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Sample records for microsecond polarized atomistic

  1. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.

    PubMed

    Shaytan, Alexey K; Armeev, Grigoriy A; Goncearenco, Alexander; Zhurkin, Victor B; Landsman, David; Panchenko, Anna R

    2016-01-16

    An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies.

  2. Experimental studies of a microsecond plasma opening switch in the positive polarity regime with inductive load/extraction ion diode

    NASA Astrophysics Data System (ADS)

    Bystritskii, V. M.; Lisitsyn, I. V.; Sinebryukhov, V. A.; Volkov, S. N.; Krasik, Ya. E.

    1992-06-01

    Systematic studies of the microsecond plasma opening switch (MPOS) operation in the positive polarity of its inner electrode with an inductive load/B-applied ion diode of the extraction type at a level of 0.3 TW of dissipated power were performed at the DOUBLE generator (300 kA, 480 kV, 1 μs). The detailed measurements of ion flow parameters in the conductive phase of the MPOS showed the considerable enhancement of the ion current amplitude over the thermal flow limit (3-10 times) which is coupled with a significant decrease of electron conductivity in the MPOS across its self-magnetic field. The positive polarity MPOS operation proved to be more critical to the stored current amplitudes and geometry of the electrodes in comparison with the negative polarity case. This fact resulted in limitations of satisfactory performance of the MPOS involving short high-voltage pulse duration, low stored current amplitudes, and a narrow region of acceptable electrode diameters. The variation of the diode anode-cathode (AC) gap provided a sensitive control of the MPOS + magnetically insulated diode (MID) system, which displayed very strong coupling, resulting in clamping of the output voltage in a wide region of diode impedances. The early long-duration (<300 ns) high-voltage (50-200 kV) prepulse improves plasma production at the anode of the MID prior to the application of the main pulse. The optimal performance of the MPOS+MID system was realized at the level of ZMPOS/ZMID = 2.5. The energy of the extracted high-power ion beam made up 3.5 kJ, its power being 120 GW with 40% efficiency of energy transfer from MPOS to the MID.

  3. Atomistic modeling of IR action spectra under circularly polarized electromagnetic fields: toward action VCD spectra.

    PubMed

    Calvo, Florent

    2015-03-01

    The nonlinear response and dissociation propensity of an isolated chiral molecule, camphor, to a circularly polarized infrared laser pulse was simulated by molecular dynamics as a function of the excitation wavelength. The results indicate similarities with linear absorption spectra, but also differences that are ascribable to dynamical anharmonic effects. Comparing the responses between left- and right-circularly polarized pulses in terms of dissociation probabilities, or equivalently between R- and S-camphor to a similarly polarized pulse, we find significant differences for the fingerprint C = O amide mode, with a sensitivity that could be sufficient to possibly enable vibrational circular dichroism as an action technique for probing molecular chirality and absolute conformations in the gas phase.

  4. Microsecond switchable thermal antenna

    SciTech Connect

    Ben-Abdallah, Philippe Benisty, Henri; Besbes, Mondher

    2014-07-21

    We propose a thermal antenna that can be actively switched on and off at the microsecond scale by means of a phase transition of a metal-insulator material, the vanadium dioxide (VO{sub 2}). This thermal source is made of a periodically patterned tunable VO{sub 2} nanolayer, which support a surface phonon-polariton in the infrared range in their crystalline phase. Using electrodes properly registered with respect to the pattern, the VO{sub 2} phase transition can be locally triggered by ohmic heating so that the surface phonon-polariton can be diffracted by the induced grating, producing a highly directional thermal emission. Conversely, when heating less, the VO{sub 2} layers cool down below the transition temperature, the surface phonon-polariton cannot be diffracted anymore so that thermal emission is inhibited. This switchable antenna could find broad applications in the domain of active thermal coatings or in those of infrared spectroscopy and sensing.

  5. Cooling rate and stress relaxation in silica melts and glasses via microsecond molecular dyanmics

    SciTech Connect

    Lane, J. Matthew D.

    2015-07-22

    We have conducted extremely long molecular dynamics simulations of glasses to microsecond times, which close the gap between experimental and atomistic simulation time scales by two to three orders of magnitude. The static, thermal, and structural properties of silica glass are reported for glass cooling rates down to 5×109 K/s and viscoelastic response in silica melts and glasses are studied over nine decades of time. We finally present results from relaxation of hydrostatic compressive stress in silica and show that time-temperature superposition holds in these systems for temperatures from 3500 to 1000 K.

  6. Cooling rate and stress relaxation in silica melts and glasses via microsecond molecular dyanmics

    DOE PAGES

    Lane, J. Matthew D.

    2015-07-22

    We have conducted extremely long molecular dynamics simulations of glasses to microsecond times, which close the gap between experimental and atomistic simulation time scales by two to three orders of magnitude. The static, thermal, and structural properties of silica glass are reported for glass cooling rates down to 5×109 K/s and viscoelastic response in silica melts and glasses are studied over nine decades of time. We finally present results from relaxation of hydrostatic compressive stress in silica and show that time-temperature superposition holds in these systems for temperatures from 3500 to 1000 K.

  7. Sub-microsecond-resolution probe microscopy

    DOEpatents

    Ginger, David; Giridharagopal, Rajiv; Moore, David; Rayermann, Glennis; Reid, Obadiah

    2014-04-01

    Methods and apparatus are provided herein for time-resolved analysis of the effect of a perturbation (e.g., a light or voltage pulse) on a sample. By operating in the time domain, the provided method enables sub-microsecond time-resolved measurement of transient, or time-varying, forces acting on a cantilever.

  8. Polar Spinel-Perovskite Interfaces: an atomistic study of Fe3O4(111)/SrTiO3(111) structure and functionality

    PubMed Central

    Gilks, Daniel; McKenna, Keith P.; Nedelkoski, Zlatko; Kuerbanjiang, Balati; Matsuzaki, Kosuke; Susaki, Tomofumi; Lari, Leonardo; Kepaptsoglou, Demie; Ramasse, Quentin; Tear, Steve; Lazarov, Vlado K.

    2016-01-01

    Atomic resolution scanning transmission electron microscopy and electron energy loss spectroscopy combined with ab initio electronic calculations are used to determine the structure and properties of the Fe3O4(111)/SrTiO3(111) polar interface. The interfacial structure and chemical composition are shown to be atomically sharp and of an octahedral Fe/SrO3 nature. Band alignment across the interface pins the Fermi level in the vicinity of the conduction band of SrTiO3. Density functional theory calculations demonstrate very high spin-polarization of Fe3O4 in the interface vicinity which suggests that this system may be an excellent candidate for spintronic applications. PMID:27411576

  9. Microsecond flares in gamma-ray bursts

    NASA Technical Reports Server (NTRS)

    Schaefer, Bradley E.; Cohen, Justin; Teegarden, Bonnard J.; Cline, Thomas L.; Fishman, Gerald J.; Meegan, Charles A.; Wilson, Robert B.; Paciesas, William S.; Pendleton, Geoffrey N.; Matteson, James L.

    1993-01-01

    It has been suggested that gamma-ray burst light curves may consist of many superposed flares with a duration shorter than 30/microsec. If true, the implications for the interpretation of burst data are enormous. With the launch of the Compton Gamma-Ray Observatory, four predictions of Mitrofanov's (1989) suggestion can be tested. Our results which contradict this suggestion are (1) the photon arrival times are not correlated between independent detectors, (2) the spectral hardness and intensity does not depend on the detector area, (3) the bursts seen by detectors which measure photon positions do not see microsecond flares, and (4) burst positions deduced from detectors with different projected areas are close to the positions deduced from time-of-flight differences between separated spacecraft. We conclude, therefore, that gamma-ray bursts are not composed of microsecond flares.

  10. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

    PubMed Central

    Pasi, Marco; Lavery, Richard

    2016-01-01

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

  11. Parallel Atomistic Simulations

    SciTech Connect

    HEFFELFINGER,GRANT S.

    2000-01-18

    Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.

  12. Atomistics of friction

    NASA Astrophysics Data System (ADS)

    Hirano, M.

    2006-03-01

    When two solid bodies contact and slide against each other, a frictional phenomenon occurs. There have been two models for the origin of the friction forces: the surface roughness model and Tomlinson's model. The surface roughness model explains the origin of the static friction force; contacting solid surfaces are so rough that surface asperities are mechanically locked against the gravitational force. From an atomistic point of view, Tomlinson explained a mechanism of the energy dissipation for the origin of the dynamic friction force. The atomistic mechanisms are described for the origin of the static and the dynamic friction forces, based on the theoretical conclusion that Tomlinson's mechanism is unlikely to occur in realistic frictional systems. The mechanism for the origin of the static friction force resembles the mechanical locking mechanism in a surface roughness model. The origin of the dynamic friction force is formulated as a problem of how the given translational kinetic energy dissipates into the internal relative motions of constituent atoms of bodies during sliding. From studying the available phase space volume of the translational motion becomes negligibly small for a large system size, compared with that of the internal motions, it is concluded that the energy dissipation occurs irreversibly from the translational motion to the internal motions. The comparison of the atomistic mechanisms with the surface roughness model and Tomlinson's model is discussed. A phenomenon of superlubricity, where two solid bodies move relatively with no resistance, is discussed.

  13. Efficient illumination for microsecond tracking microscopy.

    PubMed

    Dulin, David; Barland, Stephane; Hachair, Xavier; Pedaci, Francesco

    2014-01-01

    The possibility to observe microsecond dynamics at the sub-micron scale, opened by recent technological advances in fast camera sensors, will affect many biophysical studies based on particle tracking in optical microscopy. A main limiting factor for further development of fast video microscopy remains the illumination of the sample, which must deliver sufficient light to the camera to allow microsecond exposure times. Here we systematically compare the main illumination systems employed in holographic tracking microscopy, and we show that a superluminescent diode and a modulated laser diode perform the best in terms of image quality and acquisition speed, respectively. In particular, we show that the simple and inexpensive laser illumination enables less than 1 μs camera exposure time at high magnification on a large field of view without coherence image artifacts, together with a good hologram quality that allows nm-tracking of microscopic beads to be performed. This comparison of sources can guide in choosing the most efficient illumination system with respect to the specific application.

  14. Microsecond subdomain folding in dihydrofolate reductase.

    PubMed

    Arai, Munehito; Iwakura, Masahiro; Matthews, C Robert; Bilsel, Osman

    2011-07-08

    The characterization of microsecond dynamics in the folding of multisubdomain proteins has been a major challenge in understanding their often complex folding mechanisms. Using a continuous-flow mixing device coupled with fluorescence lifetime detection, we report the microsecond folding dynamics of dihydrofolate reductase (DHFR), a two-subdomain α/β/α sandwich protein known to begin folding in this time range. The global dimensions of early intermediates were monitored by Förster resonance energy transfer, and the dynamic properties of the local Trp environments were monitored by fluorescence lifetime detection. We found that substantial collapse occurs in both the locally connected adenosine binding subdomain and the discontinuous loop subdomain within 35 μs of initiation of folding from the urea unfolded state. During the fastest observable ∼550 μs phase, the discontinuous loop subdomain further contracts, concomitant with the burial of Trp residue(s), as both subdomains achieve a similar degree of compactness. Taken together with previous studies in the millisecond time range, a hierarchical assembly of DHFR--in which each subdomain independently folds, subsequently docks, and then anneals into the native conformation after an initial heterogeneous global collapse--emerges. The progressive acquisition of structure, beginning with a continuously connected subdomain and spreading to distal regions, shows that chain entropy is a significant organizing principle in the folding of multisubdomain proteins and single-domain proteins. Subdomain folding also provides a rationale for the complex kinetics often observed.

  15. Biomembranes in atomistic and coarse-grained simulations

    NASA Astrophysics Data System (ADS)

    Pluhackova, Kristyna; Böckmann, Rainer A.

    2015-08-01

    The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.

  16. Microsecond protein dynamics observed at the single-molecule level

    PubMed Central

    Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

    2015-01-01

    How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. PMID:26151767

  17. Microsecond delays on non-real time operating systems

    SciTech Connect

    Angstadt, R.; Estrada, J.; Diehl, H.T.; Flaugher, B.; Johnson, M.; /Fermilab

    2007-05-01

    We have developed microsecond timing and profiling software that runs on standard Windows and Linux based operating systems. This software is orders of magnitudes better than most of the standard native functions in wide use. Our software libraries calibrate RDTSC in microseconds or seconds to provide two different types of delays: a ''Guaranteed Minimum'' and a precision ''Long Delay'', which releases to the kernel. Both return profiling information of the actual delay.

  18. Atomistic k ṡ p theory

    NASA Astrophysics Data System (ADS)

    Pryor, Craig E.; Pistol, M.-E.

    2015-12-01

    Pseudopotentials, tight-binding models, and k ṡ p theory have stood for many years as the standard techniques for computing electronic states in crystalline solids. Here, we present the first new method in decades, which we call atomistic k ṡ p theory. In its usual formulation, k ṡ p theory has the advantage of depending on parameters that are directly related to experimentally measured quantities, however, it is insensitive to the locations of individual atoms. We construct an atomistic k ṡ p theory by defining envelope functions on a grid matching the crystal lattice. The model parameters are matrix elements which are obtained from experimental results or ab initio wave functions in a simple way. This is in contrast to the other atomistic approaches in which parameters are fit to reproduce a desired dispersion and are not expressible in terms of fundamental quantities. This fitting is often very difficult. We illustrate our method by constructing a four-band atomistic model for a diamond/zincblende crystal and show that it is equivalent to the sp3 tight-binding model. We can thus directly derive the parameters in the sp3 tight-binding model from experimental data. We then take the atomistic limit of the widely used eight-band Kane model and compute the band structures for all III-V semiconductors not containing nitrogen or boron using parameters fit to experimental data. Our new approach extends k ṡ p theory to problems in which atomistic precision is required, such as impurities, alloys, polytypes, and interfaces. It also provides a new approach to multiscale modeling by allowing continuum and atomistic k ṡ p models to be combined in the same system.

  19. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    DTIC Science & Technology

    2014-03-28

    Approved for Public Release; Distribution Unlimited Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic...non peer-reviewed journals: Final report on the project "Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration" Report Title In... nanoscience of multifunctional materials: atomistic exploration” PI:Inna Ponomareva We have accomplished the following. 1. We have developed a set of

  20. Numerical tools for atomistic simulations.

    SciTech Connect

    Fang, H.; Gullett, Philip Michael; Slepoy, Alexander; Horstemeyer, Mark F.; Baskes, Michael I.; Wagner, Gregory John; Li, Mo

    2004-01-01

    The final report for a Laboratory Directed Research and Development project entitled 'Parallel Atomistic Computing for Failure Analysis of Micromachines' is presented. In this project, atomistic algorithms for parallel computers were developed to assist in quantification of microstructure-property relations related to weapon micro-components. With these and other serial computing tools, we are performing atomistic simulations of various sizes, geometries, materials, and boundary conditions. These tools provide the capability to handle the different size-scale effects required to predict failure. Nonlocal continuum models have been proposed to address this problem; however, they are phenomenological in nature and are difficult to validate for micro-scale components. Our goal is to separately quantify damage nucleation, growth, and coalescence mechanisms to provide a basis for macro-scale continuum models that will be used for micromachine design. Because micro-component experiments are difficult, a systematic computational study that employs Monte Carlo methods, molecular statics, and molecular dynamics (EAM and MEAM) simulations to compute continuum quantities will provide mechanism-property relations associated with the following parameters: specimen size, number of grains, crystal orientation, strain rates, temperature, defect nearest neighbor distance, void/crack size, chemical state, and stress state. This study will quantify sizescale effects from nanometers to microns in terms of damage progression and thus potentially allow for optimized micro-machine designs that are more reliable and have higher fidelity in terms of strength. In order to accomplish this task, several atomistic methods needed to be developed and evaluated to cover the range of defects, strain rates, temperatures, and sizes that a material may see in micro-machines. Therefore we are providing a complete set of tools for large scale atomistic simulations that include pre-processing of

  1. Atomistic details of protein dynamics and the role of hydration water

    SciTech Connect

    Khodadadi, Sheila; Sokolov, Alexei P.

    2016-05-04

    The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread over a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.

  2. Atomistic details of protein dynamics and the role of hydration water

    DOE PAGES

    Khodadadi, Sheila; Sokolov, Alexei P.

    2016-05-04

    The importance of protein dynamics for their biological activity is nowwell recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. But, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. Internal protein dynamics spread overmore » a wide time range fromfaster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10 100 ps time scale. Our process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.« less

  3. Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases.

    PubMed

    Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

    2013-01-01

    A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions.

  4. Atomistic modeling at experimental strain rates and timescales

    NASA Astrophysics Data System (ADS)

    Yan, Xin; Cao, Penghui; Tao, Weiwei; Sharma, Pradeep; Park, Harold S.

    2016-12-01

    Modeling physical phenomena with atomistic fidelity and at laboratory timescales is one of the holy grails of computational materials science. Conventional molecular dynamics (MD) simulations enable the elucidation of an astonishing array of phenomena inherent in the mechanical and chemical behavior of materials. However, conventional MD, with our current computational modalities, is incapable of resolving timescales longer than microseconds (at best). In this short review article, we briefly review a recently proposed approach—the so-called autonomous basin climbing (ABC) method—that in certain instances can provide valuable information on slow timescale processes. We provide a general summary of the principles underlying the ABC approach, with emphasis on recent methodological developments enabling the study of mechanically-driven processes at slow (experimental) strain rates and timescales. Specifically, we show that by combining a strong physical understanding of the underlying phenomena, kinetic Monte Carlo, transition state theory and minimum energy pathway methods, the ABC method has been found to be useful in a variety of mechanically-driven problems ranging from the prediction of creep-behavior in metals, constitutive laws for grain boundary sliding, void nucleation rates, diffusion in amorphous materials to protein unfolding. Aside from reviewing the basic ideas underlying this approach, we emphasize some of the key challenges encountered in our own personal research work and suggest future research avenues for exploration.

  5. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.

    PubMed

    Wassenaar, Tsjerk A; Ingólfsson, Helgi I; Priess, Marten; Marrink, Siewert J; Schäfer, Lars V

    2013-04-04

    Hybrid molecular dynamics simulations of atomistic (AA) solutes embedded in coarse-grained (CG) environment can substantially reduce the computational cost with respect to fully atomistic simulations. However, interfacing both levels of resolution is a major challenge that includes a balanced description of the relevant interactions. This is especially the case for polar solvents such as water, which screen the electrostatic interactions and thus require explicit electrostatic coupling between AA and CG subsystems. Here, we present and critically test computationally efficient hybrid AA/CG models. We combined the Gromos atomistic force field with the MARTINI coarse-grained force field. To enact electrostatic coupling, two recently developed CG water models with explicit electrostatic interactions were used: the polarizable MARTINI water model and the BMW model. The hybrid model was found to be sensitive to the strength of the AA-CG electrostatic coupling, which was adjusted through the relative dielectric permittivity εr(AA-CG). Potentials of mean force (PMFs) between pairs of amino acid side chain analogues in water and partitioning free enthalpies of uncharged amino acid side chain analogues between apolar solvent and water show significant differences between the hybrid simulations and the fully AA or CG simulations, in particular for charged and polar molecules. For apolar molecules, the results obtained with the hybrid AA/CG models are in better agreement with the fully atomistic results. The structures of atomistic ubiquitin solvated in CG water and of a single atomistic transmembrane α-helix and the transmembrane portion of an atomistic mechanosensitive channel in CG lipid bilayers were largely maintained during 50-100 ns of AA/CG simulations, partly due to an overstabilization of intramolecular interactions. This work highlights some key challenges on the way toward hybrid AA/CG models that are both computationally efficient and sufficiently accurate for

  6. Microsecond-resolved SDR-based cavity ring down ellipsometry.

    PubMed

    Sofikitis, D; Spiliotis, A K; Stamataki, K; Katsoprinakis, G E; Bougas, L; Samartzis, P C; Loppinet, B; Rakitzis, T P; Surligas, M; Papadakis, S

    2015-06-20

    We present an experimental apparatus that allows microsecond-resolved ellipsometric and absorption measurements. The apparatus is based on an optical cavity containing a Dove prism, in which light undergoes total internal reflection (TIR), while the data acquisition is based on software defined radio technology and custom-built drivers. We demonstrate the ability to sense rapid variations in the refractive index above the TIR interface for arbitrarily long times with a temporal resolution of at least 2 μs.

  7. ASTROPULSE: A SEARCH FOR MICROSECOND TRANSIENT RADIO SIGNALS USING DISTRIBUTED COMPUTING. I. METHODOLOGY

    SciTech Connect

    Von Korff, J.; Heien, E.; Korpela, E.; Werthimer, D.; Cobb, J.; Lebofsky, M.; Anderson, D.; Bankay, B.; Siemion, A.; Demorest, P.

    2013-04-10

    We are performing a transient, microsecond timescale radio sky survey, called 'Astropulse', using the Arecibo telescope. Astropulse searches for brief (0.4 {mu}s to 204.8 {mu}s ), wideband (relative to its 2.5 MHz bandwidth) radio pulses centered at 1420 MHz. Astropulse is a commensal (piggyback) survey, and scans the sky between declinations of -1. Degree-Sign 33 and 38. Degree-Sign 03. We obtained 1540 hr of data in each of seven beams of the ALFA receiver, with two polarizations per beam. The data are one-bit complex sampled at the Nyquist limit of 0.4 {mu}s per sample. Examination of timescales on the order of microseconds is possible because we used coherent dedispersion, a technique that has frequently been used for targeted observations, but has never been associated with a radio sky survey. The more usual technique, incoherent dedispersion, cannot resolve signals below a minimum timescale which depends on the signal's dispersion measure (DM) and frequency. However, coherent dedispersion requires more intensive computation than incoherent dedispersion. The required processing power was provided by BOINC, the Berkeley Open Infrastructure for Network Computing. BOINC is a distributed computing system, allowing us to utilize hundreds of thousands of volunteers' computers to perform the necessary calculations for coherent dedispersion. Astrophysical events that might produce brief radio pulses include giant pulses from pulsars, rotating radio transients, exploding primordial black holes, or new sources yet to be imagined. Radio frequency interference and noise contaminate the data; these are mitigated by a number of techniques including multi-polarization correlation, DM repetition detection, and frequency profiling.

  8. Astropulse: A Search for Microsecond Transient Radio Signals Using Distributed Computing. I. Methodology

    NASA Astrophysics Data System (ADS)

    Von Korff, J.; Demorest, P.; Heien, E.; Korpela, E.; Werthimer, D.; Cobb, J.; Lebofsky, M.; Anderson, D.; Bankay, B.; Siemion, A.

    2013-04-01

    We are performing a transient, microsecond timescale radio sky survey, called "Astropulse," using the Arecibo telescope. Astropulse searches for brief (0.4 μs to 204.8 μs ), wideband (relative to its 2.5 MHz bandwidth) radio pulses centered at 1420 MHz. Astropulse is a commensal (piggyback) survey, and scans the sky between declinations of -1.°33 and 38.°03. We obtained 1540 hr of data in each of seven beams of the ALFA receiver, with two polarizations per beam. The data are one-bit complex sampled at the Nyquist limit of 0.4 μs per sample. Examination of timescales on the order of microseconds is possible because we used coherent dedispersion, a technique that has frequently been used for targeted observations, but has never been associated with a radio sky survey. The more usual technique, incoherent dedispersion, cannot resolve signals below a minimum timescale which depends on the signal's dispersion measure (DM) and frequency. However, coherent dedispersion requires more intensive computation than incoherent dedispersion. The required processing power was provided by BOINC, the Berkeley Open Infrastructure for Network Computing. BOINC is a distributed computing system, allowing us to utilize hundreds of thousands of volunteers' computers to perform the necessary calculations for coherent dedispersion. Astrophysical events that might produce brief radio pulses include giant pulses from pulsars, rotating radio transients, exploding primordial black holes, or new sources yet to be imagined. Radio frequency interference and noise contaminate the data; these are mitigated by a number of techniques including multi-polarization correlation, DM repetition detection, and frequency profiling.

  9. Developing Single-Molecule Technique with Microsecond Resolution

    NASA Astrophysics Data System (ADS)

    Akhterov, Maxim V.

    Molecular machines like proteins are responsible for many regulatory and catalytic functions. Specifically, molecular motions of proteins and their flexibility determine conformational states required for enzyme catalysis, signal transduction, and protein-protein interactions. However, the mechanisms for protein transitions between conformational states are often poorly understood, especially in the milli- to microsecond ranges where conventional optical techniques and computational modeling are most limited. This work describes development of an electronic single-molecule technique for monitoring microsecond motions of biological molecules. Dynamic changes of conductance through a transistor made of a single-walled carbon nanotube (SWNT-FET) report conformational changes of a protein molecule tethered to the SWNT sidewall. In principle, the high operating speed of SWNT-FETs could allow this technique to resolve molecular events with nanosecond resolution. This project focused on improving the technique to a 200 kHz effective bandwidth in order to resolve microsecond-scale dynamics. The improvement was achieved with a home-built electrochemical flow cell. By minimizing parasitic capacitance due to liquid coupling to electrodes and eliminating noise pickup, the flow cell enabled low-noise, high bandwidth measurement of molecular events as short as 2 mus. The apparatus was used to observe closing and opening motions of lysozyme. Preliminary results suggest that lysozyme has a distribution of possible velocities with the most probable speed approaching our experimental resolution of 2 mus.

  10. Atomistic properties of γ uranium.

    PubMed

    Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

    2012-02-22

    The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

  11. [The sub-microsecond pulser applied for electroporation effect].

    PubMed

    Tan, Yafang; Yang, Hongchun; Wu, Jianxing; Yang, Xiaolin; Zhang, Yi; Zeng, Gang; Zhang, Xiaoyu

    2012-08-01

    A sub-microsecond pulse generation applied for electroporation effects of tumor cell is presented in this paper. The principle of the generator is that the expected pulse waveform is intercepted from the RC discharge curve by controlling the on-off states of two IGBT modules with a synchronous controller. Experimental tests indicate that the generator can produce adjustable pulse waveform parameters with 0.5-3.5kV amplitude, 300-800 ns pulse duration, 1-400Hz repetition frequency rate, and it is suitable for the study of the electroporation effect experiments.

  12. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect

    Hertzog, D E; Santiago, J G; Bakajin, O

    2005-02-10

    We have developed and characterized a mixer to study the reaction kinetics of protein folding on a microsecond timescale. The mixer uses hydrodynamic focusing of pressure-driven flow in a microfluidic channel to reduce diffusion times as first demonstrated by Knight et al.[1]. Features of the mixer include 1 {micro}s mixing times, sample consumptions of order 1 nl/s, loading sample volumes on the order of microliters, and the ability to manufacture in fused silica for compatibility with most spectroscopic methods.

  13. X-rays from a microsecond X-pinch

    SciTech Connect

    Appartaim, R. K.

    2013-08-28

    The characteristics of x-rays emitted by X-pinches driven by discharging a current of ∼320 kA with a quarter period of 1 μs in crossed 25 μm wires have been investigated. The x-ray emissions are studied using filtered silicon photodiodes, diamond radiation detectors, and pinhole cameras. The results show that predominantly x-rays from the microsecond X-pinch tend to be emitted in two distinct sets of bursts. The first is predominantly “soft,” i.e., with photon energy hν < 5 keV, followed by a second set of bursts beginning up to 100 ns following the initial bursts, and usually consisting of higher photon energies. Our results show, however, that the x-ray emissions do not contain a significant component with hν > 10 keV as might be expected from electron beam activity within the plasma or from the X-pinch diode. High-resolution images obtained with the observed x-rays suggest a well-defined small source of soft x-rays that demonstrates the potential of the microsecond X-pinch.

  14. Connecting Atomistic and Continuous Models of Elastodynamics

    NASA Astrophysics Data System (ADS)

    Braun, Julian

    2017-02-01

    We prove the long-time existence of solutions for the equations of atomistic elastodynamics on a bounded domain with time-dependent boundary values as well as their convergence to a solution of continuum nonlinear elastodynamics as the interatomic distances tend to zero. Here, the continuum energy density is given by the Cauchy-Born rule. The models considered allow for general finite range interactions. To control the stability of large deformations we also prove a new atomistic Gårding inequality.

  15. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

    PubMed

    Pande, Vijay S; Baker, Ian; Chapman, Jarrod; Elmer, Sidney P; Khaliq, Siraj; Larson, Stefan M; Rhee, Young Min; Shirts, Michael R; Snow, Christopher D; Sorin, Eric J; Zagrovic, Bojan

    2003-01-01

    Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.

  16. Virus capsid dissolution studied by microsecond molecular dynamics simulations.

    PubMed

    Larsson, Daniel S D; Liljas, Lars; van der Spoel, David

    2012-01-01

    Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacco necrosis virus with and without the 92 structural calcium ions. The capsid expanded 2.5% upon removal of the calcium, in good agreement with experimental estimates. The water permeability of the native capsid was similar to that of a phospholipid membrane, but the permeability increased 10-fold after removing the calcium, predominantly between the 2-fold and 3-fold related subunits. The two calcium binding sites close to the icosahedral 3-fold symmetry axis were pivotal in the expansion and capsid-opening process, while the binding site on the 5-fold axis changed little structurally. These findings suggest that the dissociation of the capsid is initiated at the 3-fold axis.

  17. Microsecond-scale electric field pulses in cloud lightning discharges

    NASA Technical Reports Server (NTRS)

    Villanueva, Y.; Rakov, V. A.; Uman, M. A.; Brook, M.

    1994-01-01

    From wideband electric field records acquired using a 12-bit digitizing system with a 500-ns sampling interval, microsecond-scale pulses in different stages of cloud flashes in Florida and New Mexico are analyzed. Pulse occurrence statistics and waveshape characteristics are presented. The larger pulses tend to occur early in the flash, confirming the results of Bils et al. (1988) and in contrast with the three-stage representation of cloud-discharge electric fields suggested by Kitagawa and Brook (1960). Possible explanations for the discrepancy are discussed. The tendency for the larger pulses to occur early in the cloud flash suggests that they are related to the initial in-cloud channel formation processes and contradicts the common view found in the atmospheric radio-noise literature that the main sources of VLF/LF electromagnetic radiation in cloud flashes are the K processes which occur in the final, or J type, part of the cloud discharge.

  18. Substrate recognition by norovirus polymerase: microsecond molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Maláč, Kamil; Barvík, Ivan

    2013-04-01

    Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP ( C5' -O5'-C4'-O4'), cocCTP ( C5' -O5'-C4'- C4'') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP—substrate, 2dCTP—poor substrate, coCTP—chain terminator, cocCTP—inhibitor). Moreover, extremely rare events—as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement—were captured.

  19. Plasma dynamics in microsecond megaampere plasma opening switches

    SciTech Connect

    Loginov, S. V.

    2011-10-15

    The paper considers the transport of a magnetic field in highly ionized plasma of microsecond megaampere plasma opening switches. Self-similar solutions for plasma aggregation by a linearly increasing magnetic field are derived. For these solutions, the magnetic field energy in the current channel is much lower than the energy of the accelerated plasma flow. The effect of Joule heating of the plasma becomes profound only with a uniform current density. It is shown that the evolution of the magnetic field in the accelerated flow is reduced to diffusion with an effective electrical conductivity proportional to the harmonic average of the Spitzer conductivity and conductivity dependent on the magnetic field in the current channel. Thus, during about the first 100 ns of the current pulse the conductivity of the current channel increases due to the plasma heating and, as the plasma is accelerated, its conductivity decreases.

  20. Optical Pumping and Laser Induced Nuclear Orientation of a Microsecond Isomeric Level in BARIUM-134

    NASA Astrophysics Data System (ADS)

    Bell, Curtis John

    Using optical pumping techniques, on and off-line experiments were performed on a microsecond nuclear isomer (('134m)Ba 10('+) ). Shifts in atomic resonances detected by changes in the angular distribution of characteristic nuclear radiations (expressed as changes in shape and size) yield information on changes in nuclear structure. The 10('+) isomeric state was produced using a 49 MeV pulsed beam of ('13)C on an isotopically enriched ('124)Sn target. The reaction products recoil out of the target and are slowed to thermal velocities in 10 torr of xenon in a region illuminated with circularly polarized light (553.5 nm) from a Coherent 699-21 dye laser. Nuclear parameters measured were the lifetime (3.8(2)(mu)s) and g-factor (g = -.20(1)) of the 10('+) state. Atomic parameters measured for barium were the depolarization cross sections of the ('1)P(,1) atomic level (6.0(6) nm('2)) in xenon, the quenching cross section for hydrogen (0.042(4) nm('2)), and the branching ratio of the metastable (('1,3)D(,1,2,3)) atomic states (0.011(1)). A possible anisotropy signal and the cumulative results (no measurable anisotropy) are presented. Difficulties encountered were insufficient neutralization, and unexpectedly large spatial distribution, and 'trapping' in metastable atomic states.

  1. Microsecond-sustained lasing from colloidal quantum dot solids

    PubMed Central

    Adachi, Michael M.; Fan, Fengjia; Sellan, Daniel P.; Hoogland, Sjoerd; Voznyy, Oleksandr; Houtepen, Arjan J.; Parrish, Kevin D.; Kanjanaboos, Pongsakorn; Malen, Jonathan A.; Sargent, Edward H.

    2015-01-01

    Colloidal quantum dots have grown in interest as materials for light amplification and lasing in view of their bright photoluminescence, convenient solution processing and size-controlled spectral tunability. To date, lasing in colloidal quantum dot solids has been limited to the nanosecond temporal regime, curtailing their application in systems that require more sustained emission. Here we find that the chief cause of nanosecond-only operation has been thermal runaway: the combination of rapid heat injection from the pump source, poor heat removal and a highly temperature-dependent threshold. We show microsecond-sustained lasing, achieved by placing ultra-compact colloidal quantum dot films on a thermally conductive substrate, the combination of which minimizes heat accumulation. Specifically, we employ inorganic-halide-capped quantum dots that exhibit high modal gain (1,200 cm−1) and an ultralow amplified spontaneous emission threshold (average peak power of ∼50 kW cm−2) and rely on an optical structure that dissipates heat while offering minimal modal loss. PMID:26493282

  2. Detonation initiation on the microsecond time scale: DDTs

    SciTech Connect

    Kuehn, Jeffery A; Kassoy, Dr. David R; Nabity, Mr. Matthew W.; Clarke, Dr. John F.

    2006-01-01

    Spatially resolved, thermal power deposition of limited duration into a finite volume of reactive gas is the initiator for a deflagration-to-detonation transition (DDT) on the microsecond time scale. The reactive Euler equations with one-step Arrhenius kinetics are used to derive novel formulas for velocity and temperature variation that describe the physical phenomena characteristic of DDTs. A nonlinear transformation of the variables is shown to yield a canonical equation system, independent of the activation energy. Numerical solutions of the reactive Euler equations are used to describe the detailed sequence of reactive gas dynamic processes leading to an overdriven planar detonation far from the power deposition location. Results are presented for deposition into a region isolated from the planar boundary of the reactive gas as well as for that adjacent to the boundary. The role of compressions and shocks reflected from the boundary into the partially reacted hot gas is described. The quantitative dependences of DDT evolution on the magnitude of thermal power deposition and activation energy are identified.

  3. Detonation initiation on the microsecond time scale: DDTs

    SciTech Connect

    Kassoy, Dr. David R; Kuehn, Jeffery A; Nabity, Mr. Matthew W.; Clarke, Dr. John F.

    2008-01-01

    Spatially resolved, thermal power deposition of limited duration into a finite volume of reactive gas is the initiator for a deflagration-to-detonation transition (DDT) on the microsecond time scale. The reactive Euler equations with one-step Arrhenius kinetics are used to derive novel formulas for velocity and temperature variation that describe the physical phenomena characteristic of DDTs. A transformation of the variables is shown to yield a canonical equation system, independent of the activation energy. Numerical solutions of the reactive Euler equations are used to describe the detailed sequence of reactive gasdynamic processes leading to an overdriven planar detonation far from the power deposition location. Results are presented for deposition into a region isolated from the planar boundary of the reactive gas as well as for that adjacent to the boundary. The role of compressions and shocks reflected from the boundary into the partially reacted hot gas is described. The quantitative dependences of DDT evolution on the magnitude of thermal power deposition and activation energy are identified.

  4. Understanding High Voltage Vacuum Insulators for Microsecond Pulses

    SciTech Connect

    J.B., J; D.A., G; T.L., H; E.J., L; R.D., S; L.K., T; G.E., V

    2007-08-15

    High voltage insulation is one of the main areas of pulsed power research and development since the surface of an insulator exposed to vacuum can fail electrically at an applied field more than an order or magnitude below the bulk dielectric strength of the insulator. This is troublesome for applications where high voltage conditioning of the insulator and electrodes is not practical and where relatively long pulses, on the order of several microseconds, are required. Here we give a summary of our approach to modeling and simulation efforts and experimental investigations for understanding flashover mechanism. The computational work is comprised of both filed and particle-in-cell modeling with state-of-the-art commercial codes. Experiments were performed in using an available 100-kV, 10-{micro}s pulse generator and vacuum chamber. The initial experiments were done with polyethylene insulator material in the shape of a truncated cone cut at +45{sup o} angle between flat electrodes with a gap of 1.0 cm. The insulator was sized so there were no flashovers or breakdowns under nominal operating conditions. Insulator flashover or gap closure was induced by introducing a plasma source, a tuft of velvet, in proximity to the insulator or electrode.

  5. Microsecond-sustained lasing from colloidal quantum dot solids.

    PubMed

    Adachi, Michael M; Fan, Fengjia; Sellan, Daniel P; Hoogland, Sjoerd; Voznyy, Oleksandr; Houtepen, Arjan J; Parrish, Kevin D; Kanjanaboos, Pongsakorn; Malen, Jonathan A; Sargent, Edward H

    2015-10-23

    Colloidal quantum dots have grown in interest as materials for light amplification and lasing in view of their bright photoluminescence, convenient solution processing and size-controlled spectral tunability. To date, lasing in colloidal quantum dot solids has been limited to the nanosecond temporal regime, curtailing their application in systems that require more sustained emission. Here we find that the chief cause of nanosecond-only operation has been thermal runaway: the combination of rapid heat injection from the pump source, poor heat removal and a highly temperature-dependent threshold. We show microsecond-sustained lasing, achieved by placing ultra-compact colloidal quantum dot films on a thermally conductive substrate, the combination of which minimizes heat accumulation. Specifically, we employ inorganic-halide-capped quantum dots that exhibit high modal gain (1,200 cm(-1)) and an ultralow amplified spontaneous emission threshold (average peak power of ∼50 kW cm(-2)) and rely on an optical structure that dissipates heat while offering minimal modal loss.

  6. Characterization of a microsecond-conduction-time plasma opening switch

    NASA Astrophysics Data System (ADS)

    Commisso, R. J.; Goodrich, P. J.; Grossmann, J. M.; Hinshelwood, D. D.; Ottinger, P. F.; Weber, B. V.

    1992-07-01

    This paper presents data and analyses from which emerges a physical picture of microsecond-conduction-time plasma opening switch operation. During conduction, a broad current channel penetrates axially through the plasma, moving it toward the load. Opening occurs when the current channel reaches the load end of the plasma, far from the load. During conduction, the axial line density in the interelectrode region is reduced from its value with no current conduction as a result of radial hydrodynamic forces associated with the current channel. A factor of 20 reduction is observed at opening in a small, localized region between the electrodes. When open, the switch plasma behaves like a section of magnetically insulated transmission line with an effective gap of 2 to 3 mm. Increasing the magnetic field in this gap by 50% results in an improvement of 50% in the peak load voltage and load current rise time, to 1.2 MV and 20 nsec, respectively. An erosion opening mechanism explains the inferred gap growth rate using the reduced line density at opening. Improved switch performance results when the maximum gap size is increased by using a rising load impedance.

  7. Atomistic simulation of nanostructured materials

    NASA Astrophysics Data System (ADS)

    Zhu, Ronghua

    Atomistic based computer modeling and simulation of nanostructured materials has become an important subfield of materials research. Based on the multiresolution method, which combines the continuum mechanics, kinetic Monte Carlo method and molecular dynamics method, we study the nanostructured materials grown by quantum-dot self-assembly, mechanical properties of strained semiconductors, and mechanical properties of carbon nanotube reinforced composites. This thesis covers the following three main contributions. 1. Self-organization of semiconductors InAs/GaAs in Stranski-Krastanov growth mode is studied using kinetic Monte Carlo simulations method coupled with the Green's function solution for the elastic strain energy distribution. The relevant growth parameters such as growth temperature, surface coverage, flux rate, and growth interruption time are investigated. It is shown clearly that when the long-range strain energy is included in the simulation, ordered uniform size distribution can be achieved. To address the effect of material anisotropy, the anisotropic substrates of GaAs with different growth orientations (001), (111), and (113) and an isotropic substrate Iso (001), reduced from cubic GaAs, are also investigated. Simulation results show that at selected growth parameters for temperature, coverage, and growth interruption time, strain energy field in the substrate is the key factor that controls the pattern of island distribution. Furthermore, layer-by-layer growth of quantum dots is also simulated briefly, and vertical alignment is observed that could lead to progressively uniform island sizes and spatial ordering. 2. Since the misfit strain will be induced during the quantum dots epitaxial growth, the mechanical property of the grown semiconductors will be influenced. In this thesis, utilizing the basic continuum mechanics, we present a molecular dynamic prediction for the elastic stiffness C11, C12 and C 44 in strained silicon and InAs as functions

  8. 10 microsecond time resolution studies of Cygnus X-1

    SciTech Connect

    Wen, H. C.

    1997-06-01

    Time variability analyses have been applied to data composed of event times of X-rays emitted from the binary system Cygnus X-1 to search for unique black hole signatures. The X-ray data analyzed was collected at ten microsecond time resolution or better from two instruments, the High Energy Astrophysical Observatory (HEAO) A-1 detector and the Rossi X-ray Timing Explorer (XTE) Proportional Counter Array (PCA). HEAO A-1 and RXTE/PCA collected data from 1977--79 and from 1996 on with energy sensitivity from 1--25 keV and 2--60 keV, respectively. Variability characteristics predicted by various models of an accretion disk around a black hole have been searched for in the data. Drop-offs or quasi-periodic oscillations (QPOs) in the Fourier power spectra are expected from some of these models. The Fourier spectral technique was applied to the HEAO A-1 and RXTE/PCA data with careful consideration given for correcting the Poisson noise floor for instrumental effects. Evidence for a drop-off may be interpreted from the faster fall off in variability at frequencies greater than the observed breaks. Both breaks occur within the range of Keplerian frequencies associated with the inner edge radii of advection-dominated accretion disks predicted for Cyg X-1. The break between 10--20 Hz is also near the sharp rollover predicted by Nowak and Wagoner`s model of accretion disk turbulence. No QPOs were observed in the data for quality factors Q > 9 with a 95% confidence level upper limit for the fractional rms amplitude at 1.2% for a 16 M⊙ black hole.

  9. Erratum: Discovery of Microsecond Time Lags in Kilohertz QPOs

    NASA Astrophysics Data System (ADS)

    Vaughan, B. A.; van der Klis, M.; Méndez, M.; van Paradijs, J.; Wijnands, R. A. D.; Lewin, W. H. G.; Lamb, F. K.; Psaltis, D.; Kuulkers, E.; Oosterbroek, T.

    1998-12-01

    In the Letter ``Discovery of Microsecond Time Lags in Kilohertz QPOs'' by B. A. Vaughan, M. van der Klis, M. Méndez, J. van Paradijs, R. A. D. Wijnands, W. H. G. Lewin, F. K. Lamb, D. Psaltis, E. Kuulkers, and T. Oosterbroek (ApJ, 483, L115 [1997]), the reported time lags, while correct in magnitude, have a sign that is incorrect. We reanalyzed the data and checked the sign of our results using the hard lags in Cyg X-1 and GX 339-4 and the soft lags in the accreting millisecond pulsar SAX J1808.4-3658, as well as by using test signals. The true time delays for 4U 1608-52 are in the sense of the soft photons lagging the hard ones. Any lags in the reported energy and frequency ranges for 4U 0614+091 are between -80 and +15 μs and for 4U 1636-53 are between -50 and +25 μs (95% confidence), respectively, where a positive sign indicates a hard lag. This strengthens the conclusion of the Letter that in simple scattering models any time lags due to inverse Compton scattering are small and imply very small (<~1-10 km) scattering geometries. The time-lag data provide no independent evidence for inverse Compton scattering affecting the X-rays in these sources; another mechanism, perhaps related to the generation of the QPOs, must be operating to produce the soft lags in 4U 1608-52.

  10. Aromatic Polyamide Reverse-Osmosis Membrane: An Atomistic Molecular Dynamics Simulation.

    PubMed

    Wei, Tao; Zhang, Lin; Zhao, Haiyang; Ma, Heng; Sajib, Md Symon Jahan; Jiang, Hua; Murad, Sohail

    2016-10-06

    Polyamide (PA) membrane-based reverse-osmosis (RO) serves as one of the most important techniques for water desalination and purification. Fundamental understanding of PA RO membranes at the atomistic level is critical to enhance their separation capabilities, leading to significant societal and commercial benefits. In this paper, a fully atomistic molecular dynamics simulation was performed to investigate PA membrane. Our simulated cross-linked membrane exhibits structural properties similar to those reported in experiments. Our results also reveal the presence of small local two-layer slip structures in PA membrane with 70% cross-linking, primarily due to short-range anisotropic interactions among aromatic benzene rings. Inside the inhomogeneous polymeric structure of the membrane, water molecules show heterogeneous diffusivities and converge adjacent to polar groups. Increased diffusion of water molecules is observed through the less cross-linked pathways. The existence of the fast pathways for water permeation has no effect on membrane's salt rejections.

  11. Seamless elastic boundaries for atomistic calculations

    NASA Astrophysics Data System (ADS)

    Pastewka, Lars; Sharp, Tristan A.; Robbins, Mark O.

    2012-08-01

    Modeling interfacial phenomena often requires both a detailed atomistic description of surface interactions and accurate calculations of long-range deformations in the substrate. The latter can be efficiently obtained using an elastic Green's function if substrate deformations are small. We present a general formulation for rapidly computing the Green's function for a planar surface given the interatomic interactions, and then coupling the Green's function to explicit atoms. The approach is fast, avoids ghost forces, and is not limited to nearest-neighbor interactions. The full system comprising explicit interfacial atoms and an elastic substrate is described by a single Hamiltonian and interactions in the substrate are treated exactly up to harmonic order. This concurrent multiscale coupling provides simple, seamless elastic boundary conditions for atomistic simulations where near-surface deformations occur, such as nanoindentation, contact, friction, or fracture. Applications to surface relaxation and contact are used to test and illustrate the approach.

  12. Atomistic molecular dynamics simulations of shock compressed quartz

    NASA Astrophysics Data System (ADS)

    Farrow, M. R.; Probert, M. I. J.

    2011-07-01

    Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)], 10.1103/PhysRevB.43.5068 to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the β-quartz phase over the α-quartz phase at zero-temperature, and that there is a β → α phase-transition at 6 GPa.

  13. Understanding and Improving High Voltage Vacuum Insulators for Microsecond Pulses

    SciTech Connect

    Javedani, J B; Goerz, D A; Houck, T L; Lauer, E J; Speer, R D; Tully, L K; Vogtlin, G E; White, A D

    2007-03-05

    High voltage insulation is one of the main areas of pulsed power research and development, and dielectric breakdown is usually the limiting factor in attaining the highest possible performance in pulsed power devices. For many applications the delivery of pulsed power into a vacuum region is the most critical aspect of operation. The surface of an insulator exposed to vacuum can fail electrically at an applied field more than an order or magnitude below the bulk dielectric strength of the insulator. This mode of breakdown, called surface flashover, imposes serious limitations on the power flow into a vacuum region. This is especially troublesome for applications where high voltage conditioning of the insulator and electrodes is not practical and for applications where relatively long pulses, on the order of several microseconds, are required. The goal of this project is to establish a sound fundamental understanding of the mechanisms that lead to surface flashover, and then evaluate the most promising techniques to improve vacuum insulators and enable high voltage operation at stress levels near the intrinsic bulk breakdown limits of the material. The approach we proposed and followed was to develop this understanding through a combination of theoretical and computation methods coupled with experiments to validate and quantify expected behaviors. In this report we summarize our modeling and simulation efforts, theoretical studies, and experimental investigations. The computational work began by exploring the limits of commercially available codes and demonstrating methods to examine field enhancements and defect mechanisms at microscopic levels. Plasma simulations with particle codes used in conjunction with circuit models of the experimental apparatus enabled comparisons with experimental measurements. The large scale plasma (LSP) particle-in-cell (PIC) code was run on multiprocessor platforms and used to simulate expanding plasma conditions in vacuum gap regions

  14. Long-time atomistic simulations with the Parallel Replica Dynamics method

    NASA Astrophysics Data System (ADS)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  15. First Principles Atomistic Model for Carbon-Doped Boron Suboxide

    DTIC Science & Technology

    2014-09-01

    First Principles Atomistic Model for Carbon-Doped Boron Suboxide by Amol B Rahane, Jennifer S Dunn, and Vijay Kumar ARL-TR-7106...2014 First Principles Atomistic Model for Carbon-Doped Boron Suboxide Amol B Rahane Dr Vijay Kumar Foundation 1969 Sector 4 Gurgaon...Final 3. DATES COVERED (From - To) October 2013–July 2014 4. TITLE AND SUBTITLE First Principles Atomistic Model for Carbon-Doped Boron Suboxide

  16. Edge energies : atomistic calculations of a continuum quantity.

    SciTech Connect

    Hamilton, John C.

    2005-06-01

    Controlling the properties of self-assembled nanostructures requires controlling their shape. Size-dependent shape transitions, frequently observed at nanolength scales, are commonly attributed to edge energy effects. To rigorously test such theories against experiment, quantitative atomistic calculations of edge energies are essential, yet none exist. I describe a fundamental ambiguity in the atomistic definition of edge energies, propose a definition based on equimolar dividing surfaces, and present an atomistic calculation of edge energies for Pd clusters.

  17. Microsecond kinetics in model single- and double-stranded amylose polymers.

    PubMed

    Sattelle, Benedict M; Almond, Andrew

    2014-05-07

    Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Starch granule packing, gelation and inclusion-complex formation result from finely balanced macromolecular kinetics that have eluded precise experimental quantification. Here, graphics processing unit (GPU) accelerated multi-microsecond aqueous simulations are employed to explore conformational kinetics in model single- and double-stranded amylose. The all-atom dynamics concur with prior X-ray and NMR data while surprising and previously overlooked microsecond helix-coil, glycosidic linkage and pyranose ring exchange are hypothesized. In a dodecasaccharide, single-helical collapse was correlated with linkages and rings transitioning from their expected syn and (4)C1 chair conformers. The associated microsecond exchange rates were dependent on proximity to the termini and chain length (comparing hexa- and trisaccharides), while kinetic features of dodecasaccharide linkage and ring flexing are proposed to be a good model for polymers. Similar length double-helices were stable on microsecond timescales but the parallel configuration was sturdier than the antiparallel equivalent. In both, tertiary organization restricted local chain dynamics, implying that simulations of single amylose strands cannot be extrapolated to dimers. Unbiased multi-microsecond simulations of amylose are proposed as a valuable route to probing macromolecular kinetics in water, assessing the impact of chemical modifications on helical stability and accelerating the development of new biotechnologies.

  18. Atomistic deformation mechanisms in twinned copper nanospheres.

    PubMed

    Bian, Jianjun; Niu, Xinrui; Zhang, Hao; Wang, Gangfeng

    2014-01-01

    In the present study, we perform molecular dynamic simulations to investigate the compression response and atomistic deformation mechanisms of twinned nanospheres. The relationship between load and compression depth is calculated for various twin spacing and loading directions. Then, the overall elastic properties and the underlying plastic deformation mechanisms are illuminated. Twin boundaries (TBs) act as obstacles to dislocation motion and lead to strengthening. As the loading direction varies, the plastic deformation transfers from dislocations intersecting with TBs, slipping parallel to TBs, and then to being restrained by TBs. The strengthening of TBs depends strongly on the twin spacing.

  19. First Demonstration of Laser-Assisted Charge Exchange for Microsecond Duration H- Beams

    NASA Astrophysics Data System (ADS)

    Cousineau, Sarah; Rakhman, Abdurahim; Kay, Martin; Aleksandrov, Alexander; Danilov, Viatcheslav; Gorlov, Timofey; Liu, Yun; Plum, Michael; Shishlo, Andrei; Johnson, David

    2017-02-01

    This Letter reports on the first demonstration of laser-assisted H- charge exchange for microsecond duration H- beam pulses. Laser-assisted charge exchange injection is a breakthrough technology that overcomes long-standing limitations associated with the traditional method of producing high intensity, time structured beams of protons in accelerators via the use of carbon foils for charge exchange injection. The central theme of this experiment is the demonstration of novel techniques that reduce the laser power requirement to allow high efficiency stripping of microsecond duration beams with commercial laser technology.

  20. Design and Performance of a 560-Microsecond Ku-Band Binary Fiber-Optic Delay Line

    DTIC Science & Technology

    2015-05-14

    photodiode. 5. Press the laser power button on the front panel. The ring illuminator on the button will light. This button activates the current drivers for...Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/5650--15-9545 Design and Performance of a 560-Microsecond Ku-Band Binary Fiber -Optic Delay...THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Design and Performance of a 560-Microsecond Ku-Band Binary Fiber -Optic Delay Line Joseph M

  1. An Optimization-based Atomistic-to-Continuum Coupling Method

    SciTech Connect

    Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell; Shapeev, Alexander V.

    2014-08-21

    In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally, we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.

  2. A robust, coupled approach for atomistic-continuum simulation.

    SciTech Connect

    Aubry, Sylvie; Webb, Edmund Blackburn, III; Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John; Kimmer, Christopher J.

    2004-09-01

    This report is a collection of documents written by the group members of the Engineering Sciences Research Foundation (ESRF), Laboratory Directed Research and Development (LDRD) project titled 'A Robust, Coupled Approach to Atomistic-Continuum Simulation'. Presented in this document is the development of a formulation for performing quasistatic, coupled, atomistic-continuum simulation that includes cross terms in the equilibrium equations that arise due to kinematic coupling and corrections used for the calculation of system potential energy to account for continuum elements that overlap regions containing atomic bonds, evaluations of thermo-mechanical continuum quantities calculated within atomistic simulations including measures of stress, temperature and heat flux, calculation used to determine the appropriate spatial and time averaging necessary to enable these atomistically-defined expressions to have the same physical meaning as their continuum counterparts, and a formulation to quantify a continuum 'temperature field', the first step towards constructing a coupled atomistic-continuum approach capable of finite temperature and dynamic analyses.

  3. An Optimization-based Atomistic-to-Continuum Coupling Method

    DOE PAGES

    Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell; ...

    2014-08-21

    In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally,more » we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.« less

  4. Atomistic simulations of nanoscale electrokinetic transport

    NASA Astrophysics Data System (ADS)

    Liu, Jin; Wang, Moran; Chen, Shiyi; Robbins, Mark

    2011-11-01

    An efficient and accurate algorithm for atomistic simulations of nanoscale electrokinetic transport will be described. The long-range interactions between charged molecules are treated using the Particle-Particle Particle-Mesh method and the Poisson equation for the electric potential is solved using an efficient multi-grid method in physical space. Using this method, we investigate two important applications in electrokinetic transport: electroosmotic flow in rough channels and electowetting on dielectric (EWOD). Simulations of electroosmotic and pressure driven flow in exactly the same geometries show that surface roughness has a much more pronounced effect on electroosmotic flow. Analysis of local quantities shows that this is because the driving force in electroosmotic flow is localized near the wall where the charge density is high. In atomistic simulations of EWOD, we find the contact angle follows the continuum theory at low voltages and always saturates at high voltages. Based on our results, a new mechanism for saturation is identified and possible techniques for controlling saturation are proposed. This work is supported by the National Science Foundation under Grant No. CMMI 0709187.

