventional transmission electron microscopy, and hardness measurements. Nucleation of high number densities (N(sub v) greater than 10(sup 23) per cubic meters) of solute-rich precipitates (mean radius = [R] = 0.75 nm), with a critical nucleus composition of Ni-18.3 plus or minus 0.9 Al-9.3 plus or minus 0.7 Cr at.%, initiates between 0.0833 and 0.167 h. With increasing aging time (a) the solute concentrations decay in spheroidal precipitates ([R] less than 10 nm); (b) the observed early-stage coalescence peaks at maximum N(sub v) in coincidence with the smallest interprecipitate spacing; and (c) the reaction enters a quasi-stationary regime where growth and coarsening operate concomitantly. During this quasi-stationary regime, the c (face-centered cubic)-matrix solute supersaturations decay with a power-law dependence of about -1/3, while the dependencies of [R] and N(sub v) are 0.29 plus or minus 0.05 and -0.64 plus or minus 0.06 at a coarsening rate slower than model predications. Coarsening models allow both equilibrium phase compositions to be determined from the compositional measurements. The observed early-stage coalescence is discussed in further detail.

Early stage aggregation of a coarse-grained model of polyglutamine

NASA Astrophysics Data System (ADS)

Haaga, Jason; Gunton, J. D.; Buckles, C. Nadia; Rickman, J. M.

2018-01-01

In this paper, we study the early stages of aggregation of a model of polyglutamine (polyQ) for different repeat lengths (number of glutamine amino acid groups in the chain). In particular, we use the Large-scale Atomic/Molecular Massively Parallel Simulator to study a generic coarse-grained model proposed by Bereau and Deserno. We focus on the primary nucleation mechanism involved and find that our results for the initial self-assembly process are consistent with the two-dimensional classical nucleation theory of Kashchiev and Auer. More specifically, we find that with decreasing supersaturation, the oligomer fibril (protofibril) transforms from a one-dimensional β sheet to two-, three-, and higher layer β sheets as the critical nucleus size increases. We also show that the results are consistent with several predictions of their theory, including the dependence of the critical nucleus size on the supersaturation. Our results for the time dependence of the mass aggregation are in reasonable agreement with an approximate analytical solution of the filament theory by Knowles and collaborators that corresponds to an additional secondary nucleation arising from filament fragmentation. Finally, we study the dependence of the critical nucleus size on the repeat length of polyQ. We find that for the larger length polyglutamine chain that we study, the critical nucleus is a monomer, in agreement with experiment and in contrast to the case for the smaller chain, for which the smallest critical nucleus size is four.

Energetic ion, atom, and molecule reactions and excitation in low-current H2 discharges: H(alpha) Doppler profiles.

PubMed

Petrović, Z Lj; Phelps, A V

2009-12-01

Absolute spectral emissivities for Doppler broadened H(alpha) profiles are measured and compared with predictions of energetic hydrogen ion, atom, and molecule behavior in low-current electrical discharges in H2 at very high electric field E to gas density N ratios E/N and low values of Nd , where d is the parallel-plate electrode separation. These observations reflect the energy and angular distributions for the excited atoms and quantitatively test features of multiple-scattering kinetic models in weakly ionized hydrogen in the presence of an electric field that are not tested by the spatial distributions of H(alpha) emission. Absolute spectral intensities agree well with predictions. Asymmetries in Doppler profiles observed parallel to the electric field at 4

Infrared dynamics of cold atoms on hot graphene membranes

NASA Astrophysics Data System (ADS)

Sengupta, Sanghita; Kotov, Valeri N.; Clougherty, Dennis P.

2016-06-01

We study the infrared dynamics of low-energy atoms interacting with a sample of suspended graphene at finite temperature. The dynamics exhibits severe infrared divergences order by order in perturbation theory as a result of the singular nature of low-energy flexural phonon emission. Our model can be viewed as a two-channel generalization of the independent boson model with asymmetric atom-phonon coupling. This allows us to take advantage of the exact nonperturbative solution of the independent boson model in the stronger channel while treating the weaker one perturbatively. In the low-energy limit, the exact solution can be viewed as a resummation (exponentiation) of the most divergent diagrams in the perturbative expansion. As a result of this procedure, we obtain the atom's Green function which we use to calculate the atom damping rate, a quantity equal to the quantum sticking rate. A characteristic feature of our results is that the Green's function retains a weak, infrared cutoff dependence that reflects the reduced dimensionality of the problem. As a consequence, we predict a measurable dependence of the sticking rate on graphene sample size. We provide detailed predictions for the sticking rate of atomic hydrogen as a function of temperature and sample size. The resummation yields an enhanced sticking rate relative to the conventional Fermi golden rule result (equivalent to the one-loop atom self-energy), as higher-order processes increase damping at finite temperature.

Deciphering chemical order/disorder and material properties at the single-atom level

DOE PAGES

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.; ...

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

A Eulerian-Lagrangian Model to Simulate Two-Phase/Particulate Flows

NASA Technical Reports Server (NTRS)

Apte, S. V.; Mahesh, K.; Lundgren, T.

2003-01-01

Figure 1 shows a snapshot of liquid fuel spray coming out of an injector nozzle in a realistic gas-turbine combustor. Here the spray atomization was simulated using a stochastic secondary breakup model (Apte et al. 2003a) with point-particle approximation for the droplets. Very close to the injector, it is observed that the spray density is large and the droplets cannot be treated as point-particles. The volume displaced by the liquid in this region is significant and can alter the gas-phase ow and spray evolution. In order to address this issue, one can compute the dense spray regime by an Eulerian-Lagrangian technique using advanced interface tracking/level-set methods (Sussman et al. 1994; Tryggvason et al. 2001; Herrmann 2003). This, however, is computationally intensive and may not be viable in realistic complex configurations. We therefore plan to develop a methodology based on Eulerian-Lagrangian technique which will allow us to capture the essential features of primary atomization using models to capture interactions between the fluid and droplets and which can be directly applied to the standard atomization models used in practice. The numerical scheme for unstructured grids developed by Mahesh et al. (2003) for incompressible flows is modified to take into account the droplet volume fraction. The numerical framework is directly applicable to realistic combustor geometries. Our main objectives in this work are: Develop a numerical formulation based on Eulerian-Lagrangian techniques with models for interaction terms between the fluid and particles to capture the Kelvin- Helmholtz type instabilities observed during primary atomization. Validate this technique for various two-phase and particulate flows. Assess its applicability to capture primary atomization of liquid jets in conjunction with secondary atomization models.

Interfacial mixing in high-energy-density matter with a multiphysics kinetic model

NASA Astrophysics Data System (ADS)

Haack, Jeffrey R.; Hauck, Cory D.; Murillo, Michael S.

2017-12-01

We have extended a recently developed multispecies, multitemperature Bhatnagar-Gross-Krook model [Haack et al., J. Stat. Phys. 168, 822 (2017), 10.1007/s10955-017-1824-9], to include multiphysics capabilities that enable modeling of a wider range of physical conditions. In terms of geometry, we have extended from the spatially homogeneous setting to one spatial dimension. In terms of the physics, we have included an atomic ionization model, accurate collision physics across coupling regimes, self-consistent electric fields, and degeneracy in the electronic screening. We apply the model to a warm dense matter scenario in which the ablator-fuel interface of an inertial confinement fusion target is heated, but for larger length and time scales and for much higher temperatures than can be simulated using molecular dynamics. Relative to molecular dynamics, the kinetic model greatly extends the temperature regime and the spatiotemporal scales over which we are able to model. In our numerical results we observe hydrogen from the ablator material jetting into the fuel during the early stages of the implosion and compare the relative size of various diffusion components (Fickean diffusion, electrodiffusion, and barodiffusion) that drive this process. We also examine kinetic effects, such as anisotropic distributions and velocity separation, in order to determine when this problem can be described with a hydrodynamic model.

The calculation of theoretical chromospheric models and the interpretation of the solar spectrum

NASA Technical Reports Server (NTRS)

Avrett, Eugene H.

