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Sample records for microsecond polarized atomistic

  1. Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel

    PubMed Central

    Bjelkmar, Pär; Niemelä, Perttu S.; Vattulainen, Ilpo; Lindahl, Erik

    2009-01-01

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins—not to mention numerous applications in drug design. Here, we present a full 1 µs atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120° rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation (∼35°) of the extracellular end of all S4 segments is present also in a reference 0.5 µs simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 310 helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4–lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5–1 µs). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations. PMID:19229308

  2. Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers.

    PubMed

    Upadhyay, Sanjay K; Wang, Yukun; Zhao, Tangzhen; Ulmschneider, Jakob P

    2015-06-01

    The membrane disruption and pore-forming mechanism of melittin has been widely explored by experiments and computational studies. However, the precise mechanism is still enigmatic, and further study is required to turn antimicrobial peptides into future promising drugs against microbes. In this study, unbiased microsecond (µs) time scale (total 17 µs) atomistic molecular dynamics simulation were performed on multiple melittin systems in 1,2-dimyristoyl-sn-glycero-3-phosphocholine membrane to capture the various events during the membrane disorder produced by melittin. We observed bent U-shaped conformations of melittin, penetrated deeply into the membrane in all simulations, and a special double U-shaped structure. However, no peptide transmembrane insertion, nor pore formation was seen, indicating that these processes occur on much longer timescales, and suggesting that many prior computational studies of melittin were not sufficiently unbiased. PMID:25963936

  3. 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. PMID:26699921

  4. Laser-driven microsecond temperature cycles analyzed by fluorescence polarization microscopy.

    PubMed

    Zondervan, Rob; Kulzer, Florian; van der Meer, Harmen; Disselhorst, Jos A J M; Orrit, Michel

    2006-04-15

    We demonstrate a novel technique to achieve fast thermal cycles of a small sample (a few femtoliters). Modulating a continuous near-infrared laser focused on a metal film, we can drive the local temperature from 130 to 300 K and back, within a few microseconds. By fluorescence microscopy of dyes in a thin glycerol film, we record images of the hot spot, calibrate its temperature, and follow its variations in real time. The temperature dependence of fluorescence anisotropy, due to photophysics and rotational diffusion, gives a steady-state temperature calibration between 200 and 350 K. From 200 to 220 K, we monitor temperature more accurately by fluorescence autocorrelation, a probe for rotational diffusion. Time-resolved measurements of fluorescence anisotropy give heating and cooling times of a few microseconds, short enough to supercool pure water. We designed our method to repeatedly cycle a single (bio)molecule between ambient and cryostat temperatures with microsecond time resolution. Successive measurements of a structurally relevant variable will decompose a dynamical process into structural snapshots. Such temperature-cycle experiments, which combine a high time resolution with long observation times, can thus be expected to yield new insights into complex processes such as protein folding. PMID:16443653

  5. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    PubMed

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-10-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

  6. PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

    PubMed Central

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-01-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  8. Understanding polarization properties of InAs quantum dots by atomistic modeling of growth dynamics

    SciTech Connect

    Tasco, Vittorianna; Todaro, Maria Teresa; De Giorgi, Milena; Passaseo, Adriana; Usman, Muhammad

    2013-12-04

    A model for realistic InAs quantum dot composition profile is proposed and analyzed, consisting of a double region scheme with an In-rich internal core and an In-poor external shell, in order to mimic the atomic scale phenomena such as In-Ga intermixing and In segregation during the growth and overgrowth with GaAs. The parameters of the proposed model are derived by reproducing the experimentally measured polarization data. Further understanding is developed by analyzing the strain fields which suggests that the two-composition model indeed results in lower strain energies than the commonly applied uniform composition model.

  9. 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.

  10. General Reactive Atomistic Simulation Program

    Energy Science and Technology Software Center (ESTSC)

    2004-09-22

    GRASP (General Reactive Atomistic Simulation Program) is primarily intended as a molecular dynamics package for complex force fields, The code is designed to provide good performance for large systems, either in parallel or serial execution mode, The primary purpose of the code is to realistically represent the structural and dynamic properties of large number of atoms on timescales ranging from picoseconds up to a microsecond. Typically the atoms form a representative sample of some material,more » such as an interface between polycrystalline silicon and amorphous silica. GRASP differs from other parallel molecular dynamics codes primarily due to it’s ability to handle relatively complicated interaction potentials and it’s ability to use more than one interaction potential in a single simulation. Most of the computational effort goes into the calculation of interatomic forces, which depend in a complicated way on the positions of all the atoms. The forces are used to integrate the equations of motion forward in time using the so-called velocity Verlet integration scheme. Alternatively, the forces can be used to find a minimum energy configuration, in which case a modified steepest descent algorithm is used.« less

  11. 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.

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

    DOE PAGESBeta

    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.

  13. Sub-microsecond-resolution probe microscopy

    SciTech Connect

    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.

  14. 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

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    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.

  17. 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.

  18. Atomistic bond relaxation, energy entrapment, and electron polarization of the RbN and CsN clusters (N ≤ 58).

    PubMed

    Guo, Yongling; Bo, Maolin; Wang, Yan; Liu, Yonghui; Huang, Yongli; Sun, Chang Q

    2015-11-11

    We systematically examined the effect of atomic undercoordination on the performance of bonds and electrons of Rb and Cs atomic clusters and their solid skins using a combination of photoelectron spectrometric analysis and density functional theory calculations. Results show that atomic coordination number reduction shortens the bonds by up to 30% for the Rb13 and Cs13 clusters, which densifies the local electrons and entraps their binding energies. Consistency between predictions and observations revealed that the Rb 4p level shifts from 13.654 eV for an isolated atom to a bulk value of 14.940 eV and the Cs 5p level shifts from 10.284 to 11.830 eV upon bulk formation. Such core-electron densification and entrapment polarize the valence charge from the inner to the outermost layer of skins, which perturbs the local Hamiltonian and hence dictates the unusual behavior of the Rb and Cs solid skins and nanocrystals. PMID:26507096

  19. 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

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

    PubMed

    Pasi, Marco; Lavery, Richard

    2016-06-20

    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

  1. Efficient Illumination for Microsecond Tracking Microscopy

    PubMed Central

    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 s 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. PMID:25251462

  2. 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.