  5. Atomistic Monte Carlo Simulation of Lipid Membranes

    PubMed Central

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. PMID:24469314

  6. Atomistic to continuum modeling of solidification microstructures

    SciTech Connect

    Karma, Alain; Tourret, Damien

    2015-09-26

    We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked to experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.

  7. Atomistic to continuum modeling of solidification microstructures

    DOE PAGES

    Karma, Alain; Tourret, Damien

    2015-09-26

    We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked tomore » experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.« less

  8. Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation

    PubMed Central

    Huang, Nan-Lan; Lin, Jung-Hsin

    2015-01-01

    Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases. PMID:26150421

  9. Parallel line raster eliminates ambiguities in reading timing of pulses less than 500 microseconds apart

    NASA Technical Reports Server (NTRS)

    Horne, A. P.

    1966-01-01

    Parallel horizontal line raster is used for precision timing of events occurring less than 500 microseconds apart for observation of hypervelocity phenomena. The raster uses a staircase vertical deflection and eliminates ambiguities in reading timing of pulses close to the end of each line.

  10. Plasma Emission Spectra of Opuntia Nopalea Obtained with Microsecond Laser Pulses

    NASA Astrophysics Data System (ADS)

    Ponce, L.; Flores, T.; Arronte, A.; Flores, A.

    2008-04-01

    Laser-induced Plasma Spectroscopy was performed during the spines ablation of Opuntia by using Nd:YAG microsecond laser pulses. The results show strong absorption in Glochids that causes the intense electronic noise on the spectra. This process is consider suitable for practical elimination of spines in alimentary products like opuntia.

  11. Plasma Emission Spectra of Opuntia Nopalea Obtained with Microsecond Laser Pulses

    SciTech Connect

    Ponce, L.; Flores, T.; Arronte, A.; Flores, A.

    2008-04-15

    Laser-induced Plasma Spectroscopy was performed during the spines ablation of Opuntia by using Nd:YAG microsecond laser pulses. The results show strong absorption in Glochids that causes the intense electronic noise on the spectra. This process is consider suitable for practical elimination of spines in alimentary products like opuntia.

  12. An atomistic model of slip formation

    NASA Technical Reports Server (NTRS)

    Halicioglu, T.; Cooper, D. M.

    1984-01-01

    The results of an atomistic model for the simulation of the early stages of crack initiation in a two-dimensional triangular lattice are presented. In the current model, each particle in the system is treated discretely and assumed to be interacting with the surrounding particles via Lennard-Jones potentials. A uniaxial load (in incremental elongations) is applied to the rectangular two-dimensional slab in either the x or the y direction. After each incremental elongation the system is equilibrated using a static method. Initially, elastic behavior in the x and y directions is observed. Continued elongation results in plastic deformation. In lattices with point defects, the defects first move to the surface, creating vacancies which trigger plastic deformation.

  13. Quantum Corrections to the 'Atomistic' MOSFET Simulations

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Slavcheva, G.; Kaya, S.; Balasubramaniam, R.

    2000-01-01

    We have introduced in a simple and efficient manner quantum mechanical corrections in our 3D 'atomistic' MOSFET simulator using the density gradient formalism. We have studied in comparison with classical simulations the effect of the quantum mechanical corrections on the simulation of random dopant induced threshold voltage fluctuations, the effect of the single charge trapping on interface states and the effect of the oxide thickness fluctuations in decanano MOSFETs with ultrathin gate oxides. The introduction of quantum corrections enhances the threshold voltage fluctuations but does not affect significantly the amplitude of the random telegraph noise associated with single carrier trapping. The importance of the quantum corrections for proper simulation of oxide thickness fluctuation effects has also been demonstrated.

  14. Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids.

    PubMed

    Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily

    2014-08-06

    Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space-time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space-time, a novel hybrid atomistic-fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided.

  15. Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

    PubMed Central

    Pasi, Marco; Maddocks, John H.; Lavery, Richard

    2015-01-01

    Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied contain all 136 distinct tetranucleotides and we are thus able to make a comprehensive analysis of base sequence effects. Using a recently developed curvilinear helicoidal coordinate method we are able to analyze the details of ion populations and densities within the major and minor grooves and in the space surrounding DNA. The results show higher ion populations than have typically been observed in earlier studies and sequence effects that go beyond the nature of individual base pairs or base pair steps. We also show that, in some special cases, ion distributions converge very slowly and, on a microsecond timescale, do not reflect the symmetry of the corresponding base sequence. PMID:25662221

  16. Use of microsecond current prepulse for dramatic improvements of wire array Z-pinch implosion

    SciTech Connect

    Calamy, H.; Lassalle, F.; Loyen, A.; Zucchini, F.; Chittenden, J. P.; Hamann, F.; Maury, P.; Georges, A.; Bedoch, J. P.; Morell, A.

    2008-01-15

    The Sphinx machine [F. Lassalle et al., 'Status on the SPHINX machine based on the 1microsecond LTD technology'] based on microsecond linear transformer driver (LTD) technology is used to implode an aluminium wire array with an outer diameter up to 140 mm and maximum current from 3.5 to 5 MA. 700 to 800 ns implosion Z-pinch experiments are performed on this driver essentially with aluminium. Best results obtained before the improvement described in this paper were 1-3 TW radial total power, 100-300 kJ total yield, and 20-30 kJ energy above 1 keV. An auxiliary generator was added to the Sphinx machine in order to allow a multi microsecond current to be injected through the wire array load before the start of the main current. Amplitude and duration of this current prepulse are adjustable, with maxima {approx}10 kA and 50 {mu}s. This prepulse dramatically changes the ablation phase leading to an improvement of the axial homogeneity of both the implosion and the final radiating column. Total power was multiplied by a factor of 6, total yield by a factor of 2.5 with a reproducible behavior. This paper presents experimental results, magnetohydrodynamic simulations, and analysis of the effect of such a long current prepulse.

  17. Pulsed Electron Beam Water Radiolysis for Sub-Microsecond Hydroxyl Radical Protein Footprinting

    PubMed Central

    Watson, Caroline; Janik, Ireneusz; Zhuang, Tiandi; Charvátová, Olga; Woods, Robert J.; Sharp, Joshua S.

    2009-01-01

    Hydroxyl radical footprinting is a valuable technique for studying protein structure, but care must be taken to ensure that the protein does not unfold during the labeling process due to oxidative damage. Footprinting methods based on sub-microsecond laser photolysis of peroxide that complete the labeling process faster than the protein can unfold have been recently described; however, the mere presence of large amounts of hydrogen peroxide can also cause uncontrolled oxidation and minor conformational changes. We have developed a novel method for sub-microsecond hydroxyl radical protein footprinting using a pulsed electron beam from a 2 MeV Van de Graaff electron accelerator to generate a high concentration of hydroxyl radicals by radiolysis of water. The amount of oxidation can be controlled by buffer composition, pulsewidth, dose, and dissolved nitrous oxide gas in the sample. Our results with ubiquitin and β-lactoglobulin A demonstrate that one sub-microsecond electron beam pulse produces extensive protein surface modifications. Highly reactive residues that are buried within the protein structure are not oxidized, indicating that the protein retains its folded structure during the labeling process. Time-resolved spectroscopy indicates that the major part of protein oxidation is complete in a timescale shorter than that of large scale protein motions. PMID:19265387

  18. Atomistic modeling of thermodynamic equilibrium of plutonium

    NASA Astrophysics Data System (ADS)

    Lee, Tongsik; Valone, Steve; Baskes, Mike; Chen, Shao-Ping; Lawson, Andrew

    2012-02-01

    Plutonium metal has complex thermodynamic properties. Among its six allotropes at ambient pressure, the fcc delta-phase exhibits a wide range of anomalous behavior: extraordinarily high elastic anisotropy, largest atomic volume despite the close-packed structure, negative thermal expansion, strong elastic softening at elevated temperature, and extreme sensitivity to dilute alloying. An accurate description of these thermodynamic properties goes far beyond the current capability of first-principle calculations. An elaborate modeling strategy at the atomic level is hence an urgent need. We propose a novel atomistic scheme to model elemental plutonium, in particular, to reproduce the anomalous characteristics of the delta-phase. A modified embedded atom method potential is fitted to two energy-volume curves that represent the distinct electronic states of plutonium in order to embody the mechanism of the two-state model of Weiss, in line with the insight originally proposed by Lawson et al. [Philos. Mag. 86, 2713 (2006)]. By the use of various techniques in Monte Carlo simulations, we are able to provide a unified perspective of diverse phenomenological aspects among thermal expansion, elasticity, and phase stability.

  19. NiTi superelasticity via atomistic simulations

    NASA Astrophysics Data System (ADS)

    Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin

    2015-12-01

    The NiTi shape memory alloys (SMAs) are promising candidates for the next-generation multifunctional materials. These materials are superelastic i.e. they can fully recover their original shape even after fairly large inelastic deformations once the mechanical forces are removed. The superelasticity reportedly stems from atomic scale crystal transformations. However, very few computer simulations have emerged, elucidating the transformation mechanisms at the discrete lattice level, which underlie the extraordinary strain recoverability. Here, we conduct breakthrough molecular dynamics modelling on the superelastic behaviour of the NiTi single crystals, and unravel the atomistic genesis thereof. The deformation recovery is clearly traced to the reversible transformation between austenite and martensite crystals through simulations. We examine the mechanistic origin of the tension-compression asymmetries and the effects of pressure/temperature/strain rate variation isolatedly. Hence, this work essentially brings a new dimension to probing the NiTi performance based on the mesoscale physics under more complicated thermo-mechanical loading scenarios.

  20. Atomistic simulation on indented defects in silicon.

    PubMed

    Trandinh, Long; Cheon, Seong Sik; Kang, Woojong

    2013-12-01

    Silicon is known as one of the widely used materials in electronic fields for its excellent semiconductive characteristics. However, these characteristics are vulnerable to internal defects, which randomly exist in any materials. In the present study, defects in single crystalline silicon thin film were investigated by atomistic simulation of nano-indentation at zero temperature. The Tersoff potential and the spherical indenter were applied to the model of silicon. The symmetric axis parameter method is novelly proposed to identify defects in the diamond cubic structure. Under the nanoindentation condition, the ring slip appears close to the indentation region on the free surface and propagates along with [110]/(111). The dislocation is initiated closely to the ring slip and emitted on the (111) plane by the dissociation into two partial dislocations. It was found that the symmetric axis parameter method successfully separated the perfect dislocations, the partial dislocations and the stacking fault from perfect structure, i.e., diamond cubic structure, even though it was not able to distinguish between glide set and shuffle set dislocations.

  1. Strain Functionals for Characterizing Atomistic Geometries

    NASA Astrophysics Data System (ADS)

    Kober, Edward; Rudin, Sven

    The development of a set of strain tensor functionals that are capable of characterizing arbitrarily ordered atomistic structures is described. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the moments of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. Other methods used to characterize atomic structures, such as the Steinhardt parameters or the centrosymmetry metric, can be derived from this more general approach. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. They allow material phases, deformations, and a large number of defect structures to be readily identified and classified. Applications to the analysis of shock-loaded samples of Cu, Ta and Ti will be presented. This strain functional basis can also then be used for developing interatomic potential functions, and an initial application to Cu will be presented.

  2. Free energy of steps using atomistic simulations

    NASA Astrophysics Data System (ADS)

    Freitas, Rodrigo; Frolov, Timofey; Asta, Mark

    The properties of solid-liquid interfaces are known to play critical roles in solidification processes. Particularly special importance is given to thermodynamic quantities that describe the equilibrium state of these surfaces. For example, on the solid-liquid-vapor heteroepitaxial growth of semiconductor nanowires the crystal nucleation process on the faceted solid-liquid interface is influenced by the solid-liquid and vapor-solid interfacial free energies, and also by the free energies of associated steps at these faceted interfaces. Crystal-growth theories and mesoscale simulation methods depend on quantitative information about these properties, which are often poorly characterized from experimental measurements. In this work we propose an extension of the capillary fluctuation method for calculation of the free energy of steps on faceted crystal surfaces. From equilibrium atomistic simulations of steps on (111) surfaces of Copper we computed accurately the step free energy for different step orientations. We show that the step free energy remains finite at all temperature up to the melting point and that the results obtained agree with the more well established method of thermodynamic integration if finite size effects are taken into account. The research of RF and MA at UC Berkeley were supported by the US National Science Foundation (Grant No. DMR-1105409). TF acknowledges support through a postdoctoral fellowship from the Miller Institute for Basic Research in Science.

  3. Atomistic Simulation of Initiation in Hexanitrostilbene

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  4. Stress in titania nanoparticles: An atomistic study

    SciTech Connect

    Darkins, Robert; Sushko, Maria L.; Liu, Jun; Duffy, Dorothy M.

    2014-04-24

    Stress engineering is becoming an increasingly important method for controlling electronic, optical, and magnetic properties of nanostructures, although the concept of stress is poorly defined at the nanoscale. We outline a methodology for computing bulk and surface stress in nanoparticles using atomistic simulation. The method is applicable to ionic and non- ionic materials alike and may be extended to other nanostructures. We apply it to spherical anatase nanoparticles ranging from 2 to 6 nm in diameter and obtain a surface stress of 0.89 N/m, in agreement with experimental measurements. Based on the extent that stress inhomogeneities at the surface are transmitted into the bulk, two characteristic length-scales are identified: below 3 nm bulk and surface regions cannot be defined and the available analytic theories for stress are not applicable, and above about 5 nm the stress becomes well-described by the theoretical Young-Laplace equation. The effect of a net surface charge on the bulk stress is also investigated. It is found that moderate surface charges can induce significant bulk stresses, on the order of 100 MPa, in nanoparticles within this size range.

  5. Anomalous dependence of the lasing parameters of dye solutions on the spectrum of microsecond pump laser pulses

    SciTech Connect

    Tarkovsky, V V; Kurstak, V Yu; Anufrik, S S

    2003-10-31

    The anomalous dependence of the lasing parameters of ethanol solutions of coumarin, rhodamine, oxazine, and laser dyes of other classes on the spectrum of microsecond pump laser pulses is found. The dependence is determined by the shape of the induced singlet - singlet absorption spectra and absorption spectra of short-lived photoproducts. The elucidation of the influence of these factors makes it possible to choose optimal pump spectra and to enhance the efficiency and stability of microsecond dye lasers. (active media)

  6. Atomistic simulation of Voronoi-based coated nanoporous metals

    NASA Astrophysics Data System (ADS)

    Onur Yildiz, Yunus; Kirca, Mesut

    2017-02-01

    In this study, a new method developed for the generation of periodic atomistic models of coated and uncoated nanoporous metals (NPMs) is presented by examining the thermodynamic stability of coated nanoporous structures. The proposed method is mainly based on the Voronoi tessellation technique, which provides the ability to control cross-sectional dimension and slenderness of ligaments as well as the thickness of coating. By the utilization of the method, molecular dynamic (MD) simulations of randomly structured NPMs with coating can be performed efficiently in order to investigate their physical characteristics. In this context, for the purpose of demonstrating the functionality of the method, sample atomistic models of Au/Pt NPMs are generated and the effects of coating and porosity on the thermodynamic stability are investigated by using MD simulations. In addition to that, uniaxial tensile loading simulations are performed via MD technique to validate the nanoporous models by comparing the effective Young’s modulus values with the results from literature. Based on the results, while it is demonstrated that coating the nanoporous structures slightly decreases the structural stability causing atomistic configurational changes, it is also shown that the stability of the atomistic models is higher at lower porosities. Furthermore, adaptive common neighbour analysis is also performed to identify the stabilized atomistic structure after the coating process, which provides direct foresights for the mechanical behaviour of coated nanoporous structures.

  7. Atomistic modeling and simulation of nanopolycrystalline solids

    NASA Astrophysics Data System (ADS)

    Yang, Zidong

    In the past decades, nanostructured materials have opened new and fascinating avenues for research. Nanopolycrystalline solids, which consist of nano-sized crystalline grains and significant volume fractions of amorphous grain boundaries, are believed to have substantially different response to the thermal-mechanical-electric-magnetic loads, as compared to the response of single-crystalline materials. Nanopolycrystalline materials are expected to play a key role in the next generation of smart materials. This research presents a framework (1) to generate full atomistic models, (2) to perform non-equilibrium molecular dynamics simulations, and (3) to study multi-physics phenomena of nanopolycrystalline solids. This work starts the physical model and mathematical representation with the framework of molecular dynamics. In addition to the latest theories and techniques of molecular dynamics simulations, this work implemented principle of objectivity and incorporates multi-physics features. Further, a database of empirical interatomic potentials is established and the combination scheme for potentials is revisited, which enables investigation of a broad spectrum of chemical elements (as in periodic table) and compounds (such as rocksalt, perovskite, wurtzite, diamond, etc.). The configurational model of nanopolycrystalline solids consists of two spatial components: (1) crystalline grains, which can be obtained through crystal structure optimization, and (2) amorphous grain boundaries, which can be obtained through amorphization process. Therefore, multi-grain multi-phase nanopolycrystalline material system can be constructed by partitioning the space for grains, followed by filling the inter-grain space with amorphous grain boundaries. Computational simulations are performed on several representative crystalline materials and their mixture, such as rocksalt, perovskite and diamond. Problems of relaxation, mechanical loading, thermal stability, heat conduction

  8. Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids

    PubMed Central

    Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily

    2014-01-01

    Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space–time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space–time, a novel hybrid atomistic–fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided. PMID:24982246

  9. Microsecond fiber laser pumped, single-frequency optical parametric oscillator for trace gas detection.

    PubMed

    Barria, Jessica Barrientos; Roux, Sophie; Dherbecourt, Jean-Baptiste; Raybaut, Myriam; Melkonian, Jean-Michel; Godard, Antoine; Lefebvre, Michel

    2013-07-01

    We report on the first microsecond doubly resonant optical parametric oscillator (OPO). It is based on a nested cavity OPO architecture allowing single longitudinal mode operation and low oscillation threshold (few microjoule). The combination with a master oscillator-power amplifier fiber pump laser provides a versatile optical source widely tunable in the 3.3-3.5 μm range with an adjustable pulse repetition rate (from 40 to 100 kHz), high duty cycle (~10(-2)) and mean power (up to 25 mW in the idler beam). The potential for trace gas sensing applications is demonstrated through photoacoustic detection of atmospheric methane.

  10. Cold Microsecond Spark Discharge Plasma Production of Active Species and Their Delivery into Tissue

    NASA Astrophysics Data System (ADS)

    Dobrynin, Danil; Fridman, Gregory; Friedman, Gary; Fridman, Alexander

    Mechanisms of the Plasma Medicine techniques, first of all plasma ­sterilization and healing of wounds, are immediately related to the effects of ­reactive neutral and charged species produced by plasma and delivered to the treated object. Here we report experimental results on measurement of production of reactive ­oxygen species in liquid media and their delivery into tissue by microsecond spark discharge plasma. We also show that a simple agarose gel model may closely mimic physicochemical characteristics of tissue.

  11. Microsecond Scale Vibrational Spectroscopic Imaging by Multiplex Stimulated Raman Scattering Microscopy

    PubMed Central

    Liao, Chien-Sheng; Slipchenko, Mikhail N.; Wang, Ping; Li, Junjie; Lee, Seung-Young; Oglesbee, Robert A.; Cheng, Ji-Xin

    2015-01-01

    Real-time vibrational spectroscopic imaging is desired for monitoring cellular states and cellular processes in a label-free manner. Raman spectroscopic imaging of highly dynamic systems is inhibited by relatively slow spectral acquisition on millisecond to second scale. Here, we report microsecond scale vibrational spectroscopic imaging by lock-in free parallel detection of spectrally dispersed stimulated Raman scattering signal. Using a homebuilt tuned amplifier array, our method enables Raman spectral acquisition, within the window defined by the broadband pulse, at the speed of 32 microseconds and with close to shot-noise limited detection sensitivity. Incorporated with multivariate curve resolution analysis, our platform allows compositional mapping of lipid droplets in single live cells, observation of intracellular retinoid metabolism, discrimination of fat droplets from protein-rich organelles in Caenorhabditis elegans, spectral detection of fast flowing tumor cells, and monitoring drug diffusion through skin tissue in vivo. The reported technique opens new opportunities for compositional analysis of cellular compartment in a microscope setting and high-throughput spectral profiling of single cells in a flow cytometer setting. PMID:26167336

  12. A study of low-current-density microsecond electron beam diodes

    NASA Astrophysics Data System (ADS)

    Ramirez, J. J.; Cook, D. L.

    1980-09-01

    The performances of various field emitters and plasma-injected diodes for the generation of low-current-density microsecond electron beams to be used in gas laser excitation are investigated and compared. The output from a microsecond high-voltage pulse-forming network was fed to a large-area vacuum diode containing metal-oxide matrix and carbon fiber field emitters and to diodes filled with plasma and containing preformed plasma on the cathode surface. Of the field emitters, a brush cathode made with 10-micron carbon filaments is found to give the best performance, with emission at fields as low as 10 kV/cm, space charge-limited flow established in 60 nsec and apparent gap closure velocities of 1.5 cm/sec. Although substantial control of the diode impedance was obtained when the plasma was allowed to fill the anode-cathode volume, the constraining of the plasma to the cathode surface is found to improve the uniformity and reproducibility of anode current density, with apparent gap closure velocities as low as 2 cm/sec.

  13. Microsecond Time Resolution Optical Photometry using a H.E.S.S. Cherenkov Telescope

    SciTech Connect

    Deil, Christoph; Domainko, Wilfried; Hermann, German

    2008-02-22

    We have constructed an optical photometer with microsecond time resolution, which is currently being operated on one of the H.E.S.S. telescopes. H.E.S.S. is an array of four Cherenkov telescopes, each with a 107 m{sup 2} mirror, located in the Khomas highland in Namibia. In its normal mode of operation H.E.S.S. observes Cherenkov light from air showers generated by very high energy gamma-rays in the upper atmosphere. Our detector consists of seven photomultipliers, one in the center to record the lightcurve from the target and six concentric photomultipliers as a veto system to reject disturbing signals e.g. from meteorites or lightning at the horizon. The data acquisition system has been designed to continuously record the signals with zero deadtime. The Crab pulsar has been observed to verify the performance of the instrument and the GPS timing system. Compact galactic targets were observed to search for flares on timescales of a few microseconds to {approx}100 ms. The design and sensitivity of the instrument as well as the data analysis method are presented.

  14. Development of a microsecond X-ray protein footprinting facility at the Advanced Light Source

    PubMed Central

    Gupta, Sayan; Celestre, Richard; Petzold, Christopher J.; Chance, Mark R.; Ralston, Corie

    2014-01-01

    X-ray footprinting (XF) is an important structural biology tool used to determine macromolecular conformations and dynamics of both nucleic acids and proteins in solution on a wide range of timescales. With the impending shut-down of the National Synchrotron Light Source, it is ever more important that this tool continues to be developed at other synchrotron facilities to accommodate XF users. Toward this end, a collaborative XF program has been initiated at the Advanced Light Source using the white-light bending-magnet beamlines 5.3.1 and 3.2.1. Accessibility of the microsecond time regime for protein footprinting is demonstrated at beamline 5.3.1 using the high flux density provided by a focusing mirror in combination with a micro-capillary flow cell. It is further reported that, by saturating samples with nitrous oxide, the radiolytic labeling efficiency is increased and the imprints of bound versus bulk water can be distinguished. These results both demonstrate the suitability of the Advanced Light Source as a second home for the XF experiment, and pave the way for obtaining high-quality structural data on complex protein samples and dynamics information on the microsecond timescale. PMID:24971962

  15. Three Dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Wijesinghe, Sanith; Hornung, Richard; Garcia, Alejandro; Hadjiconstantinou, Nicolas

    2002-11-01

    An adaptive mesh and algorithmic refinement (AMAR) scheme to model multi-scale, compressible continuum-atomistic hydrodynamics is presented. The AMAR technique applies the atomistic description as the finest level of refinement in regions where the continuum description is expected to fail, such as in regions of high flow gradients and discontinous material interfaces. In the current implementation the atomistic description is provided by the direct simulation Monte Carlo (DSMC). The continuum flow is modeled using the compressible flow Euler equations and is solved using a second order Godunov scheme. Coupling is achieved by conservation of fluxes across the continuum-atomistic grid boundaries. The AMAR data structures are supported by a C++ object oriented framework (Structured Adaptive Mesh Refinement Application Infrastructure - SAMRAI) which allows for efficient parallel implementation. Current work is focused on extending AMAR to simulations of gas mixtures. This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract number W-7405-Eng-48.

  16. Atomistic and Coarse-grained Simulations of Hexabenzocoronene Crystals

    NASA Astrophysics Data System (ADS)

    Ziogos, G.; Megariotis, G.; Theodorou, D. N.

    2016-08-01

    This study concerns atomistic and coarse-grained Molecular Dynamics simulations of pristine hexabenzocoronene (HBC) molecular crystals. HBC is a symmetric graphene flake of nanometric size that falls in the category of polyaromatic hydrocarbons, finding numerous applications in the field of organic electronics. The HBC molecule is simulated in its crystalline phase initially by means of an all-atom representation, where the molecules self- organize into well aligned molecular stacks, which in turn create a perfect monoclinic molecular crystal. The atomistic model reproduces fairly well the structural experimental properties and thus can be used as a reliable starting point for the development of a coarsegrained model following a bottom-up approach. The coarse-grained model is developed by applying Iterative Boltzmann Inversion, a systematic coarse-graining method which reproduces a set of target atomistic radial distribution functions and intramolecular distributions at the coarser level of description. This model allows the simulation of HBC crystals over longer time and length scales. The crystalline phase is analyzed in terms of the Saupe tensor and thermomechanical properties are probed at the atomistic level.

  17. Bridging the macroscopic and atomistic descriptions of the electrocaloric effect.

    PubMed

    Ponomareva, I; Lisenkov, S

    2012-04-20

    First-principles-based simulations are used to simulate the electrocaloric effect (ECE) in Ba(0.5)Sr(0.5)TiO(3) alloys. In analogy with experimental studies we simulate the effect directly and indirectly (via the use of Maxwell thermodynamics). Both direct and indirect simulations utilize the same atomistic framework that allows us to compare them in a systematic way and with an atomistic precision for the very first time. Such precise comparison allows us to provide a bridge between the atomistic and macroscopic descriptions of the ECE and identify the factors that may critically compromise or even destroy their equivalence. Our computational data reveal the intrinsic features of ECE in ferroelectrics with multiple ferroelectric transitions and confirm the potential of these materials to exhibit giant electrocaloric response. The coexistence of negative and positive ECE in one material as well as an unusual field-driven transition between them is predicted, explained at an atomistic level, and proposed as a potential way to enhance the electrocaloric efficiency.

  18. A concurrent atomistic-continuum methodolody and its applications

    NASA Astrophysics Data System (ADS)

    Xiong, Liming

    The objective of my dissertation research is to develop a concurrent atomistic-continuum (CAC) modeling and simulation tool for crystalline solids. The theoretical foundation of the methodology is a newly developed atomistic field theory (AFT). In this work, finite element method (FEM) is implemented to pursue the numerical solutions of the governing equations in AFT, where atomistic information has been naturally built in. Since those governing equations are constructed in terms of local densities, in the finite element implementations, different meshes can be used in the regions of different concerns. When the finest mesh is used, there is a finite element node corresponding to each lattice point embedded with multiple atoms, the computational model becomes identical to a fully atomistic model. When a coarse mesh is used, that is, the size of the finite element is much larger than lattice spacing, the majority of the degrees of freedom are eliminated and the computational cost can be largely reduced, the resulting model is a coarse grained (CG) model. When the coarse mesh and finest mesh are concurrently implemented within one computational model, that is, the finest mesh is used within the critical regions and the coarser mesh is used away from the critical regions. The resulting model is naturally a CAC model governed by one single theoretical framework. With much less computational resources requested than that by fully atomistic simulations, the simulation packages developed in this work has been applied to model and simulate critical phenomena such as dislocations, phase transformations and fracture in various crystalline materials including ceramics such as MgO, silicon and silicon carbide and also metals such as copper under mechanical loading. All of the simulations conducted in this work are verified through the direct comparisons with that from the corresponding full molecular dynamics (MD) simulations. In addition, the limitations, potential

  19. Study of Vacuum Insulator Flashover for Pulse Lengths of Multi-Microseconds

    SciTech Connect

    Houck, T; Goerz, D; Javedani, J; Lauer, E; Tully, L; Vogtlin, G

    2006-07-31

    We are studying the flashover of vacuum insulators for applications where high voltage conditioning of the insulator and electrodes is not practical and for pulse lengths on the order of several microseconds. The study is centered about experiments performed with a 100-kV, 10-ms pulsed power system and supported by a combination of theoretical and computational modeling. The base line geometry is a cylindrically symmetric, +45{sup o} insulator between flat electrodes. In the experiments, flashovers or breakdowns are localized by operating at field stresses slightly below the level needed for explosive emissions with the base line geometry. The electrodes and/or insulator are then seeded with an emission source, e.g. a tuft of velvet, or a known mechanical defect. Various standard techniques are employed to suppress cathode-originating flashovers/breakdowns. We present the results of our experiments and discuss the capabilities of modeling insulator flashover.

  20. From microseconds to seconds and minutes—time computation in insect hearing

    PubMed Central

    Hartbauer, Manfred; Römer, Heiner

    2014-01-01

    The computation of time in the auditory system of insects is of relevance at rather different time scales, covering a large range from microseconds to several minutes. At the one end of this range, only a few microseconds of interaural time differences are available for directional hearing, due to the small distance between the ears, usually considered too small to be processed reliably by simple nervous systems. Synapses of interneurons in the afferent auditory pathway are, however, very sensitive to a time difference of only 1–2 ms provided by the latency shift of afferent activity with changing sound direction. At a much larger time scale of several tens of milliseconds to seconds, time processing is important in the context species recognition, but also for those insects where males produce acoustic signals within choruses, and the temporal relationship between song elements strongly deviates from a random distribution. In these situations, some species exhibit a more or less strict phase relationship of song elements, based on phase response properties of their song oscillator. Here we review evidence on how this may influence mate choice decisions. In the same dimension of some tens of milliseconds we find species of katydids with a duetting communication scheme, where one sex only performs phonotaxis to the other sex if the acoustic response falls within a very short time window after its own call. Such time windows show some features unique to insects, and although its neuronal implementation is unknown so far, the similarity with time processing for target range detection in bat echolocation will be discussed. Finally, the time scale being processed must be extended into the range of many minutes, since some acoustic insects produce singing bouts lasting quite long, and female preferences may be based on total signaling time. PMID:24782783

  1. Near-IR absorbance changes and electrogenic reactions in the microsecond-to-second time domain in Photosystem I.

    PubMed

    Vassiliev, I R; Jung, Y S; Mamedov, M D; Semenov AYu; Golbeck, J H

    1997-01-01

    The back-reaction kinetics in Photosystem I (PS I) were studied on the microsecond-to-s time scale in cyanobacterial preparations, which differed in the number of iron-sulfur clusters to assess the contributions of particular components to the reduction of P700+. In membrane fragments and in trimeric P700-FA/FB complexes, the major contribution to the absorbance change at 820 nm (delta A820) was the back-reaction of FA- and/or FB- with lifetimes of approximately 10 and 80 ms (approximately 10% and 40% relative amplitude). The decay of photoinduced electric potential (delta psi) across a membrane with directionally incorporated P700-FA/FB complexes had similar kinetics. HgCl2-treated PS I complexes, which contain FA but no FB, retain both of these kinetic components, indicating that neither can be assigned uniquely to a specific acceptor. These results suggest that FA- reduces P700+ directly and argue for a rapid electron equilibration between FA and FB, which would eliminate their kinetic distinction in a back-reaction. In PsaC-depleted P700-Fx cores, as well as in P700-FA/FB complexes with chemically reduced FA and FB, the major contribution to the delta A820 and the delta psi decay is a biphasic back-reaction of F-X (approximately 400 microseconds and 1.5 ms) with some contribution from A-1 (approximately 10 microseconds and 100 microseconds), the latter of which is variable depending on experimental conditions. The delta A820 decay in a P700-A1 core devoid of all iron-sulfur clusters comprises two phases with lifetimes of 10 microseconds and 130 microseconds (2.7:1 ratio). The biexponential back-reaction kinetics found for each of the electron acceptors may be related to existence of different conformational states of the PS I complex. In all preparations studied, excitation at 532 nm with flash energies exceeding 10 mJ gives rise to formation of antenna 3Chl, which also contributes to delta A820 decay on the tens-of-microsecond time scale. A distinction between

  2. Atomistic modeling of carbon Cottrell atmospheres in bcc iron.

    PubMed

    Veiga, R G A; Perez, M; Becquart, C S; Domain, C

    2013-01-16

    Atomistic simulations with an EAM interatomic potential were used to evaluate carbon-dislocation binding energies in bcc iron. These binding energies were then used to calculate the occupation probability of interstitial sites in the vicinity of an edge and a screw dislocation. The saturation concentration due to carbon-carbon interactions was also estimated by atomistic simulations in the dislocation core and taken as an upper limit for carbon concentration in a Cottrell atmosphere. We obtained a maximum concentration of 10 ± 1 at.% C at T = 0 K within a radius of 1 nm from the dislocation lines. The spatial carbon distributions around the line defects revealed that the Cottrell atmosphere associated with an edge dislocation is denser than that around a screw dislocation, in contrast with the predictions of the classical model of Cochardt and colleagues. Moreover, the present Cottrell atmosphere model is in reasonable quantitative accord with the three-dimensional atom probe data available in the literature.

  3. Asymptotic analysis of microscopic impenetrability constraints for atomistic systems

    NASA Astrophysics Data System (ADS)

    Braides, A.; Gelli, M. S.

    2016-11-01

    We analyze systems of atomistic interactions on a triangular lattice allowing for fracture under a geometric condition on the triangles corresponding to a microscopic impenetrability constraint. Such systems can be thought as a computational simulation of materials undergoing brittle fracture. We show that in the small-deformation regime such approximation can be validated analytically in the framework of variational models of fracture. Conversely, in a finite-deformation regime various pathologies show that the continuum approximation of such a system differs from the usual variational representations of fracture and either needs new types of formulations on the continuum, or a proper interpretation of the atomistic constraints limiting their range and adapting them to a dynamical framework.

  4. The notion of a plastic material spin in atomistic simulations

    NASA Astrophysics Data System (ADS)

    Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

    2016-12-01

    A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

  5. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    PubMed

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  6. Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

    DTIC Science & Technology

    2006-02-01

    Ab Initio Atomistic Thermodynamics for Surfaces: A Primer Jutta Rogal and Karsten Reuter Fritz - Haber -Institut der Max-Planck-Gesellschaft... Fritz - Haber -Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...of the Fritz - Haber -Institut, in particular Wei-Xue Li, Cathy Stampfl and Mira Todorova. Particular thanks go to Matthias Scheffler for his continued

  7. The atomistic representation of first strain-gradient elastic tensors

    NASA Astrophysics Data System (ADS)

    Admal, Nikhil Chandra; Marian, Jaime; Po, Giacomo

    2017-02-01

    We derive the atomistic representations of the elastic tensors appearing in the linearized theory of first strain-gradient elasticity for an arbitrary multi-lattice. In addition to the classical second-Piola) stress and elastic moduli tensors, these include the rank-three double-stress tensor, the rank-five tensor of mixed elastic moduli, and the rank-six tensor of strain-gradient elastic moduli. The atomistic representations are closed-form analytical expressions in terms of the first and second derivatives of the interatomic potential with respect to interatomic distances, and dyadic products of relative atomic positions. Moreover, all expressions are local, in the sense that they depend only on the atomic neighborhood of a lattice site. Our results emanate from the condition of energetic equivalence between continuum and atomistic representations of a crystal, when the kinematics of the latter is governed by the Cauchy-Born rule. Using the derived expressions, we prove that the odd-order tensors vanish if the lattice basis admits central-symmetry. The analytical expressions are implemented as a KIM compliant algorithm to compute the strain gradient elastic tensors for various materials. Numerical results are presented to compare representative interatomic potentials used in the literature for cubic crystals, including simple lattices (fcc Al and Cu and bcc Fe and W) and multi-lattices (diamond-cubic Si). We observe that central potentials exhibit generalized Cauchy relations for the rank-six tensor of strain-gradient elastic moduli. In addition, this tensor is found to be indefinite for many potentials. We discuss the relationship between indefiniteness and material stability. Finally, the atomistic representations are specialized to central potentials in simple lattices. These expressions are used with analytical potentials to study the sensitivity of the elastic tensors to the choice of the cutoff radius.

  8. Atomistic Modeling of Co Growth on Cu(111

    NASA Technical Reports Server (NTRS)

    Khalil, Joseph; Bozzolo, Guillermo; Farias, Daniel; deParga, Vazquez; deMiguel, J. J.; Miranda, R.

    2002-01-01

    The BFS method for alloys is applied to the study of Co growth on Cu(111). The parameterization of the Co-Cu system is obtained from first-principles calculations, and tested against known experimental features for low coverage Co deposition on Cu(100) and Cu(111). Atomistic simulations are performed to investigate the behavior of Co on Cu(111) as a function of coverage.

  9. High-power QCW microsecond-pulse solid-state sodium beacon laser with spiking suppression and D2b re-pumping.

    PubMed

    Bian, Qi; Bo, Yong; Zuo, Jun-wei; Guo, Chuan; Xu, Chang; Tu, Wei; Shen, Yu; Zong, Nan; Yuan, Lei; Gao, Hong-wei; Peng, Qin-jun; Chen, Hong-bin; Feng, Lu; Jin, Kai; Wei, Kai; Cui, Da-fu; Xue, Sui-jian; Zhang, Yu-dong; Xu, Zu-yan

    2016-04-15

    A 65 W quasi-continuous-wave microsecond-pulse solid-state sodium beacon laser tuned to the sodium D2a line has been developed with a linewidth of 0.3 GHz, beam quality of M2=1.38, and pulse width of 120 μs at a repetition rate of 500 Hz by sum-frequency mixing 1319 and 1064 nm diode-pumped Nd:YAG master-oscillator power-amplifier systems. The laser wavelength stability is less than ±0.15 GHz through feedback controlling. The laser spiking due to relaxation oscillations is suppressed by inserting frequency doublers in both 1319 and 1064 nm oscillators. Sodium D2b re-pumping is accomplished by tuning the frequency of the electro-optic modulator with the right D2a-D2b offset. A bright sodium laser guide star with a photon return of 1820 photons/cm2/s was achieved with the laser system when a 32 W circular polarized beam was projected to the sky during our field test at the Xinglong Observatory.

  10. Polarized cells, polar actions.

    PubMed

    Maddock, J R; Alley, M R; Shapiro, L

    1993-11-01

    The recognition of polar bacterial organization is just emerging. The examples of polar localization given here are from a variety of bacterial species and concern a disparate array of cellular functions. A number of well-characterized instances of polar localization of bacterial proteins, including the chemoreceptor complex in both C. crescentus and E. coli, the maltose-binding protein in E. coli, the B. japonicum surface attachment proteins, and the actin tail of L. monocytogenes within a mammalian cell, involve proteins or protein complexes that facilitate bacterial interaction with the environment, either the extracellular milieux or that within a plant or mammalian host. The significance of this observation remains unclear. Polarity in bacteria poses many problems, including the necessity for a mechanism for asymmetrically distributing proteins as well as a mechanism by which polar localization is maintained. Large structures, such as a flagellum, are anchored at the pole by means of the basal body that traverses the peptidoglycan wall. But for proteins and small complexes, whether in the periplasm or the membrane, one must invoke a mechanism that prevents the diffusion of these proteins away from the cell pole. Perhaps the periplasmic proteins are retained at the pole by the presence of the periseptal annulus (35). The constraining features for membrane components are not known. For large aggregates, such as the clusters of MCP, CheA, and CheW complexes, perhaps the size of the aggregate alone prevents displacement. In most cases of cellular asymmetry, bacteria are able to discriminate between the new pole and the old pole and to utilize this information for localization specificity. The maturation of new pole to old pole appears to be a common theme as well. Given numerous examples reported thus far, we propose that bacterial polarity displays specific rules and is a more general phenomenon than has been previously recognized.

  11. Observations of multi-microsecond VHF pulsetrains in energetic intracloud lightning discharges

    NASA Astrophysics Data System (ADS)

    Jacobson, A. R.; Holzworth, R. H.; Shao, X.-M.

    2011-09-01

    Certain intracloud lightning discharges emit energetic, multi-microsecond pulsetrains of radio noise. Observations of this distinctive form of lightning date from 1980 and have involved both ground-based and satellite-based radio recording systems. The underlying intracloud lightning discharges have been referred to as "Narrow Bipolar Pulses", "Narrow Bipolar Events", and "Compact Intracloud Discharges". An important discriminant for this species of radio emission is that, in the range above ~30 MHz, it consists of several microseconds of intense radio noise. When the intracloud emission is viewed from a satellite, each radio pulsetrain is received both from a direct lightning-to-satellite path, and after some delay, from a path via ground. Thus one recording of the radio emission, if of sufficient length, contains the "view" of the intracloud emission from two different angles. One view is of radiation exiting the emitter into the upper hemisphere, the other for radiation exiting into the lower hemisphere. However, the propagation conditions are similar, except that one path includes a ground reflection, while the other does not. One would normally expect a stereoscopic double view of the "same" emission process to provide two almost congruent time series, one delayed from the other, and also differing due to the different propagation effects along the two signal paths, namely, the ground reflection. We present somewhat unexpected results on this matter, using recordings from the FORTE satellite at a passband 118-141 MHz, with simultaneous data at 26-49 MHz. We find that the 118-141 MHz pulsetrain's detailed time-dependence is completely uncorrelated between the two views of the process. We examine statistics of the 118-141 MHz pulsetrain's integrated power and show that the power emitted into the lower hemisphere, on average, exceeds the power emitted into the upper hemisphere. Finally, we examine statistical measures of the amplitude distribution and show that

  12. Atomistic Simulation of Sea Spray Particles

    NASA Astrophysics Data System (ADS)

    Gokturk, H.

    2012-12-01

    Particles generated by ocean wave spray play an important role in many atmospheric processes such as cloud condensation, cycling of elements like chlorine, and scattering of sunlight reaching the ocean surface [1-2]. Indeed, artificially spraying droplets of seawater to the atmosphere by marine vessels roaming the ocean has been suggested as a geoengineering method to combat global warming [3]. One of the interesting aspects of ocean spray particles is that they include dissolved salt ions. Typically a liter of seawater contains about 3.5 g of salt which is mostly sodium chloride. Hydrated salt ions of the particle create a molecular structure which is different from that of pure water. An objective of this research is to investigate the influence of the dissolved ions on the properties of the particles by using first principle quantum mechanical calculations. Another objective is to probe the interaction of carbon dioxide (CO2) with such particles to understand whether the ions might enhance the absorption of atmospheric CO2 into the particles. Atomic models used in the calculations consist of a salt ion, for example sodium (Na+) ion surrounded by water molecules. Calculations are performed by using the DFT method with B3LYP hybrid functional and Pople type basis sets augmented with polarization and diffuse functions. Results of the calculations indicate that average binding energy of water molecules nearest to the ion is 0.7 eV per molecule for Na+ and 0.5 eV per molecule for Cl-. Water molecules are bound to the ion with significantly greater energy than that of the hydrogen bond (~0.2 eV) which is the binding mechanism of pure water. Higher binding energy of the particles explains why they serve well as condensation nuclei. As expected, binding energy decreases with increasing distance from the ion. It becomes comparable to that of the hydrogen bond at a distance of about 2 nm which corresponds to approximately 7 layers of water molecules surrounding the ion

  13. A Comparative Study on the Effects of Millisecond- and Microsecond-Pulsed Electric Field Treatments on the Permeabilization and Extraction of Pigments from Chlorella vulgaris.

    PubMed

    Luengo, Elisa; Martínez, Juan Manuel; Coustets, Mathilde; Álvarez, Ignacio; Teissié, Justin; Rols, Marie-Pierre; Raso, Javier

    2015-10-01

    The interdependencies of the two main processing parameters affecting "electroporation" (electric field strength and pulse duration) while using pulse duration in the range of milliseconds and microseconds on the permeabilization, inactivation, and extraction of pigments from Chlorella vulgaris was compared. While irreversible "electroporation" was observed above 4 kV/cm in the millisecond range, electric field strengths of ≥10 kV/cm were required in the microseconds range. However, to cause the electroporation of most of the 90 % of the population of C. vulgaris in the millisecond (5 kV/cm, 20 pulses) or microsecond (15 kV/cm, 25 pulses) range, the specific energy that was delivered was lower for microsecond treatments (16.87 kJ/L) than in millisecond treatments (150 kJ/L). In terms of the specific energy required to cause microalgae inactivation, treatments in the microsecond range also resulted in greater energy efficiency. The comparison of extraction yields in the range of milliseconds (5 kV, 20 ms) and microseconds (20, 25 pulses) under the conditions in which the maximum extraction was observed revealed that the improvement in the carotenoid extraction was similar and chlorophyll a and b extraction was slightly higher for treatments in the microsecond range. The specific energy that was required for the treatment in the millisecond range (150 kJ/L) was much higher than those required in the microsecond range (30 kJ/L). The comparison of the efficacy of both types of pulses on the extraction enhancement just after the treatment and after a post-pulse incubation period seemed to indicate that PEF in the millisecond range created irreversible alterations while, in the microsecond range, the defects were a dynamic structure along the post-pulse time that caused a subsequent increment in the extraction yield.

  14. STROBE-X: X-ray Timing & Spectroscopy on Dynamical Timescales from Microseconds to Years

    NASA Astrophysics Data System (ADS)

    Ray, Paul; Wilson-Hodge, Colleen; Gendreau, Keith; Chakrabarty, Deepto; Feroci, Marco; Maccarone, Thomas; Arzoumanian, Zaven; Remillard, Ron; Wood, Kent; Griffith, Chris; Strobe-X Collaboration

    2017-01-01

    We describe a proposed probe-class mission concept that will provide an unprecedented view of the X-ray sky, performing timing and spectroscopy over a broad band (0.2-30 keV) probing timescale from microseconds to years. The Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X) comprises two primary instruments, one based on technology developed for the NICER mission and the other based on the European LOFT mission. The broad coverage will enable thermal components, non-thermal components, iron lines, and reflection features to be studied simultaneously from a single platform for the first time in accreting black holes at all scales. The massive collecting area will enable studies of the dense matter equation of state using multiple techniques. A broad range of other revolutionary science, such as high quality spectroscopy of clusters of galaxies and unprecedented timing investigations of active galactic nuclei, would also be obtained. We describe the mission concept and the planned trade studies that will optimize the mission to maximize the science return. This mission is being developed in collaboration with members of the European LOFT team, and a hardware contribution from Europe is expected.

  15. Microsecond light-induced proton transfer to flavin in the blue light sensor plant cryptochrome.

    PubMed

    Langenbacher, Thomas; Immeln, Dominik; Dick, Bernhard; Kottke, Tilman

    2009-10-14

    Plant cryptochromes are blue light photoreceptors that regulate key responses in growth and daily rhythm of plants and might be involved in magnetoreception. They show structural homology to the DNA repair enzyme photolyase and bind flavin adenine dinucleotide as chromophore. Blue light absorption initiates the photoreduction from the oxidized dark state of flavin to the flavin neutral radical, which is the signaling state of the sensor. Previous time-resolved studies of the photoreduction process have been limited to observation of the decay of the radical in the millisecond time domain. We monitored faster, light-induced changes in absorption of an algal cryptochrome covering a spectral range of 375-750 nm with a streak camera setup. Electron transfer from tryptophan to flavin is completed before 100 ns under formation of the flavin anion radical. Proton transfer takes place with a time constant of 1.7 micros leading to the flavin neutral radical. Finally, the flavin radical and a tryptophan neutral radical decay with a time constant >200 micros in the millisecond and second time domain. The microsecond proton transfer has not been observed in animal cryptochromes from insects or photolyases. Furthermore, the strict separation in time of electron and proton transfer is novel in the field of flavin-containing photoreceptors. The reaction rate implies that the proton donor is not in hydrogen bonding distance to the flavin N5. Potential candidates for the proton donor and the involvement of the tryptophan triad are discussed.

  16. Microsecond folding and domain motions of a spider silk protein structural switch.

    PubMed

    Ries, Julia; Schwarze, Simone; Johnson, Christopher M; Neuweiler, Hannes

    2014-12-10

    Web spiders rapidly assemble protein monomers, so-called spidroins, into extraordinarily tough silk fibers. The process involves the pH-triggered self-association of the spidroin N-terminal domain (NTD), which contains a structural switch connecting spidroins to supermolecules. Single-molecule spectroscopy can detect conformational heterogeneity that is hidden to conventional methods, but motions of the NTD are beyond the resolution limit. Here, we engineered probes for 1 nm conformational changes based on the phenomenon of fluorescence quenching by photoinduced electron transfer into the isolated NTD of a spidroin from the nursery web spider Euprosthenops australis. Correlation analysis of single-molecule fluorescence fluctuations uncovered site-dependent nanosecond-to-microsecond movement of secondary and tertiary structure. Kinetic amplitudes were most pronounced for helices that are part of the association interface and where structural studies show large displacements between monomeric and dimeric conformations. A single tryptophan at the center of the five-helix bundle toggled conformations in ∼100 μs and in a pH-dependent manner. Equilibrium denaturation and temperature-jump relaxation experiments revealed cooperative and ultrafast folding in only 60 μs. We deduced a free-energy surface that exhibits native-state ruggedness with apparently similar barrier heights to folding and native motions. Observed equilibrium dynamics within the domain suggest a conformational selection mechanism in the rapid association of spidroins through their NTDs during silk synthesis by web spiders.

  17. Three-dimensional multispectral hand-held optoacoustic imaging with microsecond-level delayed laser pulses

    NASA Astrophysics Data System (ADS)

    Deán-Ben, X. L.; Bay, Erwin; Razansky, Daniel

    2015-03-01

    Three-dimensional hand-held optoacoustic imaging comes with important advantages that prompt the clinical translation of this modality, with applications envisioned in cardiovascular and peripheral vascular disease, disorders of the lymphatic system, breast cancer, arthritis or inflammation. Of particular importance is the multispectral acquisition of data by exciting the tissue at several wavelengths, which enables functional imaging applications. However, multispectral imaging of entire three-dimensional regions is significantly challenged by motion artefacts in concurrent acquisitions at different wavelengths. A method based on acquisition of volumetric datasets having a microsecond-level delay between pulses at different wavelengths is described in this work. This method can avoid image artefacts imposed by a scanning velocity greater than 2 m/s, thus, does not only facilitate imaging influenced by respiratory, cardiac or other intrinsic fast movements in living tissues, but can achieve artifact-free imaging in the presence of more significant motion, e.g., abrupt displacements during handheld-mode operation in a clinical environment.

  18. Evaluating letter recognition, flicker fusion, and the Talbot-Plateau law using microsecond-duration flashes.

    PubMed

    Greene, Ernest

    2015-01-01

    Four experiments examined the ability of respondents to identify letters that were displayed on an LED array with flashes lasting little more than a microsecond. The first experiment displayed each letter with a single, simultaneous flash of all the dots forming the letter and established the relation of flash intensity to the probability of letter identification. The second experiment displayed the letters with multiple flashes at different frequencies to determine the probability that the sequence of flashes would be perceived as fused. The third experiment displayed the letters at a frequency that was above the flicker-fusion frequency, varying flash intensity to establish the amount needed to elicit a given probability of letter identification. The fourth experiment displayed each letter twice, once at a frequency where no flicker was perceived and also with steady light emission. The intensity of each flash was fixed and the steady intensity was varied; respondents were asked to judge whether the fused-flicker display and the steady display appeared to be the same brightness. Steady intensity was about double the average flash intensity where the two conditions were perceived as being equal in brightness. This is at odds with Talbot-Plateau law, which predicts that these two values should be equal. The law was formulated relative to a flash lasting half of each period, so it is surprising that it comes this close to being correct where the flash occupies only a millionth of the total period.

  19. Studies of the dynamics of a 1-microsecond X-pinch

    NASA Astrophysics Data System (ADS)

    Appartaim, Richard; Green, Danielle

    2015-11-01

    The 1- μs X-pinch (0.3 kA/ns) has been shown to produce intense soft x-rays with a spatially reproducible source location and fine size (i .e . < 10 μm) . For certain applications these x-rays are comparable in their utility to those produced on pulsed-power devices but have the advantage of a much lower component of hard x-rays. Many of the critical plasma dynamics are also similar to those observed in the fast rise-time (1 kA/ns) experiments. However, the longer rise time of the microsecond discharge can lead to important differences in wire ablation rates and transition to coronal plasma, plasma current distribution and plasma dynamics. We present recent results of these plasma dynamics using optical techniques such as shadowgraphy, schlieren and framing photography, as well as x-ray observation techniques including filtered PCD and Si diode measurements, pinhole photography and x-ray spectroscopy. We demonstrate potential applications including the relevance of the observed plasma jets to astrophysical jets. Supported by DOE Grant DE-FG02-0547253ER.

  20. Molecular recognition of oxygen by protein mimics: dynamics on the femtosecond to microsecond time scale.

    PubMed

    Zou, Shouzhong; Baskin, J Spencer; Zewail, Ahmed H

    2002-07-23

    Molecular recognition by biological macromolecules involves many elementary steps, usually convoluted by diffusion processes. Here we report studies of the dynamics, from the femtosecond to the microsecond time scale, of the different elementary processes involved in the bimolecular recognition of a protein mimic, cobalt picket-fence porphyrin, with varying oxygen concentration at controlled temperatures. Electron transfer, bond breakage, and thermal "on" (recombination) and "off" (dissociation) reactions are the different processes involved. The reaction on-rate is 30 to 60 times smaller than that calculated from standard Smoluchowski theory. Introducing a two-step recognition model, with reversibility being part of both steps, removes the discrepancy and provides consistency for the reported thermodynamics, kinetics, and dynamics. The transient intermediates are configurations defined by the contact between oxygen (diatomic) and the picket-fence porphyrin (macromolecule). This intermediate is critical in the description of the potential energy landscape but, as shown here, both enthalpic and entropic contributions to the free energy are important. In the recognition process, the net entropy decrease is -33 cal mol(-1) K(-1); Delta H is -13.4 kcal mol(-1).

  1. Microsecond gain-switched master oscillator power amplifier (1958 nm) with high pulse energy

    SciTech Connect

    Ke Yin; Weiqiang Yang; Bin Zhang; Ying Li; Jing Hou

    2014-02-28

    An all-fibre master oscillator power amplifier (MOPA) emitting high-energy pulses at 1958 nm is presented. The seed laser is a microsecond gain-switched thulium-doped fibre laser (TDFL) pumped with a commercial 1550-nm pulsed fibre laser. The TDFL operates at a repetition rate f in the range of 10 to 100 kHz. The two-stage thulium-doped fibre amplifier is built to scale the energy of the pulses generated by the seed laser. The maximum output pulse energy higher than 0.5 mJ at 10 kHz is achieved which is comparable with the theoretical maximum extractable pulse energy. The slope efficiency of the second stage amplifier with respect to the pump power is 30.4% at f = 10 kHz. The wavelength of the output pulse laser is centred near 1958 nm at a spectral width of 0.25 nm after amplification. Neither nonlinear effects nor significant amplified spontaneous emission (ASE) is observed in the amplification experiments. (lasers)

  2. Polarization measurement through combination polarizers

    NASA Astrophysics Data System (ADS)

    Bai, Yunfeng; Li, Linjun; He, Zhelong; Liu, Yanwei; Ma, Cheng; Shi, Guang; Liu, Lu

    2014-02-01

    Polarization measurement approaches only using polarizer and grating is present. The combination polarizers consists of two polarizers: one is γ degree with the X axis; the other is along the Y axis. Binary grating is covered by the combination polarizers, and based on Fraunhofer diffraction, the diffraction intensity formula is deduced. The polarization state of incident light can be gotten by fitting the diffraction pattern with the deduced formula. Compared with the traditional polarization measurement method, this measurement only uses polarizer and grating, therefore, it can be applied to measure a wide wavelength range without replacing device in theory.