1994-01-01

Since the early 1970s we have been developing the extensive computer programs needed to construct models of the solar atmosphere and to calculate detailed spectra for use in the interpretation of solar observations. This research involves two major related efforts: work by Avrett and Loeser on the Pandora computer program for non-LTE modeling of the solar atmosphere including a wide range of physical processes, and work by Kurucz on the detailed synthesis of the solar spectrum based on opacity data for over 58 million atomic and molecular lines. Our goals are to determine models of the various features observed on the sun (sunspots, different components of quiet and active regions, and flares) by means of physically realistic models, and to calculate detailed spectra at all wavelengths that match observations of those features. These two goals are interrelated: discrepancies between calculated and observed spectra are used to determine improvements in the structure of the models, and in the detailed physical processes used in both the model calculations and the spectrum calculations. The atmospheric models obtained in this way provide not only the depth variation of various atmospheric parameters, but also a description of the internal physical processes that are responsible for nonradiative heating, and for solar activity in general.

The calculation of theoretical chromospheric models and the interpretation of solar spectra from rockets and spacecraft

NASA Technical Reports Server (NTRS)

Avrett, Eugene H.

1993-01-01

Since the early 1970s we have been developing the extensive computer programs needed to construct models of the solar atmosphere and to calculate detailed spectra for use in the interpretation of solar observations. This research involves two major related efforts: work by Avrett and Loeser on the Pandora computer program for non-LTE modeling of the solar atmosphere including a wide range of physical processes, and work by Kurucz on the detailed synthesis of the solar spectrum based on opacity data for over 58 million atomic and molecular lines. Our goals are to determine models of the various features observed on the Sun (sunspots, different components of quiet and active regions, and flares) by means of physically realistic models, and to calculate detailed spectra at all wavelengths that match observations of those features. These two goals are interrelated: discrepancies between calculated and observed spectra are used to determine improvements in the structure of the models, and in the detailed physical processes used in both the model calculations and the spectrum calculations. The atmospheric models obtained in this way provide not only the depth variation of various atmospheric parameters, but also a description of the internal physical processes that are responsible for non-radiative heating, and for solar activity in general.

Gas-phase reactions of carbon dioxide with atomic transition-metal and main-group cations: room-temperature kinetics and periodicities in reactivity.

PubMed

Koyanagi, Gregory K; Bohme, Diethard K

2006-02-02

The chemistry of carbon dioxide has been surveyed systematically with 46 atomic cations at room temperature using an inductively-coupled plasma/selected-ion flow tube (ICP/SIFT) tandem mass spectrometer. The atomic cations were produced at ca. 5500 K in an ICP source and allowed to cool radiatively and to thermalize by collisions with Ar and He atoms prior to reaction downstream in a flow tube in helium buffer gas at 0.35 +/- 0.01 Torr and 295 +/- 2 K. Rate coefficients and products were measured for the reactions of first-row atomic ions from K(+) to Se(+), of second-row atomic ions from Rb(+) to Te(+) (excluding Tc(+)), and of third-row atomic ions from Cs(+) to Bi(+). CO(2) was found to react in a bimolecular fashion by O atom transfer only with 9 early transition-metal cations: the group 3 cations Sc(+), Y(+), and La(+), the group 4 cations Ti(+), Zr(+), and Hf(+), the group 5 cations Nb(+) and Ta(+), and the group 6 cation W(+). Electron spin conservation was observed to control the kinetics of O atom transfer. Addition of CO(2) was observed for the remaining 37 cations. While the rate of addition was not measurable some insight was obtained into the standard free energy change, DeltaG(o), for CO(2) ligation from equilibrium constant measurements. A periodic variation in DeltaG(o) was observed for first row cations that is consistent with previous calculations of bond energies D(0)(M(+)-CO(2)). The observed trends in D(0) and DeltaG(o) are expected from the variation in electrostatic attraction between M(+) and CO(2) which follows the trend in atomic-ion size and the trend in repulsion between the orbitals of the atomic cations and the occupied orbitals of CO(2). Higher-order CO(2) cluster ions with up to four CO(2) ligands also were observed for 24 of the atomic cations while MO(2)(+) dioxide formation by sequential O atom transfer was seen only with Hf(+), Nb(+), Ta(+), and W(+).

Femtosecond two-photon photoassociation of hot magnesium atoms: A quantum dynamical study using thermal random phase wavefunctions

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kosloff, Ronnie; Tomza, Michał; Skomorowski, Wojciech; Pawłowski, Filip; Moszynski, Robert; Rybak, Leonid; Levin, Liat; Amitay, Zohar; Berglund, J. Martin; Reich, Daniel M.; Koch, Christiane P.

2013-10-01

Two-photon photoassociation of hot magnesium atoms by femtosecond laser pulses, creating electronically excited magnesium dimer molecules, is studied from first principles, combining ab initio quantum chemistry and molecular quantum dynamics. This theoretical framework allows for rationalizing the generation of molecular rovibrational coherence from thermally hot atoms [L. Rybak, S. Amaran, L. Levin, M. Tomza, R. Moszynski, R. Kosloff, C. P. Koch, and Z. Amitay, Phys. Rev. Lett. 107, 273001 (2011)]. Random phase thermal wavefunctions are employed to model the thermal ensemble of hot colliding atoms. Comparing two different choices of basis functions, random phase wavefunctions built from eigenstates are found to have the fastest convergence for the photoassociation yield. The interaction of the colliding atoms with a femtosecond laser pulse is modeled non-perturbatively to account for strong-field effects.

Restoring the lattice of Si-based atom probe reconstructions for enhanced information on dopant positioning.

PubMed

Breen, Andrew J; Moody, Michael P; Ceguerra, Anna V; Gault, Baptiste; Araullo-Peters, Vicente J; Ringer, Simon P

2015-12-01

The following manuscript presents a novel approach for creating lattice based models of Sb-doped Si directly from atom probe reconstructions for the purposes of improving information on dopant positioning and directly informing quantum mechanics based materials modeling approaches. Sophisticated crystallographic analysis techniques are used to detect latent crystal structure within the atom probe reconstructions with unprecedented accuracy. A distortion correction algorithm is then developed to precisely calibrate the detected crystal structure to the theoretically known diamond cubic lattice. The reconstructed atoms are then positioned on their most likely lattice positions. Simulations are then used to determine the accuracy of such an approach and show that improvements to short-range order measurements are possible for noise levels and detector efficiencies comparable with experimentally collected atom probe data. Copyright © 2015 Elsevier B.V. All rights reserved.

NLTE atomic kinetics modeling in ICF target simulations

NASA Astrophysics Data System (ADS)

Patel, Mehul V.; Mauche, Christopher W.; Scott, Howard A.; Jones, Ogden S.; Shields, Benjamin T.

2017-10-01

Radiation hydrodynamics (HYDRA) simulations using recently developed 1D spherical and 2D cylindrical hohlraum models have enabled a reassessment of the accuracy of energetics modeling across a range of NIF target configurations. Higher-resolution hohlraum calculations generally find that the X-ray drive discrepancies are greater than previously reported. We identify important physics sensitivities in the modeling of the NLTE wall plasma and highlight sensitivity variations between different hohlraum configurations (e.g. hohlraum gas fill). Additionally, 1D capsule only simulations show the importance of applying a similar level of rigor to NLTE capsule ablator modeling. Taken together, these results show how improved target performance predictions can be achieved by performing inline atomic kinetics using more complete models for the underlying atomic structure and transitions. Prepared by LLNL under Contract DE-AC52-07NA27344.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

Good scientists and honest people

NASA Astrophysics Data System (ADS)

Robinson, Andrew

2014-06-01

In early 1948, less than three years after the end of the Second World War in Europe, Werner Heisenberg - the Nobel laureate and physicist leader of the failed German atomic bomb project - was invited to the UK as part of an attempt to repair relations between British and German physicists.

Acoustic effects of sprays

NASA Technical Reports Server (NTRS)

Pindera, Maciej Z.; Przekwas, Andrzej J.

1994-01-01

Since the early 1960's, it has been known that realistic combustion models for liquid fuel rocket engines should contain at least a rudimentary treatment of atomization and spray physics. This is of particular importance in transient operations. It has long been recognized that spray characteristics and droplet vaporization physics play a fundamental role in determining the stability behavior of liquid fuel rocket motors. This paper gives an overview of work in progress on design of a numerical algorithm for practical studies of combustion instabilities in liquid rocket motors. For flexibility, the algorithm is composed of semi-independent solution modules, accounting for different physical processes. Current findings are report and future work is indicated. The main emphasis of this research is the development of an efficient treatment to interactions between acoustic fields and liquid fuel/oxidizer sprays.

Towards quantum chemistry on a quantum computer.