  3. 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

  4. Microsecond linear optical response in the unusual nematic phase of achiral bimesogens

    NASA Astrophysics Data System (ADS)

    Panov, V. P.; Balachandran, R.; Nagaraj, M.; Vij, J. K.; Tamba, M. G.; Kohlmeier, A.; Mehl, G. H.

    2011-12-01

    Some hydrocarbon linked mesogenic dimers are known to exhibit an additional nematic phase (Nx) below a conventional uniaxial nematic (Nu) phase. Although composed of non-chiral molecules, the Nx phase is found to exhibit linear (polar) switching under applied electric field. This switching has remarkably low response time of the order of a few microseconds. Two chiral domains with opposite handedness and consequently opposite responses are found in planar cells. Uniformly lying helix, electroclinic, and flexoelectric effects are given as possible causes for this intriguing phenomenon.

  5. Fragmentation process induced by microsecond laser pulses during lithotripsy

    NASA Astrophysics Data System (ADS)

    Rink, K.; Delacrétaz, G.; Salathé, R. P.

    1992-07-01

    A fiber optic stress sensing technique is applied to evaluate the fragmentation mechanism for pulsed dye-laser lithotripsy. We demonstrate for the first time that the fragmentation process with microsecond laser pulses originates from the shock wave induced by the cavitation bubble collapse. This shock occurs some hundreds of microseconds after the laser pulse. The shock induced by the plasma expansion, which occurs during laser irradiation, has a minor effect.

  6. 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.

  7. 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

  8. Atomistic Simulation of the Transition from Atomistic to Macroscopic Cratering

    SciTech Connect

    Samela, Juha; Nordlund, Kai

    2008-07-11

    Using large-scale atomistic simulations, we show that the macroscopic cratering behavior emerges for projectile impacts on Au at projectile sizes between 1000 and 10 000 Au atoms at impact velocities comparable to typical meteoroid velocities. In this size regime, we detect a compression of material in Au nanoparticle impacts similar to that observed for hypervelocity macroscopic impacts. The simulated crater volumes agree with the values calculated using the macroscopic crater size scaling law, in spite of a downwards extrapolation over more than 15 orders of magnitude in terms of the impactor volume. The result demonstrates that atomistic simulations can be used as a tool to understand the strength properties of materials in cases where only continuum models have been possible before.

  9. 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. PMID:24009494

  10. 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

    2013-04-01

    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

  11. Progress Towards Atomistic Simulations that Reach Anthropological Timescale and Beyond

    NASA Astrophysics Data System (ADS)

    Li, Ju

    2012-02-01

    Atomistic and first-principles modeling, which describe the world as assembly of atoms and electrons, provide the most fundamental answer to problems of materials. However, they also suffer the most severe timescale limitations. For instance, in molecular dynamics (MD) simulations, in order to resolve atomic vibrations, the integration time step is limited to hundredth of a picosecond, and therefore the simulation duration is limited to sub-microsecond due to computational cost. Although a nanosecond simulation is often enough (surprisingly) for many physical and chemical properties, it is usually insufficient for predicting microstructural evolution and thermo-mechanical properties of materials. In this invited talk I will discuss recent attempts at overcoming the timescale challenges of atomic-resolution simulations: (a) strain-boost hyperdynamics [Phys. Rev. B 82 (2010) 184114] for simulating primarily displacive events and associated issues of activation entropy and the Meyer-Neldel compensation rule, (b) diffusive molecular dynamics (DMD) [Phys. Rev. B 84 (2011) 054103] for microstructural evolution driven by repetitive diffusion events and coupled displacive-diffusive processes, and (c) a Markovian network statistical mechanical treatment of the energy-landscape basin connectivity and a formula for the viscosity of supercooled liquid and glass [PLoS ONE 6 (2011) e17909]. Challenges and future directions are discussed.

  12. Using the USCCS for sub microsecond spacecraft clock calibration

    NASA Technical Reports Server (NTRS)

    Sank, Victor J.

    1993-01-01

    The Return Data Delay technique which requires knowledge of spacecraft range is commonly used for correlating a spacecraft clock against a ground time standard when millisecond accuracy is required. An analysis is presented that allows using the user spacecraft clock calibration system (USCCS) to correlate a spacecraft clock to better than one microsecond accuracy. The basic USCCS algorithm has been simplified and it is shown to result in about one microsecond accuracy without requiring orbital information. By considering the relative motion of the user satellite, the TDRS and the earth station about the center of the earth, a correction of almost two orders of magnitude can be made. Such accuracy is required for scientific investigations that require correlating coincident radiation or particle detection with a remote laboratory.

  13. 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.

  14. 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.

  15. Lasing efficiency of ethanol dye solutions under coherent microsecond pumping

    NASA Astrophysics Data System (ADS)

    Tarkovskiĭ, V. V.; Anufrik, S. S.

    2008-11-01

    It is established that the excitation wavelength plays an important role in the attainment of maximum efficiency and the time dependence of the pump and lasing pulses under coherent microsecond pumping of dye solutions because the losses due to the molecular absorption in the channel of excited triplet levels, thermooptical distortions, and products of photochemical transformations play a minor role in the total energy balance in comparison with the spectrally dependent loss in the channel of excited singlet levels.