  3. On-the-fly decoding luminescence lifetimes in the microsecond region for lanthanide-encoded suspension arrays

    NASA Astrophysics Data System (ADS)

    Lu, Yiqing; Lu, Jie; Zhao, Jiangbo; Cusido, Janet; Raymo, Françisco M.; Yuan, Jingli; Yang, Sean; Leif, Robert C.; Huo, Yujing; Piper, James A.; Paul Robinson, J.; Goldys, Ewa M.; Jin, Dayong

    2014-05-01

    Significant multiplexing capacity of optical time-domain coding has been recently demonstrated by tuning luminescence lifetimes of the upconversion nanoparticles called ‘τ-Dots’. It provides a large dynamic range of lifetimes from microseconds to milliseconds, which allows creating large libraries of nanotags/microcarriers. However, a robust approach is required to rapidly and accurately measure the luminescence lifetimes from the relatively slow-decaying signals. Here we show a fast algorithm suitable for the microsecond region with precision closely approaching the theoretical limit and compatible with the rapid scanning cytometry technique. We exploit this approach to further extend optical time-domain multiplexing to the downconversion luminescence, using luminescence microspheres wherein lifetimes are tuned through luminescence resonance energy transfer. We demonstrate real-time discrimination of these microspheres in the rapid scanning cytometry, and apply them to the multiplexed probing of pathogen DNA strands. Our results indicate that tunable luminescence lifetimes have considerable potential in high-throughput analytical sciences.

  4. On-the-fly decoding luminescence lifetimes in the microsecond region for lanthanide-encoded suspension arrays.

    PubMed

    Lu, Yiqing; Lu, Jie; Zhao, Jiangbo; Cusido, Janet; Raymo, Françisco M; Yuan, Jingli; Yang, Sean; Leif, Robert C; Huo, Yujing; Piper, James A; Paul Robinson, J; Goldys, Ewa M; Jin, Dayong

    2014-05-06

    Significant multiplexing capacity of optical time-domain coding has been recently demonstrated by tuning luminescence lifetimes of the upconversion nanoparticles called 'τ-Dots'. It provides a large dynamic range of lifetimes from microseconds to milliseconds, which allows creating large libraries of nanotags/microcarriers. However, a robust approach is required to rapidly and accurately measure the luminescence lifetimes from the relatively slow-decaying signals. Here we show a fast algorithm suitable for the microsecond region with precision closely approaching the theoretical limit and compatible with the rapid scanning cytometry technique. We exploit this approach to further extend optical time-domain multiplexing to the downconversion luminescence, using luminescence microspheres wherein lifetimes are tuned through luminescence resonance energy transfer. We demonstrate real-time discrimination of these microspheres in the rapid scanning cytometry, and apply them to the multiplexed probing of pathogen DNA strands. Our results indicate that tunable luminescence lifetimes have considerable potential in high-throughput analytical sciences.

  5. Structure identification methods for atomistic simulations of crystalline materials

    DOE PAGES

    Stukowski, Alexander

    2012-05-28

    Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

  6. Atomistic Modeling of Mechanical Loss in Amorphous Oxides

    NASA Astrophysics Data System (ADS)

    Hamdan, Rashid; Trinastic, Jonathan; Cheng, Hai-Ping

    2013-03-01

    The mechanical and optical loss in amorphous solids, described by the internal friction and light scattering susceptibility are investigated using classical, atomistic molecular dynamics simulation. We implemented the trajectory bisection method and the non-local ridge method in DL-POLY molecular dynamics simulation software. These methods were used to locate the different local potential energy minima that a system visits through an MD trajectory and the transition state between any two consecutive minima. From the distributions of the barrier height and asymmetry, and the relaxation time of the different transition states we calculated the internal friction of pure amorphous silica and mixed oxides. Acknowledgment: NSF/PHYS

  7. Atomistic simulations of grain and interphase boundary mobility

    NASA Astrophysics Data System (ADS)

    Hoyt, J. J.

    2014-04-01

    In recent years, atomistic simulations have provided valuable insights into the thermodynamic and kinetic properties of grain and interphase boundaries. In this work, we provide a brief overview of kinetic processes occurring at migrating interfaces and survey various molecular dynamics techniques for extracting grain boundary mobilities. The advantages and disadvantages of fluctuation and applied driving force methods will be discussed. In addition, we review recent examples of simulations that have identified structural phase transformations at grain boundaries. Finally, simulations that have investigated the mobility and atomic mechanisms of growth of an fcc-bcc interphase boundary are summarized.

  8. Predicting dislocation climb and creep from explicit atomistic details.

    PubMed

    Kabir, Mukul; Lau, Timothy T; Rodney, David; Yip, Sidney; Van Vliet, Krystyn J

    2010-08-27

    Here we report kinetic Monte Carlo simulations of dislocation climb in heavily deformed, body-centered cubic iron comprising a supersaturation of vacancies. This approach explicitly incorporates the effect of nonlinear vacancy-dislocation interaction on vacancy migration barriers as determined from atomistic calculations, and enables observations of diffusivity and climb over time scales and temperatures relevant to power-law creep. By capturing the underlying microscopic physics, the calculated stress exponents for steady-state creep rates agree quantitatively with the experimentally measured range, and qualitatively with the stress dependence of creep activation energies.

  9. Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

    PubMed Central

    2015-01-01

    The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previously been limited to coarse-grained models (at varying levels of resolution). This Communication demonstrates the extraction of Kc from fully atomistic molecular dynamics simulations for three different single-component lipid bilayers (DPPC, DOPC, and DOPE). The results agree quantitatively with experiments that measure thermal shape fluctuations in giant unilamellar vesicles. Lipid tilt, twist, and compression moduli are also reported. PMID:25202918

  10. Polarization Maintaining, Very-Large-Mode Area, Er Fiber Amplifier for High Energy Pulses at 1572.3 nm

    NASA Technical Reports Server (NTRS)

    Nicholoson, J. W.; DeSantolo, A.; Yan, M. F.; Wisk, P.; Mangan, B.; Puc, G.; Yu, A.; Stephen, M.

    2016-01-01

    We demonstrate the first polarization maintaining, very-large-mode-area Er-doped fiber amplifier with 1000 square micron effective area. The amplifier is core pumped by a Raman fiber laser and is used to generate single frequency one microsecond pulses with pulse energy of 368 microJoules, M2 of 1.1, and polarization extinction greater than 20 dB. The amplifier operates at 1572.3 nm, a wavelength useful for trace atmospheric CO2 detection.

  11. Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

    DOE PAGES

    Taylor, Christopher D.

    2012-01-01

    Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies ofmore » the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.« less

  12. Methods for the Detection and Characterization of Silica Colloids by Microsecond spICP-MS.

    PubMed

    Montaño, Manuel D; Majestic, Brian J; Jämting, Åsa K; Westerhoff, Paul; Ranville, James F

    2016-05-03

    The rapid development of nanotechnology has led to concerns over their environmental risk. Current analytical techniques are underdeveloped and lack the sensitivity and specificity to characterize these materials in complex environmental and biological matrices. To this end, single particle ICP-MS (spICP-MS) has been developed in the past decade, with the capability to detect and characterize nanomaterials at environmentally relevant concentrations in complex environmental and biological matrices. However, some nanomaterials are composed of elements inherently difficult to quantify by quadrupole ICP-MS due to abundant molecular interferences, such as dinitrogen ions interfering with the detection of silicon. Three approaches aimed at reducing the contribution of these background molecular interferences in the analysis of (28)Si are explored in an attempt to detect and characterize silica colloids. Helium collision cell gases and reactive ammonia gas are investigated for their conventional use in reducing the signal generated from the dinitrogen interference and background silicon ions leaching from glass components of the instrumentation. A new approach brought on by the advent of microsecond dwell times in single particle ICP-MS allows for the detection and characterization of silica colloids without the need for these cell gases, as at shorter dwell times the proportion of signal attributed to a nanoparticle event is greater relative to the constant dinitrogen signal. It is demonstrated that the accurate detection and characterization of these materials will be reliant on achieving a balance between reducing the contribution of the background interference, while still registering the maximum amount of signal generated by the particle event.

  13. Microsecond pulsed hydrogen/deuterium exchange of electrosprayed ubiquitin ions stored in a linear ion trap.

    PubMed

    Rajabi, Khadijeh

    2015-02-07

    A pulse of D2O vapour on the order of microseconds is allowed to react with the +6 to +9 charge states of ubiquitin confined in a linear ion trap (LIT). Two envelopes of peaks are detected for the ions of ubiquitin, corresponding to the ions that exchange more quickly and more slowly. The deuterium uptake of the protonated sites on ubiquitin ions accounts for the ion population with the fast exchange. The hydrogen/deuterium exchange (HDX) kinetics of ubiquitin ions trapped in the LIT for 200 ms showed comparable structural transitions to those trapped for 300 ms. When ions are trapped for longer, i.e. up to 2000 ms, mainly the slow exchanging ion population is detected. In all experiments the +7 ions exchange the most, suggesting a short distance between the surface protonated sites and nearby charged sites, and concomitantly high accessibility of surface protonated sites towards D2O. The +6 ions are more compact than the +7 ions but have one fewer protonated site, therefore fewer surface availabilities for D2O attack. The data suggest that the +6 ions keep most of their solution-phase contacts intact while the hydrophobic core is slightly interrupted in the +7 ions, possibly due to the exposure of charged His68 that is normally buried in the hydrophobic pocket. The +8 and +9 ions have more protonated sites but are less compact than the +7 ions because of Coulombic repulsion, resulting in a larger distance between the protonated sites and the basic sites. The data indicate that the HDX mechanism of ions with the slower exchange corresponding to the second envelope of peaks is primarily governed via a relay mechanism. The results suggest that the pulsed HDX MS method is sampling a population of ubiquitin ions with a similar backbone fold to the solution.

  14. 3d visualization of atomistic simulations on every desktop

    NASA Astrophysics Data System (ADS)

    Peled, Dan; Silverman, Amihai; Adler, Joan

    2013-08-01

    Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

  15. Atomistically-informed Dislocation Dynamics in fcc Crystals

    SciTech Connect

    Martinez, E; Marian, J; Arsenlis, T; Victoria, M; Perlado, J M

    2006-09-06

    We develop a nodal dislocation dynamics (DD) model to simulate plastic processes in fcc crystals. The model explicitly accounts for all slip systems and Burgers vectors observed in fcc systems, including stacking faults and partial dislocations. We derive simple conservation rules that describe all partial dislocation interactions rigorously and allow us to model and quantify cross-slip processes, the structure and strength of dislocation junctions and the formation of fcc-specific structures such as stacking fault tetrahedra. The DD framework is built upon isotropic non-singular linear elasticity, and supports itself on information transmitted from the atomistic scale. In this fashion, connection between the meso and micro scales is attained self-consistently with core parameters fitted to atomistic data. We perform a series of targeted simulations to demonstrate the capabilities of the model, including dislocation reactions and dissociations and dislocation junction strength. Additionally we map the four-dimensional stress space relevant for cross-slip and relate our findings to the plastic behavior of monocrystalline fcc metals.

  16. Concurrent atomistic-continuum simulation of polycrystalline strontium titanate

    NASA Astrophysics Data System (ADS)

    Yang, Shengfeng; Zhang, Ning; Chen, Youping

    2015-08-01

    This paper presents the new development of a concurrent atomistic-continuum (CAC) method in simulation of the dynamic evolution of defects in polycrystalline polyatomic materials. The CAC method is based on a theoretical formulation that extends Kirkwood's statistical mechanical theory of transport processes to a multiscale description of crystalline materials. It solves for both the deformation of lattice cells and the internal deformation within each lattice cell, making it a suitable method for simulations of polyatomic materials. The simulation results of this work demonstrate that CAC can simulate the nucleation of dislocations and cracks from atomistically resolved grain boundary (GB) regions and the subsequent propagation into coarsely meshed grain interiors in polycrystalline strontium titanate without the need of supplemental constitutive equations or additional numerical treatments. With a significantly reduced computational cost, CAC predicts not only the GB structures, but also the dynamic behaviour of dislocations, cracks and GBs, all of which are comparable with those obtained from atomic-level molecular dynamics simulations. Simulation results also show that dislocations tend to initiate from GBs and triple junctions. The angle between the slip planes and the GB planes plays a key role in determining the GB-dislocation reactions.

  17. Quantum transport in RTD and atomistic modeling of nanostructures

    NASA Astrophysics Data System (ADS)

    Jiang, Zhengping

    As devices are scaled down to nanometer scale, new materials and device structures are introduced to extend Moore's law beyond Si devices. In this length scale, carrier transport moves from classical transport to quantum transport; material granularity has more and more impacts on performance. Computer Aided Design (CAD) becomes essential for both industrial and educational purposes. First part focuses on physical models and numerical issues in nano-scale devices modeling. Resonance Tunneling Diode (RTD) is simulated and used to illustrate phenomena in carrier transport. Non-Equilibrium Green's Function (NEGF) formulism is employed in quantum transport simulation. Inhomogeneous energy grid is used in energy integration, which is critical to capture essential physics in RTD simulation. All simulation results could be reproduced by developed simulators RTDNEGF and NEMO5. In nanostructures, device length becomes comparable to material granularity; it is not proper to consider materials as continuous in many situations. Second part of this work resolves this problem by introducing atomistic modeling method. Valley degeneracy in Si (110) QW is investigated. Inconsistency of experimental observations is resolved by introducing miscut in surface. Impacts of strain and electric field on electronic bandstructure are studied. Research of SiGe barrier disorder effects on valley splitting in Si (100) QW is then conducted. Behaviors of valley splitting in different well widths under electric field are predicted by atomistic simulation. Nearest neighbor empirical tight-binding method is used in electronic calculation and VFF Keating model is used in strain relaxation.

  18. 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

  19. Adaptive resolution simulation of an atomistic protein in MARTINI water

    NASA Astrophysics Data System (ADS)

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-02-01

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

  20. Shape-controlled growth of metal nanoparticles: an atomistic view.

    PubMed

    Konuk, Mine; Durukanoğlu, Sondan

    2016-01-21

    Recent developments in shape-controlled synthesis of metallic nano-particles present a promising path for precisely tuning chemical activity, selectivity, and stability of nano-materials. While previous studies have highlighted the macroscopic description of synthesis processes, there is less understanding as to whether individual atomic-scale processes possess any significant role in controlling the growth of nano-products. The presented molecular static and dynamic simulations are the first simulations to understand the underlying atomistic mechanisms of the experimentally determined growth modes of metal nano-clusters. Our simulations on Ag nano-cubes confirm that metal nano-seeds enclosed by {100} facets can be directed to grow into octopods, concave, truncated cubes, and cuboctahedra when the relative surface diffusion and deposition rates are finely tuned. Here we further showed that atomic level processes play a significant role in controllably fine tuning the two competing rates: surface diffusion and deposition. We also found that regardless of temperature and the initial shape of the nano-seeds, the exchange of the deposited atom with an edge atom of the seed is by far the governing diffusion mechanism between the neighboring facets, and thus is the leading atomistic process determining the conditions for fine tuning of macroscopic processes.

  1. Atomistic simulation of ion beam patterning with crater functions

    NASA Astrophysics Data System (ADS)

    Yang, Zhangcan; Lively, Michael; Allain, Jean Paul

    2013-07-01

    In this study, an atomistic model is developed to simulate ripple pattern formation when a surface is irradiated by incident low-energy energetic ions. The model treats individual ion impacts using crater functions, which represent the average change in the surface shape due to a single-ion impact. These functions incorporate the complete redistribution of mass along the surface due to an impact, and not just that due to sputtering. While most models only treat erosion, analysis of the craters reveals that the amount of mass redistributed across the surface is an order of magnitude greater than the mass removed by sputtering. Simulations in this study are conducted for 500 eV Ar+ bombardments of Si at angles of 0° to 60° with 5° increment at temperature of 350 K. Initial simulations with this model have shown agreement with prior observations of ripple pattern formation. However, some significant departures from other models based on the Bradley-Harper theory have emerged; the key difference is that the presence of crater rims plays a key role in ripple formation, which could explain phenomena such as maximum ripple amplitudes which most models do not account for. These results show that atomistic crater functions are a viable method for modeling ion beam patterning. They indicate that mass redistribution is a key mechanism for surface patterning.

  2. Atomistic Molecular Dynamics Simulations of Crude Oil/Brine Displacement in Calcite Mesopores.

    PubMed

    Sedghi, Mohammad; Piri, Mohammad; Goual, Lamia

    2016-04-12

    Unconventional reservoirs such as hydrocarbon-bearing shale formations and ultratight carbonates generate a large fraction of oil and gas production in North America. The characteristic feature of these reservoirs is their nanoscale porosity that provides significant surface areas between the pore walls and the occupying fluids. To better assess hydrocarbon recovery from these formations, it is crucial to develop an improved insight into the effects of wall-fluid interactions on the interfacial phenomena in these nanoscale confinements. One of the important properties that controls the displacement of fluids inside the pores is the threshold capillary pressure. In this study, we present the results of an integrated series of large-scale molecular dynamics (MD) simulations performed to investigate the effects of wall-fluid interactions on the threshold capillary pressures of oil-water/brine displacements in a calcite nanopore with a square cross section. Fully atomistic models are utilized to represent crude oil, brine, and calcite in order to accommodate electrostatic interactions and H-bonding between the polar molecules and the calcite surface. To this end, we create mixtures of various polar and nonpolar organic molecules to better represent the crude oil. The interfacial tension between oil and water/brine and their contact angle on calcite surface are simulated. We study the effects of oil composition, water salinity, and temperature and pressure conditions on these properties. The threshold capillary pressure values are also obtained from the MD simulations for the calcite nanopore. We then compare the MD results against those generated using the Mayer-Stowe-Princen (MSP) method and explain the differences.

  3. Amp: A modular approach to machine learning in atomistic simulations

    NASA Astrophysics Data System (ADS)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

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

  4. STROBE-X: X-ray Timing & Spectroscopy on Dynamical Timescales from Microseconds to Years

    NASA Astrophysics Data System (ADS)

    Wilson-Hodge, Colleen A.; Ray, Paul S.; Gendreau, Keith; Chakrabarty, Deepto; Feroci, Marco; Maccarone, Tom; Arzoumanian, Zaven; Remillard, Ronald A.; Wood, Kent; Griffith, Christopher; STROBE-X Collaboration

    2017-01-01

    We describe a proposed probe-class mission concept that will provide an unprecedented view of the X-ray sky, performing timing and spectroscopy over a broad band (0.2-30 keV) probing timescales from microseconds to years. The Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X) comprises two primary instruments. The soft band (0.2-12 keV) will be covered by an array of lightweight optics (3-m focal length) that concentrate incident photons onto small solid state detectors with CCD-level (85-130 eV) energy resolution, 100 ns time resolution, and low background rates. This technology, fully developed for NICER, would be scaled up with enhanced optics to take advantage of the longer focal length of STROBE-X. The harder band (2 to at least 30 keV) would be covered by large-area collimated silicon drift detectors,developed for the European LOFT mission concept. Each instrument would provide an order of magnitude improvement in effective area compared with its predecessor (NICER in the soft band and RXTE in the hard band). A sensitive sky monitor would act as a trigger for pointed observations, provide high duty cycle, high time resolution, high spectral resolution monitoring of the X-ray sky with ~20 times the sensitivity of the RXTE ASM, and enable multi-wavelength and multi-messenger studies on a continuous, rather than scanning basis.The broad coverage will enable thermal components, non-thermal components, iron lines, and reflection features to be studied simultaneously from a single platform for the first time in accreting black holes at all scales. The enormous collecting area will enable studies of the dense matter equation of state using both soft thermal emission from rotation-powered pulsars and harder emission from X-ray burst oscillations. Revolutionary science, such as high quality spectroscopy of clusters of galaxies and unprecedented timing investigations of active galactic nuclei, would also be obtained.We describe the mission

  5. The Soft Mode Driven Dynamics in Ferroelectric Perovskites at the Nanoscale: An Atomistic Study

    NASA Astrophysics Data System (ADS)

    McCash, Kevin

    The discovery of ferroelectricity at the nanoscale has incited a lot of interest in perovskite ferroelectrics not only for their potential in device application but also for their potential to expand fundamental understanding of complex phenomena at very small size scales. Unfortunately, not much is known about the dynamics of ferroelectrics at this scale. Many of the widely held theories for ferroelectric materials are based on bulk dynamics which break down when applied to smaller scales. In an effort to increase understanding of nanoscale ferroelectric materials we use atomistic resolution computational simulations to investigate the dynamics of polar perovskites. Within the framework of a well validated effective Hamiltonian model we are able to accurately predict many of the properties of ferroelectric materials at the nanoscale including the response of the soft mode to mechanical boundary conditions and the polarization reversal dynamics of ferroelectric nanowires. Given that the focus of our study is the dynamics of ferroelectric perovskites we begin by developing an effective Hamiltonian based model that could simultaneously describe both static and dynamic properties of such materials. Our study reveals that for ferroelectric perovskites that undergo a sequence of phase transitions, such as BaTiO3. for example, the minimal parameter effective Hamiltonian model is unable to reproduce both static and dynamical properties simultaneously. Nevertheless we developed two sets of parameters that accurately describes the static properties and dynamic properties of BaTiO3 independently. By creating a tool that accurately models the dynamical properties of perovskite ferroelectrics we are able to investigate the frequencies of the soft modes in the perovskite crystal. The lowest energy transverse optical soft modes in perovskite ferroelectrics are known to be cause of the ferroelectric phase transition in these materials and affect a number of electrical properties

  6. Shock Hugoniot behavior of single crystal titanium using atomistic simulations

    NASA Astrophysics Data System (ADS)

    Mackenchery, Karoon; Dongare, Avinash

    2017-01-01

    Atomistic shock simulations are performed for single crystal titanium using four different interatomic potentials at impact velocities ranging from 0.5 km/s to 2.0 km/s. These potentials comprise of three parameterizations in the formulation of the embedded atom method and one formulation of the modified embedded atom method. The capability of the potentials to model the shock deformation and failure behavior is investigated by computing the shock hugoniot response of titanium and comparing to existing experimental data. In addition, the capability to reproduce the shock induced alpha (α) to omega (ω) phase transformation seen in Ti is investigated. The shock wave structure is discussed and the velocities for the elastic, plastic and the α-ω phase transformation waves are calculated for all the interatomic potentials considered.

  7. Atomistic Simulation of Polymer Crystallization at Realistic Length Scales

    SciTech Connect

    Gee, R H; Fried, L E

    2005-01-28

    Understanding the dynamics of polymer crystallization during the induction period prior to crystal growth is a key goal in polymer physics. Here we present the first study of primary crystallization of polymer melts via molecular dynamics simulations at physically realistic (about 46 nm) length scales. Our results show that the crystallization mechanism involves a spinodal decomposition microphase separation caused by an increase in the average length of rigid trans segments along the polymer backbone during the induction period. Further, the characteristic length of the growing dense domains during the induction period is longer than predicted by classical nucleation theory. These results indicate a new 'coexistence period' in the crystallization, where nucleation and growth mechanisms coexist with a phase separation mechanism. Our results provide an atomistic verification of the fringed micelle model.

  8. Impacts of atomistic coating on thermal conductivity of germanium nanowires.

    PubMed

    Chen, Jie; Zhang, Gang; Li, Baowen

    2012-06-13

    By using nonequilibrium molecular dynamics simulations, we demonstrated that thermal conductivity of germanium nanowires can be reduced more than 25% at room temperature by atomistic coating. There is a critical coating thickness beyond which thermal conductivity of the coated nanowire is larger than that of the host nanowire. The diameter-dependent critical coating thickness and minimum thermal conductivity are explored. Moreover, we found that interface roughness can induce further reduction of thermal conductivity in coated nanowires. From the vibrational eigenmode analysis, it is found that coating induces localization for low-frequency phonons, while interface roughness localizes the high-frequency phonons. Our results provide an available approach to tune thermal conductivity of nanowires by atomic layer coating.

  9. Redox reactions with empirical potentials: atomistic battery discharge simulations.

    PubMed

    Dapp, Wolf B; Müser, Martin H

    2013-08-14

    Batteries are pivotal components in overcoming some of today's greatest technological challenges. Yet to date there is no self-consistent atomistic description of a complete battery. We take first steps toward modeling of a battery as a whole microscopically. Our focus lies on phenomena occurring at the electrode-electrolyte interface which are not easily studied with other methods. We use the redox split-charge equilibration (redoxSQE) method that assigns a discrete ionization state to each atom. Along with exchanging partial charges across bonds, atoms can swap integer charges. With redoxSQE we study the discharge behavior of a nano-battery, and demonstrate that this reproduces the generic properties of a macroscopic battery qualitatively. Examples are the dependence of the battery's capacity on temperature and discharge rate, as well as performance degradation upon recharge.

  10. Atomistic modeling of ion implantation technologies in silicon

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    Requirements for the manufacturing of electronic devices at the nanometric scale are becoming more and more demanding on each new technology node, driving the need for the fabrication of ultra-shallow junctions and finFET structures. Main implantation strategies, cluster and cold implants, are aimed to reduce the amount of end-of-range defects through substrate amorphization. During finFET doping the device body gets amorphized, and its regrowth is more problematic than in the case of conventional planar devices. Consequently, there is a renewed interest on the modeling of amorphization and recrystallization in the front-end processing of Si. We present multi-scale simulation schemes to model amorphization and recrystallization in Si from an atomistic perspective. Models are able to correctly predict damage formation, accumulation and regrowth, both in the ballistic and thermal-spike regimes, in very good agreement with conventional molecular dynamics techniques but at a much lower computational cost.

  11. Atomistic pathways of the pressure-induced densification of quartz

    NASA Astrophysics Data System (ADS)

    Liang, Yunfeng; Miranda, Caetano R.; Scandolo, Sandro

    2015-10-01

    When quartz is compressed at room temperature it retains its crystal structure at pressures well above its stability domain (0-2 GPa), and collapses into denser structures only when pressure reaches 20 GPa. Depending on the experimental conditions, pressure-induced densification can be accompanied by amorphization; by the formation of crystalline, metastable polymorphs; and can be preceded by the appearance of an intermediate phase, quartz II, with unknown structure. Based on molecular dynamic simulations, we show that this rich phenomenology can be rationalized through a unified theoretical framework of the atomistic pathways leading to densification. The model emphasizes the role played by the oxygen sublattice, which transforms from a bcc-like order in quartz into close-packed arrangements in the denser structures, through a ferroelastic instability of martensitic nature.

  12. Atomistic molecular dynamics simulations of model C36 fullerite

    NASA Astrophysics Data System (ADS)

    Abramo, Maria C.; Caccamo, C.

    2008-02-01

    We report atomistic molecular dynamics investigations of a model C36 fullerite in which the fullerene molecules are modeled as rigid cages over which the carbon atoms occupy fixed interaction sites, distributed in space according to the experimentally known atomic positions in the molecule. Carbon sites belonging to different molecules are assumed to interact via a 12-6 Lennard-Jones-type potential; the parameters of the latter are employed in the framework of a molecular dynamics fitting procedure, through which the ambient condition physical quantities characterizing the hcp structure of solid C36 are eventually reproduced. We discuss applications of the adopted modelization to the C36 phases in a temperature range spanning from 300to1500K, and compare the obtained results to the available data for C36 and other fullerenes, and to the predictions of the well known Girifalco central potential modelization of interactions in fullerenes, as applied to the C36 case.

  13. Pathfinder: A parallel search algorithm for concerted atomistic events

    NASA Astrophysics Data System (ADS)

    Nakano, Aiichiro

    2007-02-01

    An algorithm has been designed to search for the escape paths with the lowest activation barriers when starting from a local minimum-energy configuration of a many-atom system. The pathfinder algorithm combines: (1) a steered eigenvector-following method that guides a constrained escape from the convex region and subsequently climbs to a transition state tangentially to the eigenvector corresponding to the lowest negative Hessian eigenvalue; (2) discrete abstraction of the atomic configuration to systematically enumerate concerted events as linear combinations of atomistic events; (3) evolutionary control of the population dynamics of low activation-barrier events; and (4) hybrid task + spatial decompositions to implement massive search for complex events on parallel computers. The program exhibits good scalability on parallel computers and has been used to study concerted bond-breaking events in the fracture of alumina.

  14. Atomistic design of semiconductor nanostructures with optimal thermoelectric properties

    NASA Astrophysics Data System (ADS)

    Galli, Giulia

    2008-03-01

    The search for novel materials with optimal thermoelectric properties (for either thermoelectric power generation or heat dissipation) is an active field of research. We present atomistic and ab-initio simulations of selected nanomaterials, aimed at predicting thermal conductivities and electronic transport properties, and ultimately at designing materials with optimal thermoelectric figure of merit. In particular we focus on carbon nanotubes [1], silicon wires [2] and nanoporous silicon [3] and we discuss both strategies and algorithms to optimize thermoelectric properties at the nanoscale. [1] D. Donadio and G.Galli, Phys. Rev. Lett. 2007 (in press). [2] T.Vo, A.Williamson, V.Lordi and G.Galli (submitted) and J.Reed, A.Williamson, E.Schwegler and G.Galli (submitted). [3] J.-H. Lee, J.C.Grossman, J.Reed and G.Galli, Appl. Phys. Lett. 2007 (in press).

  15. Effects of Atomistic Domain Size on Hybrid Lattice Boltzmann-Molecular Dynamics Simulations of Dense Fluids

    NASA Astrophysics Data System (ADS)

    Dupuis, A.; Koumoutsakos, P.

    We present a convergence study for a hybrid Lattice Boltzmann-Molecular Dynamics model for the simulation of dense liquids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The velocity field from the atomistic domain is introduced as forcing terms to the Lattice Boltzmann model of the continuum while the mean field of the continuum imposes mean field conditions for the atomistic domain. In the present paper we investigate the effect of varying the size of the atomistic subdomain in simulations of two dimensional flows of liquid argon past carbon nanotubes and assess the efficiency of the method.

  16. Analysis of an optimization-based atomistic-to-continuum coupling method for point defects

    DOE PAGES

    Olson, Derek; Shapeev, Alexander V.; Bochev, Pavel B.; ...

    2015-11-16

    Here, we formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Application of a potential-based atomistic model near the defect core enables accurate simulation of the defect. Away from the core, where site energies become nearly independent of the lattice position, the method switches to a more efficient continuum model. The two models are merged by minimizing the mismatch of their states on an overlap region, subject to the atomistic and continuum force balance equations acting independently in their domains. We prove that the optimization problem is well-posed and establish error estimates.

  17. Experimentally driven atomistic model of 1,2 polybutadiene

    SciTech Connect

    Gkourmpis, Thomas; Mitchell, Geoffrey R.

    2014-02-07

    We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles, and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120–400 K. Analysis of the experimental data yields bond lengths for Cî—¸C and C î—» C of 1.54 Å and 1.35 Å, respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently, the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

  18. Numerical algorithms for the atomistic dopant profiling of semiconductor materials

    NASA Astrophysics Data System (ADS)

    Aghaei Anvigh, Samira

    In this dissertation, we investigate the possibility to use scanning microscopy such as scanning capacitance microscopy (SCM) and scanning spreading resistance microscopy (SSRM) for the "atomistic" dopant profiling of semiconductor materials. For this purpose, we first analyze the discrete effects of random dopant fluctuations (RDF) on SCM and SSRM measurements with nanoscale probes and show that RDF significantly affects the differential capacitance and spreading resistance of the SCM and SSRM measurements if the dimension of the probe is below 50 nm. Then, we develop a mathematical algorithm to compute the spatial coordinates of the ionized impurities in the depletion region using a set of scanning microscopy measurements. The proposed numerical algorithm is then applied to extract the (x, y, z) coordinates of ionized impurities in the depletion region in the case of a few semiconductor materials with different doping configuration. The numerical algorithm developed to solve the above inverse problem is based on the evaluation of doping sensitivity functions of the differential capacitance, which show how sensitive the differential capacitance is to doping variations at different locations. To develop the numerical algorithm we first express the doping sensitivity functions in terms of the Gâteaux derivative of the differential capacitance, use Riesz representation theorem, and then apply a gradient optimization approach to compute the locations of the dopants. The algorithm is verified numerically using 2-D simulations, in which the C-V curves are measured at 3 different locations on the surface of the semiconductor. Although the cases studied in this dissertation are much idealized and, in reality, the C-V measurements are subject to noise and other experimental errors, it is shown that if the differential capacitance is measured precisely, SCM measurements can be potentially used for the "atomistic" profiling of ionized impurities in doped semiconductors.

  19. LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Spectral characteristics of fragmentation of kidney stones by microsecond laser radiation

    NASA Astrophysics Data System (ADS)

    Batishche, S. A.; Tarkovsky, V. V.

    1995-07-01

    A study of the action of single microsecond laser pulses on kidney stones revealed a strong spectral dependence of the efficiency K of mass removal. This should be taken into account in the development of apparatus for laser lithotripsy. An increase in the energy of the laser pulses acting on a stone resulted in saturation of K when a certain energy, specific to each wavelength, was exceeded. The radiation energy should be less than the saturation threshold in order to reduce the effects on the surrounding tissues.

  20. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing.

    PubMed

    Zagrovic, Bojan; Snow, Christopher D; Shirts, Michael R; Pande, Vijay S

    2002-11-08

    By employing thousands of PCs and new worldwide-distributed computing techniques, we have simulated in atomistic detail the folding of a fast-folding 36-residue alpha-helical protein from the villin headpiece. The total simulated time exceeds 300 micros, orders of magnitude more than previous simulations of a molecule of this size. Starting from an extended state, we obtained an ensemble of folded structures, which is on average 1.7A and 1.9A away from the native state in C(alpha) distance-based root-mean-square deviation (dRMS) and C(beta) dRMS sense, respectively. The folding mechanism of villin is most consistent with the hydrophobic collapse view of folding: the molecule collapses non-specifically very quickly ( approximately 20ns), which greatly reduces the size of the conformational space that needs to be explored in search of the native state. The conformational search in the collapsed state appears to be rate-limited by the formation of the aromatic core: in a significant fraction of our simulations, the C-terminal phenylalanine residue packs improperly with the rest of the hydrophobic core. We suggest that the breaking of this interaction may be the rate-determining step in the course of folding. On the basis of our simulations we estimate the folding rate of villin to be approximately 5micros. By analyzing the average features of the folded ensemble obtained by simulation, we see that the mean folded structure is more similar to the native fold than any individual folded structure. This finding highlights the need for simulating ensembles of molecules and averaging the results in an experiment-like fashion if meaningful comparison between simulation and experiment is to be attempted. Moreover, our results demonstrate that (1) the computational methodology exists to simulate the multi-microsecond regime using distributed computing and (2) that potential sets used to describe interatomic interactions may be sufficiently accurate to reach the folded state

  1. Control of density fluctuations in atomistic-continuum simulations of dense liquids

    NASA Astrophysics Data System (ADS)

    Kotsalis, E. M.; Walther, J. H.; Koumoutsakos, P.

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation. We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

  2. Control of density fluctuations in atomistic-continuum simulations of dense liquids.

    PubMed

    Kotsalis, E M; Walther, J H; Koumoutsakos, P

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation. We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

  3. Breaking the millisecond barrier on SpiNNaker: implementing asynchronous event-based plastic models with microsecond resolution

    PubMed Central

    Lagorce, Xavier; Stromatias, Evangelos; Galluppi, Francesco; Plana, Luis A.; Liu, Shih-Chii; Furber, Steve B.; Benosman, Ryad B.

    2015-01-01

    Spike-based neuromorphic sensors such as retinas and cochleas, change the way in which the world is sampled. Instead of producing data sampled at a constant rate, these sensors output spikes that are asynchronous and event driven. The event-based nature of neuromorphic sensors implies a complete paradigm shift in current perception algorithms toward those that emphasize the importance of precise timing. The spikes produced by these sensors usually have a time resolution in the order of microseconds. This high temporal resolution is a crucial factor in learning tasks. It is also widely used in the field of biological neural networks. Sound localization for instance relies on detecting time lags between the two ears which, in the barn owl, reaches a temporal resolution of 5 μs. Current available neuromorphic computation platforms such as SpiNNaker often limit their users to a time resolution in the order of milliseconds that is not compatible with the asynchronous outputs of neuromorphic sensors. To overcome these limitations and allow for the exploration of new types of neuromorphic computing architectures, we introduce a novel software framework on the SpiNNaker platform. This framework allows for simulations of spiking networks and plasticity mechanisms using a completely asynchronous and event-based scheme running with a microsecond time resolution. Results on two example networks using this new implementation are presented. PMID:26106288

  4. Search of the energetic gamma-ray experiment telescope (EGRET) data for high-energy gamma-ray microsecond bursts

    NASA Technical Reports Server (NTRS)

    Fichtel, C. E.; Bertsch, D. L.; Dingus, B. L.; Esposito, J. A.; Hartman, R. C.; Hunter, S. D.; Kanbach, G.; Kniffen, D. A.; Lin, Y. C.; Mattox, J. R.

    1994-01-01

    Hawking (1974) and Page & Hawking (1976) investigated theoretically the possibility of detecting high-energy gamma rays produced by the quantum-mechanical decay of a small black hole created in the early universe. They concluded that, at the very end of the life of the small black hole, it would radiate a burst of gamma rays peaked near 250 MeV with a total energy of about 10(exp 34) ergs in the order of a microsecond or less. The characteristics of a black hole are determined by laws of physics beyond the range of current particle accelerators; hence, the search for these short bursts of high-energy gamma rays provides at least the possibility of being the first test of this region of physics. The Compton Observatory Energetic Gamma-Ray Experiment Telescope (EGRET) has the capability of detecting directly the gamma rays from such bursts at a much fainter level than SAS 2, and a search of the EGRET data has led to an upper limit of 5 x 10(exp -2) black hole decays per cu pc per yr, placing constraints on this and other theories predicting microsecond high-energy gamma-ray bursts.

  5. Breaking the millisecond barrier on SpiNNaker: implementing asynchronous event-based plastic models with microsecond resolution.

    PubMed

    Lagorce, Xavier; Stromatias, Evangelos; Galluppi, Francesco; Plana, Luis A; Liu, Shih-Chii; Furber, Steve B; Benosman, Ryad B

    2015-01-01

    Spike-based neuromorphic sensors such as retinas and cochleas, change the way in which the world is sampled. Instead of producing data sampled at a constant rate, these sensors output spikes that are asynchronous and event driven. The event-based nature of neuromorphic sensors implies a complete paradigm shift in current perception algorithms toward those that emphasize the importance of precise timing. The spikes produced by these sensors usually have a time resolution in the order of microseconds. This high temporal resolution is a crucial factor in learning tasks. It is also widely used in the field of biological neural networks. Sound localization for instance relies on detecting time lags between the two ears which, in the barn owl, reaches a temporal resolution of 5 μs. Current available neuromorphic computation platforms such as SpiNNaker often limit their users to a time resolution in the order of milliseconds that is not compatible with the asynchronous outputs of neuromorphic sensors. To overcome these limitations and allow for the exploration of new types of neuromorphic computing architectures, we introduce a novel software framework on the SpiNNaker platform. This framework allows for simulations of spiking networks and plasticity mechanisms using a completely asynchronous and event-based scheme running with a microsecond time resolution. Results on two example networks using this new implementation are presented.

  6. On-the-fly decoding luminescence lifetimes in the microsecond region for lanthanide-encoded suspension arrays

    PubMed Central

    Lu, Yiqing; Lu, Jie; Zhao, Jiangbo; Cusido, Janet; Raymo, Françisco M; Yuan, Jingli; Yang, Sean; Leif, Robert C.; Huo, Yujing; Piper, James A.; Paul Robinson, J; Goldys, Ewa M.; Jin, Dayong

    2014-01-01

    Significant multiplexing capacity of optical time-domain coding has been recently demonstrated by tuning luminescence lifetimes of the upconversion nanoparticles called ‘τ-Dots’. It provides a large dynamic range of lifetimes from microseconds to milliseconds, which allows creating large libraries of nanotags/microcarriers. However, a robust approach is required to rapidly and accurately measure the luminescence lifetimes from the relatively slow-decaying signals. Here we show a fast algorithm suitable for the microsecond region with precision closely approaching the theoretical limit and compatible with the rapid scanning cytometry technique. We exploit this approach to further extend optical time-domain multiplexing to the downconversion luminescence, using luminescence microspheres wherein lifetimes are tuned through luminescence resonance energy transfer. We demonstrate real-time discrimination of these microspheres in the rapid scanning cytometry, and apply them to the multiplexed probing of pathogen DNA strands. Our results indicate that tunable luminescence lifetimes have considerable potential in high-throughput analytical sciences. PMID:24796249

  7. Polarization Aberrations

    NASA Technical Reports Server (NTRS)

    Mcguire, James P., Jr.; Chipman, Russell A.

    1990-01-01

    The analysis of the polarization characteristics displayed by optical systems can be divided into two categories: geometrical and physical. Geometrical analysis calculates the change in polarization of a wavefront between pupils in an optical instrument. Physical analysis propagates the polarized fields wherever the geometrical analysis is not valid, i.e., near the edges of stops, near images, in anisotropic media, etc. Polarization aberration theory provides a starting point for geometrical design and facilitates subsequent optimization. The polarization aberrations described arise from differences in the transmitted (or reflected) amplitudes and phases at interfaces. The polarization aberration matrix (PAM) is calculated for isotropic rotationally symmetric systems through fourth order and includes the interface phase, amplitude, linear diattenuation, and linear retardance aberrations. The exponential form of Jones matrices used are discussed. The PAM in Jones matrix is introduced. The exact calculation of polarization aberrations through polarization ray tracing is described. The report is divided into three sections: I. Rotationally Symmetric Optical Systems; II. Tilted and Decentered Optical Systems; and Polarization Analysis of LIDARs.

  8. Quantifying sampling noise and parametric uncertainty in atomistic-to-continuum simulations using surrogate models

    SciTech Connect

    Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.; Najm, Habib N.; Debusschere, Bert

    2015-08-11

    We present a methodology to assess the predictive fidelity of multiscale simulations by incorporating uncertainty in the information exchanged between the components of an atomistic-to-continuum simulation. We account for both the uncertainty due to finite sampling in molecular dynamics (MD) simulations and the uncertainty in the physical parameters of the model. Using Bayesian inference, we represent the expensive atomistic component by a surrogate model that relates the long-term output of the atomistic simulation to its uncertain inputs. We then present algorithms to solve for the variables exchanged across the atomistic-continuum interface in terms of polynomial chaos expansions (PCEs). We also consider a simple Couette flow where velocities are exchanged between the atomistic and continuum components, while accounting for uncertainty in the atomistic model parameters and the continuum boundary conditions. Results show convergence of the coupling algorithm at a reasonable number of iterations. As a result, the uncertainty in the obtained variables significantly depends on the amount of data sampled from the MD simulations and on the width of the time averaging window used in the MD simulations.

  9. Quantifying sampling noise and parametric uncertainty in atomistic-to-continuum simulations using surrogate models

    DOE PAGES

    Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.; ...

    2015-08-11

    We present a methodology to assess the predictive fidelity of multiscale simulations by incorporating uncertainty in the information exchanged between the components of an atomistic-to-continuum simulation. We account for both the uncertainty due to finite sampling in molecular dynamics (MD) simulations and the uncertainty in the physical parameters of the model. Using Bayesian inference, we represent the expensive atomistic component by a surrogate model that relates the long-term output of the atomistic simulation to its uncertain inputs. We then present algorithms to solve for the variables exchanged across the atomistic-continuum interface in terms of polynomial chaos expansions (PCEs). We alsomore » consider a simple Couette flow where velocities are exchanged between the atomistic and continuum components, while accounting for uncertainty in the atomistic model parameters and the continuum boundary conditions. Results show convergence of the coupling algorithm at a reasonable number of iterations. As a result, the uncertainty in the obtained variables significantly depends on the amount of data sampled from the MD simulations and on the width of the time averaging window used in the MD simulations.« less

  10. 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

  11. Polar Bear

    USGS Publications Warehouse

    Amstrup, S.D.; ,; Lentfer, J.W.

    1988-01-01

    Polar bears are long-lived, late-maturing carnivores that have relatively low rates of reproduction and natural mortality. Their populations are susceptible to disturbance from human activities, such as the exploration and development of mineral resources or hunting. Polar bear populations have been an important renewable resource available to coastal communities throughout the Arctic for thousands of years.

  12. Atomistic modeling of electronic structure and transport in disordered nanostructures

    NASA Astrophysics Data System (ADS)

    Kharche, Neerav

    As the Si-CMOS technology approaches the end of the International Technology Roadmap for Semiconductors (ITRS), the semiconductor industry faces a formidable challenge to continue the transistor scaling according to Moore's law. To continue the scaling of classical devices, alternative channel materials such as SiGe, carbon nanotubes, nanowires, and III-V based materials are being investigated along with novel 3D device geometries. Researchers are also investigating radically new quantum computing devices, which are expected to perform calculations faster than the existing classical Si-CMOS based structures. Atomic scale disorders such as interface roughness, alloy randomness, non-uniform strain, and dopant fluctuations are routinely present in the experimental realization of such devices. These disorders now play an increasingly important role in determining the electronic structure and transport properties as device sizes enter the nanometer regime. This work employs the atomistic tight-binding technique, which is ideally suited for modeling systems with local disorders on an atomic scale. High-precision multi-million atom electronic structure calculations of (111) Si surface quantum wells and (100) SiGe/Si/SiGe heterostructure quantum wells are performed to investigate the modulation of valley splitting induced by atomic scale disorders. The calculations presented here resolve the existing discrepancies between theoretically predicted and experimentally measured valley splitting, which is an important design parameter in quantum computing devices. Supercell calculations and the zone-unfolding method are used to compute the bandstructures of inhomogeneous nanowires made of AlGaAs and SiGe and their connection with the transmission coefficients computed using non-equilibrium Green's function method is established. A unified picture of alloy nanowires emerges, in which the nanodevice (transmission) and nanomaterials (bandstructure) viewpoints complement each other

  13. Polarization control at spin-driven ferroelectric domain walls.

    PubMed

    Leo, Naëmi; Bergman, Anders; Cano, Andres; Poudel, Narayan; Lorenz, Bernd; Fiebig, Manfred; Meier, Dennis

    2015-04-14

    Unusual electronic states arise at ferroelectric domain walls due to the local symmetry reduction, strain gradients and electrostatics. This particularly applies to improper ferroelectrics, where the polarization is induced by a structural or magnetic order parameter. Because of the subordinate nature of the polarization, the rigid mechanical and electrostatic boundary conditions that constrain domain walls in proper ferroics are lifted. Here we show that spin-driven ferroelectricity promotes the emergence of charged domain walls. This provides new degrees of flexibility for controlling domain-wall charges in a deterministic and reversible process. We create and position a domain wall by an electric field in Mn0.95Co0.05WO4. With a magnetic field we then rotate the polarization and convert neutral into charged domain walls, while its magnetic properties peg the wall to its location. Using atomistic Landau-Lifshitz-Gilbert simulations we quantify the polarization changes across the two wall types and highlight their general occurrence.

  14. Macrophage Polarization.

    PubMed

    Murray, Peter J

    2017-02-10

    Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and the normal tissue environment. Three broad pathways control polarization: epigenetic and cell survival pathways that prolong or shorten macrophage development and viability, the tissue microenvironment, and extrinsic factors, such as microbial products and cytokines released in inflammation. A plethora of advances have provided a framework for rationally purifying, describing, and manipulating macrophage polarization. Here, I assess the current state of knowledge about macrophage polarization and enumerate the major questions about how activated macrophages regulate the physiology of normal and damaged tissues.

  15. GPUbased, Microsecond Latency, HectoChannel MIMO Feedback Control of Magnetically Confined Plasmas

    NASA Astrophysics Data System (ADS)

    Rath, Nikolaus

    Feedback control has become a crucial tool in the research on magnetic confinement of plasmas for achieving controlled nuclear fusion. This thesis presents a novel plasma feedback control system that, for the first time, employs a Graphics Processing Unit (GPU) for microsecond-latency, real-time control computations. This novel application area for GPU computing is opened up by a new system architecture that is optimized for low-latency computations on less than kilobyte sized data samples as they occur in typical plasma control algorithms. In contrast to traditional GPU computing approaches that target complex, high-throughput computations with massive amounts of data, the architecture presented in this thesis uses the GPU as the primary processing unit rather than as an auxiliary of the CPU, and data is transferred from A-D/D-A converters directly into GPU memory using peer-to-peer PCI Express transfers. The described design has been implemented in a new, GPU-based control system for the High-Beta Tokamak - Extended Pulse (HBT-EP) device. The system is built from commodity hardware and uses an NVIDIA GeForce GPU and D-TACQ A-D/D-A converters providing a total of 96 input and 64 output channels. The system is able to run with sampling periods down to 4 μs and latencies down to 8 μs. The GPU provides a total processing power of 1.5 x 1012 floating point operations per second. To illustrate the performance and versatility of both the general architecture and concrete implementation, a new control algorithm has been developed. The algorithm is designed for the control of multiple rotating magnetic perturbations in situations where the plasma equilibrium is not known exactly and features an adaptive system model: instead of requiring the rotation frequencies and growth rates embedded in the system model to be set a priori, the adaptive algorithm derives these parameters from the evolution of the perturbation amplitudes themselves. This results in non-linear control

  16. Quantifying grain boundary damage tolerance with atomistic simulations

    NASA Astrophysics Data System (ADS)

    Foley, Daniel; Tucker, Garritt J.

    2016-10-01

    Grain boundaries play a pivotal role in defect evolution and accommodation within materials. Irradiated metals have been observed to form defect denuded zones in the vicinity of grain boundaries. This is especially apparent in nanocrystalline metals, which have an increased grain boundary concentration, as compared to their polycrystalline counterparts. Importantly, the effect of individual grain boundaries on microstructural damage tolerance is related to the character or structural state of the grain boundary. In this work, the damage accommodation behavior of a variety of copper grain boundaries is studied using atomistic simulations. Damage accumulation behavior is found to reach a saturation point where both the free volume and energy of a grain boundary fluctuate within an elliptical manifold, which varies in size for different boundary characters. Analysis of the grain boundaries shows that extrinsic damage accommodation occurs due to localized atomic shuffling accompanied by free volume rearrangement within the boundary. Continuous damage accumulation leads to altered atomic structural states that oscillate around a mean non-equilibrium state, that is energetically metastable. Our results suggest that variation of grain boundary behavior, both from equilibrium and under saturation, is directly related to grain boundary equilibrium energy and some boundaries have a greater propensity to continually accommodate damage, as compared to others.

  17. Scoring multipole electrostatics in condensed-phase atomistic simulations.

    PubMed

    Bereau, Tristan; Kramer, Christian; Monnard, Fabien W; Nogueira, Elisa S; Ward, Thomas R; Meuwly, Markus

    2013-05-09

    Permanent multipoles (MTPs) embody a natural extension to common point-charge (PC) representations in atomistic simulations. In this work, we propose an alternative to the computationally expensive MTP molecular dynamics simulations by running a simple PC simulation and later reevaluate-"score''-all energies using the more detailed MTP force field. The method, which relies on the assumption that the PC and MTP force fields generate closely related phase spaces, is accomplished by enforcing identical sets of monopoles between the two force fields-effectively highlighting the higher MTP terms as a correction to the PC approximation. We first detail our consistent parametrization of the electrostatics and van der Waals interactions for the two force fields. We then validate the method by comparing the accuracy of protein-ligand binding free energies from both PC and MTP-scored representations with experimentally determined binding constants obtained by us. Specifically, we study the binding of several arylsulfonamide ligands to human carbonic anhydrase II. We find that both representations yield an accuracy of 1 kcal/mol with respect to experiment. Finally, we apply the method to rank the energetic contributions of individual atomic MTP coefficients for molecules solvated in water. All in all, MTP scoring is a computationally appealing method that can provide insight into the multipolar electrostatic interactions of condensed-phase systems.

  18. Dislocation climb models from atomistic scheme to dislocation dynamics

    NASA Astrophysics Data System (ADS)

    Niu, Xiaohua; Luo, Tao; Lu, Jianfeng; Xiang, Yang

    2017-02-01

    We develop a mesoscopic dislocation dynamics model for vacancy-assisted dislocation climb by upscalings from a stochastic model on the atomistic scale. Our models incorporate microscopic mechanisms of (i) bulk diffusion of vacancies, (ii) vacancy exchange dynamics between bulk and dislocation core, (iii) vacancy pipe diffusion along the dislocation core, and (iv) vacancy attachment-detachment kinetics at jogs leading to the motion of jogs. Our mesoscopic model consists of the vacancy bulk diffusion equation and a dislocation climb velocity formula. The effects of these microscopic mechanisms are incorporated by a Robin boundary condition near the dislocations for the bulk diffusion equation and a new contribution in the dislocation climb velocity due to vacancy pipe diffusion driven by the stress variation along the dislocation. Our climb formulation is able to quantitatively describe the translation of prismatic loops at low temperatures when the bulk diffusion is negligible. Using this new formulation, we derive analytical formulas for the climb velocity of a straight edge dislocation and a prismatic circular loop. Our dislocation climb formulation can be implemented in dislocation dynamics simulations to incorporate all the above four microscopic mechanisms of dislocation climb.

  19. Coarse-Grained and Atomistic Modeling of Polyimides

    NASA Technical Reports Server (NTRS)

    Clancy, Thomas C.; Hinkley, Jeffrey A.

    2004-01-01

    A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

  20. An efficient fully atomistic potential model for dense fluid methane

    NASA Astrophysics Data System (ADS)

    Jiang, Chuntao; Ouyang, Jie; Zhuang, Xin; Wang, Lihua; Li, Wuming

    2016-08-01

    A fully atomistic model aimed to obtain a general purpose model for the dense fluid methane is presented. The new optimized potential for liquid simulation (OPLS) model is a rigid five site model which consists of five fixed point charges and five Lennard-Jones centers. The parameters in the potential model are determined by a fit of the experimental data of dense fluid methane using molecular dynamics simulation. The radial distribution function and the diffusion coefficient are successfully calculated for dense fluid methane at various state points. The simulated results are in good agreement with the available experimental data shown in literature. Moreover, the distribution of mean number hydrogen bonds and the distribution of pair-energy are analyzed, which are obtained from the new model and other five reference potential models. Furthermore, the space-time correlation functions for dense fluid methane are also discussed. All the numerical results demonstrate that the new OPLS model could be well utilized to investigate the dense fluid methane.

  1. Atomistic simulation of defects in alkaline-earth fluorohalide crystals

    NASA Astrophysics Data System (ADS)

    Baetzold, Roger C.

    1987-12-01

    Defect properties of BaFBr, BaFCl, and SrFCl were calculated using the atomistic simulation technique. Two-body potentials were developed starting from potentials in related crystals or calculated by the electron-gas method and then fit to minimize strain in the equilibrium structure. Agreement of calculated elastic, dielectric, and cohesive properties with available experimental and theoretical data was reasonable. Generally, Frenkel energies for the larger-size halogen ion were less than for the fluorine ion and less than the Schottky energy for the metal, fluoride, and other halide ions set. A Schottky energy for vacancies of the metal ion and two of the larger-size halide ions was small. Energies of formation of Vk and H centers were computed with the aid of thermodynamic cycles. The most stable Vk center forms on the halide ion site where the Madelung potential is most favorable for holes. H centers occupy off-center sites in these low-symmetry materials. Stable geometries are discussed.