PubMed

Lanyon, B P; Whitfield, J D; Gillett, G G; Goggin, M E; Almeida, M P; Kassal, I; Biamonte, J D; Mohseni, M; Powell, B J; Barbieri, M; Aspuru-Guzik, A; White, A G

2010-02-01

Exact first-principles calculations of molecular properties are currently intractable because their computational cost grows exponentially with both the number of atoms and basis set size. A solution is to move to a radically different model of computing by building a quantum computer, which is a device that uses quantum systems themselves to store and process data. Here we report the application of the latest photonic quantum computer technology to calculate properties of the smallest molecular system: the hydrogen molecule in a minimal basis. We calculate the complete energy spectrum to 20 bits of precision and discuss how the technique can be expanded to solve large-scale chemical problems that lie beyond the reach of modern supercomputers. These results represent an early practical step toward a powerful tool with a broad range of quantum-chemical applications.

Design rules for biomolecular adhesion: lessons from force measurements.

PubMed

Leckband, Deborah

2010-01-01

Cell adhesion to matrix, other cells, or pathogens plays a pivotal role in many processes in biomolecular engineering. Early macroscopic methods of quantifying adhesion led to the development of quantitative models of cell adhesion and migration. The more recent use of sensitive probes to quantify the forces that alter or manipulate adhesion proteins has revealed much greater functional diversity than was apparent from population average measurements of cell adhesion. This review highlights theoretical and experimental methods that identified force-dependent molecular properties that are central to the biological activity of adhesion proteins. Experimental and theoretical methods emphasized in this review include the surface force apparatus, atomic force microscopy, and vesicle-based probes. Specific examples given illustrate how these tools have revealed unique properties of adhesion proteins and their structural origins.

Roles of Vacancy/Interstitial Diffusion and Segregation in the Microchemistry at Grain Boundaries of Irradiated Fe-Cr-Ni alloys

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

Yang, Ying; Field, Kevin G.; Allen, Todd R.

2016-02-23

A detailed analysis of the diffusion fluxes near and at grain boundaries of irradiated Fe–Cr–Ni alloys, induced by preferential atom-vacancy and atom-interstitial coupling, is presented. The diffusion flux equations were based on the Perks model formulated through the linear theory of the thermodynamics of irreversible processes. The preferential atom-vacancy coupling was described by the mobility model, whereas the preferential atom-interstitial coupling was described by the interstitial binding model. The composition dependence of the thermodynamic factor was modeled using the CALPHAD approach. The calculated fluxes up to 10 dpa suggested the dominant diffusion mechanism for chromium and iron is via vacancy,more » while that for nickel can swing from the vacancy to the interstitial dominant mechanism. The diffusion flux in the vicinity of a grain boundary was found to be greatly modified by the segregation induced by irradiation, leading to the oscillatory behavior of alloy compositions in this region.« less

Detecting an atomic clock frequency anomaly using an adaptive Kalman filter algorithm

NASA Astrophysics Data System (ADS)

Song, Huijie; Dong, Shaowu; Wu, Wenjun; Jiang, Meng; Wang, Weixiong

2018-06-01

The abnormal frequencies of an atomic clock mainly include frequency jump and frequency drift jump. Atomic clock frequency anomaly detection is a key technique in time-keeping. The Kalman filter algorithm, as a linear optimal algorithm, has been widely used in real-time detection for abnormal frequency. In order to obtain an optimal state estimation, the observation model and dynamic model of the Kalman filter algorithm should satisfy Gaussian white noise conditions. The detection performance is degraded if anomalies affect the observation model or dynamic model. The idea of the adaptive Kalman filter algorithm, applied to clock frequency anomaly detection, uses the residuals given by the prediction for building ‘an adaptive factor’ the prediction state covariance matrix is real-time corrected by the adaptive factor. The results show that the model error is reduced and the detection performance is improved. The effectiveness of the algorithm is verified by the frequency jump simulation, the frequency drift jump simulation and the measured data of the atomic clock by using the chi-square test.

Comment on atomic independent-particle models

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

Doda, D.D.; Gravey, R.H.; Green, A.E.S.

1975-08-01

The Hartree-Fock-Slater (HFS) independent-particle model in the form developed by Hermann and Skillman (HS) and the Green, Sellin, and Zachor (GSZ) analytic independent-particle model are being used for many types of applications of atomic theory to avoid cumbersome, albeit more rigorous, many-body calculations. The single-electron eigenvalues obtained with these models are examined and it is found that the GSZ model is capable of yielding energy eigenvalues for valence electrons which are substantially closer to experimental values than are the results of HS-HFS calculations. With the aid of an analytic representation of the equivalent HS-HFS screening function, the difficulty with thismore » model is identified as a weakness of the potential in the neighborhood of the valence shell. Accurate representations of valence states are important in most atomic applications of the independent-particle model. (auth)« less

Effective Hubbard model for Helium atoms adsorbed on a graphite

NASA Astrophysics Data System (ADS)

Motoyama, Yuichi; Masaki-Kato, Akiko; Kawashima, Naoki

Helium atoms adsorbed on a graphite is a two-dimensional strongly correlated quantum system and it has been an attractive subject of research for a long time. A helium atom feels Lennard-Jones like potential (Aziz potential) from another one and corrugated potential from the graphite. Therefore, this system may be described by a hardcore Bose Hubbard model with the nearest neighbor repulsion on the triangular lattice, which is the dual lattice of the honeycomb lattice formed by carbons. A Hubbard model is easier to simulate than the original problem in continuous space, but we need to know the model parameters of the effective model, hopping constant t and interaction V. In this presentation, we will present an estimation of the model parameters from ab initio quantum Monte Carlo calculation in continuous space in addition to results of quantum Monte Carlo simulation for an obtained discrete model.

Gaussian approximation potential modeling of lithium intercalation in carbon nanostructures

NASA Astrophysics Data System (ADS)

Fujikake, So; Deringer, Volker L.; Lee, Tae Hoon; Krynski, Marcin; Elliott, Stephen R.; Csányi, Gábor

2018-06-01

We demonstrate how machine-learning based interatomic potentials can be used to model guest atoms in host structures. Specifically, we generate Gaussian approximation potential (GAP) models for the interaction of lithium atoms with graphene, graphite, and disordered carbon nanostructures, based on reference density functional theory data. Rather than treating the full Li-C system, we demonstrate how the energy and force differences arising from Li intercalation can be modeled and then added to a (prexisting and unmodified) GAP model of pure elemental carbon. Furthermore, we show the benefit of using an explicit pair potential fit to capture "effective" Li-Li interactions and to improve the performance of the GAP model. This provides proof-of-concept for modeling guest atoms in host frameworks with machine-learning based potentials and in the longer run is promising for carrying out detailed atomistic studies of battery materials.

Student Misapplication of a Gas-Like Model to Explain Particle Movement in Heated Solids: Implications for Curriculum and Instruction towards Students' Creation and Revision of Accurate Explanatory Models

ERIC Educational Resources Information Center

Bouwma-Gearhart, Jana; Stewart, James; Brown, Keffrelyn

2009-01-01

Understanding the particulate nature of matter (PNM) is vital for participating in many areas of science. We assessed 11 students' atomic/molecular-level explanations of real-world phenomena after their participation in a modelling-based PNM unit. All 11 students offered a scientifically acceptable model regarding atomic/molecular behaviour in…

Development of quantitative atomic modeling for tungsten transport study using LHD plasma with tungsten pellet injection

NASA Astrophysics Data System (ADS)

Murakami, I.; Sakaue, H. A.; Suzuki, C.; Kato, D.; Goto, M.; Tamura, N.; Sudo, S.; Morita, S.

2015-09-01

Quantitative tungsten study with reliable atomic modeling is important for successful achievement of ITER and fusion reactors. We have developed tungsten atomic modeling for understanding the tungsten behavior in fusion plasmas. The modeling is applied to the analysis of tungsten spectra observed from plasmas of the large helical device (LHD) with tungsten pellet injection. We found that extreme ultraviolet (EUV) emission of W24+ to W33+ ions at 1.5-3.5 nm are sensitive to electron temperature and useful to examine the tungsten behavior in edge plasmas. We can reproduce measured EUV spectra at 1.5-3.5 nm by calculated spectra with the tungsten atomic model and obtain charge state distributions of tungsten ions in LHD plasmas at different temperatures around 1 keV. Our model is applied to calculate the unresolved transition array (UTA) seen at 4.5-7 nm tungsten spectra. We analyze the effect of configuration interaction on population kinetics related to the UTA structure in detail and find the importance of two-electron-one-photon transitions between 4p54dn+1- 4p64dn-14f. Radiation power rate of tungsten due to line emissions is also estimated with the model and is consistent with other models within factor 2.