  16. Atomistic Properties of Y Uranium

    SciTech Connect

    Benjamin Beeler; Chaitanya Deo; Mmichael Baskes; Maria Okuniewski

    2012-02-01

    The properties of the body-centered cubic y 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 (y) 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 y 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 y calculation of U properties above 0 K with interatomic potentials.

  17. Wire Array Z-pinches on Sphinx Machine: Experimental Results and Relevant Points of Microsecond Implosion Physics

    NASA Astrophysics Data System (ADS)

    Calamy, H.; Hamann, F.; Lassalle, F.; Bayol, F.; Mangeant, C.; Morell, A.; Huet, D.; Bedoch, J. P.; Chittenden, J. P.; Lebedev, S. V.; Jennings, C. A.; Bland, S. N.

    2006-01-01

    Centre d'Etudes de Gramat (France) has developed an efficient long implosion time (800 ns) Aluminum plasma radiation source (PRS). Based on the LTD technology, the SPHINX facility is developed as a 1-3MJ, 1μs rise time, 4-10 MA current driver. In this paper, it was used in 1MJ, 4MA configuration to drive Aluminum nested wire arrays Z-pinches with K-shell yield up to 20 kJ and a FWHM of the x-ray pulse of about 50 ns. We present latest SPHINX experiments and some of the main physic issues of the microsecond regime. Experimental setup and results are described with the aim of giving trends that have been obtained. The main features of microsecond implosion of wire arrays can be analyzed thanks to same methods and theories as used for faster Z-pinches. The effect of load polarity was examined. The stability of the implosion , one of the critical point of microsecond wire arrays due to the load dimensions imposed by the time scale, is tackled. A simple scaling from 100 ns Z-pinch results to 800 ns ones gives good results and the use of nested arrays improves dramatically the implosion quality and the Kshell yield of the load. However, additional effects such as the impact of the return current can geometry on the implosion have to be taken into account on our loads. Axial inhomogeneity of the implosion the origin of which is not yet well understood occurs in some shots and impacts the radiation output. The shape of the radiative pulse is discussed and compared with the homogeneity of the implosion. Numerical 2D R-Z and R-θ simulations are used to highlight some experimental results and understand the plasma conditions during these microsecond wire arrays implosions.

  18. Wire Array Z-pinches on Sphinx Machine: Experimental Results and Relevant Points of Microsecond Implosion Physics

    SciTech Connect

    Calamy, H.; Hamann, F.; Lassalle, F.; Bayol, F.; Mangeant, C.; Morell, A.; Huet, D.; Bedoch, J.P.; Chittenden, J.P.; Lebedev, S.V.; Jennings, C.A.; Bland, S.N.

    2006-01-05

    Centre d'Etudes de Gramat (France) has developed an efficient long implosion time (800 ns) Aluminum plasma radiation source (PRS). Based on the LTD technology, the SPHINX facility is developed as a 1-3MJ, 1{mu}s rise time, 4-10 MA current driver. In this paper, it was used in 1MJ, 4MA configuration to drive Aluminum nested wire arrays Z-pinches with K-shell yield up to 20 kJ and a FWHM of the x-ray pulse of about 50 ns. We present latest SPHINX experiments and some of the main physic issues of the microsecond regime. Experimental setup and results are described with the aim of giving trends that have been obtained. The main features of microsecond implosion of wire arrays can be analyzed thanks to same methods and theories as used for faster Z-pinches. The effect of load polarity was examined. The stability of the implosion , one of the critical point of microsecond wire arrays due to the load dimensions imposed by the time scale, is tackled. A simple scaling from 100 ns Z-pinch results to 800 ns ones gives good results and the use of nested arrays improves dramatically the implosion quality and the Kshell yield of the load. However, additional effects such as the impact of the return current can geometry on the implosion have to be taken into account on our loads. Axial inhomogeneity of the implosion the origin of which is not yet well understood occurs in some shots and impacts the radiation output. The shape of the radiative pulse is discussed and compared with the homogeneity of the implosion. Numerical 2D R-Z and R-{theta} simulations are used to highlight some experimental results and understand the plasma conditions during these microsecond wire arrays implosions.

  19. 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.

  20. Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response

    PubMed Central

    Cino, Elio A.; Wong-ekkabut, Jirasak; Karttunen, Mikko; Choy, Wing-Yiu

    2011-01-01

    Intrinsically disordered proteins (IDPs) are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTα) and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2), with a common binding partner, Kelch-like ECH-associated protein 1(Keap1), are essential for regulating cellular response to oxidative stress. Misregulation of this pathway can lead to neurodegenerative diseases, premature aging and cancer. In order to understand the mechanisms these two disordered proteins employ to bind to Keap1, we performed extensive 0.5–1.0 microsecond atomistic molecular dynamics (MD) simulations and isothermal titration calorimetry experiments to investigate the structure/dynamics of free-state ProTα and Neh2 and their thermodynamics of bindings. The results show that in their free states, both ProTα and Neh2 have propensities to form bound-state-like β-turn structures but to different extents. We also found that, for both proteins, residues outside the Keap1-binding motifs may play important roles in stabilizing the bound-state-like structures. Based on our findings, we propose that the binding of disordered ProTα and Neh2 to Keap1 occurs synergistically via preformed structural elements (PSEs) and coupled folding and binding, with a heavy bias towards PSEs, particularly for Neh2. Our results provide insights into the molecular mechanisms Neh2 and ProTα bind to Keap1, information that is useful for developing therapeutics to enhance the oxidative stress response. PMID:22125611

  1. Microsecond yellow laser for subfoveal leaks in central serous chorioretinopathy

    PubMed Central

    Ambiya, Vikas; Goud, Abhilash; Mathai, Annie; Rani, Padmaja Kumari; Chhablani, Jay