  2. Crystallized Silicon Nanostructures - Experimental Characterization and Atomistic Simulations

    SciTech Connect

    Agbo, Solomon; Sutta, Pavol; Calta, Pavel; Biswas, Rana; Pan, Bicai

    2014-07-01

    We have synthesized silicon nanocrystalline structures from thermal annealing of thin film amorphous silicon-based multilayers. The annealing procedure that was carried out in vacuum at temperatures up to 1100 °C is integrated in a X-ray diffraction (XRD) setup for real-time monitoring of the formation phases of the nanostructures. The microstructure of the crystallized films is investigated through experimental measurements combined with atomistic simulations of realistic nanocrystalline silicon (nc-Si) models. The multilayers consisting of uniformly alternating thicknesses of hydrogenated amorphous silicon and silicon oxide (SiO2) were deposited by plasma enhanced chemical vapor deposition on crystalline silicon and Corning glass substrates. The crystallized structure consisting of nc-Si structures embedded in an amorphous matrix were further characterized through XRD, Raman spectroscopy, and Fourier transform infrared measurements. We are able to show the different stages of nanostructure formation and how the sizes and the crystallized mass fraction can be controlled in our experimental synthesis. The crystallized silicon structures with large crystalline filling fractions exceeding 50% have been simulated with a robust classical molecular dynamics technique. The crystalline filling fractions and structural order of nc-Si obtained from this simulation are compared with our Raman and XRD measurements.

  3. Equilibrium at the edge and atomistic mechanisms of graphene growth

    PubMed Central

    Artyukhov, Vasilii I.; Liu, Yuanyue; Yakobson, Boris I.

    2012-01-01

    The morphology of graphene is crucial for its applications, yet an adequate theory of its growth is lacking: It is either simplified to a phenomenological-continuum level or is overly detailed in atomistic simulations, which are often intractable. Here we put forward a comprehensive picture dubbed nanoreactor, which draws from ideas of step-flow crystal growth augmented by detailed first-principles calculations. As the carbon atoms migrate from the feedstock to catalyst to final graphene lattice, they go through a sequence of states whose energy levels can be computed and arranged into a step-by-step map. Analysis begins with the structure and energies of arbitrary edges to yield equilibrium island shapes. Then, it elucidates how the atoms dock at the edges and how they avoid forming defects. The sequence of atomic row assembly determines the kinetic anisotropy of growth, and consequently, graphene island morphology, explaining a number of experimental facts and suggesting how the growth product can further be improved. Finally, this analysis adds a useful perspective on the synthesis of carbon nanotubes and its essential distinction from graphene. PMID:22949702

  4. Optimization Algorithms in Optimal Predictions of Atomistic Properties by Kriging.

    PubMed

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

    2016-04-12

    The machine learning method kriging is an attractive tool to construct next-generation force fields. Kriging can accurately predict atomistic properties, which involves optimization of the so-called concentrated log-likelihood function (i.e., fitness function). The difficulty of this optimization problem quickly escalates in response to an increase in either the number of dimensions of the system considered or the size of the training set. In this article, we demonstrate and compare the use of two search algorithms, namely, particle swarm optimization (PSO) and differential evolution (DE), to rapidly obtain the maximum of this fitness function. The ability of these two algorithms to find a stationary point is assessed by using the first derivative of the fitness function. Finally, the converged position obtained by PSO and DE is refined through the limited-memory Broyden-Fletcher-Goldfarb-Shanno bounded (L-BFGS-B) algorithm, which belongs to the class of quasi-Newton algorithms. We show that both PSO and DE are able to come close to the stationary point, even in high-dimensional problems. They do so in a reasonable amount of time, compared to that with the Newton and quasi-Newton algorithms, regardless of the starting position in the search space of kriging hyperparameters. The refinement through L-BFGS-B is able to give the position of the maximum with whichever precision is desired.

  5. Atomistic mechanisms for bilayer growth of graphene on metal substrates

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Cui, Ping; Zhu, Wenguang; Kaxiras, Efthimios; Gao, Yanfei; Zhang, Zhenyu

    2015-01-01

    Epitaxial growth on metal substrates has been shown to be the most powerful approach in producing large-scale high-quality monolayer graphene, yet it remains a major challenge to realize uniform bilayer graphene growth. Here we carry out a comparative study of the atomistic mechanisms for bilayer graphene growth on the (111) surfaces of Cu and Ni, using multiscale approaches combining first-principles calculations and rate-equation analysis. We first show that the relatively weak graphene-Cu interaction enhances the lateral diffusion and effective nucleation of C atoms underneath the graphene island, thereby making it more feasible to grow bilayer graphene on Cu. In contrast, the stronger graphene-Ni interaction suppresses the lateral mobility and dimerization of C atoms underneath the graphene, making it unlikely to achieve controlled growth of bilayer graphene on Ni. We then determine the critical graphene size beyond which nucleation of the second layer will take place. Intriguingly, the critical size exhibits an effective inverse "Ehrlich-Schwoebel barrier" effect, becoming smaller for faster C migration from the Cu surface to the graphene-Cu interface sites across the graphene edge. These findings allow us to propose a novel alternating growth scheme to realize mass production of bilayer graphene.

  6. Atomistic simulations of CO vibrations in ices relevant to astrochemistry.

    PubMed

    Plattner, Nuria; Meuwly, Markus

    2008-06-23

    The experimental absorption band of carbon monoxide (CO) in mixed ices has been extensively studied in the past. The astrophysical interest in this band is related to its characteristic shape, which appears to depend on the surrounding ice structure. Herein, molecular dynamics simulations are carried out to analyze the relationship between the structure of the ice and the infrared (IR) spectrum of embedded CO molecules at different concentrations. Instead of conventional force fields, anharmonic potentials are used for the bonded interactions. The electrostatic interactions are more accurately described by means of fluctuating atomic multipole moments (up to quadrupole). The experimentally observed splitting of the CO absorption band (gas phase: 2143 cm(-1)) into a blue- (2152 cm(-1)) and a red-shifted (2138 cm(-1)) signal is also found in the simulations. Complementary atomistic simulations allow us to relate the spectra with the structural features. The distinction between interstitial and substitutional CO molecules as the origin of this splitting is found to be qualitatively correct. However, at increasing CO concentrations, additional effects-such as mutual interactions between CO molecules-become important, and the simplistic picture needs to be revised.

  7. Transistor roadmap projection using predictive full-band atomistic modeling

    SciTech Connect

    Salmani-Jelodar, M. Klimeck, G.; Kim, S.; Ng, K.

    2014-08-25

    In this letter, a full band atomistic quantum transport tool is used to predict the performance of double gate metal-oxide-semiconductor field-effect transistors (MOSFETs) over the next 15 years for International Technology Roadmap for Semiconductors (ITRS). As MOSFET channel lengths scale below 20 nm, the number of atoms in the device cross-sections becomes finite. At this scale, quantum mechanical effects play an important role in determining the device characteristics. These quantum effects can be captured with the quantum transport tool. Critical results show the ON-current degradation as a result of geometry scaling, which is in contrast to previous ITRS compact model calculations. Geometric scaling has significant effects on the ON-current by increasing source-to-drain (S/D) tunneling and altering the electronic band structure. By shortening the device gate length from 20 nm to 5.1 nm, the ratio of S/D tunneling current to the overall subthreshold OFF-current increases from 18% to 98%. Despite this ON-current degradation by scaling, the intrinsic device speed is projected to increase at a rate of at least 8% per year as a result of the reduction of the quantum capacitance.

  8. Seawater Pervaporation through Zeolitic Imidazolate Framework Membranes: Atomistic Simulation Study.

    PubMed

    Gupta, Krishna M; Qiao, Zhiwei; Zhang, Kang; Jiang, Jianwen

    2016-06-01

    An atomistic simulation study is reported for seawater pervaporation through five zeolitic imidazolate framework (ZIF) membranes including ZIF-8, -93, -95, -97, and -100. Salt rejection in the five ZIFs is predicted to be 100%. With the largest aperture, ZIF-100 possesses the highest water permeability of 5 × 10(-4) kg m/(m(2) h bar), which is substantially higher compared to commercial reverse osmosis membranes, as well as zeolite and graphene oxide pervaporation membranes. In ZIF-8, -93, -95, and -97 with similar aperture size, water flux is governed by framework hydrophobicity/hydrophilicity; in hydrophobic ZIF-8 and -95, water flux is higher than in hydrophilic ZIF-93 and -97. Furthermore, water molecules in ZIF-93 move slowly and remain in the membrane for a long time but undergo to-and-fro motion in ZIF-100. The lifetime of hydrogen bonds in ZIF-93 is found to be longer than in ZIF-100. This simulation study quantitatively elucidates the dynamic and structural properties of water in ZIF membranes, identifies the key governing factors (aperture size and framework hydrophobicity/hydrophilicity), and suggests that ZIF-100 is an intriguing membrane for seawater pervaporation.

  9. Atomistic Simulations of Poly(N-isopropylacrylamide) Surfactants in Water

    NASA Astrophysics Data System (ADS)

    Abbott, Lauren J.; Stevens, Mark J.

    2015-03-01

    The amphiphilic polymer poly(N-isopropylacrylamide) (PNIPAM) displays a sharp phase transition at its LCST around 32 °C, which results from competing interactions of the hydrophobic and hydrophilic groups with water. This thermoresponsive behavior can be exploited in more complex architectures, such as block copolymers or surfactants, to provide responsive PNIPAM head groups. In these systems, however, changes to the hydrophobic/hydrophilic balance can alter the transition behavior. In this work, we perform atomistic simulations of PNIPAM-alkyl surfactants to study the temperature dependence of their structures. A single chain of the surfactant does not show temperature-responsive behavior. Instead, below and above the LCST of PNIPAM, the surfactant folds to bring the hydrophobic alkyl tail in contact with the PNIPAM backbone, shielding it from water. In addition to single chains, we explore the self-assembly of multiple surfactants into micelles and how the temperature-dependent behavior is changed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  10. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

    Zhou, X. W.; Sills, R. B.; Ward, D. K.; ...

    2017-02-16

    A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin2β + B·cos2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less

  11. Atomistic simulations of elastic deformation and dislocation nucleation during nanoindentation

    NASA Astrophysics Data System (ADS)

    Lilleodden, E. T.; Zimmerman, J. A.; Foiles, S. M.; Nix, W. D.

    2003-05-01

    Nanoindentation experiments have shown that microstructural inhomogeneities across the surface of gold thin films lead to position-dependent nanoindentation behavior [Phys. Rev. B (2002), to be submitted]. The rationale for such behavior was based on the availability of dislocation sources at the grain boundary for initiating plasticity. In order to verify or refute this theory, a computational approach has been pursued. Here, a simulation study of the initial stages of indentation using the embedded atom method (EAM) is presented. First, the principles of the EAM are given, and a comparison is made between atomistic simulations and continuum models for elastic deformation. Then, the mechanism of dislocation nucleation in single crystalline gold is analyzed, and the effects of elastic anisotropy are considered. Finally, a systematic study of the indentation response in the proximity of a high angle, high sigma (low symmetry) grain boundary is presented; indentation behavior is simulated for varying indenter positions relative to the boundary. The results indicate that high angle grain boundaries are a ready source of dislocations in indentation-induced deformation.

  12. Atomistic simulations of uranium incorporation into iron (hydr)oxides.

    PubMed

    Kerisit, Sebastien; Felmy, Andrew R; Ilton, Eugene S

    2011-04-01

    Atomistic simulations were carried out to characterize the coordination environments of U incorporated in three Fe-(hydr)oxide minerals: goethite, magnetite, and hematite. The simulations provided information on U-O and U-Fe distances, coordination numbers, and lattice distortion for U incorporated in different sites (e.g., unoccupied versus occupied sites, octahedral versus tetrahedral) as a function of the oxidation state of U and charge compensation mechanisms (i.e., deprotonation, vacancy formation, or reduction of Fe(III) to Fe(II)). For goethite, deprotonation of first shell hydroxyls enables substitution of U for Fe(III) with a minimal amount of lattice distortion, whereas substitution in unoccupied octahedral sites induced appreciable distortion to 7-fold coordination regardless of U oxidation states and charge compensation mechanisms. Importantly, U-Fe distances of ∼3.6 Å were associated with structural incorporation of U and cannot be considered diagnostic of simple adsorption to goethite surfaces. For magnetite, the octahedral site accommodates U(V) or U(VI) with little lattice distortion. U substituted for Fe(III) in hematite maintained octahedral coordination in most cases. In general, comparison of the simulations with available experimental data provides further evidence for the structural incorporation of U in iron (hydr)oxide minerals.

  13. Water in hydrated orthorhombic lysozyme crystal: Insight from atomistic simulations.

    PubMed

    Hu, Zhongqiao; Jiang, Jianwen; Sandler, Stanley I

    2008-08-21

    Biologically important water in orthorhombic lysozyme crystal is investigated using atomistic simulations. A distinct hydration shell surrounding lysozyme molecules is found from the number distribution of water molecules. While the number of water molecules in the hydration shell increases, the percentage decreases as the hydration level rises. Adsorption of water in the lysozyme crystal shows type-IV behavior. At low hydration levels, water molecules primarily intercalate the minor pores and cavity in the crystal due to the strong affinity between protein and water. At high hydration levels, the major pores are filled with liquidlike water as capillary condensation occurs. A type-H4 hysteresis loop is observed in the adsorption and desorption isotherms. The locations of the water molecules identified from simulation match fairly well with the experimentally determined crystallographic hydration sites. As observed in experiment, water exhibits anomalous subdiffusion because of the geometric restrictions and interactions of protein. With increasing hydration level, this anomaly is reduced and the diffusion of water tends to progressively approach normal Brownian diffusion. The flexibility of protein framework slightly enhances water mobility, but this enhancement decreases with increasing hydration level.

  14. Water in hydrated orthorhombic lysozyme crystal: Insight from atomistic simulations

    NASA Astrophysics Data System (ADS)

    Hu, Zhongqiao; Jiang, Jianwen; Sandler, Stanley I.

    2008-08-01

    Biologically important water in orthorhombic lysozyme crystal is investigated using atomistic simulations. A distinct hydration shell surrounding lysozyme molecules is found from the number distribution of water molecules. While the number of water molecules in the hydration shell increases, the percentage decreases as the hydration level rises. Adsorption of water in the lysozyme crystal shows type-IV behavior. At low hydration levels, water molecules primarily intercalate the minor pores and cavity in the crystal due to the strong affinity between protein and water. At high hydration levels, the major pores are filled with liquidlike water as capillary condensation occurs. A type-H4 hysteresis loop is observed in the adsorption and desorption isotherms. The locations of the water molecules identified from simulation match fairly well with the experimentally determined crystallographic hydration sites. As observed in experiment, water exhibits anomalous subdiffusion because of the geometric restrictions and interactions of protein. With increasing hydration level, this anomaly is reduced and the diffusion of water tends to progressively approach normal Brownian diffusion. The flexibility of protein framework slightly enhances water mobility, but this enhancement decreases with increasing hydration level.

  15. Atomistic calculations of dislocation core energy in aluminium

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Sills, R. B.; Ward, D. K.; Karnesky, R. A.

    2017-02-01

    A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy: Ec=A sin2β +B cos2β , and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. With our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.

  16. Atomistic mechanisms for bilayer growth of graphene on metal substrates

    DOE PAGES

    Chen, Wei; Cui, Ping; Zhu, Wenguang; ...

    2015-01-08

    Epitaxial growth on metal substrates has been shown to be the most powerful approach in producing large-scale high-quality monolayer graphene, yet it remains a major challenge to realize uniform bilayer graphene growth. Here we carry out a comparative study of the atomistic mechanisms for bilayer graphene growth on the (111) surfaces of Cu and Ni, using multiscale approaches combining first-principles calculations and rate-equation analysis. We first show that the relatively weak graphene-Cu interaction enhances the lateral diffusion and effective nucleation of C atoms underneath the graphene island, thereby making it more feasible to grow bilayer graphene on Cu. In contrast,more » the stronger graphene-Ni interaction suppresses the lateral mobility and dimerization of C atoms underneath the graphene, making it unlikely to achieve controlled growth of bilayer graphene on Ni. We then determine the critical graphene size beyond which nucleation of the second layer will take place. Intriguingly, the critical size exhibits an effective inverse "Ehrlich-Schwoebel barrier" effect, becoming smaller for faster C migration from the Cu surface to the graphene-Cu interface sites across the graphene edge. Lastly, these findings allow us to propose a novel alternating growth scheme to realize mass production of bilayer graphene.« less

  17. Atomistic mechanisms for bilayer growth of graphene on metal substrates

    SciTech Connect

    Chen, Wei; Cui, Ping; Zhu, Wenguang; Kaxiras, Efthimios; Gao, Yanfei; Zhang, Zhenyu

    2015-01-08

    Epitaxial growth on metal substrates has been shown to be the most powerful approach in producing large-scale high-quality monolayer graphene, yet it remains a major challenge to realize uniform bilayer graphene growth. Here we carry out a comparative study of the atomistic mechanisms for bilayer graphene growth on the (111) surfaces of Cu and Ni, using multiscale approaches combining first-principles calculations and rate-equation analysis. We first show that the relatively weak graphene-Cu interaction enhances the lateral diffusion and effective nucleation of C atoms underneath the graphene island, thereby making it more feasible to grow bilayer graphene on Cu. In contrast, the stronger graphene-Ni interaction suppresses the lateral mobility and dimerization of C atoms underneath the graphene, making it unlikely to achieve controlled growth of bilayer graphene on Ni. We then determine the critical graphene size beyond which nucleation of the second layer will take place. Intriguingly, the critical size exhibits an effective inverse "Ehrlich-Schwoebel barrier" effect, becoming smaller for faster C migration from the Cu surface to the graphene-Cu interface sites across the graphene edge. Lastly, these findings allow us to propose a novel alternating growth scheme to realize mass production of bilayer graphene.

  18. Atomistic Simulations of Uranium Incorporation into Iron (Hydr)Oxides

    SciTech Connect

    Kerisit, Sebastien N.; Felmy, Andrew R.; Ilton, Eugene S.

    2011-04-29

    Atomistic simulations were carried out to characterize the coordination environments of U incorporated in three Fe-(hydr)oxide minerals: goethite, magnetite, and hematite. The simulations provided information on U-O and U-Fe distances, coordination numbers, and lattice distortion for U incorporated in different sites (e.g., unoccupied versus occupied sites, octahedral versus tetrahedral) as a function of the oxidation state of U and charge compensation mechanisms (i.e., deprotonation, vacancy formation, or reduction of Fe(III) to Fe(II)). For goethite, deprotonation of first shell hydroxyls enables substitution of U for Fe(III) with a minimal amount of lattice distortion, whereas substitution in unoccupied octahedral sites induced appreciable distortion to 7-fold coordination regardless of U oxidation states and charge compensation mechanisms. Importantly, U-Fe distances of ~3.6 Å were associated with structural incorporation of U and cannot be considered diagnostic of simple adsorption to goethite surfaces. For magnetite, the octahedral site accommodates U(V) or U(VI) with little lattice distortion. U substituted for Fe(III) in hematite maintained octahedral coordination in most cases. In general, comparison of the simulations with available experimental data provides further evidence for the structural incorporation of U in iron (hydr)oxide minerals.

  19. Atomistic simulation of the differences between calcite and dolomite surfaces

    SciTech Connect

    Titiloye, J.O.; Leeuw, N.H. de; Parker, S.C.

    1998-08-01

    Atomistic simulation methods have been used to calculate and compare the surface structures and energies of the {l_brace}10{bar 1}4{r_brace}, {l_brace}0001{r_brace}, {l_brace}10{bar 1}0{r_brace}, {l_brace}11{bar 2}0{r_brace} and {l_brace}10{bar 1}1{r_brace} surfaces of calcite and dolomite and to evaluate their equilibrium morphologies. The calcite {l_brace}10{bar 1}4{r_brace} and the dolomite {l_brace}10{bar 1}0{r_brace} and {l_brace}11{bar 2}0{r_brace} surfaces are the most stable crystal planes. Investigation of the segregation of Mg and Ca ions in the dolomite crystal shows a clear preference for Ca{sup 2+} ions at the surface sites and for Mg{sup 2+} ions in the bulk sites and hence growth onto dolomite results in calcium carbonate or high magnesian calcite crystals which helps explain the difficulty in crystallizing dolomite vs. calcite under laboratory conditions.

  20. Polar Glaciology

    NASA Technical Reports Server (NTRS)

    Robin, G. D.

    1984-01-01

    Two fields of research on polar ice sheets are likely to be of dominant interest during the 1990s. These are: the role of polar ice sheets in the hydrological cycle ocean-atmosphere-ice sheets-oceans, especially in relation to climate change; and the study and interpretation of material in deep ice cores to provide improved knowledge of past climates and of the varying levels of atmospheric constituents such as CO2, NOx, SO2, aerosols, etc., over the past 200,000 years. Both topics require a better knowledge of ice dynamics. Many of the studies that should be undertaken in polar regions by Earth Observing System require similar instruments and techniques to those used elsewhere over oceans and inland surfaces. However to study polar regions two special requirements need to be met: Earth Observing System satellite(s) need to be in a sufficiently high inclination orbit to cover most of the polar regions. Instruments must also be adapted, often by relatively limited changes, to give satisfactory data over polar ice. The observational requirements for polar ice sheets in the 1990s are summarized.

  1. INTERACTION OF LASER RADIATION WITH MATTER. LASER PLASMA: Composition and dynamics of an erosion plasma produced by microsecond laser pulses

    NASA Astrophysics Data System (ADS)

    Anisimov, V. N.; Grishina, V. G.; Derkach, O. N.; Sebrant, A. Yu; Stepanova, M. A.

    1995-08-01

    The ion and energy compositions were determined and the dynamics was studied of an erosion plume formed by microsecond CO2 laser pulses incident on a graphite target. The ionic emission lines were used to find the electron density and temperature of the plasma on the target surface. The temperature of the plasma source did not change throughout the line emission time (4 μs). At the plasma recombination stage the lines of the C II, C III, and C IV ions were accompanied by bands of the C2 molecule near the target surface and also near the surface of an substrate when a plasma flow interacted with it. Ways were found for controlling the plume expansion anisotropy and for producing plasma flows with controlled parameters by selection of the conditions during formation of a quasisteady erosion plasma flow.

  2. Cholesterol Flip-Flop Dynamics in a Phospholipid Bilayer: A 10 Microsecond All-Atom Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Choubey, Amit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    2012-02-01

    Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes, and controlling intracellular transport and signal transduction. Using all-atom molecular dynamics and the parallel replica approach, we study the effect of CHOL molecules on mechanical stresses across a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer, and the mechanism by which CHOL molecules migrate from one bilayer leaflet to the other (flip-flop events). On average, we observe a CHOL flip-flop event in half-a-microsecond. Once a CHOL flip-flop event is triggered, the inter-leaflet migration occurs in about 62 nanoseconds. The energy barrier associated with flip-flop events is found to be 73 kJ/mol. Results for membrane rigidity as a function of CHOL concentration will also be presented.

  3. The action of microsecond-pulsed plasma-activated media on the inactivation of human lung cancer cells

    NASA Astrophysics Data System (ADS)

    Kumar, Naresh; Park, Ji Hoon; Jeon, Su Nam; Park, Bong Sang; Choi, Eun Ha; Attri, Pankaj

    2016-03-01

    In the present work, we have generated reactive species (RS) through microsecond-pulsed plasma (MPP) in the cell culture media using a Marx generator with point-point electrodes of approximately 0.06 J discharge energy/pulse. RS generated in culture media through MPP have a selective action between growth of the H460 lung cancer cells and L132 normal lung cells. We observed that MPP-activated media (MPP-AM) induced apoptosis on H460 lung cancer cells through an oxidative DNA damage cascade. Additionally, we studied the apoptosis-related mRNA expression, DNA oxidation and polymerase-1 (PARP-1) cleaved analysis from treated cancer cells. The result proves that radicals generated through MPP play a pivotal role in the activation of media that induces the selective killing effect.

  4. Evaluation of electrical conductivity and equations of state of non-ideal plasma through microsecond timescale underwater electrical wire explosion

    SciTech Connect

    Sheftman, D.; Krasik, Ya. E.

    2011-09-15

    Experimental and simulation results of underwater electrical Cu, Al, and W wire explosions in the microsecond timescale are presented. It was shown that the electrical conductivity results for Cu and Al agree well with modified Lee-More and quantum molecular dynamic models for temperatures above 10 kK. The equation of state (EOS) values based on SESAME tables for Cu and Al were slightly modified for intermediate temperatures in order to obtain fitting between experimental and simulated exploding wire radial expansion. Also, it was shown that the electrical conductivity results and the EOS evaluation differ significantly from the results obtained in nanosecond timescale experiments. Finally, it was found that underwater electrical W wire explosion is characterized by the appearance of non-uniformities along the z-axis of the wire. This phenomena adds uncertainty to the possibility of applying this type of experiments for evaluation of the electrical conductivity and EOS of W.

  5. Evaluation of electrical conductivity and equations of state of non-ideal plasma through microsecond timescale underwater electrical wire explosion

    NASA Astrophysics Data System (ADS)

    Sheftman, D.; Krasik, Ya. E.

    2011-09-01

    Experimental and simulation results of underwater electrical Cu, Al, and W wire explosions in the microsecond timescale are presented. It was shown that the electrical conductivity results for Cu and Al agree well with modified Lee-More and quantum molecular dynamic models for temperatures above 10 kK. The equation of state (EOS) values based on SESAME tables for Cu and Al were slightly modified for intermediate temperatures in order to obtain fitting between experimental and simulated exploding wire radial expansion. Also, it was shown that the electrical conductivity results and the EOS evaluation differ significantly from the results obtained in nanosecond timescale experiments. Finally, it was found that underwater electrical W wire explosion is characterized by the appearance of non-uniformities along the z-axis of the wire. This phenomena adds uncertainty to the possibility of applying this type of experiments for evaluation of the electrical conductivity and EOS of W.

  6. Outlook for the use of microsecond plasma opening switches to generate high-power nanosecond current pulses

    NASA Astrophysics Data System (ADS)

    Dolgachev, G. I.; Maslennikov, D. D.; Ushakov, A. G.

    2006-12-01

    An analysis is made of the current break process in microsecond plasma opening switches and their possible application in high-current generators. Necessary conditions are determined for generating megavolt pulses in the erosion mode of a plasma opening switch with the gap insulated by an external magnetic field. Under these conditions, efficient sharpening of high-power submegampere current pulses can be achieved. The possibility of using plasma opening switches operating at voltages of 5 6 MV to generate X-ray and gamma emission is discussed. The main operating and design parameters of a six-module plasma opening switch with a current pulse amplitude of 3.7 MA and voltage of 4 6 MV for use in the MOL generator, which is the prototype of one of the 24 modules of the projected Baikal multimegajoule generator, are estimated by using the available scalings.

  7. High pulse energy, high beam quality microsecond-pulse Ti:sapphire laser at 819.7 nm

    NASA Astrophysics Data System (ADS)

    Xu, Chang; Guo, Chuan; Yu, Hai-Bo; Wang, Zhi-Min; Zuo, Jun-Wei; Xia, Yuan-Qin; Bian, Qi; Bo, Yong; Gao, Hong-Wei; Guo, Ya-Ding; Zhang, Sheng; Cui, Da-Fu; Peng, Qin-Jun; Xu, Zu-Yan

    2017-03-01

    In this letter, a high pulse energy and high beam quality 819.7 nm Ti:sapphire laser pumped by a frequency-doubled Nd:YAG laser is demonstrated. At incident pump energy of 774 mJ, the maximum output energy of 89 mJ at 819.7 nm with a pulse width of 100 μs is achieved at a repetition rate of 5 Hz. To the best of our knowledge, this is the highest pulse energy at 819.7 nm with pulse width of hundred microseconds for a Ti:sapphire laser. The beam quality factor M 2 is measured to be 1.18. This specific wavelength with the high pulse energy and high beam quality at 819.7 nm is a promising light source to create a polychromatic laser guide star together with a home-made 589 nm laser via exciting the sodium atoms in the mesospheric atmosphere.

  8. Microsecond-range optical shutter for unpolarized light with chiral nematic liquid crystal

    SciTech Connect

    Mohammadimasoudi, Mohammad Neyts, Kristiaan; Beeckman, Jeroen; Shin, Jungsoon; Lee, Keechang

    2015-04-15

    A fast electro-optic shutter is fabricated and demonstrated. The device works independently of the polarization state of the incoming light beam. Modulation between 3% transmission and 60% transmission is obtained within a wavelength range of 50 nm with a response time of 20 μs. The device consists of two partly polymerized chiral nematic liquid crystal layers separated by a half wave plate. The transmission modulation is due to a 50 nm wavelength shift of the photonic band gap of the chiral liquid crystal realized by applying an electric field over a mixture of photo-polymerized LC and non-reactive nematic LC containing a chiral dopant. The shutter features high reflectivity in the photonic band gap. We investigate the influence of the amplitude of the applied voltage on the width and the depth of the reflection band.

  9. Microsecond-range optical shutter for unpolarized light with chiral nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Mohammadimasoudi, Mohammad; Shin, Jungsoon; Lee, Keechang; Neyts, Kristiaan; Beeckman, Jeroen

    2015-04-01

    A fast electro-optic shutter is fabricated and demonstrated. The device works independently of the polarization state of the incoming light beam. Modulation between 3% transmission and 60% transmission is obtained within a wavelength range of 50 nm with a response time of 20 μs. The device consists of two partly polymerized chiral nematic liquid crystal layers separated by a half wave plate. The transmission modulation is due to a 50 nm wavelength shift of the photonic band gap of the chiral liquid crystal realized by applying an electric field over a mixture of photo-polymerized LC and non-reactive nematic LC containing a chiral dopant. The shutter features high reflectivity in the photonic band gap. We investigate the influence of the amplitude of the applied voltage on the width and the depth of the reflection band.

  10. Organometal halide perovskite solar cell materials rationalized: ultrafast charge generation, high and microsecond-long balanced mobilities, and slow recombination.

    PubMed

    Ponseca, Carlito S; Savenije, Tom J; Abdellah, Mohamed; Zheng, Kaibo; Yartsev, Arkady; Pascher, Tobjörn; Harlang, Tobias; Chabera, Pavel; Pullerits, Tonu; Stepanov, Andrey; Wolf, Jean-Pierre; Sundström, Villy

    2014-04-09

    Organometal halide perovskite-based solar cells have recently been reported to be highly efficient, giving an overall power conversion efficiency of up to 15%. However, much of the fundamental photophysical properties underlying this performance has remained unknown. Here, we apply photoluminescence, transient absorption, time-resolved terahertz and microwave conductivity measurements to determine the time scales of generation and recombination of charge carriers as well as their transport properties in solution-processed CH3NH3PbI3 perovskite materials. We found that electron-hole pairs are generated almost instantaneously after photoexcitation and dissociate in 2 ps forming highly mobile charges (25 cm(2) V(-1) s(-1)) in the neat perovskite and in perovskite/alumina blends; almost balanced electron and hole mobilities remain very high up to the microsecond time scale. When the perovskite is introduced into a TiO2 mesoporous structure, electron injection from perovskite to the metal oxide is efficient in less than a picosecond, but the lower intrinsic electron mobility of TiO2 leads to unbalanced charge transport. Microwave conductivity measurements showed that the decay of mobile charges is very slow in CH3NH3PbI3, lasting up to tens of microseconds. These results unravel the remarkable intrinsic properties of CH3NH3PbI3 perovskite material if used as light absorber and charge transport layer. Moreover, finding a metal oxide with higher electron mobility may further increase the performance of this class of solar cells.

  11. Polarizing cues.

    PubMed

    Nicholson, Stephen P

    2012-01-01

    People categorize themselves and others, creating ingroup and outgroup distinctions. In American politics, parties constitute the in- and outgroups, and party leaders hold sway in articulating party positions. A party leader's endorsement of a policy can be persuasive, inducing co-partisans to take the same position. In contrast, a party leader's endorsement may polarize opinion, inducing out-party identifiers to take a contrary position. Using survey experiments from the 2008 presidential election, I examine whether in- and out-party candidate cues—John McCain and Barack Obama—affected partisan opinion. The results indicate that in-party leader cues do not persuade but that out-party leader cues polarize. This finding holds in an experiment featuring President Bush in which his endorsement did not persuade Republicans but it polarized Democrats. Lastly, I compare the effect of party leader cues to party label cues. The results suggest that politicians, not parties, function as polarizing cues.

  12. Atomistic Insight into Tetraalkylphosphonium-Bis(oxalato)borate Ionic Liquid/Water Mixtures. I. Local Microscopic Structure.

    PubMed

    Wang, Yong-Lei; Sarman, Sten; Glavatskih, Sergei; Antzutkin, Oleg N; Rutland, Mark W; Laaksonen, Aatto

    2015-04-23

    Atomistic simulations have been performed to investigate the microscopic structural organization of aqueous solutions of trihexyltetradecylphosphonium bis(oxalato)borate ([P6,6,6,14][BOB]) ionic liquid (IL). The evolution of the microscopic liquid structure and the local ionic organization of IL/water mixtures as a function of the water concentration is visualized and systematically analyzed via radial and spatial distribution functions, coordination numbers, hydrogen bond network, and water clustering analysis. The microscopic liquid structure in neat IL is characterized by a connected apolar network composed of the alkyl chains of [P6,6,6,14] cations and isolated polar domains consisting of the central segments of [P6,6,6,14] cations and [BOB] anions, and the corresponding local ionic environment is described by direct contact ion pairs. In IL/water mixtures with lower water mole fractions, the added water molecules are dispersed and embedded in cavities between neighboring ionic species and the local ionic structure is characterized by solvent-shared ion pairs through cation-water-anion triple complexes. With a gradual increase in the water concentration in IL/water mixtures, the added water molecules tend to aggregate and form small clusters, intermediate chain-like structures, large aggregates, and eventually a water network in water concentrated simulation systems. A further progressive dilution of IL/water mixtures leads to the formation of self-organized micelle-like aggregates characterized by a hydrophobic core and hydrophilic shell consisting of the central polar segments in [P6,6,6,14] cations and [BOB] anions in a highly branched water network. The striking structural evolution of the [P6,6,6,14][BOB] IL/water mixtures is rationalized by the competition between favorable hydrogen bonded interactions and strong electrostatic interactions between the polar segments in ionic species and the dispersion interactions between the hydrophobic alkyl chains in

  13. Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.

    SciTech Connect

    Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

    2010-09-01

    This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and

  14. Atomistic Mechanisms for Viscoelastic Damping in Inorganic Solids

    NASA Astrophysics Data System (ADS)

    Ranganathan, Raghavan

    Viscoelasticity, a ubiquitous material property, can be tuned to engineer a wide range of fascinating applications such as mechanical dampers, artificial tissues, functional foams and optoelectronics, among others. Traditionally, soft matter such as polymers and polymer composites have been used extensively for viscoelastic damping applications, owing to the inherent viscous nature of interactions between polymer chains. Although this leads to good damping characteristics, the stiffness in these materials is low, which in turn leads to limitations. In this context, hard inorganic materials and composites are promising candidates for enhanced damping, owing to their large stiffness and, in some cases large loss modulus. Viscoelasticity in these materials has been relatively unexplored and atomistic mechanisms responsible for damping are not apparent. Therefore, the overarching goal of this work is to understand mechanisms for viscoelastic damping in various classes of inorganic composites and alloys at an atomistic level from molecular dynamics simulations. We show that oscillatory shear deformation serves as a powerful probe to explain mechanisms for exceptional damping in hitherto unexplored systems. The first class of inorganic materials consists of crystalline phases of a stiff inclusion in a soft matrix. The two crystals within the composite, namely the soft and a stiff phase, individually show a highly elastic behavior and a very small loss modulus. On the other hand, a composite with the two phases is seen to exhibit damping that is about 20 times larger than predicted theoretical bounds. The primary reason for the damping is due to large anharmonicity in phonon-phonon coupling, resulting from the composite microstructure. A concomitant effect is the distribution of shear strain, which is observed to be highly inhomogeneous and mostly concentrated in the soft phase. Interestingly, the shear frequency at which the damping is greatest is observed to scale with

  15. Megasonic cleaning, cavitation, and substrate damage: an atomistic approach

    NASA Astrophysics Data System (ADS)

    Kapila, Vivek; Deymier, Pierre A.; Shende, Hrishikesh; Pandit, Viraj; Raghavan, Srini; Eschbach, Florence O.

    2006-05-01

    Megasonic cleaning has been a traditional approach for the cleaning of photomasks. Its feasibility as a damage free approach to sub 50 nm particulate removal is under investigation for the cleaning of optical and EUV photomasks. Two major mechanisms are active in a megasonic system, namely, acoustic streaming and acoustic cavitation. Acoustic streaming is instrumental in contaminant removal via application of drag force and rolling of particles, while cavitation may dislodge particles by the release of large energy during cavity implosion or by acting as a secondary source of microstreaming. Often times, the structures (substrates with or without patterns) subjected to megasonic cleaning show evidence of damage. This is one of the impediments in the implementation of megasonic technology for 45 nm and future technology nodes. Prior work suggests that acoustic streaming does not lead to sufficiently strong forces to cause damage to the substrates or patterns. However, current knowledge of the effects of cavitation on cleaning and damage can be described, at best, as speculative. Recent experiments suggest existence of a cavity size and energy distributions in megasonic systems that may be responsible for cleaning and damage. In the current work, we develop a two-dimensional atomistic model to study such multibubble cavitation phenomena. The model consists of a Lennard-Jones liquid which is subjected to sinusoidal pressure changes leading to the formation of cavitation bubbles. The current work reports on the effects of pressure amplitude (megasonic power) and frequency on cavity size distributions in vaporous and gaseous cavitation. The findings of the work highlight the role of multibubble cavitation as cleaning and damage mechanism in megasonic cleaning.

  16. Atomistic simulations of the yielding of gold nanowires.

    SciTech Connect

    Zimmerman, Jonathan A.; Dunn, Martin L.; Diao, Jiankuai; Gall, Ken

    2004-07-01

    We performed atomistic simulations to study the effect of free surfaces on the yielding of gold nanowires. Tensile surface stresses on the surfaces of the nanowires cause them to contract along the length with respect to the bulk face-centered cubic lattice and induce compressive stress in the interior. When the cross-sectional area of a (100) nanowire is less than 2.45 nm x 2.45 nm, the wire yields under its surface stresses. Under external forces and surface stresses, nanowires yield via the nucleation and propagation of the {l_brace}111{r_brace}<112> partial dislocations. The magnitudes of the tensile and compressive yield stress of (100) nanowires increase and decrease, respectively, with a decrease of the wire width. The magnitude of the tensile yield stress is much larger than that of the compressive yield stress for small (100) nanowires, while for small <111> nanowires, tensile and compressive yield stresses have similar magnitudes. The critical resolved shear stress (RSS) by external forces depends on wire width, orientation and loading condition (tension vs. compression). However, the critical RSS in the interior of the nanowires, which is exerted by both the external force and the surface-stress-induced compressive stress, does not change significantly with wire width for same orientation and same loading condition, and can thus serve as a 'local' criterion. This local criterion is invoked to explain the observed size dependence of yield behavior and tensile/compressive yield stress asymmetry, considering surface stress effects and different slip systems active in tensile and compressive yielding.

  17. Hepatocyte Polarity

    PubMed Central

    Treyer, Aleksandr; Müsch, Anne

    2013-01-01

    Hepatocytes, like other epithelia, are situated at the interface between the organism’s exterior and the underlying internal milieu and organize the vectorial exchange of macromolecules between these two spaces. To mediate this function, epithelial cells, including hepatocytes, are polarized with distinct luminal domains that are separated by tight junctions from lateral domains engaged in cell-cell adhesion and from basal domains that interact with the underlying extracellular matrix. Despite these universal principles, hepatocytes distinguish themselves from other nonstriated epithelia by their multipolar organization. Each hepatocyte participates in multiple, narrow lumina, the bile canaliculi, and has multiple basal surfaces that face the endothelial lining. Hepatocytes also differ in the mechanism of luminal protein trafficking from other epithelia studied. They lack polarized protein secretion to the luminal domain and target single-spanning and glycosylphosphatidylinositol-anchored bile canalicular membrane proteins via transcytosis from the basolateral domain. We compare this unique hepatic polarity phenotype with that of the more common columnar epithelial organization and review our current knowledge of the signaling mechanisms and the organization of polarized protein trafficking that govern the establishment and maintenance of hepatic polarity. The serine/threonine kinase LKB1, which is activated by the bile acid taurocholate and, in turn, activates adenosine monophosphate kinase-related kinases including AMPK1/2 and Par1 paralogues has emerged as a key determinant of hepatic polarity. We propose that the absence of a hepatocyte basal lamina and differences in cell-cell adhesion signaling that determine the positioning of tight junctions are two crucial determinants for the distinct hepatic and columnar polarity phenotypes. PMID:23720287

  18. Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical Theory with Generalized Quantum Master Equations.

    PubMed

    Pfalzgraff, William C; Kelly, Aaron; Markland, Thomas E

    2015-12-03

    The development of methods that can efficiently and accurately treat nonadiabatic dynamics in quantum systems coupled to arbitrary atomistic environments remains a significant challenge in problems ranging from exciton transport in photovoltaic materials to electron and proton transfer in catalysis. Here we show that our recently introduced MF-GQME approach, which combines Ehrenfest mean field theory with the generalized quantum master equation framework, is able to yield quantitative accuracy over a wide range of charge-transfer regimes in fully atomistic environments. This is accompanied by computational speed-ups of up to 3 orders of magnitude over a direct application of Ehrenfest theory. This development offers the opportunity to efficiently investigate the atomistic details of nonadiabatic quantum relaxation processes in regimes where obtaining accurate results has previously been elusive.

  19. Origin of unrealistic blunting during atomistic fracture simulations based on MEAM potentials

    NASA Astrophysics Data System (ADS)

    Ko, Won-Seok; Lee, Byeong-Joo

    2014-06-01

    Atomistic simulations based on interatomic potentials have frequently failed to correctly reproduce the brittle fracture of materials, showing an unrealistic blunting. We analyse the origin of the unrealistic blunting during atomistic simulations by modified embedded-atom method (MEAM) potentials for experimentally well-known brittle materials such as bcc tungsten and diamond silicon. The radial cut-off which has been thought to give no influence on MEAM calculations is found to have a decisive effect on the crack propagation behaviour. Extending both cut-off distance and truncation range can prevent the unrealistic blunting, reproducing many well-known fracture behaviour which have been difficult to reproduce. The result provides a guideline for future atomistic simulations that focus on various fracture-related phenomena including the failure of metallic-covalent bonding material systems using MEAM potentials.

  20. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. I. Structural modeling.

    PubMed

    Kim, Nayong; Kim, Yongman; Tsotsis, Theodore T; Sahimi, Muhammad

    2005-06-01

    An atomistic model of layered double hydroxides, an important class of nanoporous materials, is presented. These materials have wide applications, ranging from adsorbents for gases and liquid ions to nanoporous membranes and catalysts. They consist of two types of metallic cations that are accommodated by a close-packed configuration of OH- and other anions in a positively charged brucitelike layer. Water and various anions are distributed in the interlayer space for charge compensation. A modified form of the consistent-valence force field, together with energy minimization and molecular dynamics simulations, is utilized for developing an atomistic model of the materials. To test the accuracy of the model, we compare the vibrational frequencies, x-ray diffraction patterns, and the basal spacing of the material, computed using the atomistic model, with our experimental data over a wide range of temperature. Good agreement is found between the computed and measured quantities.

  1. Atomistic simulation of nanoporous layered double hydroxide materials and their properties. I. Structural modeling

    NASA Astrophysics Data System (ADS)

    Kim, Nayong; Kim, Yongman; Tsotsis, Theodore T.; Sahimi, Muhammad

    2005-06-01

    An atomistic model of layered double hydroxides, an important class of nanoporous materials, is presented. These materials have wide applications, ranging from adsorbents for gases and liquid ions to nanoporous membranes and catalysts. They consist of two types of metallic cations that are accommodated by a close-packed configuration of OH- and other anions in a positively charged brucitelike layer. Water and various anions are distributed in the interlayer space for charge compensation. A modified form of the consistent-valence force field, together with energy minimization and molecular dynamics simulations, is utilized for developing an atomistic model of the materials. To test the accuracy of the model, we compare the vibrational frequencies, x-ray diffraction patterns, and the basal spacing of the material, computed using the atomistic model, with our experimental data over a wide range of temperature. Good agreement is found between the computed and measured quantities.

  2. A polarized photobleaching study of DNA reorientation in agarose gels

    SciTech Connect

    Scalettar, B.A.; Klein, M.P. ); Selvin, P.R.; Hearst, J.E. Univ. of California, Berkeley ); Axelrod, D. )

    1990-05-22

    Polarized fluorescence recovery after photobleaching (pFRAP) has been used to study the internal dynamics of relatively long DNA molecules embedded in gels that range in concentration from 1% to 5% agarose. The data indicate that, even in very congested gels, rapid internal relaxation of DNA is largely unhindered; however, interactions with gel matrices apparently do perturb the larger amplitude, more slowly (microseconds to milliseconds) relaxing internal motions of large DNAs. The relationship between this work and recent studies which indicate that internal motions of DNA play an important role in the separation achieved with pulsed-field gel electrophoresis techniques is discussed. The polarized photobleaching technique is also analyzed in some detail. In particular, it is shown that reversible photobleaching phenomena are probably related to depletion of the ground state by intersystem crossing to the triplet state.

  3. Single channel currents at six microsecond resolution elicited by acetylcholine in mouse myoballs

    PubMed Central

    Parzefall, Franz; Wilhelm, Robert; Heckmann, Manfred; Dudel, Josef

    1998-01-01

    A patch-clamp set-up was optimized for low noise and high time resolution. An Axoclamp 200B amplifier was modified to incorporate a Teflon connector to the electrode. An electrode puller was equipped with a hydrogen-oxygen burner to produce quartz-glass pipettes with optimally 0.2μm openings and 20 MΩ resistance.The r.m.s. (root mean square) noise of sealed pipettes in the bath ranged from 3.6 fA with 100 Hz filter cut-off to 1.5 pA with 61 kHz filter cut-off. At these extremes currents of 17 fA and more than 3 ms, or 9 pA and more than 6μs could be resolved with a negligible error rate.The system was tested on mouse myoballs, recording 9–10 pA single channel currents on-cell at −200 mV polarization which were elicited by 0.1–5000μm acetylcholine (ACh).Distributions of open and closed times and of correlations of open times to the preceding closed time defined several open states: single openings with mean durations of 1.2 and 25μs, from single-liganded receptors, and bursts of 10 ms mean duration containing on average 800μs openings and 16μs closings, from double liganded receptors. Above 0.1 mm ACh these openings are interrupted increasingly by on average 18μs and 72μs channel blocks by ACh. PMID:9729627

  4. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc{sub 1} complex

    SciTech Connect

    Martin, Daniel R.; Matyushov, Dmitry V.

    2015-04-28

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc{sub 1} bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

  5. Ionic diffusion in quartz studied by transport measurements, SIMS and atomistic simulations

    NASA Astrophysics Data System (ADS)

    Sartbaeva, Asel; Wells, Stephen A.; Redfern, Simon A. T.; Hinton, Richard W.; Reed, Stephen J. B.

    2005-02-01

    Ionic diffusion in the quartz-β-eucryptite system is studied by DC transport measurements, SIMS and atomistic simulations. Transport data show a large transient increase in ionic current at the α-β phase transition of quartz (the Hedvall effect). The SIMS data indicate two diffusion processes, one involving rapid Li+ motion and the other involving penetration of Al and Li atoms into quartz at the phase transition. Atomistic simulations explain why the fine microstructure of twin domain walls in quartz near the transition does not hinder Li+ diffusion.

  6. Atomistic modeling of BN nanofillers for mechanical and thermal properties: a review

    NASA Astrophysics Data System (ADS)

    Kumar, Rajesh; Parashar, Avinash

    2015-12-01

    Due to their exceptional mechanical properties, thermal conductivity and a wide band gap (5-6 eV), boron nitride nanotubes and nanosheets have promising applications in the field of engineering and biomedical science. Accurate modeling of failure or fracture in a nanomaterial inherently involves coupling of atomic domains of cracks and voids as well as a deformation mechanism originating from grain boundaries. This review highlights the recent progress made in the atomistic modeling of boron nitride nanofillers. Continuous improvements in computational power have made it possible to study the structural properties of these nanofillers at the atomistic scale.

  7. Real-Time Examination of Atomistic Mechanisms during Shock-Induced Structural Transformation in Silicon

    DOE PAGES

    Turneaure, Stefan J.; Sinclair, N.; Gupta, Y. M.

    2016-07-20

    Experimental determination of atomistic mechanisms linking crystal structures during a compression driven solid-solid phase transformation is a long standing and challenging scientific objective. Also, when using new capabilities at the Dynamic Compression Sector at the Advanced Photon Source, the structure of shocked Si at 19 GPa was identified as simple hexagonal and the lattice orientations between ambient cubic diamond and simple hexagonal structures were related. Furthermore, this approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes.

  8. Hypercrosslinked polystyrene networks: An atomistic molecular dynamics simulation combined with a mapping/reverse mapping procedure

    SciTech Connect

    Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R.

    2014-04-07

    An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.

  9. Atomistic Simulation of Non-Equilibrium Phenomena in Hypersonic Flows

    NASA Astrophysics Data System (ADS)

    Norman, Paul Erik

    The goal of this work is to model the heterogeneous recombination of atomic oxygen on silica surfaces, which is of interest for accurately predicting the heating on vehicles traveling at hypersonic speeds. This is accomplished by creating a finite rate catalytic model, which describes recombination with a set of elementary gas-surface reactions. Fundamental to a description of surface catalytic reactions are the in situ chemical structures on the surface where recombination can occur. Using molecular dynamics simulations with the Reax GSISiO potential, we find that the chemical sites active in direct gas-phase reactions on silica surfaces consist of a small number of specific structures (or defects). The existence of these defects on real silica surfaces is supported by experimental results and the structure and energetics of these defects have been verified with quantum chemical calculations. The reactions in the finite rate catalytic model are based on the interaction of molecular and atomic oxygen with these defects. Trajectory calculations are used to find the parameters in the forward rate equations, while a combination of detailed balance and transition state theory are used to find the parameters in the reverse rate equations. The rate model predicts that the oxygen recombination coefficient is relatively constant at T (300-1000 K), in agreement with experimental results. At T > 1000 K the rate model predicts a drop off in the oxygen recombination coefficient, in disagreement with experimental results, which predict that the oxygen recombination coefficient increases with temperature. A discussion of the possible reasons for this disagreement, including non-adiabatic collision dynamics, variable surface site concentrations, and additional recombination mechanisms is presented. This thesis also describes atomistic simulations with Classical Trajectory Calculation Direction Simulation Monte Carlo (CTC-DSMC), a particle based method for modeling non

  10. Understanding atomistic phenomenon for hydrogen storage in complex metal hydrides

    NASA Astrophysics Data System (ADS)

    Chopra, Irinder Singh

    The storage of hydrogen into metals in the form of complex metal hydrides is one of the most promising methods. However, the incorporation and release of hydrogen requires very high temperatures. The discovery that the addition of Ti compounds lowers NaAlH4 decomposition barriers closer to ambient conditions, has re-ignited the field, and it is believed that surface processes are responsible for H2 dissociation and mass transport required to form the hydrogenated materials. Such surface reactions mechanisms are however difficult to study with typical spectroscopic and imaging surface science tools. Alanes lack contrast under electron microscopes and can modify the Scanning Tunneling Microscopy (STM) tips. Infrared spectroscopy would be a sensitive probe to investigate the adsorption of hydrogen providing, but has so far failed to detect chemisorbed hydrogen on Ti-doped Al surfaces due to the weak Al-H dynamic dipole moment. Thus despite extensive investigations, the fundamental mechanisms of the role of Ti and alane formation have remained elusive. In this study combining surface infrared (IR) spectroscopy and density functional theory (DFT), we provide atomistic details about the role of Ti as a catalyst for hydrogen uptake and alane formation and evolution on single crystal Al(111) and Al(100) surfaces. We are able to detect H indirectly by using CO as a probe molecule of the weak Al-H species. We demonstrate that aluminum doped with very small amounts of titanium (in a specific configuration) can activate molecular hydrogen at temperatures as low as 90K. Once dissociated, hydrogen spills over from these catalytic sites on to the Al surface and protects the surface from further reactions. We also show that, on Ti-doped Al surfaces, the diffusion dynamics are severely altered by Ti doping (Atomic hydrogen and AlH3 are trapped at the Ti sites) as indicated by a marked decrease of higher alane concentrations, which is deleterious for hydrogen storage for which mass

  11. Scalable and portable visualization of large atomistic datasets

    NASA Astrophysics Data System (ADS)

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

    2004-10-01

    A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data

  12. Polarized Campuses.

    ERIC Educational Resources Information Center

    Parr, Susan Resneck

    1991-01-01

    On college campuses, the climate is polarized because of intolerance and discrimination, censorship, factionalism, and anger among students and faculty. As a result, the campus is in danger of becoming dominated by political issues and discouraging the exchange of ideas characteristic of a true liberal arts education. (MSE)

  13. Atomistic Method Applied to Computational Modeling of Surface Alloys

    NASA Technical Reports Server (NTRS)

    Bozzolo, Guillermo H.; Abel, Phillip B.

    2000-01-01

    The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on

  14. Space charge polarization induced memory in SmNiO3/Si transistors

    NASA Astrophysics Data System (ADS)

    Hyeon Lee, Sang; Kim, Moonkyung; Ha, Sieu D.; Lee, Jo-Won; Ramanathan, Shriram; Tiwari, Sandip

    2013-02-01

    The correlated oxide, SmNiO3 (SNO), is characterized and explored as a phase transition material in silicon capacitors and transistors with SNO as a floating gate sandwiched between silicon dioxide gate insulators. The structures show hysteresis at low bias voltages. The capacitance and its voltage hysteresis window increase as the frequency of the applied field decreases with a response time of polarization of above a microsecond. This suggests a space charge polarization dominated by low frequency permittivity response. Instability of 3+ oxidation state of Ni and presence of oxygen vacancies are believed to lead to a polarization effect through Poole-Frenkel charge trapping/de-trapping. Metal-oxide-semiconductor transistors show counterclockwise voltage hysteresis consistent with polarization switching effect. The stored information decays gradually due to the depolarization field with retention times of the order of 10 s at room temperature.

  15. Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: power law rate coefficients in cyclisation reactions.

    PubMed

    Shalashilin, Dmitrii V; Beddard, Godfrey S; Paci, Emanuele; Glowacki, David R

    2012-10-28

    Molecular dynamics (MD) methods are increasingly widespread, but simulation of rare events in complex molecular systems remains a challenge. We recently introduced the boxed molecular dynamics (BXD) method, which accelerates rare events, and simultaneously provides both kinetic and thermodynamic information. We illustrate how the BXD method may be used to obtain high-resolution kinetic data from explicit MD simulations, spanning picoseconds to microseconds. The method is applied to investigate the loop formation dynamics and kinetics of cyclisation for a range of polypeptides, and recovers a power law dependence of the instantaneous rate coefficient over six orders of magnitude in time, in good agreement with experimental observations. Analysis of our BXD results shows that this power law behaviour arises when there is a broad and nearly uniform spectrum of reaction rate coefficients. For the systems investigated in this work, where the free energy surfaces have relatively small barriers, the kinetics is very sensitive to the initial conditions: strongly non-equilibrium conditions give rise to power law kinetics, while equilibrium initial conditions result in a rate coefficient with only a weak dependence on time. These results suggest that BXD may offer us a powerful and general algorithm for describing kinetics and thermodynamics in chemical and biochemical systems.

  16. Artifact Free and Detection Profile Independent Higher Order Fluorescence Correlation Spectroscopy for Microsecond Resolved Kinetics. 2. Mixtures and Reactions.