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

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

Defining Tropospheric Chemistry As A Heterogeneous Ensemble Of Reactive Air Parcels

NASA Astrophysics Data System (ADS)

Prather, M. J.; Zhu, X.; Flynn, C.; Mao, J.; Strode, S. A.; Steenrod, S. D.; Strahan, S. E.; Lamarque, J. F.; Fiore, A. M.; Horowitz, L. W.; Shindell, D. T.; Murray, L. T.

2016-12-01

Two major challenges in model-measurement comparisons have been: Which measurements are the most important to match? At what level do models need to simulate the variegated fine structures observed in trace gases and aerosols? This talk presents a novel approach for evaluating high-resolution global chemistry models (1/2 to 1 deg) that is integral to NASA's Atmospheric Tomography (ATom) mission. The approach seeks to develop a chemical climatology for tropospheric regions rather than just event-based testing of specific observations. It enables chemistry-climate models to be readily compared and more severely tested with observations. It uses the reactivity of air parcels (e.g., loss of methane, production and loss of ozone) to weight each parcel in terms of its importance in controlling the two most important chemically reactive greenhouse gases. It looks at the entire statistical distribution of air parcels in terms of a chemical phase space for those species that control the reactivity (e.g., O3, H2O, CH4, CO, NOx, HNO3, HNO4, PAN, CH3NO3, HCHO, HOOH, CH3OOH, C2H6, C3H6O, and other VOCs when present in sufficiently large abundances). It builds statistics of chemically extreme air parcels such as pollution layers to determine if a model failure to match such cases affects the overall reactivity of the region. This approach was designed for the ATom in situ measurements using the DC-8 to slice through the middle of the Pacific and Atlantic Ocean basins each season. The ATom payload will measure the above key trace gases and many other gases and aerosols in every designated air parcel (i.e., 10-sec averages). The first ATom measurements will not be available until mid-2017 and this presentation shows how this climatology looks when sampled with different models. Six global chemistry models have simulated one day in August (no particular year), and we sample all six showing how the 2D probability density plots highlight different regions when weighted by chemical reactivity. These models pre-simulation of ATom provide a target for the ATom measurements. The models also enable us to estimate the representativeness of ATom's single tomographic slice down the ocean basins, and therefore just how well we can observationally determine this chemical climatology of the reactivity of the troposphere.

Free-free opacity in dense plasmas with an average atom model

DOE PAGES

Shaffer, Nathaniel R.; Ferris, Natalie G.; Colgan, James Patrick; ...

2017-02-28

A model for the free-free opacity of dense plasmas is presented. The model uses a previously developed average atom model, together with the Kubo-Greenwood model for optical conductivity. This, in turn, is used to calculate the opacity with the Kramers-Kronig dispersion relations. Furthermore, comparisons to other methods for dense deuterium results in excellent agreement with DFT-MD simulations, and reasonable agreement with a simple Yukawa screening model corrected to satisfy the conductivity sum rule.

Free-free opacity in dense plasmas with an average atom model

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

Shaffer, Nathaniel R.; Ferris, Natalie G.; Colgan, James Patrick

A model for the free-free opacity of dense plasmas is presented. The model uses a previously developed average atom model, together with the Kubo-Greenwood model for optical conductivity. This, in turn, is used to calculate the opacity with the Kramers-Kronig dispersion relations. Furthermore, comparisons to other methods for dense deuterium results in excellent agreement with DFT-MD simulations, and reasonable agreement with a simple Yukawa screening model corrected to satisfy the conductivity sum rule.

A Framework to Learn Physics from Atomically Resolved Images

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

Vlcek, L.; Maksov, A.; Pan, M.

Here, we present a generalized framework for physics extraction, i.e., knowledge, from atomically resolved images, and show its utility by applying it to a model system of segregation of chalcogen atoms in an FeSe 0.45Te 0.55 superconductor system. We emphasize that the framework can be used for any imaging data for which a generative physical model exists. Consider that a generative physical model can produce a very large number of configurations, not all of which are observable. By applying a microscope function to a sub-set of this generated data, we form a simulated dataset on which statistics can be computed.

Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics.

PubMed

Rudik, Anastasia V; Dmitriev, Alexander V; Lagunin, Alexey A; Filimonov, Dmitry A; Poroikov, Vladimir V

2016-01-01

The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site of a molecule at which a particular metabolic reaction occurs could be used as a starting point for metabolite identification. The prediction of the site of metabolism does not always correspond to the particular atom that is modified by the enzyme but rather is often associated with a group of atoms. To overcome this problem, we propose to operate with the term "reacting atom", corresponding to a single atom in the substrate that is modified during the biotransformation reaction. The prediction of the reacting atom(s) in a molecule for the major classes of biotransformation reactions is necessary to generate drug metabolites. Substrates of the major human cytochromes P450 and UDP-glucuronosyltransferases from the Biovia Metabolite database were divided into nine groups according to their reaction classes, which are aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation. Each training set consists of positive and negative examples of structures with one labelled atom. In the positive examples, the labelled atom is the reacting atom of a particular reaction that changed adjacency. Negative examples represent non-reacting atoms of a particular reaction. We used Labelled Multilevel Neighbourhoods of Atoms descriptors for the designation of reacting atoms. A Bayesian-like algorithm was applied to estimate the structure-activity relationships. The average invariant accuracy of prediction obtained in leave-one-out and 20-fold cross-validation procedures for five human isoforms of cytochrome P450 and all isoforms of UDP-glucuronosyltransferase varies from 0.86 to 0.99 (0.96 on average). We report that reacting atoms may be predicted with reasonable accuracy for the major classes of metabolic reactions-aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation. The proposed method is implemented as a freely available web service at http://www.way2drug.com/RA and may be used for the prediction of the most probable biotransformation reaction(s) and the appropriate reacting atoms in drug-like compounds.Graphical abstract.

Surface structure and chemistry of Pt/Cu/Pt(1 1 1) near surface alloy model catalyst in CO

NASA Astrophysics Data System (ADS)

Zeng, Shibi; Nguyen, Luan; Cheng, Fang; Liu, Lacheng; Yu, Ying; Tao, Franklin (Feng)

2014-11-01

Near surface alloy (NSA) model catalyst Pt/Cu/Pt(1 1 1) was prepared on Pt(1 1 1) through a controlled vapor deposition of Cu atoms. Different coordination environments of Pt atoms of the topmost Pt layer with the underneath Cu atoms in the subsurface result in different local electronic structures of surface Pt atoms. Surface structure and chemistry of the NAS model catalyst in Torr pressure of CO were studied with high pressure scanning tunneling microscopy (HP-STM) and ambient pressure X-ray photoelectron spectroscopy (AP-XPS). In Torr pressure of CO, the topmost Pt layer of Pt/Cu/Pt(1 1 1) is restructured to thin nanoclusters with size of about 1 nm. Photoemission feature of O 1s of CO on Pt/Cu/Pt(1 1 1) suggests CO adsorbed on both edge and surface of these formed nanoclusters. This surface is active for CO oxidation. Atomic layers of carbon are formed on Pt/Cu/Pt(1 1 1) at 573 K in 2 Torr of CO.

Structure and property of metal melt I: The number of residual bonds after solid-liquid phase changes

NASA Astrophysics Data System (ADS)

Mi, Guangbao; Li, Peijie; He, Liangju

2010-09-01

Based on the mechanism of metal solid-liquid phase change and the theory of liquid metal’s micro-inhomogeneity, a physical model is established between latent heats of fusion and vaporization and the numbers of residual bonds and short-range ordered atoms at the melting point inside a metal melt. Meanwhile, the mathematical derivation and proof are also offered. This model produces the numbers of residual bonds and short-range ordered atoms after the solid-liquid phase change only by using basic parameters and thermophysical properties of the crystal structure. Therefore, it presents a more effective way to analyze the melt’s structural information. By using this model, this study calculates the numbers of residual bonds and short-range ordered atoms in Al and Ni melts. The calculated results are consistent with the experimental results. Simultaneously, this study discusses the atomic number’s influence on the numbers of residual bonds and short-range ordered atoms in the melts within the first (IA) and second main group (IIA) elements.