    2016-01-01

    Purpose To evaluate the role of navigated yellow microsecond laser in treating subfoveal leaks in nonresolving central serous chorioretinopathy (CSC). Methods This prospective study included ten eyes of ten consecutive patients with nonresolving CSC with subfoveal leaks. All eyes were treated with 577 nm navigated yellow microsecond laser (5% duty cycle). Key inclusion criteria include a vision loss for a duration of minimum 3 months duration due to focal subfoveal leak on fluorescein angiography. Key exclusion criteria include prior treatment for CSC and any signs of chronic CSC. Comprehensive examination, in addition to low-contrast visual acuity assessment, microperimetry, autofluorescence, spectral domain optical coherence tomography, and fundus fluorescein angiography, was done at baseline, 1, 3, and 6 months after treatment. Rescue laser was performed as per predefined criteria at 3 months. Results The average best-corrected visual acuity improved from 73.3±16.1 letters to 75.8±14.0 (P=0.69) at 3 months and 76.9±13.0 (P=0.59) at 6 months, but was not statistically significant. Low-contrast visual acuity assessment (logMAR) improved from 0.41±0.32 to 0.35±0.42 (P=0.50) at 3 months and 0.28±0.33 (P=0.18) at 6 months. Average retinal sensitivity significantly improved from baseline 18.93±7.19 dB to 22.49±6.67 dB (P=0.01) at 3 months and 21.46±8.47 dB (P=0.04) at 6 months. Rescue laser was required only in one eye at 3 months; however, laser was required in three eyes at 6 months. Conclusion Microsecond laser is a safe and effective modality for treating cases of nonresolving CSC with subfoveal leaks. PMID:27570446

  2. Microsecond Microfluidic Mixing for Investigation of Protein Folding Kinetics

    SciTech Connect

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

    2003-06-25

    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.

  3. 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.

  4. [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. PMID:23016402

  5. 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.

  6. Atomistic k ⋅ p theory

    SciTech Connect

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

    2015-12-14

    Pseudopotentials, tight-binding models, and k ⋅ 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 ⋅ p theory. In its usual formulation, k ⋅ 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 ⋅ 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 sp{sup 3} tight-binding model. We can thus directly derive the parameters in the sp{sup 3} 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 ⋅ 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 ⋅ p models to be combined in the same system.

  7. Polarization-independent electro-optic depolarizer

    NASA Astrophysics Data System (ADS)

    Heismann, F.; Tokuda, K. L.

    1995-05-01

    We demonstrate a compact electro-optic polarization scrambler that depolarizes arbitrarily polarized light with less than 2.5% residual degree of polarization and variable depolarization times in the microsecond to millisecond range. The integrated-optic depolarizer is fabricated on lithium niobate and operates with a single-mode waveguide designed for a 1.5- mu m wavelength. The scrambler introduces negligible intensity modulation of less than 1.6% in the depolarized output light.

  8. Atomistic simulations of bulk, surface and interfacial polymer properties

    NASA Astrophysics Data System (ADS)

    Natarajan, Upendra

    In chapter I, quasi-static molecular mechanics based simulations are used to estimate the activation energy of phenoxy rings flips in the amorphous region of a semicrystalline polyimide. Intra and intermolecular contributions to the flip activation energy, the torsional cooperativity accompanying the flip, and the effect of the flip on the motion in the glassy bulk state, are looked at. Also, comparison of the weighted mean activation energy is made with experimental data from solid state NMR measurements; the simulated value being 17.5 kcal/mol., while the experimental value was observed to be 10.5 kcal/mol. Chapter II deals with construction of random copolymer thin films of styrene-butadiene (SB) and styrene-butadiene-acrylonitrile (SBA). The structure and properties of the free surfaces presented by these thin films are analysed by, the atom mass density profiles, backbone bond orientation function, and the spatial distribution of acrylonitrile groups and styrene rings. The surface energies of SB and SBA are calculated using an atomistic equation and are compared with experimental data in the literature. In chapter III, simulations of polymer-polymer interfaces between like and unlike polymers, specifically cis-polybutadiene (PBD) and atatic polypropylene (PP), are presented. The structure of an incompatible polymer-polymer interface, and the estimation of the thermodynamic work of adhesion and interfacial energy between different incompatible polymers, form the focus here. The work of adhesion is calculated using an atomistic equation and is further used in a macroscopic equation to estimate the interfacial energy. The interfacial energy is compared with typical values for other immiscible systems in the literature. The interfacial energy compared very well with interfacial energy values for a few other immiscible hydrocarbon pairs. In chapter IV, the study proceeds to look at the interactions between nonpolar and polar small molecules with SB and SBA thin

  9. Atomistic modeling of dropwise condensation

    NASA Astrophysics Data System (ADS)

    Sikarwar, B. S.; Singh, P. L.; Muralidhar, K.; Khandekar, S.

    2016-05-01

    The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smaller sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.

  10. Faraday rotation imaging microscope with microsecond pulse magnet

    NASA Astrophysics Data System (ADS)

    Suwa, Masayori; Tsukahara, Satoshi; Watarai, Hitoshi

    2015-11-01

    We have fabricated a high-performance Faraday rotation (FR) imaging microscope that uses a microsecond pulse magnet comprising an insulated gated bipolar transistor and a 2 μF capacitor. Our microscope produced images with greater stability and sensitivity than those of previous microscopes that used millisecond pulse magnet; these improvements are likely due to high repetition rate and negligible Joule heating effects. The mechanical vibrations in the magnet coil caused by the pulsed current were significantly reduced. The present FR microscope constructed an averaged image from 1000 FR images within 10 min under 1.7 T. Applications of the FR microscope to discriminating three benzene derivatives in micro-capillaries and oscillation-free imaging of spherical polystyrene and polymethyl methacrylate microparticles demonstrated its high performance.