    PubMed

    Abdollah-Nia, Farshad; Gelfand, Martin P; Van Orden, Alan K

    2017-02-09

    Fluorescence correlation spectroscopy (FCS) is a primary tool in the time-resolved analysis of non-reacting or reacting molecules in solution, based on fluorescence intensity fluctuations. However, conventional FCS alone is insufficient for complete determination of reaction or mixture parameters. In an accompanying article, a technique for computation of artifact-free higher-order correlations with microsecond time resolution was described. Here, we demonstrate applications of the technique to analyze systems of fast and slow reactions. As an example of slow- or non-reacting systems, the technique is applied to resolve two-component mixtures of labeled oligonucleotides. Next, the protonation reaction of fluorescein isothiocyanate (FITC) in phosphate buffer is analyzed as an example of fast reactions (relaxation time <1 μs ). By reference to an (apparent) non-reacting system, the simple factorized form of cumulant-based higher-order correlations is exploited to remove the dependence on the molecular detection function (MDF). Therefore, there is no need to model and characterize the experimental MDF, and the precision and the accuracy of the technique are enhanced. It is verified that higher-order correlation analysis enables complete and simultaneous determination of number and brightness parameters of mixing or reacting molecules, the reaction relaxation time, and forward and reverse reaction rates.

  17. Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials.

    PubMed

    De Biase, Pablo M; Markosyan, Suren; Noskov, Sergei

    2014-04-05

    We developed a novel scheme based on the grand-canonical Monte Carlo/Brownian dynamics simulations and have extended it to studies of ion currents across three nanopores with the potential for single-stranded DNA (ssDNA) sequencing: solid-state nanopore Si₃N₄, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the inverse Monte Carlo protocol, which maps the relevant ion-nucleotide distribution functions from all-atom molecular dynamics (MD) simulations. Combined with the previously developed simulation platform for Brownian dynamics simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in the nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations.

  18. Physical and biological mechanisms of nanosecond- and microsecond-pulsed FE-DBD plasma interaction with biological objects

    NASA Astrophysics Data System (ADS)

    Dobrynin, Danil

    2013-09-01

    Mechanisms of plasma interaction with living tissues and cells can be quite complex, owing to the complexity of both the plasma and the tissue. Thus, unification of all the mechanisms under one umbrella might not be possible. Here, analysis of interaction of floating electrode dielectric barrier discharge (FE-DBD) with living tissues and cells is presented and biological and physical mechanisms are discussed. In physical mechanisms, charged species are identified as the major contributors to the desired effect and a mechanism of this interaction is proposed. Biological mechanisms are also addressed and a hypothesis of plasma selectivity and its effects is offered. Spatially uniform nanosecond and sub-nanosecond short-pulsed dielectric barrier discharge plasmas are gaining popularity in biological and medical applications due to their increased uniformity, lower plasma temperature, lower surface power density, and higher concentration of the active species produced. In this presentation we will compare microsecond pulsed plasmas with nanosecond driven systems and their applications in biology and medicine with specific focus on wound healing and tissue regeneration. Transition from negative to positive streamer will be discussed with proposed hypothesis of uniformity mechanisms of positive streamer and the reduced dependence on morphology and surface chemistry of the second electrode (human body) being treated. Uniform plasma offers a more uniform delivery of active species to the tissue/surface being treated thus leading to better control over the biological results.

  19. Membrane Permeabilization of Pathogenic Yeast in Alternating Sub-microsecond Electromagnetic Fields in Combination with Conventional Electroporation.

    PubMed

    Novickij, Vitalij; Lastauskienė, Eglė; Švedienė, Jurgita; Grainys, Audrius; Staigvila, Gediminas; Paškevičius, Algimantas; Girkontaitė, Irutė; Zinkevičienė, Auksė; Markovskaja, Svetlana; Novickij, Jurij

    2017-02-25

    Recently, a novel contactless treatment method based on high-power pulsed electromagnetic fields (PEMF) was proposed, which results in cell membrane permeabilization effects similar to electroporation. In this work, a new PEMF generator based on multi-stage Marx circuit topology, which is capable of delivering 3.3 T, 0.19 kV/cm sub-microsecond pulses was used to permeabilize pathogenic yeast Candida albicans separately and in combination with conventional square wave electroporation (8-17 kV/cm, 100 μs). Bursts of 10, 25, and 50 PEMF pulses were used. The yeast permeabilization rate was evaluated using flow cytometric analysis and propidium iodide (PI) assay. A statistically significant (P < 0.05) combinatorial effect of electroporation and PEMF treatment was detected. Also the PEMF treatment (3.3 T, 50 pulses) resulted in up to 21% loss of yeast viability, and a dose-dependent additive effect with pulsed electric field was observed. As expected, increase of the dB/dt and subsequently the induced electric field amplitude resulted in a detectable effect solely by PEMF, which was not achievable before for yeasts in vitro.

  20. FAST TRACK COMMUNICATION: Contrasting characteristics of sub-microsecond pulsed atmospheric air and atmospheric pressure helium-oxygen glow discharges

    NASA Astrophysics Data System (ADS)

    Walsh, J. L.; Liu, D. X.; Iza, F.; Rong, M. Z.; Kong, M. G.

    2010-01-01

    Glow discharges in air are often considered to be the ultimate low-temperature atmospheric pressure plasmas for numerous chamber-free applications. This is due to the ubiquitous presence of air and the perceived abundance of reactive oxygen and nitrogen species in air plasmas. In this paper, sub-microsecond pulsed atmospheric air plasmas are shown to produce a low concentration of excited oxygen atoms but an abundance of excited nitrogen species, UV photons and ozone molecules. This contrasts sharply with the efficient production of excited oxygen atoms in comparable helium-oxygen discharges. Relevant reaction chemistry analysed with a global model suggests that collisional excitation of O2 by helium metastables is significantly more efficient than electron dissociative excitation of O2, electron excitation of O and ion-ion recombination. These results suggest different practical uses of the two oxygen-containing atmospheric discharges, with air plasmas being well suited for nitrogen and UV based chemistry and He-O2 plasmas for excited atomic oxygen based chemistry.

  1. Structural, electronic, and optical properties of m -plane InGaN/GaN quantum wells: Insights from experiment and atomistic theory

    NASA Astrophysics Data System (ADS)

    Schulz, S.; Tanner, D. P.; O'Reilly, E. P.; Caro, M. A.; Martin, T. L.; Bagot, P. A. J.; Moody, M. P.; Tang, F.; Griffiths, J. T.; Oehler, F.; Kappers, M. J.; Oliver, R. A.; Humphreys, C. J.; Sutherland, D.; Davies, M. J.; Dawson, P.

    2015-12-01

    In this paper we present a detailed analysis of the structural, electronic, and optical properties of an m -plane (In,Ga)N/GaN quantum well structure grown by metal organic vapor phase epitaxy. The sample has been structurally characterized by x-ray diffraction, scanning transmission electron microscopy, and 3D atom probe tomography. The optical properties of the sample have been studied by photoluminescence (PL), time-resolved PL spectroscopy, and polarized PL excitation spectroscopy. The PL spectrum consisted of a very broad PL line with a high degree of optical linear polarization. To understand the optical properties we have performed atomistic tight-binding calculations, and based on our initial atom probe tomography data, the model includes the effects of strain and built-in field variations arising from random alloy fluctuations. Furthermore, we included Coulomb effects in the calculations. Our microscopic theoretical description reveals strong hole wave function localization effects due to random alloy fluctuations, resulting in strong variations in ground state energies and consequently the corresponding transition energies. This is consistent with the experimentally observed broad PL peak. Furthermore, when including Coulomb contributions in the calculations we find strong exciton localization effects which explain the form of the PL decay transients. Additionally, the theoretical results confirm the experimentally observed high degree of optical linear polarization. Overall, the theoretical data are in very good agreement with the experimental findings, highlighting the strong impact of the microscopic alloy structure on the optoelectronic properties of these systems.

  2. Polar Diving

    NASA Technical Reports Server (NTRS)

    2006-01-01

    3 July 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows layers exposed by erosion in a trough within the north polar residual cap of Mars, diving beneath a younger covering of polar materials. The layers have, since the Mariner 9 mission in 1972, been interpreted to be composed of a combination of dust and ice in unknown proportions. In this scene, a layer of solid carbon dioxide, which was deposited during the previous autumn and winter, blankets the trough as well as the adjacent terrain. Throughout northern spring, the carbon dioxide will be removed; by summer, the layers will be frost-free.

    Location near: 81.4oN, 352.2oW Image width: 3 km (1.9 mi) Illumination from: lower left Season: Northern Spring

  3. Cell polarity

    PubMed Central

    Romereim, Sarah M

    2011-01-01

    Despite extensive genetic analysis of the dynamic multi-phase process that transforms a small population of lateral plate mesoderm into the mature limb skeleton, the mechanisms by which signaling pathways regulate cellular behaviors to generate morphogenetic forces are not known. Recently, a series of papers have offered the intriguing possibility that regulated cell polarity fine-tunes the morphogenetic process via orienting cell axes, division planes and cell movements. Wnt5a-mediated non-canonical signaling, which may include planar cell polarity, has emerged as a common thread in the otherwise distinct signaling networks that regulate morphogenesis in each phase of limb development. These findings position the limb as a key model to elucidate how global tissue patterning pathways direct local differences in cell behavior that, in turn, generate growth and form. PMID:22064549

  4. A Mathematical Analysis of Atomistic-to-Continuum (AtC) Multiscale Coupling Methods

    SciTech Connect

    Gunzburger, Max

    2013-11-13

    We have worked on several projects aimed at improving the efficiency and understanding of multiscale methods, especially those applicable to problems involving atomistic-to-continuum coupling. Activities include blending methods for AtC coupling and efficient quasi-continuum methods for problems with long-range interactions.

  5. Atomistic study on the FCC/BCC interface structure with {112}KS orientation

    SciTech Connect

    Kang, Keonwook; Beyerlein, Irene; Han, Weizhong; Wang, Jian; Mara, Nathan

    2011-09-23

    In this study, atomistic simulation is used to explore the atomic interface structure, the intrinsic defect network, and mechanism of twin formation from the {112}KS Cu-Nb interface. The interface structure of different material systems AI-Fe and AI-Nb are also compared with Cu-Nb interface.

  6. Numerical investigation of temperature field Induced by dual wavelength lasers in sub-microsecond laser annealing technology for insulated gate bipolar transistor

    NASA Astrophysics Data System (ADS)

    Cui, GuoDong; Ma, Mingying; Wang, Fan; Sun, Gang; Lan, Yanping; Xu, Wen

    2015-07-01

    To enhance the performance of the Insulated Gate Bipolar Transistor (IGBT), sub-microsecond laser annealing (LA) is propitious to achieve maximal dopant activation with minimal diffusion. In this work, two different lasers are used as annealing resource: a continuous 808 nm laser with larger spot is applied to preheat the wafer and another sub-microsecond pulsed 527 nm laser is responsible to activate the dopant. To optimize the system's performance, a physical model is presented to predict the thermal effect of two laser fields interacting on wafer. Using the Finite-Element method (FEM), we numerically investigate the temperature field induced by lasers in detail. The process window corresponding to the lasers is also acquired which can satisfy the requirements of the IGBT's annealing.

  7. Molecular cooperativity and compatibility via full atomistic simulation

    NASA Astrophysics Data System (ADS)

    Kwan Yang, Kenny

    Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules

  8. Experimental characterization of a micro-hole drilling process with short micro-second pulses by a CW single-mode fiber laser

    NASA Astrophysics Data System (ADS)

    Tu, Jay; Paleocrassas, Alexander G.; Reeves, Nicholas; Rajule, Nilesh

    2014-04-01

    Laser ablation with pulse durations in a few microseconds is a viable solution for micro-hole drilling applications which require large material removal rate (MRR) with moderate hole quality. However, the body of work regarding short microsecond laser drilling/ablation is small. The objective of this paper is to experimentally characterize this short micro-second laser micro-hole drilling technique using a 300 W, CW, single-mode fiber laser. This CW fiber laser is controlled to produce modulated pulses from 1 μs to 8 μs and these modulated laser pulses have a unique profile which contains an initial spike with a peak power of 1500 W for 1 μs, followed by the steady state power of 300 W. Because of its excellent beam quality, the laser beam produced by this fiber laser can be focused to a small spot size of 10 μm to achieve very high power density up to 1.9 GW/cm2. With one single laser pulse at approximately 1 μs, a blind hole of 167 μm in depth and 23 μm in opening diameter can be created in a stainless substrate. The experimental characterization of this micro-hole drilling process includes laser control, laser beam characterization, hole formation, photodiode measurements of the vapor intensity, high-speed photography of vapor/plasma formation, and spectroscopic measurements of plasma. The results show that, due to very high irradiance of the fiber laser beam, the absorbed energy not only is sufficient to melt and vaporize the material, but also is able to dissociate vapor into intense plasma at temperatures over 16,000 K. The hole drilling mechanism by this short microsecond laser ablation is due to a combination of adiabatic evaporation and ejection of fine droplets.

  9. Electrocaloric effect in ferroelectric nanowires from atomistic simulations

    NASA Astrophysics Data System (ADS)

    Herchig, R.; Chang, C.-M.; Mani, B. K.; Ponomareva, I.

    2015-11-01

    Electrocaloric effect is presently under active investigation owing to both the recent discoveries of giant electrocaloric effects and its potential for solid state cooling applications. We use first-principles-based direct simulations to predict the electrocaloric temperature change in ferroelectric ultrathin nanowires. Our findings suggest that in nanowires with axial polarization direction the maximum electrocaloric response is reduced when compared to bulk, while the room temperature electrocaloric properties can be enhanced by tuning the ferroelectric transition temperature. The potential of ferroelectric nanowires for electrocaloric cooling applications is discussed.

  10. Electrocaloric effect in ferroelectric nanowires from atomistic simulations

    PubMed Central

    Herchig, R.; Chang, C.-M.; Mani, B. K.; Ponomareva, I.

    2015-01-01

    Electrocaloric effect is presently under active investigation owing to both the recent discoveries of giant electrocaloric effects and its potential for solid state cooling applications. We use first-principles-based direct simulations to predict the electrocaloric temperature change in ferroelectric ultrathin nanowires. Our findings suggest that in nanowires with axial polarization direction the maximum electrocaloric response is reduced when compared to bulk, while the room temperature electrocaloric properties can be enhanced by tuning the ferroelectric transition temperature. The potential of ferroelectric nanowires for electrocaloric cooling applications is discussed. PMID:26612267

  11. Electrocaloric effect in ferroelectric nanowires from atomistic simulations.

    PubMed

    Herchig, R; Chang, C-M; Mani, B K; Ponomareva, I

    2015-11-27

    Electrocaloric effect is presently under active investigation owing to both the recent discoveries of giant electrocaloric effects and its potential for solid state cooling applications. We use first-principles-based direct simulations to predict the electrocaloric temperature change in ferroelectric ultrathin nanowires. Our findings suggest that in nanowires with axial polarization direction the maximum electrocaloric response is reduced when compared to bulk, while the room temperature electrocaloric properties can be enhanced by tuning the ferroelectric transition temperature. The potential of ferroelectric nanowires for electrocaloric cooling applications is discussed.

  12. Understanding materials behavior from atomistic simulations: Case study of al-containing high entropy alloys and thermally grown aluminum oxide

    NASA Astrophysics Data System (ADS)

    Yinkai Lei

    Atomistic simulation refers to a set of simulation methods that model the materials on the atomistic scale. These simulation methods are faster and cheaper alternative approaches to investigate thermodynamics and kinetics of materials compared to experiments. In this dissertation, atomistic simulation methods have been used to study the thermodynamic and kinetic properties of two material systems, i.e. the entropy of Al-containing high entropy alloys (HEAs) and the vacancy migration energy of thermally grown aluminum oxide. (Abstract shortened by ProQuest.).

  13. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations

    PubMed Central

    Khelashvili, George; Grossfield, Alan; Feller, Scott E.; Pitman, Michael C.; Weinstein, Harel

    2014-01-01

    An unresolved question about GPCR function is the role of membrane components in receptor stability and activation. In particular, cholesterol is known to affect the function of membrane proteins, but the details of its effect on GPCRs are still elusive. Here, we describe how cholesterol modulates the behavior of the TM1-TM2-TM7-helix 8(H8) functional network that comprises the highly conserved NPxxY(x)5,6F motif, through specific interactions with the receptor. The inferences are based on the analysis of microsecond length molecular dynamics (MD) simulations of rhodopsin in an explicit membrane environment. Three regions on the rhodopsin exhibit the highest cholesterol density throughout the trajectory: the extracellular end of TM7, a location resembling the high-density sterol area from the electron microscopy data; the intracellular parts of TM1, TM2, and TM4, a region suggested as the cholesterol binding site in the recent X-ray crystallography data on β2-adrenergic GPCR; and the intracellular ends of TM2-TM3, a location that was categorized as the high cholesterol density area in multiple independent 100 ns MD simulations of the same system. We found that cholesterol primarily affects specific local perturbations of the helical TM domains such as the kinks in TM1, TM2, and TM7. These local distortions, in turn, relate to rigid-body motions of the TMs in the TM1-TM2-TM7-H8 bundle. The specificity of the effects stems from the nonuniform distribution of cholesterol around the protein. Through correlation analysis we connect local effects of cholesterol on structural perturbations with a regulatory role of cholesterol in the structural rearrangements involved in GPCR function. PMID:19173312

  14. Characterization of neutron emission from mega-ampere deuterium gas puff Z-pinch at microsecond implosion times

    NASA Astrophysics Data System (ADS)

    Klir, D.; Shishlov, A. V.; Kokshenev, V. A.; Kubes, P.; Labetsky, A. Yu; Rezac, K.; Cikhardt, J.; Fursov, F. I.; Kovalchuk, B. M.; Kravarik, J.; Kurmaev, N. E.; Ratakhin, N. A.; Sila, O.; Stodulka, J.

    2013-08-01

    Experiments with deuterium (D2) triple shell gas puffs were carried out on the GIT-12 generator at a 3 MA current level and microsecond implosion times. The outer, middle and inner nozzle diameters were 160 mm, 80 mm and 30 mm, respectively. The influence of the mass of deuterium shells on neutron emission times, neutron yields and neutron energy spectra was studied. The injected linear mass of deuterium varied between 50 and 255 µg cm-1. Gas puffs imploded onto the axis before the peak of generator current at 700-1100 ns. Most of the neutrons were emitted during the second neutron pulse after the development of instabilities. Despite higher currents, heavier gas puffs produced lower neutron yields. Optimal mass and a short time delay between the valve opening and the generator triggering were more important than the better coincidence of stagnation with peak current. The peak neutron yield from D(d, n)3He reactions reached 3 × 1011 at 2.8 MA current, 90 µg cm-1 injected linear mass and 37 mm anode-cathode gap. In the case of lower mass shots, a large number of 10 MeV neutrons were produced either by secondary DT reactions or by DD reactions of deuterons with energies above 7 MeV. The average neutron yield ratio Y>10 MeV/Y2.5 MeV reached (6 ± 3) × 10-4. Such a result can be explained by a power law distribution for deuterons as \\rmd N_d/\\rmd E_d\\propto E_d^{-3} . The optimization of a D2 gas puff Z-pinch and similarities to a plasma focus and its drive parameter are described.

  15. High longitudinal relaxivity of ultra-small gadolinium oxide prepared by microsecond laser ablation in diethylene glycol

    SciTech Connect

    Luo Ningqi; Xiao Jun; Hu Wenyong; Chen Dihu; Tian Xiumei; Yang Chuan; Li Li

    2013-04-28

    Ultra-small gadolinium oxide (Gd{sub 2}O{sub 3}) can be used as T{sub 1}-weighted Magnetic Resonance Imaging (MRI) contrast agent own to its high longitudinal relaxivity (r{sub 1}) and has attracted intensive attention in these years. In this paper, ultra-small Gd{sub 2}O{sub 3} nanoparticles of 3.8 nm in diameter have been successfully synthesized by a microsecond laser ablating a gadolinium (Gd) target in diethylene glycol (DEG). The growth inhibition effect induced by the large viscosity of DEG makes it possible to synthesize ultra-small Gd{sub 2}O{sub 3} by laser ablation in DEG. The r{sub 1} value and T{sub 1}-weighted MR images are measured by a 3.0 T MRI spectroscope. The results show these nanoparticles with a high r{sub 1} value of 9.76 s{sup -1} mM{sup -1} to be good MRI contrast agents. We propose an explanation for the high r{sub 1} value of ultra-small Gd{sub 2}O{sub 3} by considering the decreasing factor (surface to volume ratio of the nanoparticles, S/V) and the increasing factor (water hydration number of the Gd{sup 3+} on Gd{sub 2}O{sub 3} surface, q), which offer a new look into the relaxivity studies of MRI contrast agents. Our research provides a new approach to preparing ultra-small Gd{sub 2}O{sub 3} of high r{sub 1} value by laser ablation in DEG and develops the understanding of high relaxivity of ultra-small Gd{sub 2}O{sub 3} MRI contrast agents.

  16. Polar Terrains

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03577 Polar Terrains

    The region surrounding the South Polar Cap contains many different terrain types. This image shows both etched terrain and a region of 'mounds'.

    Image information: VIS instrument. Latitude 75S, Longitude 286.5E. 17 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  17. Polar ozone

    NASA Technical Reports Server (NTRS)

    Solomon, S.; Grose, W. L.; Jones, R. L.; Mccormick, M. P.; Molina, Mario J.; Oneill, A.; Poole, L. R.; Shine, K. P.; Plumb, R. A.; Pope, V.

    1990-01-01

    The observation and interpretation of a large, unexpected ozone depletion over Antarctica has changed the international scientific view of stratospheric chemistry. The observations which show the veracity, seasonal nature, and vertical structure of the Antarctic ozone hole are presented. Evidence for Arctic and midlatitude ozone loss is also discussed. The chemical theory for Antarctic ozone depletion centers around the occurrence of polar stratospheric clouds (PSCs) in Antarctic winter and spring; the climatology and radiative properties of these clouds are presented. Lab studies of the physical properties of PSCs and the chemical processes that subsequently influence ozone depletion are discussed. Observations and interpretation of the chemical composition of the Antarctic stratosphere are described. It is shown that the observed, greatly enhanced abundances of chlorine monoxide in the lower stratosphere are sufficient to explain much if not all of the ozone decrease. The dynamic meteorology of both polar regions is given, interannual and interhemispheric variations in dynamical processes are outlined, and their likely roles in ozone loss are discussed.

  18. Coupling length scales for multiscale atomistics-continuum simulations: atomistically induced stress distributions in Si/Si3N4 nanopixels.

    PubMed

    Lidorikis, E; Bachlechner, M E; Kalia, R K; Nakano, A; Vashishta, P; Voyiadjis, G Z

    2001-08-20

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  19. Coupling-of-length-scale approach for multiscale atomistic-continuum simulations: Atomistically-induced stress distributions in Si/Si_3N4 nanopixels

    NASA Astrophysics Data System (ADS)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George; Madhukar, Anupam

    2001-03-01

    A hybrid molecular-dynamics and finite-element simulation approach has been used to investigate stress distributions in Si(111) nanopixels covered with both crystalline and amorphous Si_3N4 thin films. Surfaces, lattice-mismatched interfaces, edges, and corners create stress fields on the order of 1 GPa inside the Si substrate with patterns that cannot be reproduced by a continuum approach alone. For these atomistically-induced inhomogeneouse stresses, the hybrid simulation approach provides an excellent agreement with the standard molecular dynamics, with considerably less computational costs.

  20. Coupling Length Scales for Multiscale Atomistics-Continuum Simulations: Atomistically Induced Stress Distributions in Si/Si3N4 Nanopixels

    NASA Astrophysics Data System (ADS)

    Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Voyiadjis, George Z.

    2001-08-01

    A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are in good agreement with full multimillion-atom MD simulations: atomic structures at the lattice-mismatched interface between amorphous silicon nitride and silicon induce inhomogeneous stress patterns in the substrate that cannot be reproduced by a continuum approach alone.

  1. Polar Barchans

    NASA Technical Reports Server (NTRS)

    2004-01-01

    20 July 2004 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows dark, barchan sand dunes of the north polar region of Mars. Barchan dunes are simple, rounded forms with two horns that extend downwind. Inequalities in local wind patterns may result in one horn being extended farther than the other, as is the case for several dunes in this image. The image also shows several barchans may merge to form a long dune ridge. The horns and attendant slip faces on these dunes indicate wind transport of sand from the upper left toward the lower right. The image is located near 77.6oN, 103.6oW. The picture covers an area about 3 km (1.9 mi) wide; sunlight illuminates the scene from the lower left.

  2. Symmetry Breaking and Fine Structure Splitting in Zincblende Quantum Dots: Atomistic Simulations of Long-Range Strain and Piezoelectric Field

    NASA Astrophysics Data System (ADS)

    Ahmed, Shaikh; Usman, Muhammad; Heitzinger, Clemens; Rahman, Rajib; Schliwa, Andrei; Klimeck, Gerhard

    2007-04-01

    Electrons and holes captured in self-assembled quantum dots (QDs) are subject to symmetry breaking that cannot be represented in with continuum material representations. Atomistic calculations reveal symmetry lowering due to effects of strain and piezo-electric fields. These effects are fundamentally based on the crystal topology in the quantum dots. This work studies these two competing effects and demonstrates the fine structure splitting that has been demonstrated experimentally can be attributed to the underlying atomistic structure of the quantum dots.

  3. Polarized fluorescence correlation spectroscopy of DNA-DAPI complexes.

    PubMed

    Barcellona, Maria Luisa; Gammon, Seth; Hazlett, Theodore; Digman, Michelle A; Gratton, Enrico

    2004-11-01

    We discuss the use of fluorescence correlation spectroscopy for the measurement of relatively slow rotations of large macromolecules in solution or attached to other macromolecular structures. We present simulations and experimental results to illustrate the range of rotational correlation times and diffusion times that the technique can analyze. In particular, we examine various methods to analyze the polarization fluctuation data. We have found that by first constructing the polarization function and then calculating the autocorrelation function, we can obtain the rotational motion of the molecule with very little interference from the lateral diffusion of the macromolecule, as long as the rotational diffusion is significantly faster than the lateral diffusion. Surprisingly, for common fluorophores the autocorrelation of the polarization function is relatively unaffected by the photon statistics. In our instrument, two-photon excitation is used to define a small volume of illumination where a few molecules are present at any instant of time. The measurements of long DNA molecules labeled with the fluorescent probe DAPI show local rotational motions of the polymers in addition to translation motions of the entire polymer. For smaller molecules such as EGFP, the viscosity of the solution must be increased to bring the relaxation due to rotational motion into the measurable range. Overall, our results show that polarized fluorescence correlation spectroscopy can be used to detect fast and slow rotational motion in the time scale from microsecond to second, a range that cannot be easily reached by conventional fluorescence anisotropy decay methods.

  4. Atomistic calculation of the thermal conductance of large scale bulk-nanowire junctions

    SciTech Connect

    Duchemin, Ivan; Donadio, Davide

    2011-09-15

    We have developed a stable and efficient kernel method to compute thermal transport in open systems, based on the scattering-matrix approach. This method is applied to compute the thermal conductance of a junction between bulk silicon and silicon nanowires with diameter up to 10 nm. We have found that beyond a threshold diameter of 7 nm, transmission spectra and contact conductances scale with the cross section of the contact surface, whereas deviations from this general trend are observed in thinner wires. This result allows us to predict the thermal resistance of bulk-nanowire interfaces with larger cross sections than those tractable with atomistic simulations, and indicate the characteristic size beyond which atomistic systems can in principle be treated accurately by mean-field theories. Our calculations also elucidate how dimensionality reduction and shape affect interfacial heat transport.

  5. Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level

    NASA Astrophysics Data System (ADS)

    Buerkle, Marius; Asai, Yoshihiro

    2017-02-01

    The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations.

  6. Atomistic Simulation of Plasticity and Fracture of Crystalline and Polycrystalline Metals Under High Strain Rate

    NASA Astrophysics Data System (ADS)

    Norman, Genri E.; Kuksin, Alexey Yu.; Stegailov, Vladimir V.; Yanilkin, Alexey V.

    2007-12-01

    We consider modeling and simulation of dynamic atomistic phenomena and processes in condensed matter under high strain rate: intensive shock compression and release, uniaxial and hydrostatic stretching. An attempt is done to draft out the atomistic theory of the phenomena. The basic concepts for the theory are the multiscale approach, the analysis of thermodynamic paths of relaxation on phase diagrams, the explicit utilization of the stochastic features of the MD method. A number of "elementary processes" (cavitation of voids at negative pressures, voids growth, dislocation formation and motion, phase transformations, etc.) are briefly considered for both single and nanocrystals. A theoretical MD based multiscale approach is presented for the spall process which could be used to extend the MD results to the larger spatial and temporal scales. Examples are presented for Al, Cu and Fe. The EAM potentials are deployed. Comparisons with the experimental data available are given. A hierarchy of dynamic and stochastic processes is discussed.

  7. Atomistic Conversion Reaction Mechanism of WO3 in Secondary Ion Batteries of Li, Na, and Ca.

    PubMed

    He, Yang; Gu, Meng; Xiao, Haiyan; Luo, Langli; Shao, Yuyan; Gao, Fei; Du, Yingge; Mao, Scott X; Wang, Chongmin

    2016-05-17

    Intercalation and conversion are two fundamental chemical processes for battery materials in response to ion insertion. The interplay between these two chemical processes has never been directly seen and understood at atomic scale. Here, using in situ HRTEM, we captured the atomistic conversion reaction processes during Li, Na, Ca insertion into a WO3 single crystal model electrode. An intercalation step prior to conversion is explicitly revealed at atomic scale for the first time for Li, Na, Ca. Nanoscale diffraction and ab initio molecular dynamic simulations revealed that after intercalation, the inserted ion-oxygen bond formation destabilizes the transition-metal framework which gradually shrinks, distorts and finally collapses to an amorphous W and Mx O (M=Li, Na, Ca) composite structure. This study provides a full atomistic picture of the transition from intercalation to conversion, which is of essential importance for both secondary ion batteries and electrochromic devices.

  8. Complete Atomistic Model of a Bacterial Cytoplasm for Integrating Physics, Biochemistry, and Systems Biology

    PubMed Central

    Feig, Michael; Harada, Ryuhei; Mori, Takaharu; Yu, Isseki; Takahashi, Koichi; Sugita, Yuji

    2015-01-01

    A model for the cytoplasm of Mycoplasma genitalium is presented that integrates data from a variety of sources into a physically and biochemically consistent model. Based on gene annotations, core genes expected to be present in the cytoplasm were determined and a metabolic reaction network was reconstructed. The set of cytoplasmic genes and metabolites from the predicted reactions were assembled into a comprehensive atomistic model consisting of proteins with predicted structures, RNA, protein/RNA complexes, metabolites, ions, and solvent. The resulting model bridges between atomistic and cellular scales, between physical and biochemical aspects, and between structural and systems views of cellular systems and is meant as a starting point for a variety of simulation studies. PMID:25765281

  9. Atomistic electrodynamics simulations of bare and ligand-coated nanoparticles in the quantum size regime.

    PubMed

    Chen, Xing; Moore, Justin E; Zekarias, Meserret; Jensen, Lasse

    2015-11-10

    The optical properties of metallic nanoparticles with nanometre dimensions exhibit features that cannot be described by classical electrodynamics. In this quantum size regime, the near-field properties are significantly modified and depend strongly on the geometric arrangements. However, simulating realistically sized systems while retaining the atomistic description remains computationally intractable for fully quantum mechanical approaches. Here we introduce an atomistic electrodynamics model where the traditional description of nanoparticles in terms of a macroscopic homogenous dielectric constant is replaced by an atomic representation with dielectric properties that depend on the local chemical environment. This model provides a unified description of bare and ligand-coated nanoparticles, as well as strongly interacting nanoparticle dimer systems. The non-local screening owing to an inhomogeneous ligand layer is shown to drastically modify the near-field properties. This will be important to consider in optimization of plasmonic nanostructures for near-field spectroscopy and sensing applications.

  10. Multiscale Modeling of Carbon/Phenolic Composite Thermal Protection Materials: Atomistic to Effective Properties

    NASA Technical Reports Server (NTRS)

    Arnold, Steven M.; Murthy, Pappu L.; Bednarcyk, Brett A.; Lawson, John W.; Monk, Joshua D.; Bauschlicher, Charles W., Jr.

    2016-01-01

    Next generation ablative thermal protection systems are expected to consist of 3D woven composite architectures. It is well known that composites can be tailored to achieve desired mechanical and thermal properties in various directions and thus can be made fit-for-purpose if the proper combination of constituent materials and microstructures can be realized. In the present work, the first, multiscale, atomistically-informed, computational analysis of mechanical and thermal properties of a present day - Carbon/Phenolic composite Thermal Protection System (TPS) material is conducted. Model results are compared to measured in-plane and out-of-plane mechanical and thermal properties to validate the computational approach. Results indicate that given sufficient microstructural fidelity, along with lowerscale, constituent properties derived from molecular dynamics simulations, accurate composite level (effective) thermo-elastic properties can be obtained. This suggests that next generation TPS properties can be accurately estimated via atomistically informed multiscale analysis.

  11. Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level

    PubMed Central

    Buerkle, Marius; Asai, Yoshihiro

    2017-01-01

    The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations. PMID:28150738

  12. Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments.

    PubMed

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  13. Atomistic simulation of tunneling magnetoresistance using extended Hückel theory

    NASA Astrophysics Data System (ADS)

    Roy, Arunanshu M.; Nikonov, Dmitri E.; Young, Ian A.

    2012-11-01

    Atomistic simulations of magnetic tunnel junctions are performed using the extended Hückel theory and non equilibrium Green's function formalism. The effect of Fermi level pinning and the corresponding change in the tunnelling barrier height on the junction resistance and magnetoresistance ratio is studied. An approximate approach to the treatment of alloyed ferromagnet bandstructure is proposed and the effect of Fe and Co fractions in the ferromagnetic electrodes is determined.

  14. Atomistic mechanisms of rapid energy transport in light-harvesting molecules

    NASA Astrophysics Data System (ADS)

    Ohmura, Satoshi; Koga, Shiro; Akai, Ichiro; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2011-03-01

    Synthetic supermolecules such as π-conjugated light-harvesting dendrimers efficiently harvest energy from sunlight, which is of significant importance for the global energy problem. Key to their success is rapid transport of electronic excitation energy from peripheral antennas to photochemical reaction cores, the atomistic mechanisms of which remains elusive. Here, quantum-mechanical molecular dynamics simulation incorporating nonadiabatic electronic transitions reveals the key molecular motion that significantly accelerates the energy transport based on the Dexter mechanism.

  15. Adaptive spacetime method using Riemann jump conditions for coupled atomistic-continuum dynamics

    SciTech Connect

    Kraczek, B. Miller, S.T. Haber, R.B. Johnson, D.D.

    2010-03-20

    We combine the Spacetime Discontinuous Galerkin (SDG) method for elastodynamics with the mathematically consistent Atomistic Discontinuous Galerkin (ADG) method in a new scheme that concurrently couples continuum and atomistic models of dynamic response in solids. The formulation couples non-overlapping continuum and atomistic models across sharp interfaces by weakly enforcing jump conditions, for both momentum balance and kinematic compatibility, using Riemann values to preserve the characteristic structure of the underlying hyperbolic system. Momentum balances to within machine-precision accuracy over every element, on each atom, and over the coupled system, with small, controllable energy dissipation in the continuum region that ensures numerical stability. When implemented on suitable unstructured spacetime grids, the continuum SDG model offers linear computational complexity in the number of elements and powerful adaptive analysis capabilities that readily bridge between atomic and continuum scales in both space and time. A special trace operator for the atomic velocities and an associated atomistic traction field enter the jump conditions at the coupling interface. The trace operator depends on parameters that specify, at the scale of the atomic spacing, the position of the coupling interface relative to the atoms. In a key finding, we demonstrate that optimizing these parameters suppresses spurious reflections at the coupling interface without the use of non-physical damping or special boundary conditions. We formulate the implicit SDG-ADG coupling scheme in up to three spatial dimensions, and describe an efficient iterative solution scheme that outperforms common explicit schemes, such as the Velocity Verlet integrator. Numerical examples, in 1dxtime and employing both linear and nonlinear potentials, demonstrate the performance of the SDG-ADG method and show how adaptive spacetime meshing reconciles disparate time steps and resolves atomic-scale signals in

  16. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions†

    PubMed Central

    2015-01-01

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https

  17. Pulpal Effects of Enamel Ablation With a Microsecond Pulsed λ=9.3-μm CO2 Laser

    PubMed Central

    Staninec, Michal; Darling, Cynthia L.; Goodis, Harold E.; Pierre, Daniel; Cox, Darren P.; Fan, Kenneth; Larson, Michael; Parisi, Renaldo; Hsu, Dennis; Manesh, Saman K.; Ho, Chi; Hosseini, Mehran; Fried, Daniel

    2011-01-01

    Background and Objectives In vitro studies have shown that CO2 lasers operating at the highly absorbed 9.3 and 9.6-μm wavelengths with a pulse duration in the range of 10–20-microsecond are well suited for the efficient ablation of enamel and dentin with minimal peripheral thermal damage. Even though these CO2 lasers are highly promising, they have yet to receive FDA approval. Clinical studies are necessary to determine if excessive heat deposition in the tooth may have any detrimental pulpal effects, particularly at higher ablative fluencies. The purpose of this study was to evaluate the pulpal safety of laser irradiation of tooth occlusal surfaces under the conditions required for small conservative preparations confined to enamel. Study Design/Materials and Methods Test subjects requiring removal of third molar teeth were recruited and teeth scheduled for extraction were irradiated using a pulsed CO2 laser at a wavelength of 9.3 μm operating at 25 or 50 Hz using a incident fluence of 20 J/cm2 for a total of 3,000 laser pulses (36 J) for both rates with water cooling. Two control groups were used, one with no treatment and one with a small cut made with a conventional high-speed hand-piece. No anesthetic was used for any of the procedures and tooth vitality was evaluated prior to treatment by heat, cold and electrical testing. Short term effects were observed on teeth extracted within 72 hours after treatment and long term effects were observed on teeth extracted 90 days after treatment. The pulps of the teeth were fixed with formalin immediately after extraction and subjected to histological examination. Additionally, micro-thermocouple measurements were used to estimate the potential temperature rise in the pulp chamber of extracted teeth employing the same irradiation conditions used in vivo. Results Pulpal thermocouple measurements showed the internal temperature rise in the tooth was within safe limits, 3.3±4°C without water cooling versus 1.7±6

  18. Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

    Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

  19. Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

    SciTech Connect

    Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; Osetskiy, Yury N.

    2015-01-29

    The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies is illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.

  20. Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

    DOE PAGES

    Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

    2015-01-29

    The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

  1. Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

    PubMed

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

    Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

  2. State Representation Approach for Atomistic Time-Dependent Transport Calculations in Molecular Junctions.

    PubMed

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

    We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville-von-Neumann equation approach of Sánchez et al. [J. Chem. Phys. 2006, 124, 214708] and Subotnik et al. [J. Chem. Phys. 2009, 130, 144105]. A key ingredient of our approach is a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to uniquely define the bias voltage across the system while maintaining a proper thermal electronic distribution within the finite lead models. Furthermore, it allows us to investigate complex molecular junctions, including multilead configurations. A heuristic derivation of our working equation leads to explicit expressions for the damping and driving terms, which serve as appropriate electron sources and sinks that effectively "open" the finite model system. Although the method does not forbid it, in practice we find neither violation of Pauli's exclusion principles nor deviation from density matrix positivity throughout our numerical simulations of various tight-binding model systems. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic molecular junction models.

  3. Phase field crystal modeling as a unified atomistic approach to defect dynamics

    NASA Astrophysics Data System (ADS)

    Berry, Joel; Provatas, Nikolas; Rottler, Jörg; Sinclair, Chad W.

    2014-06-01

    Material properties controlled by evolving defect structures, such as mechanical response, often involve processes spanning many length and time scales which can not be modeled using a single approach. We present a variety of results that demonstrate the ability of phase field crystal (PFC) models to describe complex defect evolution phenomena on atomistic length scales and over long, diffusive time scales. Primary emphasis is given to the unification of conservative and nonconservative dislocation creation mechanisms in three-dimensional fcc and bcc materials. These include Frank-Read-type glide mechanisms involving closed dislocation loops or grain boundaries as well as Bardeen-Herring-type climb mechanisms involving precipitates, inclusions, and/or voids. Both source classes are naturally and simultaneously captured at the atomistic level by PFC descriptions, with arbitrarily complex defect configurations, types, and environments. An unexpected dipole-to-quadrupole source transformation is identified, as well as various complex geometrical features of loop nucleation via climb from spherical particles. Results for the strain required to nucleate a dislocation loop from such a particle are in agreement with analytic continuum theories. Other basic features of fcc and bcc dislocation structure and dynamics are also outlined, and initial results for dislocation-stacking fault tetrahedron interactions are presented. These findings together highlight various capabilities of the PFC approach as a coarse-grained atomistic tool for the study of three-dimensional crystal plasticity.

  4. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

    PubMed

    Yang, Shengfeng; Chen, Youping

    2015-03-08

    In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

  5. The space-angular characteristics of a microsecond solid laser on the basis of a nano-porous glass polymer composite activated with dyes

    NASA Astrophysics Data System (ADS)

    Tarkovsky, V.; Anufrik, S.; Koldunov, M.; Manenkov, A.

    2007-06-01

    The optimum conditions of excitation in a two-spool laser are determined, in which the pumping of a solid laser on the basis of nanoporous glass - polymer composite with the inserted dyes is made by a laser on dyes emission with a lamp pumping of microsecond duration, which provides overlapping of a broad spectral range with laser momentums with energy up to 500 mJ at the duration of 1 mcs and the divergence of 1 millirad and the increase of the radiance in 140-700 times.

  6. The polarization properties of a tilted polarizer.

    PubMed

    Korger, Jan; Kolb, Tobias; Banzer, Peter; Aiello, Andrea; Wittmann, Christoffer; Marquardt, Christoph; Leuchs, Gerd

    2013-11-04

    Polarizers are key components in optical science and technology. Thus, understanding the action of a polarizer beyond oversimplifying approximations is crucial. In this work, we study the interaction of a polarizing interface with an obliquely incident wave experimentally. To this end, a set of Mueller matrices is acquired employing a novel procedure robust against experimental imperfections. We connect our observation to a geometric model, useful to predict the effect of polarizers on complex light fields.

  7. Polarized internal target apparatus

    DOEpatents

    Holt, R.J.

    1984-10-10

    A polarized internal target apparatus with a polarized gas target of improved polarization and density (achieved by mixing target gas atoms with a small amount of alkali metal gas atoms, and passing a high intensity polarized light source into the mixture to cause the alkali metal gas atoms to become polarized which interact in spin exchange collisions with target gas atoms yielding polarized target gas atoms) is described.

  8. Polarized internal target apparatus

    DOEpatents

    Holt, Roy J.

    1986-01-01

    A polarized internal target apparatus with a polarized gas target of improved polarization and density achieved by mixing target gas atoms with a small amount of alkali metal gas atoms, and passing a high intensity polarized light source into the mixture to cause the alkali metal gas atoms to become polarized which interact in spin exchange collisions with target gas atoms yielding polarized target gas atoms.

  9. Polarization in Scattering

    DTIC Science & Technology

    2010-09-01

    we refer to the linear polarization as parallel if the polarization vector is in the scattering plane or perpendicular if the polarization vector is...obvious that the different polarization states can all be represented as linear combinations of any of the independent pairs of polarization states...J.C. (1976) “Improvement of underwater visibility by reduction of backscatter with a circular polarization technique, Applied Optics, 6, 321-330

  10. Polar Color

    NASA Technical Reports Server (NTRS)

    2004-01-01

    [figure removed for brevity, see original site]

    Released 3 May 2004 This nighttime visible color image was collected on January 1, 2003 during the Northern Summer season near the North Polar Troughs.

    This daytime visible color image was collected on September 4, 2002 during the Northern Spring season in Vastitas Borealis. The THEMIS VIS camera is capable of capturing color images of the martian surface using its five different color filters. In this mode of operation, the spatial resolution and coverage of the image must be reduced to accommodate the additional data volume produced from the use of multiple filters. To make a color image, three of the five filter images (each in grayscale) are selected. Each is contrast enhanced and then converted to a red, green, or blue intensity image. These three images are then combined to produce a full color, single image. Because the THEMIS color filters don't span the full range of colors seen by the human eye, a color THEMIS image does not represent true color. Also, because each single-filter image is contrast enhanced before inclusion in the three-color image, the apparent color variation of the scene is exaggerated. Nevertheless, the color variation that does appear is representative of some change in color, however subtle, in the actual scene. Note that the long edges of THEMIS color images typically contain color artifacts that do not represent surface variation.

    Image information: VIS instrument. Latitude 79, Longitude 346 East (14 West). 19 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with

  11. Broadband graphene polarizer

    NASA Astrophysics Data System (ADS)

    Bao, Qiaoliang; Zhang, Han; Wang, Bing; Ni, Zhenhua; Lim, Candy Haley Yi Xuan; Wang, Yu; Tang, Ding Yuan; Loh, Kian Ping

    2011-07-01

    Conventional polarizers can be classified into three main modes of operation: sheet polarizer using anisotropic absorption media, prism polarizer by refraction and Brewster-angle polarizer by reflection. These polarizing components are not easily integrated with photonic circuits. The in-line fibre polarizer, which relies on polarization-selective coupling between the evanescent field and birefringent crystal or metal, is a promising alternative because of its compatibility with most fibre-optic systems. Here, we demonstrate the operation of a broadband fibre polarizer based on graphene, an ultrathin two-dimensional carbon material. The out-coupled light in the telecommunication band shows a strong s-polarization effect with an extinction ratio of 27 dB. Unlike polarizers made from thin metal film, a graphene polarizer can support transverse-electric-mode surface wave propagation due to its linear dispersion of Dirac electrons.

  12. Tuneable microsecond-pulsed glow discharge design for the simultaneous acquisition of elemental and molecular chemical information using a time-of-flight mass spectrometer.

    PubMed

    Solà-Vázquez, Auristela; Martín, Antonio; Costa-Fernández, José M; Pereiro, Rosario; Sanz-Medel, Alfredo

    2009-04-01

    A microsecond-pulsed direct current glow discharge (GD) was interfaced and synchronized to a time-of-flight mass spectrometer MS(TOF) for time-gated generation and detection of elemental, structural, and molecular ions. In this way, sequential collection of the mass spectra at different temporal regimes occurring during the GD pulse cycle is allowed. The capabilities of this setup were explored using bromochloromethane as model analyte. A simple GD chamber, developed in our laboratory and characterized by a low plasma volume minimizing dilution of the sample but showing great robustness to the entrance of organic compounds in the microsecond-pulsed plasma, has been used. An exhaustive analytical characterization of the GD-MS(TOF) prototype has been performed. Calibration curves for bromochloromethane observed at the different time regimes of the GD pulse cycle (that is, for elemental, fragment, and molecular ions from the analyte) showed very good linearity for the measurement of the different involved ions, with precisions in the range of 7-13% (relative standard deviation). Actual detection limits obtained for bromochloromethane were in the range of 1-3 microg/L for elements monitoring in the GD pulse "prepeak", in the range of 11-13 microg/L when monitoring analyte fragments in the plateau, and about 238 microg/L when measuring the molecular peak in the afterpeak regime.

  13. Polarized maser growth

    SciTech Connect

    Melrose, D.B.; Judge, A.C.

    2004-11-01

    A polarized maser is assumed to operate in an anisotropic medium with natural modes polarized differently to the maser. It is shown that when the spatial growth rate and the generalized Faraday rotation rate are comparable, the polarization of the growing radiation is different from those of the maser and medium. In particular, for a lineary polarized maser operating in a medium with linearly polarized natural modes, the growing radiation is partially circularly polarized. This provides a previously unrecognized source of circular polarization that may be relevant to pulsar radio emission.

  14. Cholesterol-induced suppression of membrane elastic fluctuations at the atomistic level.

    PubMed

    Molugu, Trivikram R; Brown, Michael F

    2016-09-01

    Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state (2)H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C-(2)H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of (13)C-(1)H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For (2)H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes.

  15. SCT: a suite of programs for comparing atomistic models with small-angle scattering data.

    PubMed

    Wright, David W; Perkins, Stephen J

    2015-06-01

    Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.

  16. Simulating Surface-Enhanced Hyper-Raman Scattering Using Atomistic Electrodynamics-Quantum Mechanical Models.

    PubMed

    Hu, Zhongwei; Chulhai, Dhabih V; Jensen, Lasse

    2016-12-13

    Surface-enhanced hyper-Raman scattering (SEHRS) is the two-photon analogue of surface-enhanced Raman scattering (SERS), which has proven to be a powerful tool to study molecular structures and surface enhancements. However, few theoretical approaches to SEHRS exist and most neglect the atomistic descriptions of the metal surface and molecular resonance effects. In this work, we present two atomistic electrodynamics-quantum mechanical models to simulate SEHRS. The first is the discrete interaction model/quantum mechanical (DIM/QM) model, which combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule. The second model is a dressed-tensors method that describes the molecule as a point-dipole and point-quadrupole object interacting with the enhanced local field and field-gradients (FG) from the nanoparticle. In both of these models, the resonance effects are treated efficiently by means of damped quadratic response theory. Using these methods, we simulate SEHRS spectra for benzene and pyridine. Our results show that the FG effects in SEHRS play an important role in determining both the surface selection rules and the enhancements. We find that FG effects are more important in SEHRS than in SERS. We also show that the spectral features of small molecules can be accurately described by accounting for the interactions between the molecule and the local field and FG of the nanoparticle. However, at short distances between the metal and molecule, we find significant differences in the SEHRS enhancements predicted using the DIM/QM and the dressed-tensors methods.

  17. Cholesterol-Induced Suppression of Membrane Elastic Fluctuations at the Atomistic Level

    PubMed Central

    Molugu, Trivikram R.

    2017-01-01

    Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state 2H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C–2H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of 13C–1H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For 2H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes. PMID:27154600

  18. Crossed elliptical polarization undulator

    SciTech Connect

    Sasaki, Shigemi

    1997-05-01

    The first switching of polarization direction is possible by installing two identical helical undulators in series in a same straight section in a storage ring. By setting each undulator in a circular polarization mode in opposite handedness, one can obtain linearly polarized radiation with any required polarization direction depending on the modulator setting between two undulators. This scheme can be used without any major degradation of polarization degree in any low energy low emittance storage ring.

  19. Polarization-balanced beamsplitter

    DOEpatents

    Decker, Derek E.

    1998-01-01

    A beamsplitter assembly that includes several beamsplitter cubes arranged to define a plurality of polarization-balanced light paths. Each polarization-balanced light path contains one or more balanced pairs of light paths, where each balanced pair of light paths includes either two transmission light paths with orthogonal polarization effects or two reflection light paths with orthogonal polarization effects. The orthogonal pairing of said transmission and reflection light paths cancels polarization effects otherwise caused by beamsplitting.

  20. Polarization-balanced beamsplitter

    DOEpatents

    Decker, D.E.

    1998-02-17

    A beamsplitter assembly is disclosed that includes several beamsplitter cubes arranged to define a plurality of polarization-balanced light paths. Each polarization-balanced light path contains one or more balanced pairs of light paths, where each balanced pair of light paths includes either two transmission light paths with orthogonal polarization effects or two reflection light paths with orthogonal polarization effects. The orthogonal pairing of said transmission and reflection light paths cancels polarization effects otherwise caused by beamsplitting. 10 figs.

  1. Methods for atomistic abrasion simulations of laterally periodic polycrystalline substrates with fractal surfaces

    NASA Astrophysics Data System (ADS)

    Eder, S. J.; Bianchi, D.; Cihak-Bayr, U.; Gkagkas, K.

    2017-03-01

    In this work we discuss a method to generate laterally periodic polycrystalline samples with fractal surfaces for use in molecular dynamics simulations of abrasion. We also describe a workflow that allows us to produce random lateral distributions of simple but realistically shaped hard abrasive particles with Gaussian size distribution and random particle orientations. We evaluate some on-the-fly analysis and visualization possibilities that may be applied during a molecular dynamics simulation to considerably reduce the post-processing effort. Finally, we elaborate on a parallelizable post-processing approach to evaluating and visualizing the surface topography, the grain structure and orientation, as well as the temperature distribution in large atomistic systems.

  2. Elastic behavior of amorphous-crystalline silicon nanocomposite: An atomistic view

    NASA Astrophysics Data System (ADS)

    Das, Suvankar; Dutta, Amlan

    2017-01-01

    In the context of mechanical properties, nanocomposites with homogeneous chemical composition throughout the matrix and the dispersed phase are of particular interest. In this study, the elastic moduli of amorphous-crystalline silicon nanocomposite have been estimated using atomistic simulations. A comparison with the theoretical model reveals that the elastic behavior is significantly influenced by the crystal-amorphous interphase. On observing the effect of volume-fraction of the crystalline phase, an anomalous trend for the bulk modulus is obtained. This phenomenon is attributed to the relaxation displacements of the amorphous atoms.

  3. Atomistic formulas for local properties in systems with many-body interactions

    NASA Astrophysics Data System (ADS)

    Hardy, Robert J.

    2016-11-01

    Atomistic formulas are derived for the local densities and fluxes used in the continuum description of energy and momentum transport. Two general methods for the distribution of potential energy among a system's constituent particles are presented and analyzed. The resulting formulas for the heat flux and stress tensor and the equations for energy and momentum transport are exact consequences of the definitions of the densities and the equations of classical mechanics. The formulas and equations obtained are valid for systems with very general types of many-body interactions.

  4. Fundamentals of mechanical behavior in structural intermetallics: A synthesis of atomistic and continuum modeling

    SciTech Connect

    Yoo, M.H.; Fu, C.L.

    1993-08-01

    After a brief account of the recent advances in computational research on mechanical behavior of structural intermetallics, currently unresolved problems and critical issues are addressed and the knowledge base for potential answers to these problems is discussed. As large-scale problems (e.g., dislocation core structures, grain boundaries, and crack tips) are treated by atomistic simulations, future development of relevant interatomic potentials should be made consistent with the results of first-principles calculations. The bulk and defect properties calculated for intermetallic compounds, both known and as yet untested, can furnish insights to alloy designers in search of new high-temperature structural intermetallics.

  5. Thermodynamic Properties of Asphaltenes: A Predictive Approach Based On Computer Assisted Structure Elucidation and Atomistic Simulations

    SciTech Connect

    Diallo, Mamadou S.; Cagin, Tahir; Faulon, Jean Loup; Goddard, William A.

    2000-08-01

    The authors describe a new methodology for predicting the thermodynamic properties of petroleum geomacromolecules (asphaltenes and resins). This methodology combines computer assisted structure elucidation (CASE) with atomistic simulations (molecular mechanics and molecular dynamics and statistical mechanics). They use quantitative and qualitative structural data as input to a CASE program (SIGNATURE) to generate a sample of ten asphaltene model structures for a Saudi crude oil (Arab Berri). MM calculations and MD simulations are used to estimate selected volumetric and thermal properties of the model structures.

  6. AGU Chapman Conference Hydrogeologic Processes: Building and Testing Atomistic- to Basin-Scale Models

    SciTech Connect

    Weaver, B.

    1994-12-31

    This report presents details of the Chapman Conference given on June 6--9, 1994 in Lincoln, New Hampshire. This conference covered the scale of processes involved in coupled hydrogeologic mass transport and a concept of modeling and testing from the atomistic- to the basin- scale. Other topics include; the testing of fundamental atomic level parameterizations in the laboratory and field studies of fluid flow and mass transport and the next generation of hydrogeologic models. Individual papers from this conference are processed separately for the database.

  7. Networks of silicon nanowires: A large-scale atomistic electronic structure analysis

    SciTech Connect

    Keleş, Ümit; Bulutay, Ceyhun; Liedke, Bartosz; Heinig, Karl-Heinz

    2013-11-11

    Networks of silicon nanowires possess intriguing electronic properties surpassing the predictions based on quantum confinement of individual nanowires. Employing large-scale atomistic pseudopotential computations, as yet unexplored branched nanostructures are investigated in the subsystem level as well as in full assembly. The end product is a simple but versatile expression for the bandgap and band edge alignments of multiply-crossing Si nanowires for various diameters, number of crossings, and wire orientations. Further progress along this line can potentially topple the bottom-up approach for Si nanowire networks to a top-down design by starting with functionality and leading to an enabling structure.