Frozen lattice and absorptive model for high angle annular dark field scanning transmission electron microscopy: A comparison study in terms of integrated intensity and atomic column position measurement.

PubMed

Alania, M; Lobato, I; Van Aert, S

2018-01-01

In this paper, both the frozen lattice (FL) and the absorptive potential (AP) approximation models are compared in terms of the integrated intensity and the precision with which atomic columns can be located from an image acquired using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM). The comparison is made for atoms of Cu, Ag, and Au. The integrated intensity is computed for both an isolated atomic column and an atomic column inside an FCC structure. The precision has been computed using the so-called Cramér-Rao Lower Bound (CRLB), which provides a theoretical lower bound on the variance with which parameters can be estimated. It is shown that the AP model results into accurate measurements for the integrated intensity only for small detector ranges under relatively low angles and for small thicknesses. In terms of the attainable precision, both methods show similar results indicating picometer range precision under realistic experimental conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Microfabricated Waveguide Atom Traps.

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

Jau, Yuan-Yu

A nanoscale , microfabricated waveguide structure can in - principle be used to trap atoms in well - defined locations and enable strong photon-atom interactions . A neutral - atom platform based on this microfabrication technology will be prealigned , which is especially important for quantum - control applications. At present, there is still no reported demonstration of evanescent - field atom trapping using a microfabricated waveguide structure. We described the capabilities established by our team for future development of the waveguide atom - trapping technology at SNL and report our studies to overcome the technical challenges of loading coldmore » atoms into the waveguide atom traps, efficient and broadband optical coupling to a waveguide, and the waveguide material for high - power optical transmission. From the atomic - physics and the waveguide modeling, w e have shown that a square nano-waveguide can be utilized t o achieve better atomic spin squeezing than using a nanofiber for first time.« less

Supporting Students in Learning with Multiple Representation to Improve Student Mental Models on Atomic Structure Concepts

ERIC Educational Resources Information Center

Sunyono; Yuanita, L.; Ibrahim, M.

2015-01-01

The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…

Atomic temporal interval relations in branching time: calculation and application

NASA Astrophysics Data System (ADS)

Anger, Frank D.; Ladkin, Peter B.; Rodriguez, Rita V.

1991-03-01

A practical method of reasoning about intervals in a branching-time model which is dense, unbounded, future-branching, without rejoining branches is presented. The discussion is based on heuristic constraint- propagation techniques using the relation algebra of binary temporal relations among the intervals over the branching-time model. This technique has been applied with success to models of intervals over linear time by Allen and others, and is of cubic-time complexity. To extend it to branding-time models, it is necessary to calculate compositions of the relations; thus, the table of compositions for the 'atomic' relations is computed, enabling the rapid determination of the composition of arbitrary relations, expressed as disjunctions or unions of the atomic relations.

Studies for the Loss of Atomic and Molecular Species from Io

NASA Technical Reports Server (NTRS)

Smyth, William H.

1998-01-01

Updated neutral emission rates for electron impact excitation of atomic oxygen and sulfur based upon the Collisional Radiative Equilibrium (COREQ) model have been incorporated in the neutral cloud models. An empirical model for the Io plasma torus wake has also been added in the neutral cloud model to describe important enhancements in the neutral emission rates and lifetime rates in this spatial region. New insights into Io's atmosphere and its interaction with the plasma torus are discussed. These insights are based upon an initial comparison of simultaneous lo observations on October 14, 1997, for [0I] 6300 Angstrom emissions acquired by groundbased facilities and several ultraviolet emissions acquired by HST/STIS in the form of high-spatial- resolution images for atomic oxygen and sulfur.

Accelerated procedure to solve kinetic equation for neutral atoms in a hot plasma

NASA Astrophysics Data System (ADS)

Tokar, Mikhail Z.

2017-12-01

The recombination of plasma charged components, electrons and ions of hydrogen isotopes, on the wall of a fusion reactor is a source of neutral molecules and atoms, recycling back into the plasma volume. Here neutral species participate, in particular, in charge-exchange (c-x) collisions with the plasma ions and, as a result, atoms of high energies with chaotically directed velocities are generated. Some fraction of these hot atoms hit the wall. Statistical Monte Carlo methods normally used to model c-x atoms are too time consuming for reasonably small level of accident errors and extensive parameter studies are problematic. By applying pass method to evaluate integrals from functions, including the ion velocity distribution, an iteration approach to solve one-dimensional kinetic equation [1], being alternative to Monte Carlo procedure, has been tremendously accelerated, at least by a factor of 30-50 [2]. Here this approach is developed further to solve the 2-D kinetic equation, applied to model the transport of c-x atoms in the vicinity of an opening in the wall, e.g., the entrance of the duct guiding to a diagnostic installation. This is necessary to determine firmly the energy spectrum of c-x atoms penetrating into the duct and to assess the erosion of the installation there. The results of kinetic modeling are compared with those obtained with the diffusion description for c-x atoms, being strictly relevant under plasma conditions of low temperature and high density, where the mean free path length between c-x collisions is much smaller than that till the atom ionization by electrons. It is demonstrated that the previous calculations [3], done with the diffusion approximation for c-x atoms, overestimate the erosion rate of Mo mirrors in a reactor by a factor of 3 compared to the result of the present kinetic study.

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

Geometric Electron Models.

ERIC Educational Resources Information Center

Nika, G. Gerald; Parameswaran, R.

1997-01-01

Describes a visual approach for explaining the filling of electrons in the shells, subshells, and orbitals of the chemical elements. Enables students to apply the principles of atomic electron configuration while using manipulatives to model the building up of electron configurations as the atomic numbers of elements increase on the periodic…

An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

NASA Astrophysics Data System (ADS)

Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.

2013-12-01

In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations to find which is the closest atom containing an arbitrary point in space. Atom sizes are according to the corresponding van der Waals radii. Restrictions: The geometrical model presented here does not include the chromosome organization level but it could be easily build up by using fragments of the 30 nm chromatin fiber. Unusual features: To our knowledge, this is the first open source atomic-resolution DNA geometrical model developed for DNA-radiation interaction Monte Carlo simulations. In our tests, the current model took into account the explicit position of about 56×106 atoms, although the user may enhance this amount according to the necessities. Running time: This subroutine can process about 2 million points within a few minutes in a typical current computer.

Quantum dynamics of a BEC interacting with a single-mode quantized field under the influence of a dissipation process: thermal and squeezed vacuum reservoirs

NASA Astrophysics Data System (ADS)

Ghasemian, E.; Tavassoly, M. K.

2017-09-01

In this paper we consider a system consisting of a number of two-level atoms in a Bose-Einstein condensate (BEC) and a single-mode quantized field, which interact with each other in the presence of two different damping sources, i.e. cavity and atomic reservoirs. The reservoirs which we consider here are thermal and squeezed vacuum ones corresponding to field and atom modes. Strictly speaking, by considering both types of reservoirs for each of the atom and field modes, we investigate the quantum dynamics of the interacting bosons in the system. Then, via solving the quantum Langevin equations for such a dissipative BEC system, we obtain analytical expressions for the time dependence of atomic population inversion, mean atom as well as photon number and quadrature squeezing in the field and atom modes. Our investigations demonstrate that for modeling the real physical systems, considering the dissipation effects is essential. Also, numerical calculations which are presented show that the atomic population inversion, the mean number of atoms in the BEC and the photons in the cavity possess damped oscillatory behavior due to the presence of reservoirs. In addition, non-classical squeezing effects in the field quadrature can be observed especially when squeezed vacuum reservoirs are taken into account. As an outstanding property of this model, we may refer to the fact that one can extract the atom-field coupling constant from the frequency of oscillations in the mentioned quantities such as atomic population inversion.

Analytical Model of the Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions for Various Acoustic-Atomic Force Microscopies

NASA Technical Reports Server (NTRS)

Cantrell, John H., Jr.; Cantrell, Sean A.

2008-01-01

A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.

Electron-impact ionization of atomic hydrogen at incident electron energies of 15.6, 17.6, 25, and 40 eV

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

Childers, J. G.; James, K. E.; Hughes, M.