  11. 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.

  12. Atomistic simulation of graphene-based polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

    2016-05-01

    Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

  13. Fireballs: Detonation Initiation on the Microsecond Time Scale

    NASA Astrophysics Data System (ADS)

    Kassoy, D. R.; Wojciechowski, K.

    2003-11-01

    A mathematical model is developed for detonation initiation following a time and spatially resolved burst of thermal power from an external source into a spherical target of reactive gas. The objective is to produce a detonation in or near the target with the least possible energy input. Source heating occurs on a sub-microsecond time scale, short compared to the acoustic time of the millimeter-sized target. This leads to a period of near inertial confinement, where the pressure rises with temperature, the density change is very small and local Mach number is extremely subsonic. As a result the thermal enegy change is maximized while the induced kinetic energy is minimized. The large temperature increase within the localized high pressure spot initiates a high activation energy, exothermic reaction which spreads hypersonically from the maximum temperature point. The chemical front is co-located with a large localized pressure gradient, responsible for rapid gas acceleration. A detonation appears at the edge of target, in the form of a strong shock with a coupled reaction zone. The evolutionary process differs fundamentally from that in a DDT and that in a traditional model of direct initiation.

  14. Microsecond-sustained lasing from colloidal quantum dot solids

    NASA Astrophysics Data System (ADS)

    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.

    2015-10-01

    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.

  15. Theoretical Insights from Facile Microsecond Simulation of the Glass Transition

    NASA Astrophysics Data System (ADS)

    Hung, Jui-Hsiang; Patra, Tarak; Simmons, David

    Despite more than half a century of research, the fundamental nature of the glass transition remains one of the major open questions in polymer science and condensed matter physics. Molecular dynamics simulations have provided key insights into this problem, but their ability to firmly establish the underlying nature of glass formation have been limited by the extreme computational difficulty of directly probing the deeply supercooled regime most relevant to this process. Here we describe a new protocol for simulation of the glass transition enabling facile access to in-equilibrium segmental relaxation times approaching and exceeding one microsecond - well into the deeply supercooled regime of most glass-forming liquids. Coupled with a well-validated strategy for extrapolation to experimental timescales, this approach provides vastly improved prediction of experimental glass transition temperatures. Here we combine data acquired through this protocol for the deeply supercooled regime of polymeric, inorganic, organic, and metallic glass formers to robustly test several theories of glass formation and identify microscopic phenomenological features shared across all classes of glass-forming liquid in the deeply supercooled regime. We acknowledge the W. M. Keck Foundation for financial support of this research.

  16. 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

  17. The microsecond old universe — Relics of QCD phase transition

    NASA Astrophysics Data System (ADS)

    Sinha, Bikash

    2014-07-01

    It is entirely plausible under reasonable conditions, that a first-order QCD phase transition occurred from quarks to hadrons when the universe was about a microsecond old. Relics, if there be any, after the quark-hadron phase transition are the most deciding signatures of the phase transition. It is shown in this paper that quark nuggets, the possible relics of first-order QCD phase transitions with baryon number larger than 1043 will survive the entire history of the universe up to now and can be considered as a candidate for the cold dark matter. The spin down core of the neutron star on the high density low temperature end of the QCD phase diagram initiates transition from hadrons to quarks. As the star spins down, the size of the core goes on increasing. Recently discovered massive Pulsar PSRJ 1614-2230 with a mass of 1.97 ± 0.04M⊙ most likely has a strongly interacting core. What possible observables can there be from these neutron stars?

  18. 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.

  19. 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.

  20. 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.

  1. Precise inhibition is essential for microsecond interaural time difference coding

    NASA Astrophysics Data System (ADS)

    Brand, Antje; Behrend, Oliver; Marquardt, Torsten; McAlpine, David; Grothe, Benedikt

    2002-05-01

    Microsecond differences in the arrival time of a sound at the two ears (interaural time differences, ITDs) are the main cue for localizing low-frequency sounds in space. Traditionally, ITDs are thought to be encoded by an array of coincidence-detector neurons, receiving excitatory inputs from the two ears via axons of variable length (`delay lines'), to create a topographic map of azimuthal auditory space. Compelling evidence for the existence of such a map in the mammalian lTD detector, the medial superior olive (MSO), however, is lacking. Equally puzzling is the role of a-temporally very precise-glycine-mediated inhibitory input to MSO neurons. Using in vivo recordings from the MSO of the Mongolian gerbil, we found the responses of ITD-sensitive neurons to be inconsistent with the idea of a topographic map of auditory space. Moreover, local application of glycine and its antagonist strychnine by iontophoresis (through glass pipette electrodes, by means of an electric current) revealed that precisely timed glycine-controlled inhibition is a critical part of the mechanism by which the physiologically relevant range of ITDs is encoded in the MSO. A computer model, simulating the response of a coincidence-detector neuron with bilateral excitatory inputs and a temporally precise contralateral inhibitory input, supports this conclusion.

  2. Validation of Force Fields of Rubber through Glass-Transition Temperature Calculation by Microsecond Atomic-Scale Molecular Dynamics Simulation.