  8. Atomistic Modeling of RuAl and (RuNi) Al Alloys

    NASA Technical Reports Server (NTRS)

    Gargano, Pablo; Mosca, Hugo; Bozzolo, Guillermo; Noebe, Ronald D.; Gray, Hugh R. (Technical Monitor)

    2002-01-01

    Atomistic modeling of RuAl and RuAlNi alloys, using the BFS (Bozzolo-Ferrante-Smith) method for alloys is performed. The lattice parameter and energy of formation of B2 RuAl as a function of stoichiometry and the lattice parameter of (Ru(sub 50-x)Ni(sub x)Al(sub 50)) alloys as a function of Ni concentration are computed. BFS based Monte Carlo simulations indicate that compositions close to Ru25Ni25Al50 are single phase with no obvious evidence of a miscibility gap and separation of the individual B2 phases.

  9. Atomistic switch of giant magnetoresistance and spin thermopower in graphene-like nanoribbons

    PubMed Central

    Zhai, Ming-Xing; Wang, Xue-Feng

    2016-01-01

    We demonstrate that the giant magnetoresistance can be switched off (on) in even- (odd-) width zigzag graphene-like nanoribbons by an atomistic gate potential or edge disorder inside the domain wall in the antiparallel (ap) magnetic configuration. A strong magneto-thermopower effect is also predicted that the spin thermopower can be greatly enhanced in the ap configuration while the charge thermopower remains low. The results extracted from the tight-binding model agree well with those obtained by first-principles simulations for edge doped graphene nanoribbons. Analytical expressions in the simplest case are obtained to facilitate qualitative analyses in general contexts. PMID:27857156

  10. Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

    SciTech Connect

    McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.; Schultz, Peter A.; Foster, Michael E.; Bartelt, Norman Charles

    2015-09-01

    In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expand the number of potential types of graphene electronic devices.

  11. An automatic and simple method for specifying dislocation features in atomistic simulations

    NASA Astrophysics Data System (ADS)

    Dai, Fu-Zhi; Zhang, Wen-Zheng

    2015-03-01

    An important aspect of atomistic simulations of imperfect crystalline materials is the characterization of dislocations. In this paper, we propose the use of singular values and singular vectors of the Nye tensor to specify the features of dislocations, including the cores, nodes, Burgers vectors and line directions. Atoms locate in dislocation cores and nodes are identified by non-trivial singular values of the Nye tensor, while Burgers vector direction and line direction are specified by those singular vectors corresponding to the biggest singular value. This method provides a powerful, intuitive and automatic tool for characterizing dislocations from simulation data. Its validity for characterizing dislocations is verified with three examples.

  12. Cold melting of beryllium: Atomistic view on Z-machine experiments

    SciTech Connect

    Dremov, V. V. Rykounov, A. A.; Sapozhnikov, F. A.; Karavaev, A. V.; Yakovlev, S. V.; Ionov, G. V.; Ryzhkov, M. V.

    2015-07-21

    Analysis of phase diagram of beryllium at high pressures and temperatures obtained as a result of ab initio calculations and large scale classical molecular dynamics simulations of beryllium shock loading have shown that the so called cold melting takes place when shock wave propagates through polycrystalline samples. Comparison of ab initio calculation results on sound speed along the Hugoniot with experimental data obtained on Z-machine also evidences for possible manifestation of the cold melting. The last may explain the discrepancy between atomistic simulations and experimental data on the onset of the melting on the Hugoniot.

  13. Near-ideal strength in metal nanotubes revealed by atomistic simulations

    SciTech Connect

    Sun, Mingfei; Xiao, Fei; Deng, Chuang

    2013-12-02

    Here we report extraordinary mechanical properties revealed by atomistic simulations in metal nanotubes with hollow interior that have been long overlooked. Particularly, the yield strength in [1 1 1] Au nanotubes is found to be up to 60% higher than the corresponding solid Au nanowire, which approaches the theoretical ideal strength in Au. Furthermore, a remarkable transition from sharp to smooth yielding is observed in Au nanotubes with decreasing wall thickness. The ultrahigh tensile strength in [1 1 1] Au nanotube might originate from the repulsive image force exerted by the interior surface against dislocation nucleation from the outer surface.

  14. Atomistic switch of giant magnetoresistance and spin thermopower in graphene-like nanoribbons

    NASA Astrophysics Data System (ADS)

    Zhai, Ming-Xing; Wang, Xue-Feng

    2016-11-01

    We demonstrate that the giant magnetoresistance can be switched off (on) in even- (odd-) width zigzag graphene-like nanoribbons by an atomistic gate potential or edge disorder inside the domain wall in the antiparallel (ap) magnetic configuration. A strong magneto-thermopower effect is also predicted that the spin thermopower can be greatly enhanced in the ap configuration while the charge thermopower remains low. The results extracted from the tight-binding model agree well with those obtained by first-principles simulations for edge doped graphene nanoribbons. Analytical expressions in the simplest case are obtained to facilitate qualitative analyses in general contexts.

  15. Using a scalar parameter to trace dislocation evolution in atomistic modeling

    SciTech Connect

    Yang, Jinbo; Zhang, Z F; Osetskiy, Yury N; Stoller, Roger E

    2015-01-01

    A scalar gamma-parameter is proposed from the Nye tensor. Its maximum value occurs along a dislocation line, either straight or curved, when the coordinate system is purposely chosen. This parameter can be easily obtained from the Nye tensor calculated at each atom in atomistic modeling. Using the gamma-parameter, a fully automated approach is developed to determine core atoms and the Burgers vectors of dislocations simultaneously. The approach is validated by revealing the smallest dislocation loop and by tracing the whole formation process of complicated dislocation networks on the fly.

  16. Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

    NASA Technical Reports Server (NTRS)

    Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

    2006-01-01

    A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

  17. Investigations on the mechanical behavior of nanowires with twin boundaries by atomistic simulations

    SciTech Connect

    Tian, Xia

    2015-03-10

    Atomistic simulations are used to study the deformation behavior of twinned Cu nanowires with a <111> growth orientation under tension. Due to the existence of the twin boundaries, the strength of the twinned nanowires is higher than that of the twin-free nanowire and the yielding stress of twinned nanowires is inversely proportional to the spacings of the twin boundaries. Moreover, The ductility of the twin-free nanowire is the highest of all and it grows with the increasing spacings of the twin boundaries for twinned nanowires. Besides, we find that the twin boundaries can be served as dislocation sources as well as the free surfaces and grain boundaries.

  18. Human Reliability Analysis in the U.S. Nuclear Power Industry: A Comparison of Atomistic and Holistic Methods

    SciTech Connect

    Ronald L. Boring; David I. Gertman; Jeffrey C. Joe; Julie L. Marble

    2005-09-01

    A variety of methods have been developed to generate human error probabilities for use in the US nuclear power industry. When actual operations data are not available, it is necessary for an analyst to estimate these probabilities. Most approaches, including THERP, ASEP, SLIM-MAUD, and SPAR-H, feature an atomistic approach to characterizing and estimating error. The atomistic approach is based on the notion that events and their causes can be decomposed and individually quantified. In contrast, in the holistic approach, such as found in ATHEANA, the analysis centers on the entire event, which is typically quantified as an indivisible whole. The distinction between atomistic and holistic approaches is important in understanding the nature of human reliability analysis quantification and the utility and shortcomings associated with each approach.

  19. Metasurface polarization splitter.

    PubMed

    Slovick, Brian A; Zhou, You; Yu, Zhi Gang; Kravchenko, Ivan I; Briggs, Dayrl P; Moitra, Parikshit; Krishnamurthy, Srini; Valentine, Jason

    2017-03-28

    Polarization beam splitters, devices that separate the two orthogonal polarizations of light into different propagation directions, are among the most ubiquitous optical elements. However, traditionally polarization splitters rely on bulky optical materials, while emerging optoelectronic and photonic circuits require compact, chip-scale polarization splitters. Here, we show that a rectangular lattice of cylindrical silicon Mie resonators functions as a polarization splitter, efficiently reflecting one polarization while transmitting the other. We show that the polarization splitting arises from the anisotropic permittivity and permeability of the metasurface due to the twofold rotational symmetry of the rectangular unit cell. The high polarization efficiency, low loss and low profile make these metasurface polarization splitters ideally suited for monolithic integration with optoelectronic and photonic circuits.This article is part of the themed issue 'New horizons for nanophotonics'.

  20. Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.

    PubMed

    Wang, Yong-Lei; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N; Laaksonen, Aatto

    2014-07-24

    We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions.

  1. Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA.

    PubMed

    Sutthibutpong, Thana; Harris, Sarah A; Noy, Agnes

    2015-06-09

    DNA molecular center-lines designed from atomistic-resolution structures are compared for the evaluation of the writhe in supercoiled DNA using molecular dynamics simulations of two sets of minicircles with 260 and 336 base pairs. We present a new method called WrLINE that systematically filters out local (i.e., subhelical turn) irregularities using a sliding-window averaged over a single DNA turn and that provides a measure of DNA writhe that is suitable for comparing atomistic resolution data with those obtained from measurements of the global molecular shape. In contrast, the contour traced by the base-pair origins defined by the 3DNA program largely overestimates writhe due to the helical periodicity of DNA. Nonetheless, this local modulation of the molecular axis emerges as an internal mechanism for the DNA to confront superhelical stress, where the adjustment between low and high twist is coupled to a high and low local periodicity, respectively, mimicking the different base-stacking conformational space of A and B canonical DNA forms.

  2. Atomistic and elastic analyses of defects and small structures. Annual report

    SciTech Connect

    Srolovitz, D.J.

    1995-11-01

    This past year, the authors have been working on several problems associated with defects in crystals and small structures. In one series of studies, they have been investigating the structure and energetics of surfaces as a function of surface orientation. One of the goals of their present research is to model non-topological defects in crystals and very small structures using elastic models as parameterized using atomistic calculations. In order to do this, they need to make sure that the atomistic and elastic models describe the same bulk system. To this end, they have developed a set of Embedded Atom Method interatomic potentials that produce an elastically isotopic perfect fcc crystal. In another project they evaluated the accuracy of the Free Energy Minimization Method. Another goal is to understand the effect of small system size on the behavior of materials. To that end, they have been performing simulations on the structure and thermodynamics of small spherical clusters of atoms and thin films, as a function of systems size. Recently, they have extended these calculations on small systems to alloys where appropriate focus is on surface segregation. Finally, they have been working to understand the effects of strain energy on the thermodynamics of a new class of highly distorted materials -- nested fullerenes.

  3. Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

    NASA Technical Reports Server (NTRS)

    Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

    2009-01-01

    Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

  4. Scaling of slip avalanches in sheared amorphous materials based on large-scale atomistic simulations

    NASA Astrophysics Data System (ADS)

    Zhang, Dansong; Dahmen, Karin A.; Ostoja-Starzewski, Martin

    2017-03-01

    Atomistic simulations of binary amorphous systems with over 4 million atoms are performed. Systems of two interatomic potentials of the Lennard-Jones type, LJ12-6 and LJ9-6, are simulated. The athermal quasistatic shearing protocol is adopted, where the shear strain is applied in a stepwise fashion with each step followed by energy minimization. For each avalanche event, the shear stress drop (Δ σ ), the hydrostatic pressure drop (Δ σh ), and the potential energy drop (Δ E ) are computed. It is found that, with the avalanche size increasing, the three become proportional to each other asymptotically. The probability distributions of avalanche sizes are obtained and values of scaling exponents fitted. In particular, the distributions follow a power law, P (Δ U )˜Δ U-τ , where Δ U is a measure of avalanche sizes defined based on shear stress drops. The exponent τ is 1.25 ±0.1 for the LJ12-6 systems, and 1.15 ±0.1 for the LJ9-6 systems. The value of τ for the LJ12-6 systems is consistent with that from an earlier atomistic simulation study by Robbins et al. [Phys. Rev. Lett. 109, 105703 (2012)], 10.1103/PhysRevLett.109.105703, but the fitted values of other scaling exponents differ, which may be because the shearing protocol used here differs from that in their study.

  5. Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

    DOE PAGES

    Neilson, James R.; McQueen, Tyrel M.

    2015-09-20

    With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

  6. Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

    SciTech Connect

    Neilson, James R.; McQueen, Tyrel M.

    2015-09-20

    With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atoms in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.

  7. Atomistic Mechanism of Plastic Deformation During Nano-indentation of Titanium Aluminide

    NASA Astrophysics Data System (ADS)

    Rino, Jose; Dasilva, Claudio

    2013-06-01

    The mechanisms governing defect nucleation in solids are of great interest in all material science branches. Atomistic computer simulations such as Molecular Dynamics (MD), has been providing more understanding of subsurface deformations, bringing out details of atomic structures and dynamics of defects within the material. In the present work we show the first simulation measurements within an atomistic resolution of the mechanical properties of titanium aluminide intermetallic compound (TiAl), which is a promising candidate for high temperature applications with remarkable properties, such as: attractive combination of low density, high melting temperature, high elastic modulus, and strength retention at elevated temperatures, besides its good creep properties. Through calculations of local pressure, local shear stress and spatial rearrangements of atoms beneath the indenter, it was possible to quantify the indentation damage on the structure. We have founded that prismatic dislocations mediate the emission and interaction of dislocations and the activated slip planes are associated with the Thompson tetrahedron. Furthermore, using the load-penetration depth response, we were able to estimate the elastic modulus and the hardness of the TiAl alloy. All our findings are in well agreement with experimental results.

  8. An atomistic model for cross-linked HNBR elastomers used in seals

    NASA Astrophysics Data System (ADS)

    Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

    2015-03-01

    Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

  9. Time scale bridging in atomistic simulation of slow dynamics: viscous relaxation and defect activation

    NASA Astrophysics Data System (ADS)

    Kushima, A.; Eapen, J.; Li, Ju; Yip, S.; Zhu, T.

    2011-08-01

    Atomistic simulation methods are known for timescale limitations in resolving slow dynamical processes. Two well-known scenarios of slow dynamics are viscous relaxation in supercooled liquids and creep deformation in stressed solids. In both phenomena the challenge to theory and simulation is to sample the transition state pathways efficiently and follow the dynamical processes on long timescales. We present a perspective based on the biased molecular simulation methods such as metadynamics, autonomous basin climbing (ABC), strain-boost and adaptive boost simulations. Such algorithms can enable an atomic-level explanation of the temperature variation of the shear viscosity of glassy liquids, and the relaxation behavior in solids undergoing creep deformation. By discussing the dynamics of slow relaxation in two quite different areas of condensed matter science, we hope to draw attention to other complex problems where anthropological or geological-scale time behavior can be simulated at atomic resolution and understood in terms of micro-scale processes of molecular rearrangements and collective interactions. As examples of a class of phenomena that can be broadly classified as materials ageing, we point to stress corrosion cracking and cement setting as opportunities for atomistic modeling and simulations.

  10. A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra.

    PubMed

    Alves, Cassio; Iacovelli, Federico; Falconi, Mattia; Cardamone, Francesca; Morozzo Della Rocca, Blasco; de Oliveira, Cristiano L P; Desideri, Alessandro

    2016-05-23

    A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures.

  11. Intergranular fracture in UO2: derivation of traction-separation law from atomistic simulations

    SciTech Connect

    Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

    2013-10-01

    In this study, the intergranular fracture behavior of UO2 was studied by molecular dynamics simulations using the Basak potential. In addition, the constitutive traction-separation law was derived from atomistic data using the cohesive-zone model. In the simulations a bicrystal model with the (100) symmetric tilt E5 grain boundaries was utilized. Uniaxial tension along the grain boundary normal was applied to simulate Mode-I fracture. The fracture was observed to propagate along the grain boundary by micro-pore nucleation and coalescence, giving an overall intergranular fracture behavior. Phase transformations from the Fluorite to the Rutile and Scrutinyite phases were identified at the propagating crack tips. These new phases are metastable and they transformed back to the Fluorite phase at the wake of crack tips as the local stress concentration was relieved by complete cracking. Such transient behavior observed at atomistic scale was found to substantially increase the energy release rate for fracture. Insertion of Xe gas into the initial notch showed minor effect on the overall fracture behavior.

  12. Mapping Strain-rate Dependent Dislocation-Defect Interactions by Atomistic Simulations

    SciTech Connect

    Fan, Yue; Osetskiy, Yury N; Yip, Sidney; Yildiz-Botterud, Bilge

    2013-01-01

    Probing the mechanisms of defect-defect interactions at strain rates lower than 106 s-1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose a novel atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation-defect interactions at virtually any strain rate, exemplified within 10-7 to 107 s-1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIA) under shear deformation. Using an activation-relaxation algorithm (1), we uncover a unique strain-rate dependent trigger mechanism that allows the SIA cluster to be absorbed during the process leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain-rate and temperature. Our predictions of a crossover from a defect recovery at the low strain rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s-1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed.

  13. Mapping strain rate dependence of dislocation-defect interactions by atomistic simulations

    PubMed Central

    Fan, Yue; Osetskiy, Yuri N.; Yip, Sidney; Yildiz, Bilge

    2013-01-01

    Probing the mechanisms of defect–defect interactions at strain rates lower than 106 s−1 is an unresolved challenge to date to molecular dynamics (MD) techniques. Here we propose an original atomistic approach based on transition state theory and the concept of a strain-dependent effective activation barrier that is capable of simulating the kinetics of dislocation–defect interactions at virtually any strain rate, exemplified within 10−7 to 107 s−1. We apply this approach to the problem of an edge dislocation colliding with a cluster of self-interstitial atoms (SIAs) under shear deformation. Using an activation–relaxation algorithm [Kushima A, et al. (2009) J Chem Phys 130:224504], we uncover a unique strain-rate–dependent trigger mechanism that allows the SIA cluster to be absorbed during the process, leading to dislocation climb. Guided by this finding, we determine the activation barrier of the trigger mechanism as a function of shear strain, and use that in a coarse-graining rate equation formulation for constructing a mechanism map in the phase space of strain rate and temperature. Our predictions of a crossover from a defect recovery at the low strain-rate regime to defect absorption behavior in the high strain-rate regime are validated against our own independent, direct MD simulations at 105 to 107 s−1. Implications of the present approach for probing molecular-level mechanisms in strain-rate regimes previously considered inaccessible to atomistic simulations are discussed. PMID:24114271

  14. New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

    NASA Technical Reports Server (NTRS)

    Saether, E.; Yamakov, V.; Glaessgen, E.

    2008-01-01

    A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

  15. Atomistic theory of excitonic fine structure in InAs/InP nanowire quantum dot molecules

    NASA Astrophysics Data System (ADS)

    Świderski, M.; Zieliński, M.

    2017-03-01

    Nanowire quantum dots have peculiar electronic and optical properties. In this work we use atomistic tight binding to study excitonic spectra of artificial molecules formed by a double nanowire quantum dot. We demonstrate a key role of atomistic symmetry and nanowire substrate orientation rather than cylindrical shape symmetry of a nanowire and a molecule. In particular for [001 ] nanowire orientation we observe a nonvanishing bright exciton splitting for a quasimolecule formed by two cylindrical quantum dots of different heights. This effect is due to interdot coupling that effectively reduces the overall symmetry, whereas single uncoupled [001 ] quantum dots have zero fine structure splitting. We found that the same double quantum dot system grown on [111 ] nanowire reveals no excitonic fine structure for all considered quantum dot distances and individual quantum dot heights. Further we demonstrate a pronounced, by several orders of magnitude, increase of the dark exciton optical activity in a quantum dot molecule as compared to a single quantum dot. For [111 ] systems we also show spontaneous localization of single particle states in one of nominally identical quantum dots forming a molecule, which is mediated by strain and origins from the lack of the vertical inversion symmetry in [111 ] nanostructures of overall C3 v symmetry. Finally, we study lowering of symmetry due to alloy randomness that triggers nonzero excitonic fine structure and the dark exciton optical activity in realistic nanowire quantum dot molecules of intermixed composition.

  16. Atomistic potentials based energy flux integral criterion for dynamic adiabatic shear banding

    NASA Astrophysics Data System (ADS)

    Xu, Yun; Chen, Jun

    2015-02-01

    The energy flux integral criterion based on atomistic potentials within the framework of hyperelasticity-plasticity is proposed for dynamic adiabatic shear banding (ASB). System Helmholtz energy decomposition reveals that the dynamic influence on the integral path dependence is originated from the volumetric strain energy and partial deviatoric strain energy, and the plastic influence only from the rest part of deviatoric strain energy. The concept of critical shear banding energy is suggested for describing the initiation of ASB, which consists of the dynamic recrystallization (DRX) threshold energy and the thermal softening energy. The criterion directly relates energy flux to the basic physical processes that induce shear instability such as dislocation nucleations and multiplications, without introducing ad-hoc parameters in empirical constitutive models. It reduces to the classical path independent J-integral for quasi-static loading and elastic solids. The atomistic-to-continuum multiscale coupling method is used to simulate the initiation of ASB. Atomic configurations indicate that DRX induced microstructural softening may be essential to the dynamic shear localization and hence the initiation of ASB.

  17. Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

    PubMed Central

    Plattner, Nuria; Noé, Frank

    2015-01-01

    Understanding the structural mechanisms of protein–ligand binding and their dependence on protein sequence and conformation is of fundamental importance for biomedical research. Here we investigate the interplay of conformational change and ligand-binding kinetics for the serine protease Trypsin and its competitive inhibitor Benzamidine with an extensive set of 150 μs molecular dynamics simulation data, analysed using a Markov state model. Seven metastable conformations with different binding pocket structures are found that interconvert at timescales of tens of microseconds. These conformations differ in their substrate-binding affinities and binding/dissociation rates. For each metastable state, corresponding solved structures of Trypsin mutants or similar serine proteases are contained in the protein data bank. Thus, our wild-type simulations explore a space of conformations that can be individually stabilized by adding ligands or making suitable changes in protein sequence. These findings provide direct evidence of conformational plasticity in receptors. PMID:26134632

  18. Effect of the Initial Load Parameters on the K-shell Output of Al Planar Wire Arrays Operating in the Microsecond Implosion Regime

    SciTech Connect

    Shishlov, A.; Chaikovsky, S.; Fedunin, A.; Fursov, F.; Kokshenev, V.; Kurmaev, N.; Labetsky, A.; Oreshkin, V.; Rousskikh, A.; Labetskaya, N.

    2009-01-21

    A set of microsecond implosion experiments was carried on the GIT-12 generator to study the radiative performance of Al planar wire arrays. The load parameters such as a wire diameter, a gap between the wires, the number of wires, and the total planar wire mass and width were varied during the experiments, however the implosion time and the peak implosion current were almost the same for all load configurations. This ensured equal energy deposition to the plasma due to kinetic mechanisms for all load configurations. Two implosion regimes with the implosion times of 1050 ns and 850 ns were investigated. The experimental data on the K-shell radiation yield and power at varying load parameters are presented.

  19. A 10 kHz Sub-microsecond High-voltage Pulse Generator using SI Thyristor for Micro-plasma Jets Generation

    NASA Astrophysics Data System (ADS)

    Jia, Li; Sakai, Natsuko; Watanabe, Masato; Hotta, Eiki

    Employing an inductive energy storage system, a stable and high-repetitive sub-microsecond pulse generator is developed for generation of micro-plasma jets. Its operation is based on the current interruption by an SI Thyristor, coupled with MOSFETs connected in series. While being operated without loads, the pulse generator can reliably generate high-voltage pulses of ∼20 kV with pulse duration of about 400 ns at the repetition rate up to 10 kHz. At the operating frequency of 1 kHz, a maximal energy transfer efficiency of ∼57 % has been obtained with 3 kΩ resistor as a dummy load. Driven by this pulse generator, a 6 mm long N2 plasma plume at atmospheric pressure was successfully produced.

  20. Photographic studies of laser-induced bubble formation in absorbing liquids and on submerged targets: implications for drug delivery with microsecond laser pulses

    NASA Astrophysics Data System (ADS)

    Shangguan, HanQun; Casperson, Lee W.; Paisley, Dennis L.; Prahl, Scott A.

    1998-08-01

    Pulsed laser ablation of blood clots in a fluid-filled blood vessel is accompanied by an explosive evaporation process. The resulting vapor bubble rapidly expands and collapses to disrupt the thrombus (blood clot). The hydrodynamic pressures following the bubble expansion and collapse can also be used as a driving force to deliver clot-dissolving agents into thrombus for enhancement of laser thrombolysis. Thus, the laser-induced bubble formation plays an important role in the thrombus removal process. We investigate the effects of boundary configurations and materials on bubble formation with time-resolved flash photography and high- speed photography. Potential applications in drug delivery using microsecond laser pulses are then discussed.

  1. An all-solid-state microsecond-range quasi-square pulse generator based on fractional-turn ratio saturable pulse transformer and anti-resonance network

    NASA Astrophysics Data System (ADS)

    Chen, Rong; Yang, Jianhua; Cheng, Xinbing; Pan, Zilong

    2017-03-01

    High voltage pulse generators are widely applied in a number of fields. Defense and industrial applications stimulated intense interests in the area of pulsed power technology towards the system with high power, high repetition rate, solid state characteristics, and compact structure. An all-solid-state microsecond-range quasi-square pulse generator based on a fractional-turn ratio saturable pulse transformer and anti-resonance network is proposed in this paper. This generator consists of a charging system, a step-up system, and a modulating system. In this generator, the fractional-turn ratio saturable pulse transformer is the key component since it acts as a step-up transformer and a main switch during the working process. Demonstrative experiments show that if the primary storage capacitors are charged to 400 V, a quasi-square pulse with amplitude of about 29 kV can be achieved on a 3500 Ω resistive load, as well as the pulse duration (full width at half maximum) of about 1.3 μs. Preliminary repetition rate experiments are also carried out, which indicate that this pulse generator could work stably with the repetition rates of 30 Hz and 50 Hz. It can be concluded that this kind of all-solid-state microsecond-range quasi-square pulse generator can not only lower both the operating voltage of the primary windings and the saturable inductance of the secondary windings, thus ideally realizing the magnetic switch function of the fractional-turn ratio saturable pulse transformer, but also achieve a quasi-square pulse with high quality and fixed flat top after the modulation of a two-section anti-resonance network. This generator can be applied in areas of large power microwave sources, sterilization, disinfection, and wastewater treatment.

  2. An all-solid-state microsecond-range quasi-square pulse generator based on fractional-turn ratio saturable pulse transformer and anti-resonance network.

    PubMed

    Chen, Rong; Yang, Jianhua; Cheng, Xinbing; Pan, Zilong

    2017-03-01

    High voltage pulse generators are widely applied in a number of fields. Defense and industrial applications stimulated intense interests in the area of pulsed power technology towards the system with high power, high repetition rate, solid state characteristics, and compact structure. An all-solid-state microsecond-range quasi-square pulse generator based on a fractional-turn ratio saturable pulse transformer and anti-resonance network is proposed in this paper. This generator consists of a charging system, a step-up system, and a modulating system. In this generator, the fractional-turn ratio saturable pulse transformer is the key component since it acts as a step-up transformer and a main switch during the working process. Demonstrative experiments show that if the primary storage capacitors are charged to 400 V, a quasi-square pulse with amplitude of about 29 kV can be achieved on a 3500 Ω resistive load, as well as the pulse duration (full width at half maximum) of about 1.3 μs. Preliminary repetition rate experiments are also carried out, which indicate that this pulse generator could work stably with the repetition rates of 30 Hz and 50 Hz. It can be concluded that this kind of all-solid-state microsecond-range quasi-square pulse generator can not only lower both the operating voltage of the primary windings and the saturable inductance of the secondary windings, thus ideally realizing the magnetic switch function of the fractional-turn ratio saturable pulse transformer, but also achieve a quasi-square pulse with high quality and fixed flat top after the modulation of a two-section anti-resonance network. This generator can be applied in areas of large power microwave sources, sterilization, disinfection, and wastewater treatment.

  3. Subnanosecond polarized fluorescence photobleaching: rotational diffusion of acetylcholine receptors on developing muscle cells.

    PubMed Central

    Yuan, Y; Axelrod, D

    1995-01-01

    Polarized fluorescence recovery after photobleaching (PFRAP) is a technique for measuring the rate of rotational motion of biomolecules on living, nondeoxygenated cells with characteristic times previously ranging from milliseconds to many seconds. Although very broad, that time range excludes the possibility of quantitatively observing freely rotating membrane protein monomers that typically should have a characteristic decay time of only several microseconds. This report describes an extension of the PFRAP technique to a much shorter time scale. With this new system, PFRAP experiments can be conducted with sample time as short as 0.4 microseconds and detection of possible characteristic times of less than 2 microseconds. The system is tested on rhodamine-alpha-bungarotoxin-labeled acetylcholine receptors (AChRs) on myotubes grown in primary cultures of embryonic rat muscle, in both endogenously clustered and nonclustered regions of AChR distribution. It is found that approximately 40% of the AChRs in nonclustered regions undergoes rotational diffusion fast enough to possibly arise from unrestricted monomer Brownian motion. The AChRs in clusters, on the other hand, are almost immobile. The effects of rat embryonic brain extract (which contains AChR aggregating factors) on the myotube AChR were also examined by the fast PFRAP system. Brain extract is known to abolish the presence of endogenous clusters and to induce the formation of new clusters. It is found here that rotational diffusion of AChR in the extract-induced clusters is as slow as that in endogenous clusters on untreated cells but that rotational diffusion in the nonclustered regions of extract-treated myotubes remains rapid. Images FIGURE 3 PMID:8527682

  4. A Translational Polarization Rotator

    NASA Technical Reports Server (NTRS)

    Chuss, David T.; Wollack, Edward J.; Pisano, Giampaolo; Ackiss, Sheridan; U-Yen, Kongpop; Ng, Ming wah

    2012-01-01

    We explore a free-space polarization modulator in which a variable phase introduction between right- and left-handed circular polarization components is used to rotate the linear polarization of the outgoing beam relative to that of the incoming beam. In this device, the polarization states are separated by a circular polarizer that consists of a quarter-wave plate in combination with a wire grid. A movable mirror is positioned behind and parallel to the circular polarizer. As the polarizer-mirror distance is separated, an incident liear polarization will be rotated through an angle that is proportional to the introduced phase delay. We demonstrate a prototype device that modulates Stokes Q and U over a 20% bandwidth.

  5. Polarized Light Corridor Demonstrations.

    ERIC Educational Resources Information Center

    Davies, G. R.

    1990-01-01

    Eleven demonstrations of light polarization are presented. Each includes a brief description of the apparatus and the effect demonstrated. Illustrated are strain patterns, reflection, scattering, the Faraday Effect, interference, double refraction, the polarizing microscope, and optical activity. (CW)

  6. Polarization at SLAC

    SciTech Connect

    Woods, M.

    1995-01-01

    A highly polarized electron beam is a key feature. for the Current physics program at SLAC. An electron beam polarization of 80% can now be routinely achieved for typically 5000 hours of machine operation per year. Two main Physics programs utilize the polarized beam. Fixed target experiments in End Station A study the collision of polarized electrons with polarized nuclear targets to elucidate the spin structure of the nucleon and to provide an important test of QCD. Using the SLAC Linear Collider, collisions of polarized electrons with unpolarized positrons allow precise measurements of parity violation in the Z-fermion couplings and provide a very precise measurement of tile weak mixing angle. This paper discusses polarized beam operation at SLAC, and gives an overview of the polarized physics program.

  7. Calculation of polarization effects

    SciTech Connect

    Chao, A.W.

    1983-09-01

    Basically there are two areas of accelerator applications that involve beam polarization. One is the acceleration of a polarized beam (most likely a proton beam) in a synchrotron. Another concerns polarized beams in an electron storage ring. In both areas, numerical techniques have been very useful.

  8. Partial polarizer filter

    NASA Technical Reports Server (NTRS)

    Title, A. M. (Inventor)

    1978-01-01

    A birefringent filter module comprises, in seriatum. (1) an entrance polarizer, (2) a first birefringent crystal responsive to optical energy exiting the entrance polarizer, (3) a partial polarizer responsive to optical energy exiting the first polarizer, (4) a second birefringent crystal responsive to optical energy exiting the partial polarizer, and (5) an exit polarizer. The first and second birefringent crystals have fast axes disposed + or -45 deg from the high transmitivity direction of the partial polarizer. Preferably, the second crystal has a length 1/2 that of the first crystal and the high transmitivity direction of the partial polarizer is nine times as great as the low transmitivity direction. To provide tuning, the polarizations of the energy entering the first crystal and leaving the second crystal are varied by either rotating the entrance and exit polarizers, or by sandwiching the entrance and exit polarizers between pairs of half wave plates that are rotated relative to the polarizers. A plurality of the filter modules may be cascaded.

  9. Playing with Polarizers.

    ERIC Educational Resources Information Center

    Hecht, Jeff

    1991-01-01

    Discussed is how polarized sunglasses block glare, help spot subtle differences in surfaces, and give a clearer view under water. Information on unpolarized and polarized light is provided. The reasons causing glare to occur and how polarizers decrease glare are discussed. (KR)

  10. Silicon Raman polarizer.

    PubMed

    Kozlov, Victor V; Wabnitz, Stefan

    2012-02-15

    We theoretically investigate the polarization properties of Raman amplifiers based on silicon-on-insulator waveguides, and show that it is possible to realize a waveguide Raman polarizer. The Raman polarizer is a special type of Raman amplifier with the property of producing an amplified and highly repolarized beam when it is fed by a relatively weak and unpolarized signal.

  11. Graphing Polar Curves

    ERIC Educational Resources Information Center

    Lawes, Jonathan F.

    2013-01-01

    Graphing polar curves typically involves a combination of three traditional techniques, all of which can be time-consuming and tedious. However, an alternative method--graphing the polar function on a rectangular plane--simplifies graphing, increases student understanding of the polar coordinate system, and reinforces graphing techniques learned…

  12. Physics with Polarized Nuclei.

    ERIC Educational Resources Information Center

    Thompson, William J.; Clegg, Thomas B.

    1979-01-01

    Discusses recent advances in polarization techniques, specifically those dealing with polarization of atomic nuclei, and how polarized beams and targets are produced. These techniques have greatly increased the scope of possible studies, and provided the tools for testing fundamental symmetries and the spin dependence of nuclear forces. (GA)

  13. Polar Ozone Workshop. Abstracts

    NASA Technical Reports Server (NTRS)

    Aikin, Arthur C.

    1988-01-01

    Results of the proceedings of the Polar Ozone Workshop held in Snowmass, CO, on May 9 to 13, 1988 are given. Topics covered include ozone depletion, ozonometry, polar meteorology, polar stratospheric clouds, remote sensing of trace gases, atmospheric chemistry and dynamical simulations.

  14. Polarity at Many Levels

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2004-01-01

    An attempt is made to find how polarity arises and is maintained, which is a central issue in development. It is a fundamental attribute of living things and cellular polarity is also important in the development of multicellular organisms and controversial new work indicates that polarization in mammals may occur much earlier than previously…

  15. Polarization feedback laser stabilization

    DOEpatents

    Esherick, Peter; Owyoung, Adelbert

    1988-01-01

    A system for locking two Nd:YAG laser oscillators includes an optical path for feeding the output of one laser into the other with different polarizations. Elliptical polarization is incorporated into the optical path so that the change in polarization that occurs when the frequencies coincide may be detected to provide a feedback signal to control one laser relative to the other.

  16. High energy, 1572.3 nm pulses for CO2 LIDAR from a polarization-maintaining, very-large-mode-area, Er-doped fiber amplifier.

    PubMed

    Nicholson, J W; DeSantolo, A; Yan, M F; Wisk, P; Mangan, B; Puc, G; Yu, A W; Stephen, M A

    2016-08-22

    We demonstrate the first polarization-maintaining, very-large-mode-area, Er-doped fiber amplifier with ~1100 μm2 effective area. The amplifier is core pumped by a Raman fiber laser and is used to generate single-frequency, one-microsecond, pulses with pulse energy of 541 μJ, peak power of 700 W, M2 of 1.1, and polarization extinction > 20 dB. The amplifier operates at 1572.3 nm, a wavelength useful for trace atmospheric CO2 detection.

  17. Influence of random defects on the mechanical behavior of carbon nanotubes through atomistic simulation

    NASA Astrophysics Data System (ADS)

    Lu, Qiang

    Carbon nanotubes (CNTs) have drawn great interest and shown great promise in recent years in the areas of composite materials, sensors, and small electronic devices owing in a large part to their extraordinary mechanical properties. Yet an enormous scatter is observed in available laboratory results on the stiffness and strength of CNTs. Surface defects including vacancies, pentagon and heptagons have been commonly observed in CNT samples, and are found to have significant influence on the mechanics of CNTs. However, any link between the randomness in CNTs mechanical properties and CNT defects has not been investigated systematically before. Moreover, the fracture of CNTs due to mechanical loading is an important issue likely to affect the durability and reliability of CNT-based materials and devices; yet, based on the author's knowledge, the fracture resistance of CNTs has not been quantified before. This dissertation, trying to build up these missing links, studies the effects of randomly distributed vacancies and Stone-Wales (SW or 5-7-7-5) defects on the mechanical properties of single-walled nanotubes (SWNTs) using the technique of atomistic simulation (AS), and quantifies the fracture resistance of zigzag SWNTs with fracture mechanics concepts. Basic principles and key issues of atomistic simulation and multiscale modeling are reviewed. A series of displacement controlled tensile tests of CNTs are modeled with atomistic simulation. Armchair and zigzag SWNTs, with and without defects are studied. A modified Morse potential is adopted to model the interatomic forces. Time histories of energies, displacements and forces are generated from the simulations, and three mechanical properties---stiffness, ultimate strength and ultimate strain---are further calculated. Effects of loading speed and geometry are discussed. Further details of CNT structure changes, especially the evolution of defects during the loading process are monitored. In studying the fracture

  18. Finite element analysis of an atomistically derived cohesive model for brittle fracture

    NASA Astrophysics Data System (ADS)

    Lloyd, J. T.; Zimmerman, J. A.; Jones, R. E.; Zhou, X. W.; McDowell, D. L.

    2011-09-01

    In order to apply information from molecular dynamics (MD) simulations in problems governed by engineering length and time scales, a coarse graining methodology must be used. In previous work by Zhou et al (2009 Acta Mater. 57 4671-86), a traction-separation cohesive model was developed using results from MD simulations with atomistic-to-continuum measures of stress and displacement. Here, we implement this cohesive model within a combined finite element/cohesive surface element framework (referred to as a finite element approach or FEA), and examine the ability for the atomistically informed FEA to directly reproduce results from MD. We find that FEA shows close agreement of both stress and crack opening displacement profiles at the cohesive interface, although some differences do exist that can be attributed to the stochastic nature of finite temperature MD. The FEA methodology is then used to study slower loading rates that are computationally expensive for MD. We find that the crack growth process initially exhibits a rate-independent relationship between crack length and boundary displacement, followed by a rate-dependent regime where, at a given amount of boundary displacement, a lower applied strain rate produces a longer crack length. Our method is also extended to larger length scales by simulating a compact tension fracture-mechanics specimen with sub-micrometer dimensions. Such a simulation shows a computational speedup of approximately four orders of magnitude over conventional atomistic simulation, while exhibiting the expected fracture-mechanics response. Finally, differences between FEA and MD are explored with respect to ensemble and temperature effects in MD, and their impact on the cohesive model and crack growth behavior. These results enable us to make several recommendations to improve the methodology used to derive cohesive laws from MD simulations. In light of this work, which has critical implications for efforts to derive continuum laws

  19. A hybrid atomistic electrodynamics-quantum mechanical approach for simulating surface-enhanced Raman scattering.

    PubMed

    Payton, John L; Morton, Seth M; Moore, Justin E; Jensen, Lasse

    2014-01-21

    Surface-enhanced Raman scattering (SERS) is a technique that has broad implications for biological and chemical sensing applications by providing the ability to simultaneously detect and identify a single molecule. The Raman scattering of molecules adsorbed on metal nanoparticles can be enhanced by many orders of magnitude. These enhancements stem from a twofold mechanism: an electromagnetic mechanism (EM), which is due to the enhanced local field near the metal surface, and a chemical mechanism (CM), which is due to the adsorbate specific interactions between the metal surface and the molecules. The local field near the metal surface can be significantly enhanced due to the plasmon excitation, and therefore chemists generally accept that the EM provides the majority of the enhancements. While classical electrodynamics simulations can accurately simulate the local electric field around metal nanoparticles, they offer few insights into the spectral changes that occur in SERS. First-principles simulations can directly predict the Raman spectrum but are limited to small metal clusters and therefore are often used for understanding the CM. Thus, there is a need for developing new methods that bridge the electrodynamics simulations of the metal nanoparticle and the first-principles simulations of the molecule to facilitate direct simulations of SERS spectra. In this Account, we discuss our recent work on developing a hybrid atomistic electrodynamics-quantum mechanical approach to simulate SERS. This hybrid method is called the discrete interaction model/quantum mechanics (DIM/QM) method and consists of an atomistic electrodynamics model of the metal nanoparticle and a time-dependent density functional theory (TDDFT) description of the molecule. In contrast to most previous work, the DIM/QM method enables us to retain a detailed atomistic structure of the nanoparticle and provides a natural bridge between the electronic structure methods and the macroscopic

  20. Predictive atomistic simulations of electronic properties of realistic nanoscale devices: A multiscale modeling approach

    NASA Astrophysics Data System (ADS)

    Vedula, Ravi Pramod Kumar

    Scaling of CMOS towards its ultimate limits, where quantum effects and atomistic variability due to fabrication, along with recent emphasis on heterogeneous integration of non-digital devices for increasing the functional diversification presents us with fundamentally new challenges. A comprehensive understanding of design and operation of these nanoscale transistors, and other electronic devices like RF-MEMS, requires an insight into their electronic and mechanical properties that are strongly influenced by underlying atomic structure. Hence, continuum descriptions of materials and use of empirical models at these scales become questionable. This increase in complexity of electronic devices necessitates an understanding at a more fundamental level to accurately predict the performance and reliability of these devices. The objective of this thesis is to outline the application of multiscale predictive modeling methods, ranging from atoms to devices, for addressing these challenges. This capability is demonstrated using two examples: characterization of (i) dielectric charging in RF-MEMS, and (ii) transport properties of Ge-nanofins. For characterizing the dielectric charging phenomenon, a continuum dielectric charging model, augmented by first principles informed trap distributions, is used to predict current transient measurements across a broad range of voltages and temperatures. These simulations demonstrate using ab initio informed model not only reduces the empiricism (number of adjustable parameters) in the model but also leads to a more accurate model over a broad range of operating conditions, and enable the precise determination of additional material parameters. These atomistic calculations also provide detailed information about the nature of charge traps and their trapping mechanisms that are not accessible experimentally; such information could prove invaluable in defect engineering. The second problem addresses the effect of the in-homogeneous strain

  1. Nonclassical Crystal Growth as Explanation for the Riddle of Polarity in Centrosymmetric Glycine Crystals.

    PubMed

    Meirzadeh, Elena; Sapir, Liel; Cohen, Hagai; Cohen, Sidney R; Ehre, David; Harries, Daniel; Lahav, Meir; Lubomirsky, Igor

    2016-11-09

    The riddle of anomalous polar behavior of the centrosymmetric crystal of α-glycine is resolved by the discovery of a polar, several hundred nanometer thick hydrated layer, created at the {010} faces during crystal growth. This layer was detected by two independent pyroelectric analytical methods: (i) periodic temperature change technique (Chynoweth) at ambient conditions and (ii) contactless X-ray photoelectron spectroscopy under ultrahigh vacuum. The total polarization of the surface layer is extremely large, yielding ≈1 μC·cm(-2), and is preserved in ultrahigh vacuum, but disappears upon heating to 100 °C. Molecular dynamics simulations corroborate the formation of polar hydrated layers at the sub-microsecond time scale, however with a thickness of only several nanometers, not several hundred. This inconsistency might be reconciled by invoking a three-step nonclassical crystal growth mechanism comprising (i) docking of clusters from the supersaturated solution onto the evolving crystal, (ii) surface recognition and polar induction, and (iii) annealing and dehydration, followed by site-selective recrystallization.

  2. The Physics of Polarization

    NASA Astrophysics Data System (ADS)

    Landi Degl'Innocenti, Egidio

    2015-10-01

    The introductory lecture that has been delivered at this Symposium is a condensed version of an extended course held by the author at the XII Canary Island Winter School from November 13 to November 21, 2000. The full series of lectures can be found in Landi Degl'Innocenti (2002). The original reference is organized in 20 Sections that are here itemized: 1. Introduction, 2. Description of polarized radiation, 3. Polarization and optical devices: Jones calculus and Muller matrices, 4. The Fresnel equations, 5. Dichroism and anomalous dispersion, 6. Polarization in everyday life, 7. Polarization due to radiating charges, 8. The linear antenna, 9. Thomson scattering, 10. Rayleigh scattering, 11. A digression on Mie scattering, 12. Bremsstrahlung radiation, 13. Cyclotron radiation, 14. Synchrotron radiation, 15. Polarization in spectral lines, 16. Density matrix and atomic polarization, 17. Radiative transfer and statistical equilibrium equations, 18. The amplification condition in polarized radiative transfer, and 19. Coupling radiative transfer and statistical equilibrium equations.

  3. Polarization effects. Volume 2

    SciTech Connect

    Courant, E.

    1981-01-01

    The use of polarized proton beams in ISABELLE is important for several general reasons: (1) With a single longitudinally polarized proton beam, effects involving parity violation can be identified and hence processes involving weak interactions can be separated from those involving strong and electromagnetic interactions. (2) Spin effects are important in the strong interactions and can be useful for testing QCD. The technique for obtaining polarized proton beams in ISABELLE appears promising, particularly in view of the present development of a polarized proton beam for the AGS. Projections for the luminosity in ISABELLE for collisions of polarized protons - one or both beams polarized with longitudinal or transverse polarization - range from 1/100 to 1 times the luminosity for unpolarized protons.

  4. Circular Polarization in AGNs: Polarity and Spectra

    NASA Astrophysics Data System (ADS)

    Aller, M. F.; Aller, H. D.; Plotkin, R. M.

    2005-12-01

    Circular polarization (Stokes V) observations potentially provide information on the nature and origin of the underlying magnetic fields in AGNs. We have been systematically monitoring a group of sources with detectable circular polarization (V>0.1 percent, a level set by the instrumental polarization of our system) in all 4 Stokes parameters at 8.0 and 4.8 GHz since 2000, and also at 14.5 GHz since November 2003, with the University of Michigan prime focus paraboloid antenna. These data are compared with historical observations obtained with the same instrument at 8.0 and 4.8 GHz extending back to 1978. Specific goals are to study the temporal spectral behavior of Stokes V and its relation to variability in total flux and linear polarization, and to investigate the question of polarity stability on decade-long time scales using data obtained with the same instrumentation and at the same frequencies. The data are consistent with linear-to-circular mode conversion in partially opaque regions of the source. We find examples of polarity changes with time at one or more frequencies associated with outbursts in total flux and linear polarization, and polarity differences within the 3 frequencies at a single epoch in one case, 3C 279. Such behavior argues against the notion that the sign of Stokes V is a simple tracer of the net flow of magnetic energy from the central engine to the jet or an indicator of the direction of rotation of the spinning central black hole/accretion disk via the winding up of the initial seed magnetic field. This work was supported in part by NSF grant AST-0307629 and by funds from the University of Michigan.

  5. Rate dependence of grain boundary sliding via time-scaling atomistic simulations

    NASA Astrophysics Data System (ADS)

    Hammami, Farah; Kulkarni, Yashashree

    2017-02-01

    Approaching experimentally relevant strain rates has been a long-standing challenge for molecular dynamics method which captures phenomena typically on the scale of nanoseconds or at strain rates of 107 s-1 and higher. Here, we use grain boundary sliding in nanostructures as a paradigmatic problem to investigate rate dependence using atomistic simulations. We employ a combination of time-scaling computational approaches, including the autonomous basin climbing method, the nudged elastic band method, and kinetic Monte Carlo, to access strain rates ranging from 0.5 s-1 to 107 s-1. Combined with a standard linear solid model for viscoelastic behavior, our simulations reveal that grain boundary sliding exhibits noticeable rate dependence only below strain rates on the order of 10 s-1 but is rate independent and consistent with molecular dynamics at higher strain rates.

  6. Fully atomistic molecular dynamics simulation of nanosilica-filled crosslinked polybutadiene

    NASA Astrophysics Data System (ADS)

    Pavlov, Alexander S.; Khalatur, Pavel G.

    2016-06-01

    We report on the first fully atomistic simulation of sulfur-crosslinked cis-1,4-polybutadiene (PB) rubbers, both unfilled and nanosilica-filled. A well-integrated network is built by crosslinking the coarse-grained precursor PB chains. The initial configurations for subsequent molecular dynamics simulations are obtained by reverse mapping of well-equilibrated coarse-grained systems. Thermal and mechanical properties of the PB-based elastomers are predicted in reasonable agreement with experiment. The inclusion of silica nanoparticles into the model rubber increases the glass transition temperature and elastic modulus. Under tensile loading conditions, the formation of structural defects (microcavities) within the polymer bulk is observed for nanocomposite at the elastomer/nanoparticle interfaces.

  7. An Analysis of Crystal Cleavage in the Passage from Atomistic Models to Continuum Theory

    NASA Astrophysics Data System (ADS)

    Friedrich, Manuel; Schmidt, Bernd

    2015-07-01

    We study the behavior of brittle atomistic models in general dimensions under uniaxial tension and investigate the system for critical fracture loads. We rigorously prove that in the discrete-to-continuum limit the minimal energy satisfies a particular cleavage law with quadratic response to small boundary displacements followed by a sharp constant cut-off beyond some critical value. Moreover, we show that the minimal energy is attained by homogeneous elastic configurations in the subcritical case and that beyond critical loading cleavage along specific crystallographic hyperplanes is energetically favorable. In particular, our results apply to mass spring models with full nearest and next-to-nearest pair interactions and provide the limiting minimal energy and minimal configurations.

  8. Study of the embedded atom method of atomistic calculations for metals and alloys

    SciTech Connect

    Johnson, R.A.

    1990-10-01

    Two projects were completed in the past year. The stability of a series of binary alloys was calculated using the embedded-atom method (EAM) with an analytic form for two-body potentials derived previously. Both disordered alloys and intermetallic compounds with the L1{sub 0} and L1{sub 2} structures were studied. The calculated heats of solution of alloys of Cu, Ag, Au, Ni, and Pt were satisfactory, while results for alloys containing Pd were too high. Atomistic calculations using the EAM were also carried out for point defects in hcp metals. By comparison with results in the literature, it was found that many body effects from the EAM significantly alter predicted physical properties of hcp metals. For example, the EAM calculations yield anisotropic vacancy diffusion with greater vacancy mobility in the basal plane, and imply that diffusion will start at a lower fraction of the melting temperature.

  9. Atomistic Modeling of Quaternary Alloys: Ti and Cu in NiAl

    NASA Technical Reports Server (NTRS)

    Bozzolo, Guillermo; Mosca, Hugo O.; Wilson, Allen W.; Noebe, Ronald D.; Garces, Jorge E.

    2002-01-01

    The change in site preference in NiAl(Ti,Cu) alloys with concentration is examined experimentally via ALCHEMI and theoretically using the Bozzolo-Ferrante-Smith (BFS) method for alloys. Results for the site occupancy of Ti and Cu additions as a function of concentration are determined experimentally for five alloys. These results are reproduced with large-scale BFS-based Monte Carlo atomistic simulations. The original set of five alloys is extended to 25 concentrations, which are modeled by means of the BFS method for alloys, showing in more detail the compositional range over which major changes in behavior occur. A simple but powerful approach based on the definition of atomic local environments also is introduced to describe energetically the interactions between the various elements and therefore to explain the observed behavior.

  10. Atomistic Simulation of the Size and Orientation Dependences of Thermal Conductivity in GaN Nanowires

    SciTech Connect

    Wang, Zhiguo; Zu, Xiaotao; Gao, Fei; Weber, William J.; Crocombette, J.-P.

    2007-04-16

    The thermal conductivity of GaN nanowires has been determined computationally, by applying nonequilibrium atomistic simulation methods using the Stillinger-Weber [Phys. Rev. B 31, 5262 (1985)] potentials. The simulation results show that the thermal conductivity of the GaN nanowires is smaller than that of a bulk crystal and increases with increasing diameter. Surface scattering of phonons and the high surface to volume ratios of the nanowires are primarily responsible for the reduced thermal conductivity and its size dependence behavior. The thermal conductivity is also found to decrease with increasing temperature, which is due to phonon-phonon interactions at high temperatures. The thermal conductivity also exhibits a dependence on axial orientation of the nanowires.

  11. Atomistic understanding of diffusion kinetics in nanocrystals from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wang, Yun-Jiang; Gao, Guo-Jie J.; Ogata, Shigenobu

    2013-09-01

    Understanding the grain size effect on diffusion in nanocrystals has been hampered by the difficulty of measuring diffusion directly in experiments. Here large-scale atomistic modeling is applied to understand the diffusion kinetics in nanocrystals. Enhanced short-circuit diffusivity is revealed to be controlled by the rule of mixtures for grain-boundary diffusion and lattice diffusion, which can be accurately described by the Maxwell-Garnett equation instead of the commonly thought Hart equation, and the thermodynamics of pure grain-boundary self-diffusion is not remarkably affected by varying grain size. Experimentally comparable Arrhenius parameters with atomic detail validate our results. We also propose a free-volume diffusion mechanism considering negative activation entropy and small activation volume. These help provide a fundamental understanding of how the activation parameters depend on size and the structure-property relationship of nanostructured materials from a physical viewpoint.

  12. Toward an atomistic model for predicting transcription-factor binding sites.

    PubMed

    Endres, Robert G; Schulthess, Thomas C; Wingreen, Ned S

    2004-11-01

    Identifying the specific DNA-binding sites of transcription-factor proteins is essential to understanding the regulation of gene expression in the cell. Bioinformatics approaches are fast compared to experiments, but require prior knowledge of multiple binding sites for each protein. Here, we present an atomistic force-field method to predict binding sites based only on the X-ray structure of a related bound complex. Specific flexible contacts between the protein and DNA are modeled by a library of amino acid side-chain rotamers. Using the example of the mouse transcription factor, Zif268, a well-studied zinc-finger protein, we show that the protein sequence alone, without the detailed experimental structure, gives a strong bias toward the consensus binding site.

  13. Permutation invariant potential energy surfaces for polyatomic reactions using atomistic neural networks

    NASA Astrophysics Data System (ADS)

    Kolb, Brian; Zhao, Bin; Li, Jun; Jiang, Bin; Guo, Hua

    2016-06-01

    The applicability and accuracy of the Behler-Parrinello atomistic neural network method for fitting reactive potential energy surfaces is critically examined in three systems, H + H2 → H2 + H, H + H2O → H2 + OH, and H + CH4 → H2 + CH3. A pragmatic Monte Carlo method is proposed to make efficient choice of the atom-centered mapping functions. The accuracy of the potential energy surfaces is not only tested by fitting errors but also validated by direct comparison in dynamically important regions and by quantum scattering calculations. Our results suggest this method is both accurate and efficient in representing multidimensional potential energy surfaces even when dissociation continua are involved.

  14. An atomistic vision of the Mass Action Law: Prediction of carbon/oxygen defects in silicon

    SciTech Connect

    Brenet, G.; Timerkaeva, D.; Caliste, D.; Pochet, P.; Sgourou, E. N.; Londos, C. A.

    2015-09-28

    We introduce an atomistic description of the kinetic Mass Action Law to predict concentrations of defects and complexes. We demonstrate in this paper that this approach accurately predicts carbon/oxygen related defect concentrations in silicon upon annealing. The model requires binding and migration energies of the impurities and complexes, here obtained from density functional theory (DFT) calculations. Vacancy-oxygen complex kinetics are studied as a model system during both isochronal and isothermal annealing. Results are in good agreement with experimental data, confirming the success of the methodology. More importantly, it gives access to the sequence of chain reactions by which oxygen and carbon related complexes are created in silicon. Beside the case of silicon, the understanding of such intricate reactions is a key to develop point defect engineering strategies to control defects and thus semiconductors properties.