2003-09-01

Absolute doubly differential cross sections for the electron-impact ionization of atomic hydrogen have been measured from near threshold to intermediate energies. The measurements are calibrated to the well-established, accurate differential cross section for electron-impact excitation of the atomic hydrogen transition H(1{sup 2}S{yields}2{sup 2}S+2{sup 2}P). In these experiments background secondary electrons are suppressed by moving the atomic hydrogen target source to and from the collision region. Measurements cover the incident electron energy range of 14.6-40 eV, for scattering angles of 10 degree sign -120 degree sign and are found to be in very good agreement with the results of the mostmore » advanced theoretical models--the convergent close-coupling model and the exterior complex scaling model.« less

Overview of the 1986--1987 atomic mass predictions

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

Haustein, P.E.

1988-07-01

The need for a comprehensive update of earlier sets of atomic mass predictions is documented. A project that grew from this need and which resulted in the preparation of the 1986--1987 Atomic Mass Predictions is summarized. Ten sets of new mass predictions and expository text from a variety of types of mass models are combined with the latest evaluation of experimentally determined atomic masses. The methodology employed in constructing these mass predictions is outlined. The models are compared with regard to their reproduction of the experimental mass surface and their use of varying numbers of adjustable parameters. Plots are presented,more » for each set of predictions, of differences between model calculations and the measured masses. These plots may be used to estimate the reliability of the new mass predictions in unmeasured regions that border the experimetally known mass surface. copyright 1988 Academic Press, Inc.« less

Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model.

PubMed

Kao, Hsiu-Fen; Lo, Ikai; Chiang, Jih-Chen; Chen, Chun-Nan; Wang, Wan-Tsang; Hsu, Yu-Chi; Ren, Chung-Yuan; Lee, Meng-En; Wu, Chieh-Lung; Gau, Ming-Hong

2012-10-17

We develop a 16-band atomic bond-orbital model (16ABOM) to compute the spin splitting induced by bulk inversion asymmetry in zincblende materials. This model is derived from the linear combination of atomic-orbital (LCAO) scheme such that the characteristics of the real atomic orbitals can be preserved to calculate the spin splitting. The Hamiltonian of 16ABOM is based on a similarity transformation performed on the nearest-neighbor LCAO Hamiltonian with a second-order Taylor expansion k at the Γ point. The spin-splitting energies in bulk zincblende semiconductors, GaAs and InSb, are calculated, and the results agree with the LCAO and first-principles calculations. However, we find that the spin-orbit coupling between bonding and antibonding p-like states, evaluated by the 16ABOM, dominates the spin splitting of the lowest conduction bands in the zincblende materials.

Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former.

PubMed

Kim, Jeongmin; Sung, Bong June

2015-06-17

The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

Controlling the atom. The beginnings of nuclear regulation 1946--1962

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

Mazuzan, G.T.; Walker, J.S.

This book traces the early history of nuclear power regulation in the US. It focuses on the Atomic Energy Commission (AEC), the federal agency that until 1975 was primarily responsible for planning and carrying out programs to protect public health and safety from the hazards of the civilian use of nuclear energy. It also describes the role of other groups that figured significantly in the development of regulatory policies, including the congressional Joint Committee on Atomic Energy, federal agencies other than the AEC, state governments, the nuclear industry, and scientific organizations. And it considers changes in public perceptions of andmore » attitudes toward atomic energy and the dangers of radiation exposure. The context in which regulatory programs evolved is a rich and complex mixture of political, legislative, legal, technological, scientific, and administrative history. The basic purpose of this book is to provide the Nuclear Regulatory Commission (NRC), which inherited responsibility for nuclear safety after Congress disbanded the AEC, and the general public with information on the historical antecedents and background of regulatory issues.« less

Statistical analysis of atom probe data: detecting the early stages of solute clustering and/or co-segregation.

PubMed

Hyde, J M; Cerezo, A; Williams, T J

2009-04-01

Statistical analysis of atom probe data has improved dramatically in the last decade and it is now possible to determine the size, the number density and the composition of individual clusters or precipitates such as those formed in reactor pressure vessel (RPV) steels during irradiation. However, the characterisation of the onset of clustering or co-segregation is more difficult and has traditionally focused on the use of composition frequency distributions (for detecting clustering) and contingency tables (for detecting co-segregation). In this work, the authors investigate the possibility of directly examining the neighbourhood of each individual solute atom as a means of identifying the onset of solute clustering and/or co-segregation. The methodology involves comparing the mean observed composition around a particular type of solute with that expected from the overall composition of the material. The methodology has been applied to atom probe data obtained from several irradiated RPV steels. The results show that the new approach is more sensitive to fine scale clustering and co-segregation than that achievable using composition frequency distribution and contingency table analyses.

Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

PubMed

Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

2010-01-19

Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

Oxygen discharge and post-discharge kinetics experiments and modeling for the electric oxygen-iodine laser system.

PubMed

Palla, A D; Zimmerman, J W; Woodard, B S; Carroll, D L; Verdeyen, J T; Lim, T C; Solomon, W C

2007-07-26

Laser oscillation at 1315 nm on the I(2P1/2)-->I(2P3/2) transition of atomic iodine has been obtained by a near resonant energy transfer from O2(a1Delta) produced using a low-pressure oxygen/helium/nitric oxide discharge. In the electric discharge oxygen-iodine laser (ElectricOIL) the discharge production of atomic oxygen, ozone, and other excited species adds levels of complexity to the singlet oxygen generator (SOG) kinetics which are not encountered in a classic purely chemical O2(a1Delta) generation system. The advanced model BLAZE-IV has been introduced to study the energy-transfer laser system dynamics and kinetics. Levels of singlet oxygen, oxygen atoms, and ozone are measured experimentally and compared with calculations. The new BLAZE-IV model is in reasonable agreement with O3, O atom, and gas temperature measurements but is under-predicting the increase in O2(a1Delta) concentration resulting from the presence of NO in the discharge and under-predicting the O2(b1Sigma) concentrations. A key conclusion is that the removal of oxygen atoms by NOX species leads to a significant increase in O2(a1Delta) concentrations downstream of the discharge in part via a recycling process; however, there are still some important processes related to the NOX discharge kinetics that are missing from the present modeling. Further, the removal of oxygen atoms dramatically inhibits the production of ozone in the downstream kinetics.

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

PubMed

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

2014-07-24

Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes

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

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C.

2014-06-25

Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagatesmore » into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Furthermore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.« less

Nanoscale wear as a stress-assisted chemical reaction

NASA Astrophysics Data System (ADS)

Jacobs, Tevis D. B.; Carpick, Robert W.

2013-02-01

Wear of sliding contacts leads to energy dissipation and device failure, resulting in massive economic and environmental costs. Typically, wear phenomena are described empirically, because physical and chemical interactions at sliding interfaces are not fully understood at any length scale. Fundamental insights from individual nanoscale contacts are crucial for understanding wear at larger length scales, and to enable reliable nanoscale devices, manufacturing and microscopy. Observable nanoscale wear mechanisms include fracture and plastic deformation, but recent experiments and models propose another mechanism: wear via atom-by-atom removal (`atomic attrition'), which can be modelled using stress-assisted chemical reaction kinetics. Experimental evidence for this has so far been inferential. Here, we quantitatively measure the wear of silicon--a material relevant to small-scale devices--using in situ transmission electron microscopy. We resolve worn volumes as small as 25 +/- 5 nm3, a factor of 103 lower than is achievable using alternative techniques. Wear of silicon against diamond is consistent with atomic attrition, and inconsistent with fracture or plastic deformation, as shown using direct imaging. The rate of atom removal depends exponentially on stress in the contact, as predicted by chemical rate kinetics. Measured activation parameters are consistent with an atom-by-atom process. These results, by direct observation, establish atomic attrition as the primary wear mechanism of silicon in vacuum at low loads.

Power from Radioisotopes, Understanding the Atom Series.

ERIC Educational Resources Information Center

Corliss, William R.; Mead, Robert L.

This 1971 revision deals with radioisotopes and their use in power generators. Early developments and applications for the Systems for Nuclear Auxiliary Power (SNAP) and Radioisotope Thermoelectric Generators (RTGs) are reviewed. Present uses in space and on earth are included. Uses in space are as power sources in various satellites and space…

Using Paperclips to Explain Empirical Formulas to Students

ERIC Educational Resources Information Center

Nassiff, Peter; Czerwinski, Wendy A.