    PubMed

    Sharma, Pragati; Roy, Sudip; Karimi-Varzaneh, Hossein Ali

    2016-02-25

    Microsecond atomic-scale molecular dynamics simulation has been employed to calculate the glass-transition temperature (Tg) of cis- and trans-1,4-polybutadiene (PB) and 1,4-polyisoprene (PI). Both all-atomistic and united-atom models have been simulated using force fields, already available in literature. The accuracy of these decade old force fields has been tested by comparing calculated glass-transition temperatures to the corresponding experimental values. Tg depicts the phase transition in elastomers and substantially affects various physical properties of polymers, and hence the reproducibility of Tg becomes very crucial from a thermodynamic point of view. Such validation using Tg also evaluates the ability of these force fields to be used for advanced materials like rubber nanocomposites, where Tg is greatly affected by the presence of fillers. We have calculated Tg for a total of eight systems, featuring all-atom and united-atom models of cis- and trans-PI and -PB, which are the major constituents of natural and synthetic rubber. Tuning and refinement of the force fields has also been done using quantum-chemical calculations to obtain desirable density and Tg. Thus, a set of properly validated force fields, capable of reproducing various macroscopic properties of rubber, has been provided. A novel polymer equilibration protocol, involving potential energy convergence as the equilibration criterion, has been proposed. We demonstrate that not only macroscopic polymer properties like density, thermal expansion coefficient, and Tg but also local structural characteristics like end-to-end distance (R) and radius of gyration (Rg) and mechanical properties like bulk modulus have also been equilibrated using our strategy. Complete decay of end-to-end vector autocorrelation function with time also supports proper equilibration using our strategy. PMID:26836395

  3. 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{sub {circle_dot}} black hole.

  4. Towards Microsecond Biological Molecular Dynamics Simulations on Hybrid Processors

    SciTech Connect

    Hampton, Scott S; Agarwal, Pratul K

    2010-01-01

    Biomolecular simulations continue to become an increasingly important component of molecular biochemistry and biophysics investigations. Performance improvements in the simulations based on molecular dynamics (MD) codes are widely desired. This is particularly driven by the rapid growth of biological data due to improvements in experimental techniques. Unfortunately, the factors, which allowed past performance improvements of MD simulations, particularly the increase in microprocessor clock frequencies, are no longer improving. Hence, novel software and hardware solutions are being explored for accelerating the performance of popular MD codes. In this paper, we describe our efforts to port and optimize LAMMPS, a popular MD framework, on hybrid processors: graphical processing units (GPUs) accelerated multi-core processors. Our implementation is based on porting the computationally expensive, non-bonded interaction terms on the GPUs, and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface (MPI) that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs as well as extend the implementation on GPU clusters. The results from a number of typically sized biomolecular systems are provided and analysis is performed on 3 generations of GPUs from NVIDIA. Our implementation allows up to 30-40 ns/day throughput on a single workstation as well as significant speedup over Cray XT5, a high-end supercomputing platform. Moreover, detailed analysis of the implementation indicates that further code optimization and improvements in GPUs will allow {approx}100 ns/day throughput on workstations and inexpensive GPU clusters, putting the widely-desired microsecond simulation time-scale within reach to a large user community.

  5. Atomistic spin dynamics and surface magnons.

    PubMed

    Etz, Corina; Bergqvist, Lars; Bergman, Anders; Taroni, Andrea; Eriksson, Olle

    2015-06-24

    Atomistic spin dynamics simulations have evolved to become a powerful and versatile tool for simulating dynamic properties of magnetic materials. It has a wide range of applications, for instance switching of magnetic states in bulk and nano-magnets, dynamics of topological magnets, such as skyrmions and vortices and domain wall motion. In this review, after a brief summary of the existing investigation tools for the study of magnons, we focus on calculations of spin-wave excitations in low-dimensional magnets and the effect of relativistic and temperature effects in such structures. In general, we find a good agreement between our results and the experimental values. For material specific studies, the atomistic spin dynamics is combined with electronic structure calculations within the density functional theory from which the required parameters are calculated, such as magnetic exchange interactions, magnetocrystalline anisotropy, and Dzyaloshinskii-Moriya vectors. PMID:26030259

  6. 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.

  7. Bulk breakdown in rexolite for non-uniform field geometries and single polarity pulses <10 microseconds.

    SciTech Connect

    Savage, Mark Edward; Stoltzfus, Brian Scott

    2005-06-01

    Although there is much written in regards to voltage breakdown of polymeric insulators under AC and DC conditions, much less is written involving Rexolite{copyright}(1422), non-uniform field geometries, and impulse conditions. Yet, in order to design optimized pulsed power systems with some desired degree of reliability, understanding the behavior of this type of insulating system is needed. Specifically, Sandia National Laboratory's ZR project, which will use anode plugs in the vacuum stack (thus increasing the electrical stress in the Rexolite insulators), needs to be able to estimate the reliability of these vacuum stack insulators. In an effort to estimate the insulator's lifetime small scale testing is in progress. Nine samples have been tested so far and at least ten more will be tested. Results from the current testing suggest that the Rexolite 'ages' from pulse to pulse, that there is some volume dependence on breakdown strength, and that the electrode-vacuum-insulator interface has an affect on the insulator lifetime.

  8. In-vitro bipolar nano- and microsecond electro-pulse bursts for irreversible electroporation therapies.

    PubMed

    Sano, Michael B; Arena, Christopher B; DeWitt, Matthew R; Saur, Dieter; Davalos, Rafael V

    2014-12-01

    Under the influence of external electric fields, cells experience a rapid potential buildup across the cell membrane. Above a critical threshold of electric field strength, permanent cell damage can occur, resulting in cell death. Typical investigations of electroporation effects focus on two distinct regimes. The first uses sub-microsecond duration, high field strength pulses while the second uses longer (50 μs+) duration, but lower field strength pulses. Here we investigate the effects of pulses between these two extremes. The charging behavior of the cell membrane and nuclear envelope is evaluated numerically in response to bipolar pulses between 250 ns and 50 μs. Typical irreversible electroporation protocols expose cells to 90 monopolar pulses, each 100 μs in duration with a 1 second inter-pulse delay. Here, we replace each monopolar waveform with a burst of alternating polarity pulses, while keeping the total energized time (100 μs), burst number (80), and inter-burst delay (1s) the same. We show that these bursts result in instantaneous and delayed cell death mechanisms and that there exists an inverse relationship between pulse-width and toxicity despite the delivery of equal quantities of energy. At 1500 V/cm only treatments with bursts containing 50 μs pulses (2×) resulted in viability below 10%. At 4000 V/cm, bursts with 1 μs (100×), 2 μs (50×), 5 μs (20×), 10 μs (10×), and 50 μs (2×) duration pulses reduced viability below 10% while bursts with 500 ns (200×) and 250 ns (400×) pulses resulted in viabilities of 31% and 92%, respectively. PMID:25131187

  9. 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

  10. A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

    SciTech Connect

    Nomura, K; Seymour, R; Wang, W; Kalia, R; Nakano, A; Vashishta, P; Shimojo, F; Yang, L H

    2009-02-17

    A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based on hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).