  15. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    DOE PAGES

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; ...

    2017-01-26

    When using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. Furthermore, by calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. A comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnonsmore » leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.« less

  16. Mechanism of the Cassie-Wenzel transition via the atomistic and continuum string methods

    SciTech Connect

    Giacomello, Alberto Casciola, Carlo Massimo; Meloni, Simone; Müller, Marcus

    2015-03-14

    The string method is a general and flexible strategy to compute the most probable transition path for an activated process (rare event). We apply here the atomistic string method in the density field to the Cassie-Wenzel transition, a central problem in the field of superhydrophobicity. We discuss in detail the mechanism of wetting of a submerged hydrophobic cavity of nanometer size and its dependence on the geometry of the cavity. Furthermore, we analyze the algorithmic analogies between the continuum “interface” string method and CREaM [Giacomello et al., Phys. Rev. Lett. 109, 226102 (2012)], a method inspired by the string that allows for a faster and simpler computation of the mechanism and of the free-energy profiles of the wetting process.

  17. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis.

    PubMed

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz; Vattulainen, Ilpo; Suomalainen, Anu; Sharma, Vivek

    2017-03-07

    DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.

  18. An atomistic vision of the Mass Action Law: Prediction of carbon/oxygen defects in silicon

    NASA Astrophysics Data System (ADS)

    Brenet, G.; Timerkaeva, D.; Sgourou, E. N.; Londos, C. A.; Caliste, D.; Pochet, P.

    2015-09-01

    We introduce an atomistic description of the kinetic Mass Action Law to predict concentrations of defects and complexes. We demonstrate in this paper that this approach accurately predicts carbon/oxygen related defect concentrations in silicon upon annealing. The model requires binding and migration energies of the impurities and complexes, here obtained from density functional theory (DFT) calculations. Vacancy-oxygen complex kinetics are studied as a model system during both isochronal and isothermal annealing. Results are in good agreement with experimental data, confirming the success of the methodology. More importantly, it gives access to the sequence of chain reactions by which oxygen and carbon related complexes are created in silicon. Beside the case of silicon, the understanding of such intricate reactions is a key to develop point defect engineering strategies to control defects and thus semiconductors properties.

  19. Atomistic full-band simulations of monolayer MoS{sub 2} transistors

    SciTech Connect

    Chang, Jiwon; Register, Leonard F.; Banerjee, Sanjay K.

    2013-11-25

    We study the transport properties of deeply scaled monolayer MoS{sub 2} n-channel metal-oxide-semiconductor field effect transistors (MOSFETs), using full-band ballistic quantum transport simulations, with an atomistic tight-binding Hamiltonian obtained from density functional theory. Our simulations suggest that monolayer MoS{sub 2} MOSFETs can provide near-ideal subthreshold slope, suppression of drain-induced barrier lowering, and gate-induced drain leakage. However, these full-band simulations exhibit limited transconductance. These ballistic simulations also exhibit negative differential resistance (NDR) in the output characteristics associated with the narrow width in energy of the lowest conduction band, but this NDR may be substantially reduced or eliminated by scattering in MoS{sub 2}.

  20. Simulating Cellulose Structure, Properties, Thermodynamics, Synthesis, and Deconstruction with Atomistic and Coarse-Grain Models

    SciTech Connect

    Crowley, M. F.; Matthews, J.; Beckham, G.; Bomble, Y.; Hynninen, A. P.; Ciesielski, P. F.

    2012-01-01

    Cellulose is still a mysterious polymer in many ways: structure of microfibrils, thermodynamics of synthesis and degradation, and interactions with other plant cell wall components. Our aim is to uncover the details and mechanisms of cellulose digestion and synthesis. We report the details of the structure of cellulose 1-beta under several temperature conditions and report here the results of these studies and connections to experimental measurements and the measurement in-silico the free energy of decrystallization of several morphologies of cellulose. In spatially large modeling, we show the most recent work of mapping atomistic and coarse-grain models into tomographic images of cellulose and extreme coarse-grain modeling of interactions of large cellulase complexes with microfibrils. We discuss the difficulties of modeling cellulose and suggest future work both experimental and theoretical to increase our understanding of cellulose and our ability to use it as a raw material for fuels and materials.

  1. Atomistic studies of formation and diffusion of helium clusters and bubbles in BCC iron

    SciTech Connect

    Stewart, David M; Stoller, Roger E; Osetskiy, Yury N

    2011-01-01

    In fusion applications, helium created by transmutation plays an important role in the response of reduced-activation ferritic/martensitic (RAFM) steels to neutron radiation damage. We have performed extensive atomistic simulations using the ORNL 3-body Fe He interatomic potential combined with three interatomic potentials for the iron matrix. Some of the results obtained are summarized in this review. Interstitial helium is very mobile and coalesces together to form interstitial clusters. We have investigated the mobility of these clusters. When an interstitial He cluster reaches sufficient size, it punches out an Fe interstitial, creating an immobile helium vacancy cluster. If more helium atoms join it, more Fe interstitials can be created; the He V defect is a nascent bubble. These mechanisms are investigated together in simulations that examine the nucleation of He defects. Mobile interstitial He clusters and helium bubbles 1 to 6 nm across are also simulated separately. Results are compared based on temperature and interatomic potentials used.

  2. Coarse-graining the computations of surface reactions: Nonlinear dynamics from atomistic simulators

    NASA Astrophysics Data System (ADS)

    Makeev, Alexei G.; Kevrekidis, Ioannis G.

    2009-06-01

    We review and discuss the use of equation-free computation in extracting coarse-grained, nonlinear dynamics information from atomistic (lattice-gas) models of surface reactions. The approach is based on circumventing the explicit derivation of macroscopic equations for the system statistics (e.g., average coverage). Short bursts of appropriately initialized computational experimentation with the lattice-gas simulator are designed "on demand" and processed in the spirit of the coarse timestepper introduced in Theodoropoulos et al. (2000) (K. Theodoropoulos, Y.-H. Qian, I.G. Kevrekidis, Proc. Natl. Acad. Sci. USA 97 (2000) 9840). The information derived from these computational experiments, processed through traditional, continuum numerical methods is used to solve the macroscopic equations without ever deriving them in closed form. The approach is illustrated through two computational examples: the CO oxidation reaction, and the NO + CO/Pt(1 0 0) reaction.

  3. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation

    PubMed Central

    Maffeo, Christopher; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-01-01

    The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures. PMID:26980283

  4. Atomistic Simulations of Ternary Polymer Electrolytes Containing Ionic Liquids: Ion Transport and Viscoelastic Behavior

    NASA Astrophysics Data System (ADS)

    Mogurampelly, Santosh; Ganesan, Venkat

    Influence of the BMIMPF6 ionic liquid on ion transport and viscoelastic properties of ternary polymer electrolytes containing polyethylene oxide solvated with LiPF6 salt and the underlying mechanisms are investigated. By employing atomistic molecular dynamics and trajectory extended kinetic Monte Carlo simulation techniques, we observe enhanced ionic mobilities and conductivities of the PEOLiPF6-BMIMPF ternary electrolytes upon the addition ionic liquid into the PEOLiPF6 binary electrolyte. The dispersion of the BMIMPF6 ionic liquid into the PEOLiPF6 electrolyte is found to (a) promote dissociation of existing LiPF6 ion-pairs and (b) slightly accelerate the polymer segmental dynamics. Together, these effects are observed to collectively give rise to an increase in ionic mobilities and conductivities of the ternary polymer electrolyte. On the other hand, Rouse analysis reveals that the storage and loss modulus of the ternary polymer electrolytes are coupled to their ion conducting properties.

  5. Computer code for the atomistic simulation of lattice defects and dynamics. [COMENT code

    SciTech Connect

    Schiffgens, J.O.; Graves, N.J.; Oster, C.A.

    1980-04-01

    This document has been prepared to satisfy the need for a detailed, up-to-date description of a computer code that can be used to simulate phenomena on an atomistic level. COMENT was written in FORTRAN IV and COMPASS (CDC assembly language) to solve the classical equations of motion for a large number of atoms interacting according to a given force law, and to perform the desired ancillary analysis of the resulting data. COMENT is a dual-purpose intended to describe static defect configurations as well as the detailed motion of atoms in a crystal lattice. It can be used to simulate the effect of temperature, impurities, and pre-existing defects on radiation-induced defect production mechanisms, defect migration, and defect stability.

  6. Large-scale atomistic simulations of helium-3 bubble growth in complex palladium alloys

    NASA Astrophysics Data System (ADS)

    Hale, Lucas M.; Zimmerman, Jonathan A.; Wong, Bryan M.

    2016-05-01

    Palladium is an attractive material for hydrogen and hydrogen-isotope storage applications due to its properties of large storage density and high diffusion of lattice hydrogen. When considering tritium storage, the material's structural and mechanical integrity is threatened by both the embrittlement effect of hydrogen and the creation and evolution of additional crystal defects (e.g., dislocations, stacking faults) caused by the formation and growth of helium-3 bubbles. Using recently developed inter-atomic potentials for the palladium-silver-hydrogen system, we perform large-scale atomistic simulations to examine the defect-mediated mechanisms that govern helium bubble growth. Our simulations show the evolution of a distribution of material defects, and we compare the material behavior displayed with expectations from experiment and theory. We also present density functional theory calculations to characterize ideal tensile and shear strengths for these materials, which enable the understanding of how and why our developed potentials either meet or confound these expectations.

  7. Thermochemistry of organic reactions in microporous oxides by atomistic simulations: benchmarking against periodic B3LYP.

    PubMed

    Bleken, Francesca; Svelle, Stian; Lillerud, Karl Petter; Olsbye, Unni; Arstad, Bjørnar; Swang, Ole

    2010-07-15

    The methylation of ethene by methyl chloride and methanol in the microporous materials SAPO-34 and SSZ-13 has been studied using different periodic atomistic modeling approaches based on density functional theory. The RPBE functional, which earlier has been used successfully in studies of surface reactions on metals, fails to yield a qualitatively correct description of the transition states under study. Employing B3LYP as functional gives results in line with experimental data: (1) Methanol is adsorbed more strongly than methyl chloride to the acid site. (2) The activation energies for the methylation of ethene are slightly lower for SSZ-13. Furthermore, the B3LYP activation energies are lower for methyl chloride than for methanol.

  8. Mechanism of the Cassie-Wenzel transition via the atomistic and continuum string methods

    NASA Astrophysics Data System (ADS)

    Giacomello, Alberto; Meloni, Simone; Müller, Marcus; Casciola, Carlo Massimo

    2015-03-01

    The string method is a general and flexible strategy to compute the most probable transition path for an activated process (rare event). We apply here the atomistic string method in the density field to the Cassie-Wenzel transition, a central problem in the field of superhydrophobicity. We discuss in detail the mechanism of wetting of a submerged hydrophobic cavity of nanometer size and its dependence on the geometry of the cavity. Furthermore, we analyze the algorithmic analogies between the continuum "interface" string method and CREaM [Giacomello et al., Phys. Rev. Lett. 109, 226102 (2012)], a method inspired by the string that allows for a faster and simpler computation of the mechanism and of the free-energy profiles of the wetting process.

  9. Elastic anisotropy and shear-induced atomistic deformation of tetragonal silicon carbon nitride

    SciTech Connect

    Yan, Haiyan; Zhang, Meiguang; Zhao, Yaru; Zhou, Xinchun; Wei, Qun

    2014-07-14

    First-principles calculations are employed to provide a fundamental understanding of the structural features, elastic anisotropy, shear-induced atomistic deformation behaviors, and its electronic origin of the recently proposed superhard t-SiCN. According to the dependences of the elastic modulus on different crystal directions, the t-SiCN exhibits a well-pronounced elastic anisotropy which may impose certain limitations and restrictions on its applications. The further mechanical calculations demonstrated that t-SiCN shows lower elastic moduli and ideal shear strength than those of typical hard substances of TiN and TiC, suggesting that it cannot be intrinsically superhard as claimed in the recent works. We find that the failure modes of t-SiCN at the atomic level during shear deformation can be attributed to the breaking of C-C bonds through the bonding evolution and electronic localization analyses.

  10. Effect of Ultrahigh Stiffness of Defective Graphene from Atomistic Point of View.

    PubMed

    Kvashnin, D G; Sorokin, P B

    2015-06-18

    Well-known effects of mechanical stiffness degradation under the influence of point defects in macroscopic solids can be controversially reversed in the case of low-dimensional materials. Using atomistic simulation, we showed here that a single-layered graphene film can be sufficiently stiffened by monovacancy defects at a tiny concentration. Our results correspond well with recent experimental data and suggest that the effect of mechanical stiffness augmentation is mainly originated from specific bonds distribution in the surrounded monovacancy defects regions. We showed that such unusual mechanical response is the feature of presence of specifically monovacancies, whereas other types of point defects such as divacancy, 555-777 and Stone-Wales defects, lead to the ordinary degradation of the graphene mechanical stiffness.

  11. Mapping between atomistic simulations and Eshelby inclusions in the shear deformation of an amorphous silicon model

    NASA Astrophysics Data System (ADS)

    Albaret, T.; Tanguy, A.; Boioli, F.; Rodney, D.

    2016-05-01

    In this paper we perform quasistatic shear simulations of model amorphous silicon bulk samples with Stillinger-Weber-type potentials. Local plastic rearrangements identified based on local energy variations are fitted through their displacement fields on collections of Eshelby spherical inclusions, allowing determination of their transformation strain tensors. The latter are then used to quantitatively reproduce atomistic stress-strain curves, in terms of both shear and pressure components. We demonstrate that our methodology is able to capture the plastic behavior predicted by different Stillinger-Weber potentials, in particular, their different shear tension coupling. These calculations justify the decomposition of plasticity into shear transformations used so far in mesoscale models and provide atomic-scale parameters that can be used to limit the empiricism needed in such models up to now.

  12. Emergence of step flow from an atomistic scheme of epitaxial growth in 1 +1 dimensions

    NASA Astrophysics Data System (ADS)

    Lu, Jianfeng; Liu, Jian-Guo; Margetis, Dionisios

    2015-03-01

    The Burton-Cabrera-Frank (BCF) model for the flow of line defects (steps) on crystal surfaces has offered useful insights into nanostructure evolution. This model has rested on phenomenological grounds. Our goal is to show via scaling arguments the emergence of the BCF theory for noninteracting steps from a stochastic atomistic scheme of a kinetic restricted solid-on-solid model in one spatial dimension. Our main assumptions are: adsorbed atoms (adatoms) form a dilute system, and elastic effects of the crystal lattice are absent. The step edge is treated as a front that propagates via probabilistic rules for atom attachment and detachment at the step. We formally derive a quasistatic step flow description by averaging out the stochastic scheme when terrace diffusion, adatom desorption, and deposition from above are present.

  13. Atomistic multiscale simulation of the structure and properties of an amorphous OXD-7 layer

    NASA Astrophysics Data System (ADS)

    Emelyanova, Svetlana; Chashchikhin, Vladimir; Bagaturyants, Alexander

    2013-12-01

    The structure and properties of an amorphous 1,3-bis(2-(4-tert-butylphenyl)-1,3,4-oxadiazol-5-yl)benzene (OXD-7) layer are investigated by atomistic multiscale simulation combining quantum chemical (DFT, TDDFT) and molecular dynamics (MD, AMBER force field) calculations. Three stable OXD-7 conformers are found on its ground-state DFT potential energy surface. The force-field parameters of torsion angles lacking in the AMBER force field are determined by fitting to the results of MP2 calculations for a model oxadiazole derivative. The OXD-7 absorption band shape and HOMO and LUMO energy distributions in an amorphous film are found by TDDFT/DFT calculations for sample points obtained by MD calculations.

  14. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    NASA Astrophysics Data System (ADS)

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; Stocks, G. Malcolm; Landau, David P.

    2017-01-01

    Using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. By calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. Comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnons leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.

  15. Coupling LAMMPS and the vl3 Framework for Co-Visualization of Atomistic Simulations

    SciTech Connect

    Rizzi, Silvio; Hereld, Mark; Insley, Joseph; Malakar, Preeti; Papka, Michael E.; Uram, Thomas; Vishwanath, Venkatram

    2016-01-01

    In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future research avenues based on our results.

  16. Atomistic Investigation of Cu-Induced Misfolding in the Onset of Parkinson's Disease

    NASA Astrophysics Data System (ADS)

    Rose, Francis; Hodak, Miroslav; Bernholc, Jerry

    2009-03-01

    A nucleation mechanism for the misfolding of α-synuclein, the protein implicated in Parkinson's Disease (PD), is investigated using computer simulations. Through a combination of ab initio and classical simulation techniques, the conformational evolution of copper-ion-initiated misfolding of α-synuclein is determined. Based on these investigations and available experimental evidence, an atomistic model detailing the nucleation-initiated pathogenesis of PD is proposed. Once misfolded, the proteins can assemble into fibrils, the primary structural components of the deleterious PD plaques. Our model identifies a process of structural modifications to an initially unfolded α-synuclein that results in a partially folded intermediate with a well defined nucleation site as a precursor to the fully misfolded protein. The identified pathway can enable studies of reversal mechanisms and inhibitory agents, potentially leading to the development of effective therapies.

  17. Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface

    PubMed Central

    He, Xibing; Guvench, Olgun; MacKerell, Alexander D.; Klein, Michael L.

    2010-01-01

    Molecular Dynamics simulations with the CHARMM atomistic force field have been used to study monolayers of a series of linear alkylbenzene sulfonates (LAS) at the water/air interface. Both the numbers of carbon atoms in the LAS alkyl tail (1 to 11), and the position of attachment of the benzene ring on the alkyl chain have been varied. Totally 36 LAS homologues and isomers have been investigated. The surface tensions of the systems and the average tilt angles of the LAS molecules are found to be related to both the length and the degree of branching of the alkyl tails, whereas the solubility and mobility are mostly determined by the tail length. PMID:20614916

  18. Atomistic origin of an ordered superstructure induced superconductivity in layered chalcogenides.

    PubMed

    Ang, R; Wang, Z C; Chen, C L; Tang, J; Liu, N; Liu, Y; Lu, W J; Sun, Y P; Mori, T; Ikuhara, Y

    2015-01-27

    Interplay among various collective electronic states such as charge density wave and superconductivity is of tremendous significance in low-dimensional electron systems. However, the atomistic and physical nature of the electronic structures underlying the interplay of exotic states, which is critical to clarifying its effect on remarkable properties of the electron systems, remains elusive, limiting our understanding of the superconducting mechanism. Here, we show evidence that an ordering of selenium and sulphur atoms surrounding tantalum within star-of-David clusters can boost superconductivity in a layered chalcogenide 1T-TaS2-xSex, which undergoes a superconducting transition in the nearly commensurate charge density wave phase. Advanced electron microscopy investigations reveal that such an ordered superstructure forms only in the x area, where the superconductivity manifests, and is destructible to the occurrence of the Mott metal-insulator transition. The present findings provide a novel dimension in understanding the relationship between lattice and electronic degrees of freedom.

  19. Biophysical and biochemical aspects of antifreeze proteins: Using computational tools to extract atomistic information.

    PubMed

    Kar, Rajiv K; Bhunia, Anirban

    2015-11-01

    Antifreeze proteins (AFPs) are the key biomolecules that protect species from extreme climatic conditions. Studies of AFPs, which are based on recognition of ice plane and structural motifs, have provided vital information that point towards the mechanism responsible for executing antifreeze activity. Importantly, the use of experimental techniques has revealed key information for AFPs, but the exact microscopic details are still not well understood, which limits the application and design of novel antifreeze agents. The present review focuses on the importance of computational tools for investigating (i) molecular properties, (ii) structure-function relationships, and (iii) AFP-ice interactions at atomistic levels. In this context, important details pertaining to the methodological approaches used in molecular dynamics studies of AFPs are also discussed. It is hoped that the information presented herein is helpful for enriching our knowledge of antifreeze properties, which can potentially pave the way for the successful design of novel antifreeze biomolecular agents.

  20. Atomistic simulation of tensile deformation behavior of ∑5 tilt grain boundaries in copper bicrystal.

    PubMed

    Zhang, Liang; Lu, Cheng; Tieu, Kiet

    2014-08-01

    Experiments on polycrystalline metallic samples have indicated that Grain boundary (GB) structure can affect many material properties related to fracture and plasticity. In this study, atomistic simulations are employed to investigate the structures and mechanical behavior of both symmetric and asymmetric ∑5[0 0 1] tilt GBs of copper bicrystal. First, the equilibrium GB structures are generated by molecular statics simulation at 0K. The results show that the ∑5 asymmetric GBs with different inclination angles (φ) are composed of only two structural units corresponding to the two ∑5 symmetric GBs. Molecular dynamics simulations are then conducted to investigate the mechanical response and the underlying deformation mechanisms of bicrystal models with different ∑5 GBs under tension. Tensile deformation is applied under both 'free' and 'constrained' boundary conditions. Simulation results revealed different mechanical properties of the symmetric and asymmetric GBs and indicated that stress state can play an important role in the deformation mechanisms of nanocrystalline materials.

  1. Atomistic modeling of the structural components of the blood-brain barrier

    NASA Astrophysics Data System (ADS)

    Glukhova, O. E.; Grishina, O. A.; Slepchenkov, M. M.

    2015-03-01

    Blood-brain barrier, which is a barrage system between the brain and blood vessels, plays a key role in the "isolation" of the brain of unnecessary information, and reduce the "noise" in the interneuron communication. It is known that the barrier function of the BBB strictly depends on the initial state of the organism and changes significantly with age and, especially in developing the "vascular accidents". Disclosure mechanisms of regulation of the barrier function will develop new ways to deliver neurotrophic drugs to the brain in the newborn. The aim of this work is the construction of atomistic models of structural components of the blood-brain barrier to reveal the mechanisms of regulation of the barrier function.

  2. Identifying early stage precipitation in large-scale atomistic simulations of superalloys

    NASA Astrophysics Data System (ADS)

    Schmidt, Eric; Bristowe, Paul D.

    2017-04-01

    A method for identifying and classifying ordered phases in large chemically and thermally disordered atomistic models is presented. The method uses Steinhardt parameters to represent local atomic configurations and develops probability density functions to classify individual atoms using naïve Bayes. The method is applied to large molecular dynamics simulations of supersaturated Ni-20 at% Al solid solutions in order to identify the formation of embryonic γ‧-Ni3Al. The composition and temperatures are chosen to promote precipitation, which is observed in the form of ordering and is found to occur more likely in regions with above average Al concentration producing ‘clusters’ of increasing size. The results are interpreted in terms of a precipitation mechanism in which the solid solution is unstable with respect to ordering and potentially followed by either spinodal decomposition or nucleation and growth.

  3. Filler reinforcement in cross-linked elastomer nanocomposites: insights from fully atomistic molecular dynamics simulation.

    PubMed

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

    Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more

  4. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    NASA Astrophysics Data System (ADS)

    Seppä, Jeremias; Reischl, Bernhard; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Raiteri, Paolo; Rohl, Andrew L.; Nordlund, Kai; Lassila, Antti

    2017-03-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation.

  5. An atomistic study of the effects of stress and hydrogen on a dislocation lock in nickel

    SciTech Connect

    Hoagland, R.G.; Baskes, M.I.

    1998-03-19

    Even though austenitic alloys are commonly used in a hydrogen environment, hydrogen-induced fracture of these alloys has been reported. Most recently it has been shown that the failure of these alloys in hydrogen is initiated by void formation at slip band intersections. It is the object of this work to investigate the atomistic mechanisms that occur at these slip band intersections in the presence of hydrogen. Specifically it has been suggested that dislocation-dislocation interactions may play a large role in the initiation of voids or cracks. Hirth has summarized the various forms of dislocation interactions, traditionally called Lomer-Cottrell Locks (LCLs), that can occur. Baskes et al. have investigated the effects of stress on a LCL using an Embedded Atom Method (EAM) model for nickel developed previously by Angelo et al. The EAM is a well-established semi-empirical method of atomistic calculation that has been successfully used for over a decade to calculate the energetics and structure of defects in transition metals. The work by Angelo et al. established that the trapping of hydrogen to single dislocations had a maximum energy of ca. 0.1 eV while the trapping to a LCL was significantly greater, {approximately}0.33 eV, thus the authors expect that a LCL could be important in explaining the fracture behavior of a fcc material in a hydrogen environment. Baskes et al. found that under uniaxial stress a LCL in the absence of hydrogen underwent a number of transitions, but it did not dissociate or form a crack nucleus. In this work the authors extend the previous work to include the effects of hydrogen. Specifically they will simulate the experiments of Moody et al. for the case of room temperature exposure of Inconel to 190 atm of hydrogen.

  6. Atomistic details of oxide surfaces and surface oxidation: the example of copper and its oxides

    NASA Astrophysics Data System (ADS)

    Gattinoni, Chiara; Michaelides, Angelos

    2015-11-01

    The oxidation and corrosion of metals are fundamental problems in materials science and technology that have been studied using a large variety of experimental and computational techniques. Here we review some of the recent studies that have led to significant advances in our atomic-level understanding of copper oxide, one of the most studied and best understood metal oxides. We show that a good atomistic understanding of the physical characteristics of cuprous (Cu2O) and cupric (CuO) oxide and of some key processes of their formation has been obtained. Indeed, the growth of the oxide has been shown to be epitaxial with the surface and to proceed, in most cases, through the formation of oxide nano-islands which, with continuous oxygen exposure, grow and eventually coalesce. We also show how electronic structure calculations have become increasingly useful in helping to characterise the structures and energetics of various Cu oxide surfaces. However a number of challenges remain. For example, it is not clear under which conditions the oxidation of copper in air at room temperature (known as native oxidation) leads to the formation of a cuprous oxide film only, or also of a cupric overlayer. Moreover, the atomistic details of the nucleation of the oxide islands are still unknown. We close our review with a brief perspective on future work and discuss how recent advances in experimental techniques, bringing greater temporal and spatial resolution, along with improvements in the accuracy, realism and timescales achievable with computational approaches make it possible for these questions to be answered in the near future.

  7. An atomistic methodology of energy release rate for graphene at nanoscale

    SciTech Connect

    Zhang, Zhen; Lee, James D.; Wang, Xianqiao

    2014-03-21

    Graphene is a single layer of carbon atoms packed into a honeycomb architecture, serving as a fundamental building block for electric devices. Understanding the fracture mechanism of graphene under various conditions is crucial for tailoring the electrical and mechanical properties of graphene-based devices at atomic scale. Although most of the fracture mechanics concepts, such as stress intensity factors, are not applicable in molecular dynamics simulation, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at nanoscale. This work introduces an atomistic simulation methodology, based on the energy release rate, as a tool to unveil the fracture mechanism of graphene at nanoscale. This methodology can be easily extended to any atomistic material system. We have investigated both opening mode and mixed mode at different temperatures. Simulation results show that the critical energy release rate of graphene is independent of initial crack length at low temperature. Graphene with inclined pre-crack possesses higher fracture strength and fracture deformation but smaller critical energy release rate compared with the graphene with vertical pre-crack. Owing to its anisotropy, graphene with armchair chirality always has greater critical energy release rate than graphene with zigzag chirality. The increase of temperature leads to the reduction of fracture strength, fracture deformation, and the critical energy release rate of graphene. Also, higher temperature brings higher randomness of energy release rate of graphene under a variety of predefined crack lengths. The energy release rate is independent of the strain rate as long as the strain rate is small enough.

  8. Atomistic simulations of adiabatic coherent electron transport in triple donor systems

    NASA Astrophysics Data System (ADS)

    Rahman, Rajib; Park, Seung H.; Cole, Jared H.; Greentree, Andrew D.; Muller, Richard P.; Klimeck, Gerhard; Hollenberg, Lloyd C. L.

    2009-07-01

    A solid-state analog of stimulated Raman adiabatic passage can be implemented in a triple-well solid-state system to coherently transport an electron across the wells with exponentially suppressed occupation in the central well at any point of time. Termed coherent-tunneling adiabatic passage (CTAP), this method provides a robust way to transfer quantum information encoded in the electronic spin across a chain of quantum dots or donors. Using large-scale atomistic tight-binding simulations involving over 3.5×106 atoms, we verify the existence of a CTAP pathway in a realistic solid-state system: gated triple donors in silicon. Realistic gate profiles from commercial tools were combined with tight-binding methods to simulate gate control of the donor to donor tunnel barriers in the presence of crosstalk. As CTAP is an adiabatic protocol, it can be analyzed by solving the time-independent problem at various stages of the pulse justifying the use of time-independent tight-binding methods to this problem. This work also involves the first atomistic treatment to translate the three-state-based quantum-optics type of modeling into a solid-state description beyond the ideal localization assumption. Our results show that a three-donor CTAP transfer, with interdonor spacing of 15 nm can occur on time scales greater than 23 ps, well within experimentally accessible regimes. The method not only provides a tool to guide future CTAP experiments but also illuminates the possibility of system engineering to enhance control and transfer times.

  9. Atomistic Pseudopotential Calculations of the Electronic and Optical Properties of Self-Assembled Quantum Dots

    NASA Astrophysics Data System (ADS)

    Bester, Gabriel

    2006-03-01

    The optical spectrum and the charging energies of semiconductor quantum dots have been recently measured with high accuracy. Both of these experimental techniques probe many-body states that are not directly described by independent particle theories such as the density functional theory. On the other hand, quasi- particle theories that can in principle address the problem, such as GW, are computationally too demanding for the study of nanostructures (as opposed to clusters) where many thousands of atoms are involved. One way to approach this problem is to use the effective mass approximation or the k.p method and choose a confinement potential that reproduces a few known experimental facts (e.g. the splitting between confined levels). These methods can provide a good initial guess but were shown to be too crude to enable a quantitative comparision with recent experiments. We therefore adopt a bottom-up atomistic approach where instead of starting from a simplified approach, such as effective mass, and progressively increase the complexity by adding parameters, we start from the accurate atomistic description (LDA or GW) and work ourselves up using a few well controlled approximations.I will first present the method, namely (i) the scheme that is used to derive the empirical pseudopotentials including the piezoelectric effect, (ii) the choices that have to be made for the basis used to expand the wave functions, (iii) the inclusion of corelations through Bethe-Salpeter-like treatment. I will then present recent applications of the theory to calculate the fine-structure [1] of excitons and charged excitons, the charging spectra of holes [2] and the degree or entanglement stored in a quantum dot molecule [3].[1] G. Bester, S.V. Nair, A. Zunger, prb 67, 161306 (2003). [2] L. He, G. Bester, A. Zunger, PRL (in press). [3] G. Bester, J. Shumway, A. Zunger, PRL 93, 047401 (2004)

  10. Polarized Solid State Target

    NASA Astrophysics Data System (ADS)

    Dutz, Hartmut; Goertz, Stefan; Meyer, Werner

    2017-01-01

    The polarized solid state target is an indispensable experimental tool to study single and double polarization observables at low intensity particle beams like tagged photons. It was one of the major components of the Crystal-Barrel experiment at ELSA. Besides the operation of the 'CB frozen spin target' within the experimental program of the Crystal-Barrel collaboration both collaborative groups of the D1 project, the polarized target group of the Ruhr Universität Bochum and the Bonn polarized target group, have made significant developments in the field of polarized targets within the CRC16. The Bonn polarized target group has focused its work on the development of technically challenging polarized solid target systems towards the so called '4π continuous mode polarized target' to operate them in combination with 4π-particle detection systems. In parallel, the Bochum group has developed various highly polarized deuterated target materials and high precision NMR-systems, in the meantime used for polarization experiments at CERN, JLAB and MAMI, too.

  11. Measurement of internal movements of the Escherichia coli ribosome using Forster resonance energy transfer and microsecond, continuous-flow turbulent mixing in micro-fabricated devices

    NASA Astrophysics Data System (ADS)

    Majumdar, Zigurts Krishna

    We have studied internal movements of the Eschericia coli ribosome with Forster Resonance Energy Transfer (FRET) using multiple donor-acceptor pairs labeled at specific ribosomal protein residues. We have developed a novel methodology that allows a more quantitative interpretation of distance data from FRET measurements, accounting for specific effects when using fluorescent probes, such as: non-stoichiometric labeling when biochemical separation is not possible, quantification of static and dynamic quenching, changes in extinction coefficients, effects of the orientation factor and the presence of random and systematic errors. From the obtained distance data, 13 donor-acceptor positions (from 18 independent FRET pairs) are used to model internal movements within the 30S subunit upon 70S association. These measurements are also applied to monitoring inter-subunit movements in functional states of the ribosome that are associated with the translocation cycle of the ribosome. This work reveals internal movements of the ribosome observed for the first time in solution, and presents in vitro evidence for large concerted inter-subunit motions associated with ribosome translocation. The second half of this thesis is independent of the above. We present the design, construction and implementation of micro-fabricated, continuous-flow, turbulent mixing devices that can mix two or three fluids to complete homogeneity on the molecular scale in the microsecond range. The prototypical designs are compact, portable, simple to fabricate and consume smaller sample volumes than current technology. We characterize the turbulent mixing process in microfluidic channels with fluorescence intensity and lifetime imaging and show that both the dependence of mixing times and pressure drop on the flow velocity and Reynolds number agree well with theoretical expectations for turbulent pipe flow. The novelties in this work are: the new methods of fabrication which enable production of three

  12. Statistical Polarization Mode Dispersion/Polarization Dependent Loss Emulator for Polarization Division Multiplexing Transmission Testing

    NASA Astrophysics Data System (ADS)

    Perlicki, Krzysztof

    2010-03-01

    A low-cost statistical polarization mode dispersion/polarization dependent loss emulator is presented in this article. The emulator was constructed by concatenating 15 highly birefringence optical-fiber segments and randomly varying the mode coupling between them by rotating the polarization state. The impact of polarization effects on polarization division multiplexing transmission quality was measured. The designed polarization mode dispersion/polarization dependent loss emulator was applied to mimic the polarization effects of real optical-fiber links.

  13. [Review] Polarization and Polarimetry

    NASA Astrophysics Data System (ADS)

    Trippe, Sascha

    2014-02-01

    Polarization is a basic property of light and is fundamentally linked to the internal geometry of a source of radiation. Polarimetry complements photometric, spectroscopic, and imaging analyses of sources of radiation and has made possible multiple astrophysical discoveries. In this article I review (i) the physical basics of polarization: electromagnetic waves, photons, and parameterizations; (ii) astrophysical sources of polarization: scattering, synchrotron radiation, active media, and the Zeeman, Goldreich-Kylafis, and Hanle effects, as well as interactions between polarization and matter (like birefringence, Faraday rotation, or the Chandrasekhar-Fermi effect); (iii) observational methodology: on-sky geometry, influence of atmosphere and instrumental polarization, polarization statistics, and observational techniques for radio, optical, and X/γ wavelengths; and (iv) science cases for astronomical polarimetry: solar and stellar physics, planetary system bodies, interstellar matter, astrobiology, astronomical masers, pulsars, galactic magnetic fields, gamma-ray bursts, active galactic nuclei, and cosmic microwave background radiation.

  14. Automatic Bayesian polarity determination

    NASA Astrophysics Data System (ADS)

    Pugh, D. J.; White, R. S.; Christie, P. A. F.

    2016-07-01

    The polarity of the first motion of a seismic signal from an earthquake is an important constraint in earthquake source inversion. Microseismic events often have low signal-to-noise ratios, which may lead to difficulties estimating the correct first-motion polarities of the arrivals. This paper describes a probabilistic approach to polarity picking that can be both automated and combined with manual picking. This approach includes a quantitative estimate of the uncertainty of the polarity, improving calculation of the polarity probability density function for source inversion. It is sufficiently fast to be incorporated into an automatic processing workflow. When used in source inversion, the results are consistent with those from manual observations. In some cases, they produce a clearer constraint on the range of high-probability source mechanisms, and are better constrained than source mechanisms determined using a uniform probability of an incorrect polarity pick.

  15. A dual polarized antenna system using a meanderline polarizer

    NASA Technical Reports Server (NTRS)

    Burger, H. A.

    1978-01-01

    Certain applications of synthetic aperture radars (e.g., aerial crop surveying) require transmission on one linear polarization and reception on two orthogonal linear polarizations for adequate characterization of the surface. To meet this requirement at minimum cost, it was desirable to use two identically polarized shaped beam antennas and to change the polarization of one of them by a polarization conversion plate. The plate was realized as a four-layer meanderline polarizer designed to convert horizontal polarization to vertical.

  16. A dual polarized antenna system using a meanderline polarizer

    NASA Technical Reports Server (NTRS)

    Burger, H. A.

    1978-01-01

    Certain applications of synthetic aperture radars require transmitting on one linear polarization and receiving on two orthogonal linear polarizations for adequate characterization of the surface. To meet the current need at minimum cost, it was desirable to use two identical horizontally polarized shaped beam antennas and to change the polarization of one of them by a polarization conversion plate. The plate was realized as a four-layer meanderline polarizer designed to convert horizontal polarization to vertical.

  17. Quantifying Coulombic and solvent polarization-mediated forces between DNA helices.

    PubMed

    He, Zhaojian; Chen, Shi-Jie

    2013-06-20

    One of the fundamental problems in nucleic acids biophysics is to predict the different forces that stabilize nucleic acid tertiary folds. Here we provide a quantitative estimation and analysis for the forces between DNA helices in an ionic solution. Using the generalized Born model and the improved atomistic tightly binding ions model, we evaluate ion correlation and solvent polarization effects in interhelix interactions. The results suggest that hydration, Coulomb correlation and ion entropy act together to cause the repulsion and attraction between nucleic acid helices in Mg(2+) and Mn(2+) solutions, respectively. The theoretical predictions are consistent with experimental findings. Detailed analysis further suggests that solvent polarization and ion correlation both are crucial for the interhelix interactions. The theory presented here may provide a useful framework for systematic and quantitative predictions of the forces in nucleic acids folding.

  18. Polarization feedback laser stabilization

    DOEpatents

    Esherick, P.; Owyoung, A.

    1987-09-28

    A system for locking two Nd:YAG laser oscillators includes an optical path for feeding the output of one laser into the other with different polarizations. Elliptical polarization is incorporated into the optical path so that the change in polarization that occurs when the frequencies coincide may be detected to provide a feedback signal to control one laser relative to the other. 4 figs.

  19. Polarized negative ions

    SciTech Connect

    Haeberli, W.

    1981-04-01

    This paper presents a survey of methods, commonly in use or under development, to produce beams of polarized negative ions for injection into accelerators. A short summary recalls how the hyperfine interaction is used to obtain nuclear polarization in beams of atoms. Atomic-beam sources for light ions are discussed. If the best presently known techniques are incorporated in all stages of the source, polarized H/sup -/ and D/sup -/ beams in excess of 10 ..mu..A can probably be achieved. Production of polarized ions from fast (keV) beams of polarized atoms is treated separately for atoms in the H(25) excited state (Lamb-Shift source) and atoms in the H(1S) ground state. The negative ion beam from Lamb-Shift sources has reached a plateau just above 1 ..mu..A, but this beam current is adequate for many applications and the somewhat lower beam current is compensated by other desirable characteristics. Sources using fast polarized ground state atoms are in a stage of intense development. The next sections summarize production of polarized heavy ions by the atomic beam method, which is well established, and by optical pumping, which has recently been demonstrated to yield very large nuclear polarization. A short discussion of proposed ion sources for polarized /sup 3/He/sup -/ ions is followed by some concluding remarks.

  20. Polarization at SLC

    SciTech Connect

    Swartz, M.L.

    1988-07-01

    The SLAC Linear Collider has been designed to readily accommodate polarized electron beams. Considerable effort has been made to implement a polarized source, a spin rotation system, and a system to monitor the beam polarization. Nearly all major components have been fabricated. At the current time, several source and polarimeter components have been installed. The installation and commissioning of the entire system will take place during available machine shutdown periods as the commissioning of SLC progresses. It is expected that a beam polarization of 45% will be achieved with no loss in luminosity. 13 refs., 15 figs.

  1. Electron trapping in polar-solvated zeolites.

    PubMed

    Ellison, Eric H

    2005-11-03

    Of current interest in our laboratory is the nature of photoinduced processes in the cavities of zeolites completely submerged in polar solvents, or polar-solvated zeolites (PSZ). The present study addresses the nature of electron trapping in PSZ with emphasis on the zeolites NaX and NaY. Free electrons were generated by two-photon, pulsed-laser excitation of either pyrene or naphthalene included in zeolite cavities. Trapped electrons were monitored by diffuse transmittance, transient absorption spectroscopy at visible wavelengths. In anhydrous alcohols, electron trapping by Na(4)(4+) ion clusters was observed in both NaX and NaY. The resulting trapped electrons decayed over the course of tens of milliseconds. No evidence for alcohol-solvated electrons was found. More varied results were observed in solvents containing water. In NaX submerged in CH(3)OH containing 5% or higher water, species having microsecond lifetimes characteristic of solvated electrons were observed. By contrast, a 2 h exposure of NaY to 95/5 CH(3)OH/H(2)O had no effect on electron trapping relative to anhydrous CH(3)OH. The difference between NaX and NaY was explained by how fast water migrates into the sodalite cage. Prolonged exposure to water at room temperature or exposure to water at elevated temperatures was necessary to place water in the sodalite cages of NaY and deactivate Na(4)(4+) as an electron trap. Additional studies in NaY revealed that solvent clusters eventually become lower energy traps than Na(4)(4+) as the water content in methanol increases. In acetonitrile-water mixtures, electron trapping by Na(4)(4+) was eliminated and no equivalent species characteristic of solvated electrons in methanol-water mixtures was observed. This result was explained by the formation of low energy solvated electrons which cannot be observed in the visible region of the spectrum. Measurements of the rate of O(2) quenching in anhydrous solvents revealed rate constants for the quenching of ion

  2. Extending atomistic scale chemistry to mesoscale model of condensed-phase deflagration

    NASA Astrophysics Data System (ADS)

    Joshi, Kaushik; Chaudhuri, Santanu

    2017-01-01

    Predictive simulations connecting chemistry that follow the shock or thermal initiation of energetic materials to subsequent deflagration or detonation events is currently outside the realm of possibilities. Molecular dynamics and first-principles based dynamics have made progress in understanding reactions in picosecond to nanosecond time scale. Results from thermal ignition of different phases of RDX show a complex reaction network and emergence of a deterministic behavior for critical temperature before ignition and hot spot growth rates. The kinetics observed is dependent on the hot spot temperature, system size and thermal conductivity. For cases where ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. The gradual temperature and pressure increase in the incubation period is accompanied by accumulation of heavier polyradicals. The challenge of connecting such chemistry in mesoscale simulations remain in reducing the complexity of chemistry. The hot spot growth kinetics in RDX grains and interfaces is an important challenge for reactive simulations aiming to fill in the gaps in our knowledge in the nanoseconds to microseconds time scale. The results discussed indicate that the mesoscale chemistry may include large polyradical molecules in dense reactive mix reaching an instability point at certain temperatures and pressures.

  3. NMR Method for Characterizing Microsecond-to-Millisecond Chemical Exchanges Utilizing Differential Multiple-Quantum Relaxation in High Molecular Weight Proteins.

    PubMed

    Toyama, Yuki; Osawa, Masanori; Yokogawa, Mariko; Shimada, Ichio

    2016-02-24

    Chemical exchange processes of proteins on the order of microseconds (μs) to milliseconds (ms) play critical roles in biological functions. Developments in methyl-transverse relaxation optimized spectroscopy (methyl-TROSY), which observes the slowly relaxing multiple quantum (MQ) coherences, have enabled the studies of biologically important large proteins. However, the analyses of μs to ms chemical exchange processes based on the methyl-TROSY principle are still challenging, because the interpretation of the chemical exchange contributions to the MQ relaxation profiles is complicated, as significant chemical shift differences occur in both (1)H and (13)C nuclei. Here, we report a new methyl-based NMR method for characterizing chemical exchanges, utilizing differential MQ relaxation rates and a heteronuclear double resonance pulse technique. The method enables quantitative evaluations of the chemical exchange processes, in which significant chemical shift differences exist in both the (1)H and (13)C nuclei. The versatility of the method is demonstrated with the application to KirBac1.1, with an apparent molecular mass of 200 kDa.

  4. EFFECT OF LASER LIGHT ON MATTER. LASER PLASMAS: Compression of hollow gaseous envelopes at a microsecond plasma generator of x radiation

    NASA Astrophysics Data System (ADS)

    Bartnik, A.; Karpinski, L.; Ivanenkov, G. V.; Pikuz, S. A.; Shelkovenko, T. A.

    1993-11-01

    Experiments with electric discharges across hollow gaseous envelopes have been carried out on a microsecond plasma generator of x radiation (200 kA, 40 kV, 1.5 μs, Ne-Ar mixture). The diagnostic complex made it possible to carry out time- and space-resolved observations in the visible range by means of streak and framing cameras. In the vacuum-UV range, a spectrograph with a transparent grating and a vacuum x-ray diode were used. In the soft x-ray range, a crystal spectrograph with convex and spherically bent crystals, a crystal x-ray microscope, pinhole cameras, and p-i-n diodes were used. The spectral range 0.3-1.5 nm contains lines of He- and H-like Ne and of He-like Ar. These ions are used for x-ray-spectral estimates of the electron temperatures and the densities of the plasma of the hot spots. These estimates lie in the ranges 1-1.3 keV and (0.5-1) · 1022 cm-3. At the optimum nozzle diameter in terms of the x-ray yield, a kink instability and the formation of hot spots are observed simultaneously. Suppressing the kink instability increases the radiation yield. Emission from the plasma column in Kα lines of argon has been observed.

  5. Polarized fluorescence depletion reports orientation distribution and rotational dynamics of muscle cross-bridges.

    PubMed Central

    Bell, Marcus G; Dale, Robert E; van der Heide, Uulke A; Goldman, Yale E

    2002-01-01

    The method of polarized fluorescence depletion (PFD) has been applied to enhance the resolution of orientational distributions and dynamics obtained from fluorescence polarization (FP) experiments on ordered systems, particularly in muscle fibers. Previous FP data from single fluorescent probes were limited to the 2(nd)- and 4(th)-rank order parameters, and , of the probe angular distribution (beta) relative to the fiber axis and , a coefficient describing the extent of rapid probe motions. We applied intense 12-micros polarized photoselection pulses to transiently populate the triplet state of rhodamine probes and measured the polarization of the ground-state depletion using a weak interrogation beam. PFD provides dynamic information describing the extent of motions on the time scale between the fluorescence lifetime (e.g., 4 ns) and the duration of the photoselection pulse and it potentially supplies information about the probe angular distribution corresponding to order parameters above rank 4. Gizzard myosin regulatory light chain (RLC) was labeled with the 6-isomer of iodoacetamidotetramethylrhodamine and exchanged into rabbit psoas muscle fibers. In active contraction, dynamic motions of the RLC on the PFD time scale were intermediate between those observed in relaxation and rigor. The results indicate that previously observed disorder of the light chain region in contraction can be ascribed principally to dynamic motions on the microsecond time scale. PMID:12124286

  6. RHIC Polarized proton operation

    SciTech Connect

    Huang, H.; Ahrens, L.; Alekseev, I.G.; Aschenauer, E.; Atoian, G.; Bai, M.; Bazilevsky, A.; Blaskiewicz, M.; Brennan, J.M.; Brown, K.A.; Bruno, D.; Connolly, R.; Dion, A.; D'Ottavio, T.; Drees, K.A.; Fischer, W.; Gardner, C.; Glenn, J.W.; Gu, X.; Harvey, M.; Hayes, T.; Hoff, L.; Hulsart, R.L.; Laster, J.; Liu, C.; Luo, Y.; MacKay, W.W.; Makdisi, Y.; Marr, G.J.; Marusic, A.; Meot, F.; Mernick, K.; Michnoff, R,; Minty, M.; Montag, C.; Morris, J.; Nemesure, S.; Poblaguev, A.; Ptitsyn, V.; Ranjibar, V.; Robert-Demolaize, G.; Roser, T.; J.; Severino, F.; Schmidke, B.; Schoefer, V.; Severino, F.; Smirnov, D.; Smith, K.; Steski, D.; Svirida, D.; Tepikian, S.; Trbojevic, D.; Tsoupas, N.; Tuozzolo, J. Wang, G.; Wilinski, M.; Yip, K.; Zaltsman, A.; Zelenski, A.; Zeno, K.; Zhang, S.Y.

    2011-03-28

    The Relativistic Heavy Ion Collider (RHIC) operation as the polarized proton collider presents unique challenges since both luminosity(L) and spin polarization(P) are important. With longitudinally polarized beams at the experiments, the figure of merit is LP{sup 4}. A lot of upgrades and modifications have been made since last polarized proton operation. A 9 MHz rf system is installed to improve longitudinal match at injection and to increase luminosity. The beam dump was upgraded to increase bunch intensity. A vertical survey of RHIC was performed before the run to get better magnet alignment. The orbit control is also improved this year. Additional efforts are put in to improve source polarization and AGS polarization transfer efficiency. To preserve polarization on the ramp, a new working point is chosen such that the vertical tune is near a third order resonance. The overview of the changes and the operation results are presented in this paper. Siberian snakes are essential tools to preserve polarization when accelerating polarized beams to higher energy. At the same time, the higher order resonances still can cause polarization loss. As seen in RHIC, the betatron tune has to be carefully set and maintained on the ramp and during the store to avoid polarization loss. In addition, the orbit control is also critical to preserve polarization. The higher polarization during this run comes from several improvements over last run. First we have a much better orbit on the ramp. The orbit feedback brings down the vertical rms orbit error to 0.1mm, much better than the 0.5mm last run. With correct BPM offset and vertical realignment, this rms orbit error is indeed small. Second, the jump quads in the AGS improved input polarization for RHIC. Third, the vertical tune was pushed further away from 7/10 snake resonance. The tune feedback maintained the tune at the desired value through the ramp. To calibrate the analyzing power of RHIC polarimeters at any energy above

  7. Mono- and polynucleation, atomistic growth, and crystal phase of III-V nanowires under varying group V flow

    SciTech Connect

    Dubrovskii, V. G.

    2015-05-28

    We present a refined model for the vapor-liquid-solid growth and crystal structure of Au-catalyzed III-V nanowires, which revisits several assumptions used so far and is capable of describing the transition from mononuclear to polynuclear regime and ultimately to regular atomistic growth. We construct the crystal phase diagrams and calculate the wurtzite percentages, elongation rates, critical sizes, and polynucleation thresholds of Au-catalyzed GaAs nanowires depending on the As flow. We find a non-monotonic dependence of the crystal phase on the group V flow, with the zincblende structure being preferred at low and high group V flows and the wurtzite structure forming at intermediate group V flows. This correlates with most of the available experimental data. Finally, we discuss the atomistic growth picture which yields zincblende crystal structure and should be very advantageous for fabrication of ternary III-V nanowires with well-controlled composition and heterointerfaces.

  8. Atomistic simulation of defects formation and structure transitions in U-Mo alloys at swift heavy ion irradiation

    NASA Astrophysics Data System (ADS)

    Kolotova, L. N.; Starikov, S. V.

    2017-01-01

    At irradiation of swift heavy ions, the track formation frequently takes place in nuclear materials. There is a large interest to understanding of the mechanisms of defects/track formation at this phenomenon. In this work, the atomistic simulation of defects formation and melting in U-Mo alloys at irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes at irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation at irradiation in the various conditions are calculated.

  9. (Ca,Sr)CO 3 aqueous-solid solution systems: From atomistic simulations to thermodynamic modelling

    NASA Astrophysics Data System (ADS)

    Kulik, D. A.; Vinograd, V. L.; Paulsen, N.; Winkler, B.

    The uptake of strontium in calcium carbonates is a topic of sustained interest in (radio)geochemistry. The available data on (Ca,Sr)CO 3 aqueous-solid solution (Aq-SS) systems with the calcite ( R3barc) and aragonite ( Pmcn) structures are reconciled using a stepwise approach from atomistic to thermodynamic modelling consisting of: (1) Quantum-mechanical and force-field calculations aimed at the prediction of standard thermodynamic properties of a hypothetical pure SrCO 3( R3barc) compound; (2) Force-field calculations on supercell structures of end members with defects of incoherent atoms in the cluster expansion framework, followed by Monte Carlo simulations of the excess SS mixing properties in both R3barc and Pmcn structures; (3) Thermodynamic modelling of Aq-SS systems with SS phases of both structures using the Gibbs Energy Minimization (GEM) code in two scenarios: (i) aqueous solution in equilibrium with one SS phase of either Pmcn or R3barc structure; (ii) aqueous solution equilibrated with two SS phases having different structures. The (ii) case was investigated using two approaches: (A) The two SS introduced as separate phases, with the excess mixing in each phase described by an own Guggenheim polynomial and (B) End members of different structures combined into a single calcite-strontianite phase using the Darken’s Quadratic Formulation (DQF) mixing model. For the aragonite-strontianite SS system, a nearly symmetric solvus is predicted in good agreement with the available calorimetric and electrochemical data. The solubility data at low Sr concentrations are qualitatively reproduced with the DQF model. For the (Ca,Sr)CO 3 SS with the calcite structure, a slightly asymmetric, moderately positive excess Gibbs free energy of mixing is predicted and shown to agree well with known equilibrium distribution coefficients for trace Sr in calcite and with the predicted solubility product of the hypothetical SrCO 3( R3barc) end member. Although each SS system

  10. Polarized Light: Three Demonstrations.

    ERIC Educational Resources Information Center

    Goehmann, Ruth; Welty, Scott

    1984-01-01

    Describes three demonstrations used in the Chicago Museum of Science and Industry polarized light show. The procedures employed are suitable for the classroom by using smaller polarizers and an overhead projector. Topic areas include properties of cellophane tape, nondisappearing arrows, and rope through a picket fence. (JN)

  11. Polar Science Is Cool!

    ERIC Educational Resources Information Center

    Weeks, Sophie

    2012-01-01

    Children are fascinated by the fact that polar scientists do research in extremely cold and dangerous places. In the Arctic they might be viewed as lunch by a polar bear. In the Antarctic, they could lose toes and fingers to frostbite and the wind is so fast it can rip skin off. They camp on ice in continuous daylight, weeks from any form of…

  12. Generalized mosaicing: polarization panorama.

    PubMed

    Schechner, Yoav Y; Nayar, Shree K

    2005-04-01

    We present an approach to image the polarization state of object points in a wide field of view, while enhancing the radiometric dynamic range of maging systems by generalizing image mosaicing. The approach is biologically-inspired, as it emulates spatially varying polarization sensitivity of some animals. In our method, a spatially varying polarization and attenuation filter is rigidly attached to a camera. As the system moves, it senses each scene point multiple times, each time filtering it through a different filter polarizing angle, polarizance, and transmittance. Polarization is an additional dimension of the generalized mosaicing paradigm, which has recently yielded high dynamic range images and multispectral images in a wide field of view using other kinds of filters. The image acquisition is as easy as in traditional image mosaics. The computational algorithm can easily handle nonideal polarization filters (partial polarizers), variable exposures, and saturation in a single framework. The resulting mosaic represents the polarization state at each scene point. Using data acquired by this method, we demonstrate attenuation and enhancement of specular reflections and semireflection separation in an image mosaic.