2014-01-01

Early in their chemistry education, students learn to do empirical formula calculations by rote without an understanding of the historical context behind them or the reason why their calculations work. In these activities, students use paperclip "atoms", construct a series of simple compounds representing real molecules, and discover,…

SURFACE FINISHES ON STAINLESS STEEL REDUCE BACTERIAL ATTACHMENT AND EARLY BIOFILM FORMATION: SCANNING ELECTRON AND ATOMIC FORCE MICROSCOPY STUDY

EPA Science Inventory

Three common finishing treatments of stainless steel that are used for equipment during poultry processing were tested for resistance to bacterial contamination. Methods were developed to measure attached bacteria and to identify factors that make surface finishes susceptible or ...

Searching for axion stars and Q-balls with a terrestrial magnetometer network

DOE PAGES

Jackson Kimball, D. F.; Budker, D.; Eby, J.; ...

2018-02-08

Light (pseudo-)scalar fields are promising candidates to be the dark matter in the Universe. Under certain initial conditions in the early Universe and/or with certain types of self-interactions, they can form compact dark-matter objects such as axion stars or Q-balls. Direct encounters with such objects can be searched for by using a global network of atomic magnetometers. It is shown that for a range of masses and radii not ruled out by existing observations, the terrestrial encounter rate with axion stars or Q-balls can be sufficiently high (at least once per year) for a detection. Furthermore, it is shown thatmore » a global network of atomic magnetometers is sufficiently sensitive to pseudoscalar couplings to atomic spins so that a transit through an axion star or Q-ball could be detected over a broad range of unexplored parameter space.« less

Searching for axion stars and Q -balls with a terrestrial magnetometer network

NASA Astrophysics Data System (ADS)

Jackson Kimball, D. F.; Budker, D.; Eby, J.; Pospelov, M.; Pustelny, S.; Scholtes, T.; Stadnik, Y. V.; Weis, A.; Wickenbrock, A.

2018-02-01

Light (pseudo-)scalar fields are promising candidates to be the dark matter in the Universe. Under certain initial conditions in the early Universe and/or with certain types of self-interactions, they can form compact dark-matter objects such as axion stars or Q -balls. Direct encounters with such objects can be searched for by using a global network of atomic magnetometers. It is shown that for a range of masses and radii not ruled out by existing observations, the terrestrial encounter rate with axion stars or Q -balls can be sufficiently high (at least once per year) for a detection. Furthermore, it is shown that a global network of atomic magnetometers is sufficiently sensitive to pseudoscalar couplings to atomic spins so that a transit through an axion star or Q -ball could be detected over a broad range of unexplored parameter space.

Searching for axion stars and Q-balls with a terrestrial magnetometer network

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

Jackson Kimball, D. F.; Budker, D.; Eby, J.

Light (pseudo-)scalar fields are promising candidates to be the dark matter in the Universe. Under certain initial conditions in the early Universe and/or with certain types of self-interactions, they can form compact dark-matter objects such as axion stars or Q-balls. Direct encounters with such objects can be searched for by using a global network of atomic magnetometers. It is shown that for a range of masses and radii not ruled out by existing observations, the terrestrial encounter rate with axion stars or Q-balls can be sufficiently high (at least once per year) for a detection. Furthermore, it is shown thatmore » a global network of atomic magnetometers is sufficiently sensitive to pseudoscalar couplings to atomic spins so that a transit through an axion star or Q-ball could be detected over a broad range of unexplored parameter space.« less

Building Atoms Shell by Shell.

ERIC Educational Resources Information Center

Sussman, Beverly

1993-01-01

Describes an atom-building activity where students construct three-dimensional models of atoms using a styrofoam ball as the nucleus and pom-poms, gum drops, minimarshmallows, or other small items of two different colors to represent protons and neutrons attached. Rings of various sizes with pom-poms attached represent electron shells and…

Atoms in carbon cages as a source of interstellar diffuse lines

NASA Technical Reports Server (NTRS)

Ballester, J. L.; Antoniewicz, P. R.; Smoluchowski, R.

1990-01-01

A model to describe the resonance absorption lines of various atoms trapped in closed carbon cages is presented. These systems may be responsible for some of the as yet unexplained diffuse interstellar bands. Model potentials for possible atom-C60 systems are obtained and used to calculate the resonance lines. The trapped atoms considered are O, N, Si, Mg, Al, Na, and S, and in all cases the resonance lines are shifted toward the red as compared to the isolated atoms. The calculated wavelengths are compared to the range of wavelengths observed for the diffuse interstellar bands, and good agreement is found for Mg and Si resonance lines. Other lines may be caused by other than resonance transitions or by trapped molecules. The oscillator strengths and the abundances are evaluated and compared with observation. Mechanisms to explain the observed band width of the lines and the existence of certain correlated pairs of lines are discussed.

Role of sulphur atoms on stress relaxation and crack propagation in monolayer MoS2

NASA Astrophysics Data System (ADS)

Wang, Baoming; Islam, Zahabul; Zhang, Kehao; Wang, Ke; Robinson, Joshua; Haque, Aman

2017-09-01

We present in-situ transmission electron microscopy of crack propagation in a freestanding monolayer MoS2 and molecular dynamic analysis of the underlying mechanisms. Chemical vapor deposited monolayer MoS2 was transferred from sapphire substrate using interfacial etching for defect and contamination minimization. Atomic resolution imaging shows crack tip atoms sustaining 14.5% strain before bond breaking, while the stress field decays at unprecedented rate of 2.15 GPa Å-1. Crack propagation is seen mostly in the zig-zag direction in both model and experiment, suggesting that the mechanics of fracture is not brittle. Our computational model captures the mechanics of the experimental observations on crack propagation in MoS2. While molybdenum atoms carry most of the mechanical load, we show that the sliding motion of weakly bonded sulphur atoms mediate crack tip stress relaxation, which helps the tip sustain very high, localized stress levels.

Growth of Ni nanoclusters on irradiated graphene: a molecular dynamics study.

PubMed

Valencia, F J; Hernandez-Vazquez, E E; Bringa, E M; Moran-Lopez, J L; Rogan, J; Gonzalez, R I; Munoz, F

2018-04-23

We studied the soft landing of Ni atoms on a previously damaged graphene sheet by means of molecular dynamics simulations. We found a monotonic decrease of the cluster frequency as a function of its size, but few big clusters comprise an appreciable fraction of the total number of Ni atoms. The aggregation of Ni atoms is also modeled by means of a simple phenomenological model. The results are in clear contrast with the case of hard or energetic landing of metal atoms, where there is a tendency to form mono-disperse metal clusters. This behavior is attributed to the high diffusion of unattached Ni atoms, together with vacancies acting as capture centers. The findings of this work show that a simple study of the energetics of the system is not enough in the soft landing regime, where it is unavoidable to also consider the growth process of metal clusters.

Revised model core potentials for third-row transition-metal atoms from Lu to Hg

NASA Astrophysics Data System (ADS)

Mori, Hirotoshi; Ueno-Noto, Kaori; Osanai, You; Noro, Takeshi; Fujiwara, Takayuki; Klobukowski, Mariusz; Miyoshi, Eisaku

2009-07-01

We have produced new relativistic model core potentials (spdsMCPs) for the third-row transition-metal atoms from Lu to Hg explicitly treating explicitly 5s and 5p electrons in addition to 5d and 6s electrons in the same manner for the first- and second-row transition-metal atoms given in the previous Letters [Y. Osanai, M.S. Mon, T. Noro, H. Mori, H. Nakashima, M. Klobukowski, E. Miyoshi, Chem. Phys. Lett. 452 (2008) 210; Y. Osanai, E. Soejima, T. Noro, H. Mori, M.S. Mon, M. Klobukowski, E. Miyoshi, Chem. Phys. Lett. 463 (2008) 230]. Using suitable correlating functions with the split-valence MCP functions, we demonstrate that the present MCP basis sets show reasonable performance in describing the electronic structures of atoms and molecules, bringing about accurate excitation energies for atoms and proper spectroscopic constants for Au 2, Hg 2, and AuH.

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.

Quantum spin dynamics with pairwise-tunable, long-range interactions

PubMed Central

Hung, C.-L.; González-Tudela, Alejandro; Cirac, J. Ignacio; Kimble, H. J.