  11. Atomistically informed solute drag in Al Mg

    NASA Astrophysics Data System (ADS)

    Zhang, F.; Curtin, W. A.

    2008-07-01

    Solute drag in solute-strengthened alloys, caused by diffusion of solute atoms around moving dislocations, controls the stress at deformation rates and temperatures useful for plastic forming processes. In the technologically important Al-Mg alloys, the solute drag stresses predicted by classical theories are much larger than experiments, which is resolved in general by eliminating the singularity of the dislocation core via Peierls-Nabarro-type models. Here, the drag stress versus dislocation velocity is computed numerically using a realistic dislocation core structure obtained from an atomistic model to investigate the role of the core and obtain quantitative stresses for comparison with experiment. The model solves a discrete diffusion equation in a reference frame moving with the dislocation, with input solute enthalpies and diffusion activation barriers in the core computed by or estimated from atomistic studies. At low dislocation velocities, the solute drag stress is controlled by bulk solute diffusion because the core diffusion occurs too quickly. In this regime, the drag stress can be obtained using a Peierls-Nabarro model with a core spreading parameter tuned to best match the atomistic models. At intermediate velocities, both bulk and core diffusion can contribute to the drag, leading to a complex stress-velocity relationship showing two peaks in stress. At high velocities, the drag stress is controlled solely by diffusion within and across the core. Like the continuum models, the drag stress is nearly linear in solute concentration. The Orowan relationship is used to connect dislocation velocity to deformation strain rate. Accounting for the dependence of mobile dislocation density on stress, the simulations are in good agreement with experiments on Al-Mg alloys over a range of concentrations and temperatures.

  12. 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.

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

    DOE PAGESBeta

    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,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

  14. 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.

  15. Web-based implementation of atomistic visualization

    NASA Astrophysics Data System (ADS)

    Bhattarai, D.; Czech, W.; Karki, B. B.; Yuen, D. A.

    2008-12-01

    Atomistic (molecular) visualization is one of the most widely studied applications of scientific visualization. It deals with time-varying three dimensional positional data representing snapshots of atomic configurations produced by molecular dynamics simulations of a variety of materials including geomaterials. We have recently developed an efficient scheme, which integrates the analysis and rendering tasks together in order to support interactive visualization at space-time multi-resolution of these data. Our scheme allows us to gain better insight into bonding, radial distribution, atomic coordination, clustering, structural stability and distortion, and diffusion. We are currently extending the support for web-based access to atomistic visualization by developing a three-level distributed application with platform independence and portability. The first layer contains off-screen rendering engine whose functionality is exposed using Web Service. This layer supports batch-style rendering that allows remote analysis of data and provides general way to access service from different types of clients. The second layer is a web application that enables user to interact with data using Web Service as entry point to rendering engine. Finally, the front-end of the system is a web browser (e.g. Firefox, Safari, Internet Explorer). We will also take the advantage of relational database to store simulation results and retrieve them from rendering service. We will present the details of the implementation and applications.

  16. 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

  17. 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.

  18. Atomistic to continuum modeling of solidification microstructures

    DOE PAGESBeta

    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

  19. 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

  20. Astropulse: A search for microsecond transient radio signals using distributed computing

    NASA Astrophysics Data System (ADS)

    von Korff, Joshua Solomon

    I performed a transient, microsecond timescale radio sky survey, called "Astropulse," using the Arecibo telescope in Puerto Rico. Astropulse searches for brief (0.4 mus to 204.8 mus), wideband (relative to its 2.5 MHz bandwidth) radio pulses centered at 1,420 MHz, a range that includes the hyperfine hydrogen line. Astropulse is a commensal survey, obtaining its data by sharing telescope time with other surveys, such as PALFA. I scanned the sky visible to Arecibo, between declinations of --1.33 and 38.03 degrees, with varying dwell times depending on the requirements of our partner surveys. I analyzed 1,540 hours of data in each of 7 beams of the ALFA receiver, with 2 polarizations per beam, for a total of 21,600 hours of data. The data were 1-bit complex sampled at the Nyquist limit of 0.4 mus per sample. Examination of timescales less than 12.8 mus would have been impossible if not for my use of coherent dedispersion, a technique that has frequently been used for targeted observations, but has never before been associated with a radio sky survey. I performed nonlinear coherent dedispersion, reversing the broadening effects on signals caused by their passage through the interstellar medium (ISM). Coherent dedispersion requires intensive computations, and needs far more processing power than the more usual incoherent dedispersion. This processing power was provided by BOINC, the Berkeley Open Infrastructure for Network Computing. BOINC is a distributed computing system, which allowed me to utilize hundreds of thousands of volunteers' computers to perform the necessary calculations for coherent dedispersion. Each volunteer's computer requires about a week to process a single 8 MB "workunit," corresponding to 13 s of data from a single beam and polarization. In all, Astropulse analyzed over 48 TB of data. I did not aim to detect any particular astrophysical source, intending rather to perform a survey of the transient radio sky. Astrophysical events that might produce

  1. 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.