  13. The Polar Insulation Investigation

    ERIC Educational Resources Information Center

    Urban-Rich, Juanita

    2006-01-01

    In this article, the author developed an activity called "The Polar Insulation Investigation." This activity builds on students' natural interest in "things polar" and introduces them to animal adaptations in a unique way. The aim of the exploration is to determine the role of animal coverings (e.g., blubber, fur, and feathers) and to see which is…

  14. Our Polar Past

    ERIC Educational Resources Information Center

    Clary, Renee; Wandersee, James

    2009-01-01

    The study of polar exploration is fascinating and offers students insights into the history, culture, and politics that affect the developing sciences at the farthest ends of Earth. Therefore, the authors think there is value in incorporating polar exploration accounts within modern science classrooms, and so they conducted research to test their…

  15. Polarization Radar Processing Technology

    DTIC Science & Technology

    1989-10-01

    Oi"C FILE ( J qII RADC-TR-89-144 In-House Report October 1989 AD-A215 242 POLARIZATION RADAR PROCESSING TECHNOLOGY Kenneth C. Stiefvater, Russell D...NO. NO. NO. ACCESSION NO. 62702F 4506 11 58 11. TITLE (Include Security Classification) POLARIZATION RADAR PROCESSING TECHNOLOGY 12. PERSONAL AUTHOR(S

  16. Nomenclature of polarized light - Elliptical polarization

    NASA Technical Reports Server (NTRS)

    Clarke, D.

    1974-01-01

    Alternative handedness and sign conventions for relating the orientation of elliptical polarization are discussed. The discussion proceeds under two headings: (1) snapshot picture, where the emphasis for the convention is contained in the concept of handedness; and (2) angular momentum consideration, where the emphasis for the convention is strongly associated with mathematical convention and the sign of the fourth Stokes parameter.

  17. Spherical ion oscillations in a positive polarity gridded inertial-electrostatic confinement device

    SciTech Connect

    Bandara, R.; Khachan, J.

    2013-07-15

    A pulsed, positive polarity gridded inertial electrostatic confinement device has been investigated experimentally, using a differential emissive probe and potential traces as primary diagnostics. Large amplitude oscillations in the plasma current and plasma potential were observed within a microsecond of the discharge onset, which are indicative of coherent ion oscillations about a temporarily confined excess of recirculating electron space charge. The magnitude of the depth of the potential well in the established virtual cathode was determined using a differential emissive Langmuir probe, which correlated well to the potential well inferred from the ion oscillation frequency for both hydrogen and argon experiments. It was found that the timescale for ion oscillation dispersion is strongly dependent on the neutral gas density, and weakly dependent on the peak anode voltage. The cessation of the oscillations was found to be due to charge exchange processes converting ions to high velocity neutrals, causing the abrupt de-coherence of the oscillations through an avalanche dispersion in phase space.

  18. Spherical ion oscillations in a positive polarity gridded inertial-electrostatic confinement device

    NASA Astrophysics Data System (ADS)

    Bandara, R.; Khachan, J.

    2013-07-01

    A pulsed, positive polarity gridded inertial electrostatic confinement device has been investigated experimentally, using a differential emissive probe and potential traces as primary diagnostics. Large amplitude oscillations in the plasma current and plasma potential were observed within a microsecond of the discharge onset, which are indicative of coherent ion oscillations about a temporarily confined excess of recirculating electron space charge. The magnitude of the depth of the potential well in the established virtual cathode was determined using a differential emissive Langmuir probe, which correlated well to the potential well inferred from the ion oscillation frequency for both hydrogen and argon experiments. It was found that the timescale for ion oscillation dispersion is strongly dependent on the neutral gas density, and weakly dependent on the peak anode voltage. The cessation of the oscillations was found to be due to charge exchange processes converting ions to high velocity neutrals, causing the abrupt de-coherence of the oscillations through an avalanche dispersion in phase space.

  19. Free energy functionals for polarization fluctuations: Pekar factor revisited

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

    2017-02-01

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  20. Free energy functionals for polarization fluctuations: Pekar factor revisited.

    PubMed

    Dinpajooh, Mohammadhasan; Newton, Marshall D; Matyushov, Dmitry V

    2017-02-14

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  1. Free energy functionals for polarization fluctuations: Pekar factor revisited

    DOE PAGES

    Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

    2017-02-13

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. This separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom, within dielectric continuum models. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parametermore » accounting for the solvent effect on electron transfer. We study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. But, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).« less

  2. Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

    Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

  3. Exploration of complex multilayer film growth morphologies: STM analysis and predictive atomistic modeling for Ag on Ag(111)

    SciTech Connect

    Li, Maozhi; Chung, P.W.; Cox, E.; Jenks, C.J.; Thiel, P.A.; Evans, J.W.

    2008-01-03

    Scanning tunneling microscopy studies are integrated with development of a realistic atomistic model to both characterize and elucidate the complex mounded morphologies formed by deposition of Ag on Ag(111) at 150 and 180 K. Threefold symmetric lateral shapes of islands and mounds are shown to reflect the influence of a nonuniform step edge barrier inhibiting interlayer transport. Modeling of structure at the mound peaks leads to a sensitive estimate of the magnitude of this large barrier.

  4. Polarization of clouds

    NASA Astrophysics Data System (ADS)

    Goloub, Philippe; Herman, Maurice; Parol, Frederic

    1995-12-01

    This paper reports the main results concerning polarization by clouds derived from POLDER (polarization and directionality of earth's reflectances) airborne version. These results tend to confirm the high information content in the polarization (phase, altimetry). The preliminary results of EUCREX'94 (European Cloud Radiation Experiment) evidenced the drastically different polarized signatures for ice crystals and water droplets. Here we report systematic and statistically significative observations over the whole EUCREX data set. The results show that the cirrus exhibit their own signature. Preliminary observations performed during CLEOPATRA'91 (Cloud Experiment Ober Pfaffenhofen And Transport) and EUCREX'94 campaigns have shown the feasibility of cloud altimetry using spectral information (443 nm and 865 nm) of the polarized light over liquid water droplets clouds. Altimetry technique has been generalized on ASTEX-SOFIA'92 and EUCREX'94 data sets. All these results are presented and discussed in this paper.

  5. Parallel Polarization State Generation

    NASA Astrophysics Data System (ADS)

    She, Alan; Capasso, Federico

    2016-05-01

    The control of polarization, an essential property of light, is of wide scientific and technological interest. The general problem of generating arbitrary time-varying states of polarization (SOP) has always been mathematically formulated by a series of linear transformations, i.e. a product of matrices, imposing a serial architecture. Here we show a parallel architecture described by a sum of matrices. The theory is experimentally demonstrated by modulating spatially-separated polarization components of a laser using a digital micromirror device that are subsequently beam combined. This method greatly expands the parameter space for engineering devices that control polarization. Consequently, performance characteristics, such as speed, stability, and spectral range, are entirely dictated by the technologies of optical intensity modulation, including absorption, reflection, emission, and scattering. This opens up important prospects for polarization state generation (PSG) with unique performance characteristics with applications in spectroscopic ellipsometry, spectropolarimetry, communications, imaging, and security.

  6. Parallel Polarization State Generation

    PubMed Central

    She, Alan; Capasso, Federico

    2016-01-01

    The control of polarization, an essential property of light, is of wide scientific and technological interest. The general problem of generating arbitrary time-varying states of polarization (SOP) has always been mathematically formulated by a series of linear transformations, i.e. a product of matrices, imposing a serial architecture. Here we show a parallel architecture described by a sum of matrices. The theory is experimentally demonstrated by modulating spatially-separated polarization components of a laser using a digital micromirror device that are subsequently beam combined. This method greatly expands the parameter space for engineering devices that control polarization. Consequently, performance characteristics, such as speed, stability, and spectral range, are entirely dictated by the technologies of optical intensity modulation, including absorption, reflection, emission, and scattering. This opens up important prospects for polarization state generation (PSG) with unique performance characteristics with applications in spectroscopic ellipsometry, spectropolarimetry, communications, imaging, and security. PMID:27184813

  7. Cell polarity: mechanochemical patterning.

    PubMed

    Goehring, Nathan W; Grill, Stephan W

    2013-02-01

    Nearly every cell type exhibits some form of polarity, yet the molecular mechanisms vary widely. Here we examine what we term 'chemical systems' where cell polarization arises through biochemical interactions in signaling pathways, 'mechanical systems' where cells polarize due to forces, stresses and transport, and 'mechanochemical systems' where polarization results from interplay between mechanics and chemical signaling. To reveal potentially unifying principles, we discuss mathematical conceptualizations of several prototypical examples. We suggest that the concept of local activation and global inhibition - originally developed to explain spatial patterning in reaction-diffusion systems - provides a framework for understanding many cases of cell polarity. Importantly, we find that the core ingredients in this framework - symmetry breaking, self-amplifying feedback, and long-range inhibition - involve processes that can be chemical, mechanical, or even mechanochemical in nature.

  8. Atomistic simulation of the structure and elastic properties of gold nanowires

    NASA Astrophysics Data System (ADS)

    Diao, Jiankuai; Gall, Ken; Dunn, Martin L.

    2004-09-01

    We performed atomistic simulations to study the effect of free surfaces on the structure and elastic properties of gold nanowires aligned in the <1 0 0> and <1 1 1> crystallographic directions. Computationally, we formed a nanowire by assembling gold atoms into a long wire with free sides by putting them in their bulk fcc lattice positions. We then performed a static relaxation on the assemblage. The tensile surface stresses on the sides of the wire cause the wire to contract along the length with respect to the original fcc lattice, and we characterize this deformation in terms of an equilibrium strain versus the cross-sectional area. While the surface stress causes wires of both orientations and all sizes to increasingly contract with decreasing cross-sectional area, when the cross-sectional area of a <1 0 0> nanowire is less than 1.83 nm×1.83 nm, the wire undergoes a phase transformation from fcc to bct, and the equilibrium strain increases by an order of magnitude. We then applied a uniform uniaxial strain incrementally to 1.2% to the relaxed nanowires in a molecular statics framework. From the simulation results we computed the effective axial Young's modulus and Poisson's ratios of the nanowire as a function of cross-sectional area. We used two approaches to compute the effective elastic moduli, one based on a definition in terms of the strain derivative of the total energy and another in terms of the virial stress often used in atomistic simulations. Both give quantitatively similar results, showing an increase in Young's modulus with a decrease of cross-sectional area in the nanowires that do not undergo a phase transformation. Those that undergo a phase transformation experience an increase of about a factor of three of Young's modulus. The Poisson's ratio of the <1 0 0> wires that do not undergo a phase transformation show little change with the cross-sectional area. Those wires that undergo a phase transformation experience an increase of about 10% in

  9. Atomistic modeling of nanowires, small-scale fatigue damage in cast magnesium, and materials for MEMS

    SciTech Connect

    Dunn, Martin L.; Talmage, Mellisa J.; David L. McDowell; West, Neil; Gullett, Philip Michael; Miller, David C.; Spark, Kevin; Diao, Jiankuai; Horstemeyer, Mark F.; Zimmerman, Jonathan A.; Gall, K.

    2006-10-01

    Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project

  10. Atomistic study of hydrogen embrittlement of grain boundaries in nickel: I. Fracture

    NASA Astrophysics Data System (ADS)

    Tehranchi, A.; Curtin, W. A.

    Hydrogen ingress into a metal is a persistent source of embrittlement. Fracture surfaces are often intergranular, suggesting favorable cleave crack growth along grain boundaries (GBs) as one driver for embrittlement. Here, atomistic simulations are used to investigate the effects of segregated hydrogen on the behavior of cracks along various symmetric tilt grain boundaries in fcc Nickel. An atomistic potential for Ni-H is first recalibrated against new quantum level computations of the energy of H in specific sites within the NiΣ5(120)⟨100⟩ GB. The binding energy of H atoms to various atomic sites in the NiΣ3(111) (twin), NiΣ5(120)⟨100⟩, NiΣ99(557)⟨110⟩, and NiΣ9(221)⟨110⟩ GBs, and to various surfaces created by separating these GBs into two possible fracture surfaces, are computed and used to determine equilibrium H concentrations at bulk H concentrations typical of embrittlement in Ni. Mode I fracture behavior is then studied, examining the influence of H in altering the competition between dislocation emission (crack blunting; "ductile" behavior) and cleavage fracture ("brittle" behavior) for intergranular cracks. Simulation results are compared with theoretical predictions (Griffith theory for cleavage; Rice theory for emission) using the computed surface energies. The deformation behavior at the GBs is, however, generally complex and not as simple as cleavage or emission at a sharp crack tip, which is not unexpected due to the complexity of the GB structures. In cases predicted to emit dislocations from the crack tip, the presence of H atoms reduces the critical load for emission of the dislocations and no cleavage is found. In the cases predicted to cleave, the presence of H atoms reduces the cleavage stress intensity and makes cleavage easier, including NiΣ9(221)⟨110⟩ which emits dislocations in the absence of H. Aside from the one unusual NiΣ9(221)⟨110⟩ case, no tendency is found for H to cause a ductile

  11. Atomistic methodologies for material properties of 2D materials at the nanoscale

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen

    Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our

  12. Atomistic modeling of phonon bandstructure and transport for optimal thermal management in nanoscale devices

    NASA Astrophysics Data System (ADS)

    Sundaresan, Sasi Sekaran

    Monte Carlo based statistical approach to solve Boltzmann Transport Equation (BTE) has become a norm to investigate heat transport in semiconductors at sub-micron regime, owing mainly to its ability to characterize realistically sized device geometries qualitatively. One of the primary issues with this technique is that the approach predominantly uses empirically fitted phonon dispersion relations as input to determine the properties of phonons so as to predict the thermal conductivity of specified material geometry. The empirically fitted dispersion relations assume harmonic approximation thereby failing to account for thermal expansion, interaction of lattice waves, effect of strain on spring stiffness, and accurate phonon-phonon interaction. To circumvent this problem, in this work, a coupled molecular mechanics-Monte Carlo (MM-MC) platform has been developed and used to solve the phonon Boltzmann Transport Equation (BTE) for the calculation of thermal conductivity of several novel and emerging nanostructures. The use of the quasi-anharmonic MM approach (as implemented in the open source NEMO 3-D software toolkit) not only allows one to capture the true atomicity of the underlying lattice but also enables the simulation of realistically-sized structures containing millions of atoms. As compared to the approach using an empirically fitted phonon dispersion relation, here, a 17% increase in the thermal conductivity for a silicon nanowire due to the incorporation of atomistic corrections in the LA (longitudinal acoustic) branch alone has been reported. The atomistically derived thermal conductivity as calculated from the MM-MC framework is then used in the modular design and analysis of (i) a silicon nanowire based thermoelectric cooler (TEC) unit, and (ii) a GaN/InN based nanostructured light emitting device (LED). It is demonstrated that the use of empirically fitted phonon bandstructure parameters overestimates the temperature difference between the hot and the

  13. EPR detected polarization transfer between Gd3+ and protons at low temperature and 3.3 T: The first step of dynamic nuclear polarization

    NASA Astrophysics Data System (ADS)

    Nagarajan, Vijayasarathi; Hovav, Yonatan; Feintuch, Akiva; Vega, Shimon; Goldfarb, Daniella

    2010-06-01

    Electron-electron double resonance pulsed electron paramagnetic resonance (EPR) at 95 GHz (3.3 T) is used to follow the dynamics of the electron spin polarization during the first stages of dynamic nuclear polarization in solids. The experiments were performed on a frozen solution of Gd+3 (S =7/2) in water/glycerol. Focusing on the central |-1/2⟩→|+1/2⟩ transition we measured the polarization transfer from the Gd3+ electron spin to the adjacent H1 protons. The dependence of the echo detected EPR signal on the length of the microwave irradiation at the EPR "forbidden" transition corresponding to an electron and a proton spin flip is measured for different powers, showing dynamics on the microsecond to millisecond time scales. A theoretical model based on the spin density matrix formalism is suggested to account for this dynamics. The central transition of the Gd3+ ion is considered as an effective S =1/2 system and is coupled to H1 (I =1/2) nuclei. Simulations based on a single electron-single nucleus four level system are shown to deviate from the experimental results and an alternative approach taking into account the more realistic multinuclei picture is shown to agree qualitatively with the experiments.

  14. Crystal plasticity model for BCC iron atomistically informed by kinetics of correlated kinkpair nucleation on screw dislocation

    NASA Astrophysics Data System (ADS)

    Narayanan, Sankar; McDowell, David L.; Zhu, Ting

    2014-04-01

    The mobility of dislocation in body-centered cubic (BCC) metals is controlled by the thermally activated nucleation of kinks along the dislocation core. By employing a recent interatomic potential and the Nudged Elastic Band method, we predict the atomistic saddle-point state of 1/2<111> screw dislocation motion in BCC iron that involves the nucleation of correlated kinkpairs and the resulting double superkinks. This unique process leads to a single-humped minimum energy path that governs the one-step activation of a screw dislocation to move into the adjacent {110} Peierls valley, which contrasts with the double-humped energy path and the two-step transition predicted by other interatomic potentials. Based on transition state theory, we use the atomistically computed, stress-dependent kinkpair activation parameters to inform a coarse-grained crystal plasticity flow rule. Our atomistically-informed crystal plasticity model quantitatively predicts the orientation dependent stress-strain behavior of BCC iron single crystals in a manner that is consistent with experimental results. The predicted temperature and strain-rate dependencies of the yield stress agree with experimental results in the 200-350 K temperature regime, and are rationalized by the small activation volumes associated with the kinkpair-mediated motion of screw dislocations.

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

    PubMed

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

    2016-08-25

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

  16. A general library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models

    PubMed Central

    Mamonov, Artem B.; Bhatt, Divesh; Cashman, Derek J.; Ding, Ying; Zuckerman, Daniel M.

    2009-01-01

    We introduce “library based Monte Carlo” (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on pre-calculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained models, as we demonstrate in this “proof of principle” report. We first verify the approach in a toy model and in implicitly solvated poly-alanine systems. We next study five proteins, up to 309 residues in size. Based on atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified Gō-like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while an arbitrary subset of interactions is “turned on.” PMID:19594147

  17. Atomistic-level non-equilibrium model for chemically reactive systems based on steepest-entropy-ascent quantum thermodynamics

    NASA Astrophysics Data System (ADS)

    Li, Guanchen; Al-Abbasi, Omar; von Spakovsky, Michael R.

    2014-10-01

    This paper outlines an atomistic-level framework for modeling the non-equilibrium behavior of chemically reactive systems. The framework called steepest- entropy-ascent quantum thermodynamics (SEA-QT) is based on the paradigm of intrinsic quantum thermodynamic (IQT), which is a theory that unifies quantum mechanics and thermodynamics into a single discipline with wide applications to the study of non-equilibrium phenomena at the atomistic level. SEA-QT is a novel approach for describing the state of chemically reactive systems as well as the kinetic and dynamic features of the reaction process without any assumptions of near-equilibrium states or weak-interactions with a reservoir or bath. Entropy generation is the basis of the dissipation which takes place internal to the system and is, thus, the driving force of the chemical reaction(s). The SEA-QT non-equilibrium model is able to provide detailed information during the reaction process, providing a picture of the changes occurring in key thermodynamic properties (e.g., the instantaneous species concentrations, entropy and entropy generation, reaction coordinate, chemical affinities, reaction rate, etc). As an illustration, the SEA-QT framework is applied to an atomistic-level chemically reactive system governed by the reaction mechanism F + H2 leftrightarrow FH + H.

  18. Interplanetary magnetic sector polarity inferred from polar geomagnetic field observations

    NASA Technical Reports Server (NTRS)

    Friis-Christensen, E.; Lassen, K.; Wilcox, J. M.; Gonzalez, W.; Colburn, D. S.

    1971-01-01

    In order to infer the interplanetary sector polarity from polar geomagnetic field diurnal variations, measurements were carried out at Godhavn and Thule (Denmark) Geomagnetic Observatories. The inferred interplanetary sector polarity was compared with the polarity observed at the same time by Explorer 33 and 35 magnetometers. It is shown that the polarity (toward or away from the sun) of the interplanetary magnetic field can be reliably inferred from observations of the polar cap geomagnetic fields.

  19. Neutron Polarizers Based on Polarized 3He

    SciTech Connect

    William M. Snow

    2005-05-01

    The goal of this work, which is a collaborative effort between Indiana University, NIST, and Hamilton College, is to extend the technique of polarized neutron scattering into new domains by the development and application of polarized 3He-based neutron spin filters. After the IPNS experiment which measured Zeeman sp[litting in surface scattered neutrons using a polarized 3He cell as a polarization analyzer transporterd by car from Bloomington to Chicago, the Indiana work focused on technical developments to improve the 3He polarization of the Indiana compression system. The compression system was rebuilt with a new valve system which allows gas trapped in the dead volume of the compressors at the end of the piston stroke to be exhausted and conducted back to the optical pumping cell where it can be repolarized. We also incorporated a new intermediate storage volume made at NIST from 1720 glass which will reduce polarization losses between the compressors. Furthermore, we improved the stability of the 1083 nm laser by cooling the LMA rod. We achieved 60% 3he polarization in the optical pumping cell and 87% preservation of the polarization during compression. In parallel we built a magnetically-shielded transport solenoid for use on neutron scattering instruments such as POSY which achieves a fractional field uniformity of better than 10-3 per cm. The field was mapped using an automated 3D field mapping system for in-situ measurement of magnetic field gradients Diluted magnetic semiconductors offer many exciting opportunities for investigation of spintronic effects in solids and are certain to be one of the most active areas of condensed matter physics over then next several years. These materials can act as efficient spin injectors for devices that make use of spin-dependent transport phenomena. We just (late July 2002) finished a neutron reflectivity experiment at NIST on a GaMnAs trilayer film. This material is a ferromagnetic semiconductor which is of interest

  20. Polarization at the SLC

    NASA Astrophysics Data System (ADS)

    Moffeit, Kenneth C.

    1989-05-01

    The Stanford Linear Collider was designed to accommodate polarized electron beams. Longitudinally polarized electrons colliding with unpolarized positrons at a center of mass energy near the Z0 mass can be used as novel and sensitive probes of the electroweak process. A gallium arsenide based photon emission source will provide a beam of longitudinally polarized electrons of about 45 percent polarization. A system of bend magnets and a superconducting solenoid will be used to rotate the spins so that the polarization is preserved while the 1.21 GeV electrons are stored in the damping ring. Another set of bend magnets and two superconducting solenoids orient the spin vectors so that longitudinal polarization of the electrons is achieved at the collision point with the unpolarized positrons. A system to monitor the polarization based on Mo/ller and Compton scattering will be used. Nearly all major components have been fabricated and tested. Subsystems of the source and polarimeters have been installed, and studies are in progress. The installation and commissioning of the entire system will take place during available machine shutdown periods as the commissioning of SLC progresses.

  1. Atomistic modeling of thermodynamic properties of Pu-Ga alloys based on the Invar mechanism

    NASA Astrophysics Data System (ADS)

    Lee, Tongsik; Taylor, Christopher D.; Lawson, A. C.; Conradson, Steven D.; Chen, Shao Ping; Caro, A.; Valone, Steven M.; Baskes, Michael I.

    2014-05-01

    We present an atomistic model that accounts for a range of anomalous thermodynamic properties of the fcc δ phase of Pu-Ga alloys in terms of the Invar mechanism. Two modified embedded atom method potentials are employed to represent competing electronic states in δ-Pu, each of which has an individual configuration dependence as well as distinct interactions with gallium. Using classical Monte Carlo simulations, we compute the temperature dependence of various thermodynamic properties for different dilute gallium concentrations. The model reproduces the observed effects of excessive volume reduction along with a rapid shift in thermal expansion from negative to positive values with increasing gallium concentration. It also predicts progressive stiffening upon dilute-gallium alloying, while the calculated thermal softening is nearly independent of the gallium concentration in agreement with resonant ultrasound spectroscopy measurements in the literature. Analysis of the local structure predicted by the model indicates that the distribution of the gallium atoms is not completely random in the δ phase due to the presence of short-range order associated with the Invar mechanism. This effect is consistent with the nanoscale heterogeneity in local gallium concentration which is observed in recent extended x-ray absorption fine structure spectroscopy experiments. Implications of the Invar effect for phase stability and physical interpretations of the two states are also discussed.

  2. DL-FIND: an open-source geometry optimizer for atomistic simulations.

    PubMed

    Kästner, Johannes; Carr, Joanne M; Keal, Thomas W; Thiel, Walter; Wander, Adrian; Sherwood, Paul

    2009-10-29

    Geometry optimization, including searching for transition states, accounts for most of the CPU time spent in quantum chemistry, computational surface science, and solid-state physics, and also plays an important role in simulations employing classical force fields. We have implemented a geometry optimizer, called DL-FIND, to be included in atomistic simulation codes. It can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalized internal coordinates, and also functions of more variables independent of atomic structures. The implementation of the optimization algorithms is independent of the coordinate transformation used. Steepest descent, conjugate gradient, quasi-Newton, and L-BFGS algorithms as well as damped molecular dynamics are available as minimization methods. The partitioned rational function optimization algorithm, a modified version of the dimer method and the nudged elastic band approach provide capabilities for transition-state search. Penalty function, gradient projection, and Lagrange-Newton methods are implemented for conical intersection optimizations. Various stochastic search methods, including a genetic algorithm, are available for global or local minimization and can be run as parallel algorithms. The code is released under the open-source GNU LGPL license. Some selected applications of DL-FIND are surveyed.

  3. A new Monte Carlo method for investigating geometrical structures of lipid membranes with atomistic detail

    NASA Astrophysics Data System (ADS)

    Cheng, Sara; Qiu, Liming; Cheng, K.; Vaughn, Mark

    2011-10-01

    The distribution statistics of the surface area, volume and voids of lipid molecules are important parameters to characterize the structures of self-assembling lipid membranes. Traditional methods are mostly based on various assumptions of the thickness of the lipid membrane and the volumes of certain types of lipid molecules. However, those methods usually lead to an over- or underestimation of the average surface area of lipid molecules when compared to the experimental results of the pure lipid systems. We developed a new Monte Carlo method that is able to estimate the distributions and averages of surface area, volume and void space of the lipid molecules in the absence and presence of proteins of the MD simulation results of lipid membranes at the atomistic scale. We successfully validated our new method on an ordered hard-sphere system and on a phospholipid/cholesterol binary lipid system, all with known structural parameters. Using this new method, the structural perturbation of the conformal annular lipids in close proximity to the embedded protein in a lipid/protein system will also be presented.

  4. Spontaneous Formation of A Nanotube From A Square Ag Nanowire: An Atomistic View

    NASA Astrophysics Data System (ADS)

    Konuk Onat, Mine; Durukanoglu, Sondan

    2012-02-01

    We have performed molecular static calculations to investigate the recently observed phenomenon of the spontaneous formation of a nanotube from a regular, square Ag nanowire[1]. In the simulations, atoms are allowed to interact via the model potential obtained from the modified embedded atom method. Our simulations predict that this particular type of structural phase transformation is controlled by the nature of applied strain, length of the wire and initial cross-sectional shape. For such a perfect structural transformation, the <100> axially oriented fcc nanowire needs (1) to be formed by stacking A and B layers of an fcc crystal, both possessing the geometry of two interpenetrating one-lattice-parameter-wide squares, containing four atoms each, (2) to have an optimum length of eight layers, and (3) to be exposed to a combination of low and high stress along the length direction. The results further offer insights into atomistic nature of this specific structural transformation into a nanotube with the smallest possible cross-section. [1] M.J. Lagos et al., Nature Nanotech. 4, 149 (2009).

  5. An adhesive contact mechanics formulation based on atomistically induced surface traction

    SciTech Connect

    Fan, Houfu; Ren, Bo; Li, Shaofan

    2015-12-01

    In this work, we have developed a novel multiscale computational contact formulation based on the generalized Derjuguin approximation for continua that are characterized by atomistically enriched constitutive relations in order to study macroscopic interaction between arbitrarily shaped deformable continua. The proposed adhesive contact formulation makes use of the microscopic interaction forces between individual particles in the interacting bodies. In particular, the double-layer volume integral describing the contact interaction (energy, force vector, matrix) is converted into a double-layer surface integral through a mathematically consistent approach that employs the divergence theorem and a special partitioning technique. The proposed contact model is formulated in the nonlinear continuum mechanics framework and implemented using the standard finite element method. With no large penalty constant, the stiffness matrix of the system will in general be well-conditioned, which is of great significance for quasi-static analysis. Three numerical examples are presented to illustrate the capability of the proposed method. Results indicate that with the same mesh configuration, the finite element computation based on the surface integral approach is faster and more accurate than the volume integral based approach. In addition, the proposed approach is energy preserving even in a very long dynamic simulation.

  6. Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations

    DOE PAGES

    Tucker, Garritt J.; Foiles, Stephen Martin

    2014-09-22

    Over the past decade, numerous efforts have sought to understand the influence of twin boundaries on the behavior of polycrystalline materials. Early results suggested that twin boundaries within nanocrystalline face-centered cubic metals have a considerable effect on material behavior by altering the activated deformation mechanisms. In this work, we employ molecular dynamics simulations to elucidate the role of twin boundaries on the deformation of <100> columnar nanocrystalline copper at room temperature under uniaxial strain. We leverage non-local kinematic metrics, formulated from continuum mechanics theory, to compute atomically-resolved rotational and strain fields during plastic deformation. These results are then utilized tomore » compute the distribution of various nanoscale mechanisms during straining, and quantitatively resolve their contribution to the total strain accommodation within the microstructure, highlighting the fundamental role of twin boundaries. Our results show that nanoscale twins influence nanocrystalline copper by altering the cooperation of fundamental deformation mechanisms and their contributed role in strain accommodation, and we present new methods for extracting useful information from atomistic simulations. The simulation results suggest a tension–compression asymmetry in the distribution of deformation mechanisms and strain accommodation by either dislocations or twin boundary mechanisms. In highly twinned microstructures, twin boundary migration can become a significant deformation mode, in comparison to lattice dislocation plasticity in non-twinned columnar microstructures, especially during compression.« less

  7. Lattice Thermal Conductivity from Atomistic Simulations: ZrB2 and HfB2

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

    Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 have a number of properties that make them attractive for applications in extreme environments. One such property is their high thermal conductivity. Computational modeling of these materials will facilitate understanding of fundamental mechanisms, elucidate structure-property relationships, and ultimately accelerate the materials design cycle. Progress in computational modeling of UHTCs however has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parameterizations of such potentials for both ZrB2 and HfB2 appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of ZrB2 and HfB2. The atomic mass difference in these binary compounds leads to oscillations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials such as Silicon, for example. Results at room temperature and at elevated temperatures will be reported.

  8. Atomistic simulations of CO2 and N2 within cage-type silica zeolites.

    PubMed

    Madison, Lindsey; Heitzer, Henry; Russell, Colin; Kohen, Daniela

    2011-03-01

    The behavior of CO(2) and N(2), both as single components and as binary mixtures, in two cage-type silica zeolites was studied using atomistic simulations. The zeolites considered, ITQ-3 and paradigm cage-type zeolite ZK4 (the all-silica analog of LTA), were chosen so that the principles illustrated can be generalized to other adsorbent/adsorbate systems with similar topology and types of interactions. N(2) was chosen both because of the potential uses of N(2)/CO(2) separations and because it differs from CO(2) most significantly in the magnitude of its Coulombic interactions with zeolites. Despite similarities between N(2) and CO(2) diffusion in other materials, we show here that the diffusion of CO(2) within cage-type zeolites is dominated by an energy barrier to diffusion located at the entrance to the narrow channels connecting larger cages. This barrier originates in Coulombic interactions between zeolites and CO(2)'s quadrupole and results in well-defined orientations for the diffusing molecules. Furthermore, CO(2)'s favorable electrostatic interactions with the zeolite framework result in preferential binding in the windows between cages. N(2)'s behavior, in contrast, is more consistent with that of molecules previously studied. Our analysis suggests that CO(2)'s behavior might be common for adsorbates with quadrupoles that interact strongly with a material that has narrow windows between cages.

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

    NASA Astrophysics Data System (ADS)

    Bondi, Robert J.; Fox, Brian P.; Marinella, Matthew J.

    2016-03-01

    First-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influence on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.

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

    DOE PAGES

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

    2016-03-22

    In this study, first-principles calculations of electrical conductivity (σo) are revisited to determine the atomistic origin of its stochasticity in a distribution generated from sampling 14 ab-initio molecular dynamics configurations from 10 independently quenched models (n = 140) of substoichiometric amorphous Ta2O5, where each structure contains a neutral O monovacancy (VO0). Structural analysis revealed a distinct minimum Ta-Ta separation (dimer/trimer) corresponding to each VO0 location. Bader charge decomposition using a commonality analysis approach based on the σo distribution extremes revealed nanostructural signatures indicating that both the magnitude and distribution of cationic charge on the Ta subnetwork have a profound influencemore » on σo. Furthermore, visualization of local defect structures and their electron densities reinforces these conclusions and suggests σo in the amorphous oxide is best suppressed by a highly charged, compact Ta cation shell that effectively screens and minimizes localized VO0 interaction with the a-Ta2O5 network; conversely, delocalization of VO0 corresponds to metallic character and high σo. The random network of a-Ta2O5 provides countless variations of an ionic configuration scaffold in which small perturbations affect the electronic charge distribution and result in a fixed-stoichiometry distribution of σo; consequently, precisely controlled and highly repeatable oxide fabrication processes are likely paramount for advancement of resistive memory technologies.« less

  11. Ash'arite's atomistic conception of the physical world: A restatement

    SciTech Connect

    Pozi, Firdaus; Othman, Mohd Yusof; Mohamed, Faizal

    2013-11-27

    Atomism plays an important role in the history of human thought. It can be traced back from Democritus atomos in the 500 BC to particle physics and quantum theory in the 21{sup st} century. However, as it being rejected and developed in the course of history of science, it still brings the fundamental question that perplexes physicists. It gives the views that the world is eternal; that the laws of nature is immutable and eternal therefore all phenomena can be determined through the laws and that there is no reality behind the quantum world. In this paper, we shall briefly describe all these three views on the nature of the physical world or universe and this include on the nature of matter. Then, we shall explain our stand on those conceptions based on the Ash'arites atomistic conception of the physical world. We hope this paper can shed a light on several fundamental issues in the conception of the universe and gives the proper response to them.

  12. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    PubMed

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  13. Unfolding proteins with mechanical forces: From toy models to atomistic simulations

    NASA Astrophysics Data System (ADS)

    Makarov, Dmitrii

    2011-03-01

    The remarkable combination of strength and toughness, displayed by certain biological materials (e.g. spider silk) and often unmatched by artificial materials, is believed to originate from the mechanical response of individual load-bearing protein domains. Single-molecule pulling experiments carried out during the last decade showed that those proteins, when loaded, respond in a non-equilibrium fashion and can dissipate large amounts of energy though the breaking of sacrificial bonds. In my talk, I will discuss what structural properties correlate with mechanical strength and toughness at the single-molecule level, how thermodynamic stability is related to the mechanical stability, and why both atomistic simulations and simple models seem to fail to reconcile the mechanical responses of the same proteins measured under varied loading regimes. I will further discuss whether it is easier to unfold a protein mechanically by pulling at its ends or by threading it through a narrow pore. The latter process is believed to commonly occur in living organisms as an intermediate step in protein degradation. Supported by the NSF and the Robert A. Welch Foundation.

  14. Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized Systems

    NASA Astrophysics Data System (ADS)

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

    We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under Contract No. DE-AC02-06CH11357.

  15. Atomistic finite element model for axial buckling and vibration analysis of single-layered graphene sheets

    NASA Astrophysics Data System (ADS)

    Rouhi, S.; Ansari, R.

    2012-01-01

    In this article, an atomistic model is developed to study the buckling and vibration characteristics of single-layered graphene sheets (SLGSs). By treating SLGSs as space-frame structures, in which the discrete nature of graphene sheets is preserved, they are modeled using three-dimensional elastic beam elements for the bonds. The elastic moduli of the beam elements are determined via a linkage between molecular mechanics and structural mechanics. Based on this model, the critical compressive forces and fundamental natural frequencies of single-layered graphene sheets with different boundary conditions and geometries are obtained and then compared. It is indicated that the compressive buckling force decreases when the graphene sheet aspect ratio increases. At low aspect ratios, the increase of aspect ratios will result in a significant decrease in the critical buckling load. It is also indicated that increasing aspect ratio at a given side length results in the convergence of buckling envelops associated with armchair and zigzag graphene sheets. The influence of boundary conditions will be studied for different geometries. It will be shown that the influence of boundary conditions is not significant for sufficiently large SLGSs.

  16. Atomistic finite element model for axial buckling of single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Rouhi, S.

    2010-11-01

    An atomistic finite element model is developed to study the buckling behavior of single-walled carbon nanotubes with different boundary conditions. By treating nanotubes as space-frame structures, in which the discrete nature of nanotubes is preserved, they are modeled using three-dimensional elastic beam elements for the bonds and point mass elements for the atoms. The elastic moduli of the beam elements are determined via a linkage between molecular mechanics and structural mechanics. Based on this model, the critical compressive forces of single-walled carbon nanotubes with different boundary conditions, geometries as well as chiralities are obtained and then compared. It is indicated that at low aspect ratios, the critical buckling load of nanotubes decreases considerably with increasing aspect ratios, whereas at higher aspect ratios, buckling load slightly decreases as the aspect ratio increases. It is also indicated that increasing aspect ratio at a given radius results in the convergence of buckling envelops associated with armchair and zigzag nanotubes.

  17. Atomistic migration mechanisms of atomically flat, stepped, and kinked grain boundaries

    NASA Astrophysics Data System (ADS)

    Hadian, R.; Grabowski, B.; Race, C. P.; Neugebauer, J.

    2016-10-01

    We studied the migration behavior of mixed tilt and twist grain boundaries in the vicinity of a symmetric tilt <111 > Σ 7 grain boundary in aluminum. We show that these grain boundaries fall into two main categories of stepped and kinked grain boundaries around the atomically flat symmetric tilt boundary. Using these structures together with size converged molecular dynamics simulations and investigating snapshots of the boundaries during migration, we obtain an intuitive and quantitative description of the kinetic and atomistic mechanisms of the migration of general mixed grain boundaries. This description is closely related to well-known concepts in surface growth such as step and kink-flow mechanisms and allows us to derive analytical kinetic models that explain the dependence of the migration barrier on the driving force. Using this insight we are able to extract energy barrier data for the experimentally relevant case of vanishing driving forces that are not accessible from direct molecular dynamics simulations and to classify arbitrary boundaries based on their mesoscopic structures.

  18. Atomistic Insight on the Charging Energetics in Sub-nanometer Pore Supercacitors

    SciTech Connect

    Qiao, Rui; Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent; Feng, Guang

    2010-01-01

    Electrodes featuring sub-nanometer pores can significantly enhance the capacitance and energy density of supercapacitors. However, ions must pay an energy penalty to enter sub-nanometer pores as they have to shed part of their solvation shell. The magnitude of such energy penalty plays a key role in determining the accessibility and charging/discharging of these sub-nanometer pores. Here we report on the atomistic simulation of Na+ and Cl ions entering a polarizable slit pore with a width of 0.82 nm. We show that the free energy penalty for these ions to enter the pore is less than 14 kJ/mol for both Na+ and Cl ions. The surprisingly small energy penalty is caused by the van der Waals attractions between ion and pore walls, the image charge effects, the moderate (19-26%) de-hydration of the ions inside the pore, and the strengthened interactions between ions and their hydration water molecules in the sub-nanometer pore. The results provide strong impetus for further developing nanoporous electrodes featuring sub- nanometer pores.

  19. Function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

    SciTech Connect

    Nutt, David; Smith, Jeremy C

    2008-10-01

    Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.

  20. Atomistic origins of high rate capability and capacity of N-doped graphene for lithium storage.

    PubMed

    Wang, Xi; Weng, Qunhong; Liu, Xizheng; Wang, Xuebin; Tang, Dai-Ming; Tian, Wei; Zhang, Chao; Yi, Wei; Liu, Dequan; Bando, Yoshio; Golberg, Dmitri

    2014-03-12

    Distinct from pure graphene, N-doped graphene (GN) has been found to possess high rate capability and capacity for lithium storage. However, there has still been a lack of direct experimental evidence and fundamental understanding of the storage mechanisms at the atomic scale, which may shed a new light on the reasons of the ultrafast lithium storage property and high capacity for GN. Here we report on the atomistic insights of the GN energy storage as revealed by in situ transmission electron microscopy (TEM). The lithiation process on edges and basal planes is directly visualized, the pyrrolic N "hole" defect and the perturbed solid-electrolyte-interface configurations are observed, and charge transfer states for three N-existing forms are also investigated. In situ high-resolution TEM experiments together with theoretical calculations provide a solid evidence that enlarged edge {0002} spacings and surface hole defects result in improved surface capacitive effects and thus high rate capability and the high capacity are owing to short-distance orderings at the edges during discharging and numerous surface defects; the phenomena cannot be understood previously by standard electron or X-ray diffraction analyses.

  1. Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene

    NASA Astrophysics Data System (ADS)

    Guin, Laurent; Raphanel, Jean L.; Kysar, Jeffrey W.

    2016-06-01

    Pristine single crystal graphene is the strongest known two-dimensional material, and its nonlinear anisotropic mechanical properties are well understood from the atomic length scale up to a continuum description. However, experiments indicate that grain boundaries in the polycrystalline form reduce the mechanical behavior of polycrystalline graphene. Herein, we perform atomistic-scale molecular dynamics simulations of the deformation and fracture of graphene grain boundaries and express the results as continuum cohesive zone models (CZMs) that embed notions of the grain boundary ultimate strength and fracture toughness. To facilitate energy balance, we employ a new methodology that simulates a quasi-static controlled crack propagation which renders the kinetic energy contribution to the total energy negligible. We verify good agreement between Griffith's critical energy release rate and the work of separation of the CZM, and we note that the energy of crack edges and fracture toughness differs by about 35%, which is attributed to the phenomenon of bond trapping. This justifies the implementation of the CZM within the context of the finite element method (FEM). To enhance computational efficiency in the FEM implementation, we discuss the use of scaled traction-separation laws (TSLs) for larger element sizes. As a final result, we have established that the failure characteristics of pristine graphene and high tilt angle bicrystals differ by less than 10%. This result suggests that one could use a unique or a few typical TSLs as a good approximation for the CZMs associated with the mechanical simulations of the polycrystalline graphene.

  2. Prediction of TF target sites based on atomistic models of protein-DNA complexes

    PubMed Central

    Angarica, Vladimir Espinosa; Pérez, Abel González; Vasconcelos, Ana T; Collado-Vides, Julio; Contreras-Moreira, Bruno

    2008-01-01

    Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition. PMID:18922190

  3. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

    NASA Astrophysics Data System (ADS)

    Zavadlav, J.; Podgornik, R.; Melo, M. N.; Marrink, S. J.; Praprotnik, M.

    2016-10-01

    We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.

  4. Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations.

    PubMed

    Delemotte, Lucie; Tarek, Mounir; Klein, Michael L; Amaral, Cristiano; Treptow, Werner

    2011-04-12

    The response of a membrane-bound Kv1.2 ion channel to an applied transmembrane potential has been studied using molecular dynamics simulations. Channel deactivation is shown to involve three intermediate states of the voltage sensor domain (VSD), and concomitant movement of helix S4 charges 10-15 Å along the bilayer normal; the latter being enabled by zipper-like sequential pairing of S4 basic residues with neighboring VSD acidic residues and membrane-lipid head groups. During the observed sequential transitions S4 basic residues pass through the recently discovered charge transfer center with its conserved phenylalanine residue, F(233). Analysis indicates that the local electric field within the VSD is focused near the F(233) residue and that it remains essentially unaltered during the entire process. Overall, the present computations provide an atomistic description of VSD response to hyperpolarization, add support to the sliding helix model, and capture essential features inferred from a variety of recent experiments.

  5. Development and assessment of atomistic models for predicting static friction coefficients

    NASA Astrophysics Data System (ADS)

    Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

    2016-08-01

    The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

  6. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity

    PubMed Central

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210

  7. Large-scale atomistic simulations of helium-3 bubble growth in complex palladium alloys

    SciTech Connect

    Hale, Lucas M.; Zimmerman, Jonathan A.; Wong, Bryan M.

    2016-05-18

    Palladium is an attractive material for hydrogen and hydrogen-isotope storage applications due to its properties of large storage density and high diffusion of lattice hydrogen. When considering tritium storage, the material’s structural and mechanical integrity is threatened by both the embrittlement effect of hydrogen and the creation and evolution of additional crystal defects (e.g., dislocations, stacking faults) caused by the formation and growth of helium-3 bubbles. Using recently developed inter-atomic potentials for the palladium-silver-hydrogen system, we perform large-scale atomistic simulations to examine the defect-mediated mechanisms that govern helium bubble growth. Our simulations show the evolution of a distribution of material defects, and we compare the material behavior displayed with expectations from experiment and theory. In conclusion, we also present density functional theory calculations to characterize ideal tensile and shear strengths for these materials, which enable the understanding of how and why our developed potentials either meet or confound these expectations.

  8. Large-scale atomistic simulations of helium-3 bubble growth in complex palladium alloys

    DOE PAGES

    Hale, Lucas M.; Zimmerman, Jonathan A.; Wong, Bryan M.

    2016-05-18

    Palladium is an attractive material for hydrogen and hydrogen-isotope storage applications due to its properties of large storage density and high diffusion of lattice hydrogen. When considering tritium storage, the material’s structural and mechanical integrity is threatened by both the embrittlement effect of hydrogen and the creation and evolution of additional crystal defects (e.g., dislocations, stacking faults) caused by the formation and growth of helium-3 bubbles. Using recently developed inter-atomic potentials for the palladium-silver-hydrogen system, we perform large-scale atomistic simulations to examine the defect-mediated mechanisms that govern helium bubble growth. Our simulations show the evolution of a distribution of materialmore » defects, and we compare the material behavior displayed with expectations from experiment and theory. In conclusion, we also present density functional theory calculations to characterize ideal tensile and shear strengths for these materials, which enable the understanding of how and why our developed potentials either meet or confound these expectations.« less

  9. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    PubMed Central

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  10. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

    PubMed Central

    Yang, Shengfeng; Chen, Youping

    2015-01-01

    In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress–strain responses, the GB–crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB–crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation. PMID:25792957

  11. Atomistic Analysis of Room Temperature Quantum Coherence in Two-Dimensional CdSe Nanostructures.

    PubMed

    Pal, Sougata; Nijjar, Parmeet; Frauenheim, Thomas; Prezhdo, Oleg V

    2017-03-02

    Recent experiments on CdSe nanoplatelets synthesized with precisely controlled thickness that eliminates ensemble disorder have allowed accurate measurement of quantum coherence at room temperature. Matching exactly the CdSe cores of the experimentally studied particles and considering several defects, we establish the atomistic origins of the loss of coherence between heavy and light hole excitations in two-dimensional CdSe and CdSe/CdZnS core/shell structures. The coherence times obtained using molecular dynamics based on tight-binding density functional theory are in excellent agreement with the measured values. We show that a long coherence time is a consequence of both small fluctuations in the energy gap between the excited state pair, which is much less than thermal energy, and a slow decay of correlation between the energies of the two states. Anionic defects at the core/shell interface have little effect on the coherence lifetime, while cationic defects strongly perturb the electronic structure, destroying the experimentally observed coherence. By coupling to the same phonon modes, the heavy and light holes synchronize their energy fluctuations, facilitating long-lived coherence. We further demonstrate that the electronic excitations are localized close to the surface of these narrow nanoscale systems, and therefore, they couple most strongly to surface acoustic phonons. The established features of electron-phonon coupling and the influence of defects, surfaces, and core/shell interfaces provide important insights into quantum coherence in nanoscale materials in general.

  12. Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations.

    PubMed

    Alessandri, Riccardo; Uusitalo, Jaakko J; de Vries, Alex H; Havenith, Remco W A; Marrink, Siewert J

    2017-03-07

    Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor-acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)-phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device.

  13. Atomistic aspects of ductile responses of cubic silicon carbide during nanometric cutting

    PubMed Central

    2011-01-01

    Cubic silicon carbide (SiC) is an extremely hard and brittle material having unique blend of material properties which makes it suitable candidate for microelectromechanical systems and nanoelectromechanical systems applications. Although, SiC can be machined in ductile regime at nanoscale through single-point diamond turning process, the root cause of the ductile response of SiC has not been understood yet which impedes significant exploitation of this ceramic material. In this paper, molecular dynamics simulation has been carried out to investigate the atomistic aspects of ductile response of SiC during nanometric cutting process. Simulation results show that cubic SiC undergoes sp3-sp2 order-disorder transition resulting in the formation of SiC-graphene-like substance with a growth rate dependent on the cutting conditions. The disorder transition of SiC causes the ductile response during its nanometric cutting operations. It was further found out that the continuous abrasive action between the diamond tool and SiC causes simultaneous sp3-sp2 order-disorder transition of diamond tool which results in graphitization of diamond and consequent tool wear. PMID:22078069

  14. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    NASA Astrophysics Data System (ADS)

    Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

    2016-08-01

    This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  15. Continuum and atomistic modeling of ion partitioning into a peptide nanotube.

    PubMed Central

    Asthagiri, D; Bashford, D

    2002-01-01

    Continuum and atomistic descriptions of the partitioning of ions into a self-assembled (D,L)-octapeptide nanotube, cyclo[-(L-Ala-D-Ala)(4)-], are presented. Perturbation free energy calculations, including Ewald electrostatics, are used to estimate the electrostatic component of the excess free energy of charging Li(+), Na(+), Rb(+), and Cl(minus sign) ions inside the nanotube. The radial density and orientational distribution of water around the ion is calculated for the ion at two different positions inside the tube; it is seen that the calculated distributions are sensitive to the location of the ions. Two different continuum electrostatic models are formulated to describe the ion solvation inside the nanotube. When enhanced orientational structuring of water dipoles is evidenced, explicitly including the first solvation shell as part of the low dielectric nanotube environment provides good agreement with molecular dynamics simulations. When water orientational structuring is as in the reference bulk solvent, we find that treating the first shell water explicitly or as a high dielectric continuum leads to similar results. These results are discussed, and their importance for continuum electrostatic modeling of ion channels are highlighted. PMID:11867436

  16. Quantifying the influence of twin boundaries on the deformation of nanocrystalline copper using atomistic simulations

    SciTech Connect

    Tucker, Garritt J.; Foiles, Stephen Martin

    2014-09-22

    Over the past decade, numerous efforts have sought to understand the influence of twin boundaries on the behavior of polycrystalline materials. Early results suggested that twin boundaries within nanocrystalline face-centered cubic metals have a considerable effect on material behavior by altering the activated deformation mechanisms. In this work, we employ molecular dynamics simulations to elucidate the role of twin boundaries on the deformation of <100> columnar nanocrystalline copper at room temperature under uniaxial strain. We leverage non-local kinematic metrics, formulated from continuum mechanics theory, to compute atomically-resolved rotational and strain fields during plastic deformation. These results are then utilized to compute the distribution of various nanoscale mechanisms during straining, and quantitatively resolve their contribution to the total strain accommodation within the microstructure, highlighting the fundamental role of twin boundaries. Our results show that nanoscale twins influence nanocrystalline copper by altering the cooperation of fundamental deformation mechanisms and their contributed role in strain accommodation, and we present new methods for extracting useful information from atomistic simulations. The simulation results suggest a tension–compression asymmetry in the distribution of deformation mechanisms and strain accommodation by either dislocations or twin boundary mechanisms. In highly twinned microstructures, twin boundary migration can become a significant deformation mode, in comparison to lattice dislocation plasticity in non-twinned columnar microstructures, especially during compression.

  17. Atomistic Modeling of Mechanical Loss in Pure and Doped Amorphous Oxides

    NASA Astrophysics Data System (ADS)

    Trinastic, Jonathan; Hamdan, Rashid; Cheng, Hai-Ping

    2014-03-01

    The mechanical dissipation in the oxide coatings of many precision measurement systems is a major source of thermal noise that limits the performance of such devices. A good candidate for a coating material to reduce the mechanical loss is tantala (Ta2O5) doped with titania (TiO2). Here, we numerically calculate the mechanical loss (internal friction) in these and other promising oxides based on the double well model. Using classical, atomistic molecular dynamics simulations, we estimate the density of double wells in the energy landscape of the amorphous oxides and the distribution of barrier heights, in addition to the deformation potentials, the elastic constants and vibrational frequencies at both the bottom of the potential wells and at the saddle points, all of which are relevant to the internal friction calculation. We use two versions of the bisection method to find the double well densities and distributions. All methods used in these calculations are implemented in DL-POLY molecular dynamics simulation software. These calculations will provide experimentalists with a better guide into which material combinations might be better choice for reducing the mechanical loss.

  18. Atomistic simulation for deforming complex alloys with application toward TWIP steel and associated physical insights

    NASA Astrophysics Data System (ADS)

    Wang, Peng; Xu, Shaofeng; Liu, Jiabin; Li, Xiaoyan; Wei, Yujie; Wang, Hongtao; Gao, Huajian; Yang, Wei

    2017-01-01

    The interest in promoting deformation twinning for plasticity is mounting for advanced materials. In contrast to disordered grain boundaries, highly organized twin boundaries are beneficial to promoting strength-ductility combination. Twinning deformation typically involves the kinetics of stacking faults, its interplay with dislocations, as well as the interactions between dislocations and twin boundaries. While the latter has been intensively studied, the dynamics of stacking faults has been rarely touched upon. In this work, we report new physical insights on the stacking fault dynamics in twin induced plasticity (TWIP) steels. The atomistic simulation is made possible by a newly introduced approach: meta-atom molecular dynamics simulation. The simulation suggests that the stacking fault interactions are dominated by dislocation reactions that take place spontaneously, different from the existing mechanisms. Whether to generate a single stacking fault, or a twinning partial and a trailing partial dislocation, depends upon a unique parameter, namely the stacking fault energy. The latter in turn determines the deformation twinning characteristics. The complex twin-slip and twin-dislocation interactions demonstrate the dual role of deformation twins as both the dislocation barrier and dislocation storage. This duality contributes to the high strength and high ductility of TWIP steels.

  19. A coupling atomistic-continuum approach for modeling mechanical behavior of nano-crystalline structures

    NASA Astrophysics Data System (ADS)

    Khoei, A. R.; Aramoon, A.; Jahanbakhshi, F.; DorMohammadi, H.

    2014-08-01

    In this article, a novel approach is presented for the concurrent coupling of continuum-atomistic model in the nano-mechanical behavior of atomic structures. The study is focused on the static concurrent multi-scale simulation, which is able to effectively capture the surface effects intrinsic in the molecular mechanics modeling. The Hamiltonian approach is applied to combine the continuum and molecular models with the same weight in the overlapping domain. A Lagrange-multiplier method is employed over the overlapping domain for coupling the continuum nodal displacement with the atomic lattice deformation. A multiple-step algorithm is developed to decouple the solution process in the atomic and continuum domains. The mass and stiffness matrices of continuum domain are computed based on the linear bridging map of the atomic lattice displacement, laid underneath the continuum grid to the element displacements. Numerical simulation results present that the stress and displacement contours of the presented coupling method are in good agreement with those obtained from the molecular mechanics simulation.

  20. Atomistic insights into dislocation-based mechanisms of void growth and coalescence

    NASA Astrophysics Data System (ADS)

    Mi, Changwen; Buttry, Daniel A.; Sharma, Pradeep; Kouris, Demitris A.

    2011-09-01

    One of the low-temperature failure mechanisms in ductile metallic alloys is the growth of voids and their coalescence. In the present work we attempt to obtain atomistic insights into the mechanisms underpinning cavitation in a representative metal, namely Aluminum. Often the pre-existing voids in metallic alloys such as Al have complex shapes (e.g. corrosion pits) and the defromation/damage mechanisms exhibit a rich size-dependent behavior across various material length scales. We focus on these two issues in this paper through large-scale calculations on specimens of sizes ranging from 18 thousand to 1.08 million atoms. In addition to the elucidation of the dislocation propagation based void growth mechanism we highlight the observed length scale effect reflected in the effective stress-strain response, stress triaxiality and void fraction evolution. Furthermore, as expected, the conventionally used Gurson's model fails to capture the observed size-effects calling for a mechanistic modification that incorporates the mechanisms observed in our (and other researchers') simulation. Finally, in our multi-void simulations, we find that, the splitting of a big void into a distribution of small ones increases the load-carrying capacity of specimens. However, no obvious dependence of the void fraction evolution on void coalescence is observed.