2016-01-01

We present a platform for the simulation of quantum magnetism with full control of interactions between pairs of spins at arbitrary distances in 1D and 2D lattices. In our scheme, two internal atomic states represent a pseudospin for atoms trapped within a photonic crystal waveguide (PCW). With the atomic transition frequency aligned inside a band gap of the PCW, virtual photons mediate coherent spin–spin interactions between lattice sites. To obtain full control of interaction coefficients at arbitrary atom–atom separations, ground-state energy shifts are introduced as a function of distance across the PCW. In conjunction with auxiliary pump fields, spin-exchange versus atom–atom separation can be engineered with arbitrary magnitude and phase, and arranged to introduce nontrivial Berry phases in the spin lattice, thus opening new avenues for realizing topological spin models. We illustrate the broad applicability of our scheme by explicit construction for several well-known spin models. PMID:27496329

Gravitational Wave Signals from the First Massive Black Hole Seeds

NASA Astrophysics Data System (ADS)

Hartwig, Tilman; Agarwal, Bhaskar; Regan, John A.

2018-05-01

Recent numerical simulations reveal that the isothermal collapse of pristine gas in atomic cooling haloes may result in stellar binaries of supermassive stars with M* ≳ 104M⊙. For the first time, we compute the in-situ merger rate for such massive black hole remnants by combining their abundance and multiplicity estimates. For black holes with initial masses in the range 104 - 6M⊙ merging at redshifts z ≳ 15 our optimistic model predicts that LISA should be able to detect 0.6 mergers per year. This rate of detection can be attributed, without confusion, to the in-situ mergers of seeds from the collapse of very massive stars. Equally, in the case where LISA observes no mergers from heavy seeds at z ≳ 15 we can constrain the combined number density, multiplicity, and coalesence times of these high-redshift systems. This letter proposes gravitational wave signatures as a means to constrain theoretical models and processes that govern the abundance of massive black hole seeds in the early Universe.

Growth Of Single Crystalline Copper Nanowhiskers

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

Kolb, Matthias; Richter, Gunther

2010-11-24

Nanowhiskers are defect free single crystals with high aspect ratios and as result exhibit superior physical, e.g. mechanical properties. This paper sheds light on the kinetics of copper nanowhisker growth and thickening. Whisker growth was provoked by covering silicon wafers with a thin carbon film and subsequently coating them with copper by molecular beam epitaxy. The whiskers grown were examined by scanning electron microscopy and the length and diameter were measured as a function of the amount of copper deposited. The experiments show that nanowhisker growth follows Ruth and Hirth's growth model. A fit of the model parameters to themore » acquired data shows that adsorption of atoms on the substrate and on the whisker surface, with subsequent surface diffusion to the whisker tip, delivers by far the greatest portion of material for whisker growth. Additionally, the experiments demonstrate that the crystallographic orientation of the substrate surface greatly influences the growth rate in the early stage of whisker growth.« less

Analysis of hydrogen Lyman-alpha observations of the coma of Comet P/Halley near the perihelion

NASA Technical Reports Server (NTRS)

Smyth, William H.; Marconi, M. L.; Combi, Michael R.

1995-01-01

The pioneer Venus Orbiter Ultraviolet Spectrometer measurements of the Lyman-alpha intensity of atomic hydrogen excited by solar resonance scattering in the coma of Comet P/Halley acquired from December 28, 1985, to January 6, 1986, and from January 31, 1986, to March 6, 1986, are simulated with the Monte Carlo Particle Trajectory Model corrected for optical depth effects. Spatially detailed comparisons between data and model show excellent agreement and are used to infer that the highest cometary activity may not be at perihelion, but about 2 1/2 weeks before. An improved set of H2O production rates is presented for the period of time that the spectrometer was observing and is found to be consistent with the rates from other types of measurements. The apparent discrepancy between Stewart (1987) in early March and International Ultraviolet Explorer OH derived rates is resolved. The problem with the conversion of 18-cm OH radio brightness to H2O production rates is also discussed.

First-principles study of twin grain boundaries in epitaxial BaSi{sub 2} on Si(111)

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

Baba, Masakazu; Suemasu, Takashi, E-mail: suemasu@bk.tsukuba.ac.jp; Kohyama, Masanori

2016-08-28

Epitaxial films of BaSi{sub 2} on Si(111) for solar cell applications possess three epitaxial variants and exhibit a minority carrier diffusion length (ca. 9.4 μm) much larger than the domain size (ca. 0.2 μm); thus, the domain boundaries (DBs) between the variants do not act as carrier recombination centers. In this work, transmission electron microscopy (TEM) was used to observe the atomic arrangements around the DBs in BaSi{sub 2} epitaxial films on Si(111), and the most stable atomic configuration was determined by first-principles calculations based on density functional theory to provide possible interface models. Bright-field TEM along the a-axis of BaSi{sub 2}more » revealed that each DB was a twin boundary between two different epitaxial variants, and that Ba{sup (II)} atoms form hexagons containing central Ba{sup (I)} atoms in both the bulk and DB regions. Four possible interface models containing Ba{sup (I)}-atom interface layers were constructed, each consistent with TEM observations and distinguished by the relationship between the Si tetrahedron arrays in the two domains adjacent across the interface. This study assessed the structural relaxation of initial interface models constructed from surface slabs terminated by Ba{sup (I)} atoms or from zigzag surface slabs terminated by Si tetrahedra and Ba{sup (II)} atoms. In these models, the interactions or relative positions between Si tetrahedra appear to dominate the relaxation behavior and DB energies. One of the four interface models whose relationship between first-neighboring Si tetrahedra across the interface was the same as that in the bulk was particularly stable, with a DB energy of 95 mJ/m{sup 2}. There were no significant differences in the partial densities of states and band gaps between the bulk and DB regions, and it was therefore concluded that such DBs do not affect the minority carrier properties of BaSi{sub 2}.« less

Thermodynamic output of single-atom quantum optical amplifiers and their phase-space fingerprint

NASA Astrophysics Data System (ADS)

Perl, Y.; Band, Y. B.; Boukobza, E.

2017-05-01

We analyze a resonant single-atom two-photon quantum optical amplifier both dynamically and thermodynamically. A detailed thermodynamic analysis shows that the nonlinear amplifier is thermodynamically equivalent to the linear amplifier. However, by calculating the Wigner quasiprobability distribution for various initial field states, we show that unique quantum features in optical phase space, absent in the linear amplifier, are retained for extended times, despite the fact that dissipation tends to wash out dynamical features observed at early evolution times. These features are related to the discrete nature of the two-photon matter-field interaction and fingerprint the initial field state at thermodynamic times.

GMI Capabilities

NASA Technical Reports Server (NTRS)

Strode, Sarah; Rodriguez, Jose; Steenrod, Steve; Liu, Junhua; Strahan, Susan; Nielsen, Eric

2015-01-01

We describe the capabilities of the Global Modeling Initiative (GMI) chemical transport model (CTM) with a special focus on capabilities related to the Atmospheric Tomography Mission (ATom). Several science results based on GMI hindcast simulations and preliminary results from the ATom simulations are highlighted. We also discuss the relationship between GMI and GEOS-5.

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

PubMed Central

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-01-01

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

Model based control of dynamic atomic force microscope.

PubMed

Lee, Chibum; Salapaka, Srinivasa M

2015-04-01

A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

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.

Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors

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

Levashov, V. A.

2016-03-07

It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids’ structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectorsmore » of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ{sub 1} ≥ λ{sub 2} ≥ λ{sub 3} ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ{sub 2}/λ{sub 1}) and (λ{sub 3}/λ{sub 2}) are essentially identical to each other in the liquids state. We also found that λ{sub 2} tends to be equal to the geometric average of λ{sub 1} and λ{sub 3}. In our view, correlations between the eigenvalues may represent “the Poisson ratio effect” at the atomic scale.« less

Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors.

PubMed

Levashov, V A

2016-03-07

It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.

Resolution Quality and Atom Positions in Sub-Angstrom Electron Microscopy

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

O'Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

2005-02-15

Ability to determine whether an image peak represents one single atom or several depends on resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to determine whether anmore » image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation. Our Rayleigh-Sparrow parameter QRS reveals the ''resolution quality'' of a microscope image. QRS values greater than 1 indicate a clearly resolved twin peak, while values between 1 and 0 mean a lower-quality resolution and an image with peaks displaced from the relative atom positions. The depth of the twin-peak minimum can be used to determine the value of QRS and the true separation of the atom peaks that sum to produce the twin peak in the image. The Rayleigh-Sparrow parameter can be used to refine relative atom positions in defect images where atoms are closer than the Rayleigh limit of the HR-(S)TEM, reducing the necessity for full image simulations from large defect models.« less