  2. Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

    PubMed Central

    Freddolino, Peter L.; Liu, Feng; Gruebele, Martin; Schulten, Klaus

    2008-01-01

    All-atom molecular dynamics (MD) simulations of protein folding allow analysis of the folding process at an unprecedented level of detail. Unfortunately, such simulations have not yet reached their full potential both due to difficulties in sufficiently sampling the microsecond timescales needed for folding, and because the force field used may yield neither the correct dynamical sequence of events nor the folded structure. The ongoing study of protein folding through computational methods thus requires both improvements in the performance of molecular dynamics programs to make longer timescales accessible, and testing of force fields in the context of folding simulations. We report a ten-microsecond simulation of an incipient downhill-folding WW domain mutant along with measurement of a molecular time and activated folding time of 1.5 microseconds and 13.3 microseconds, respectively. The protein simulated in explicit solvent exhibits several metastable states with incorrect topology and does not assume the native state during the present simulations. PMID:18339748

  3. 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.

  4. Microsecond-long lasing delays in thin P-clad InGaAs QW lasers

    SciTech Connect

    Wu, C.H.; Miester, C.F; Zory, P.S.; Emanuel, M.A.

    1996-06-01

    Microsecond-long lasing delays have been observed in wide-stripe, thin p-clad, InGaAs single quantum well (QW) lasers with ``thick`` p{sup +} cap layers. Computer modeling indicates that localized refractive index changes in the cap layer due to ohmic heating from the con- tact resistance may be the root cause.

  5. 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.

  6. 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.

  7. Atomistic modeling of metallic nanowires in silicon.

    PubMed

    Ryu, Hoon; Lee, Sunhee; Weber, Bent; Mahapatra, Suddhasatta; Hollenberg, Lloyd C L; Simmons, Michelle Y; Klimeck, Gerhard

    2013-09-21

    Scanning tunneling microscope (STM) lithography has recently demonstrated the ultimate in device scaling with buried, conducting nanowires just a few atoms wide and the realization of single atom transistors, where a single P atom has been placed inside a transistor architecture with atomic precision accuracy. Despite the dimensions of the critical parts of these devices being defined by a small number of P atoms, the device electronic properties are influenced by the surrounding 10(4) to 10(6) Si atoms. Such effects are hard to capture with most modeling approaches, and prior to this work no theory existed that could explore the realistic size of the complete device in which both dopant disorder and placement are important. This work presents a comprehensive study of the electronic and transport properties of ultra-thin (<10 nm wide) monolayer highly P δ-doped Si (Si:P) nanowires in a fully atomistic self-consistent tight-binding approach. This atomistic approach covering large device volumes allows for a systematic study of disorder on the physical properties of the nanowires. Excellent quantitative agreement is observed with recent resistance measurements of STM-patterned nanowires [Weber et al., Science, 2012, 335, 64], confirming the presence of metallic behavior at the scaling limit. At high doping densities the channel resistance is shown to be insensitive to the exact channel dopant placement highlighting their future use as metallic interconnects. This work presents the first theoretical study of Si:P nanowires that are realistically extended and disordered, providing a strong theoretical foundation for the design and understanding of atomic-scale electronics. PMID:23897026

  8. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

    PubMed Central

    2015-01-01

    In this Perspective, we summarize recent efforts to include the explicit treatment of induced electronic polarization in biomolecular force fields. Methods used to treat polarizability, including the induced dipole, fluctuating charge, and classical Drude oscillator models, are presented, including recent advances in force fields using those methods. This is followed by recent results obtained with the Drude model, including microsecond molecular dynamics (MD) simulations of multiple proteins in explicit solvent. Results show significant variability of backbone and side-chain dipole moments as a function of environment, including significant changes during individual simulations. Dipole moments of water in the vicinity of the proteins reveal small but systematic changes, with the direction of the changes dependent on the environment. Analyses of the full proteins show that the polarizable Drude model leads to larger values of the dielectric constant of the protein interior, especially in the case of hydrophobic regions. These results indicate that the inclusion of explicit electronic polarizability leads to significant differences in the physical forces affecting the structure and dynamics of proteins, which can be investigated in a computationally tractable fashion in the context of the Drude model. PMID:25247054

  9. Atomistic Cohesive Zone Models for Interface Decohesion in Metals

    NASA Technical Reports Server (NTRS)

    Yamakov, Vesselin I.; Saether, Erik; Glaessgen, Edward H.

    2009-01-01

    Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship characterizing the load transfer across the plane of a growing edge crack is extracted from atomistic simulations for use within a continuum finite element model. The methodology for the atomistic derivation of a cohesive-zone law is presented. This procedure can be implemented to build cohesive-zone finite element models for simulating fracture in nanocrystalline or ultrafine grained materials.

  10. Pushing single molecule techniques to microsecond resolution proves that T4 Lysozyme is a Brownian ratchet

    NASA Astrophysics Data System (ADS)

    Akhterov, Maxim V.; Choi, Yongki; Olsen, Tivoli J.; Sims, Patrick C.; Iftikhar, Mariam; Gul, O. Tolga; Corso, Brad L.; Weiss, Gregory A.; Collins, Philip G.

    2015-03-01

    Single-molecule techniques can monitor conformational dynamics of proteins, but such methods usually lack the resolution to directly observe conformational pathways or intermediate conformational states. We have recently described a single-molecule electronic technique that breaks this barrier. Using a 1 MHz-bandwidth carbon nanotube transistor, the transition pathways between open and closed conformations of T4 lysozyme have been recorded with a microsecond resolution. We directly resolve a smooth, continuous transition with an average duration of 37 microseconds. Unexpectedly, the mechanical closing and re-opening of the enzyme have identical distributions of transition durations, and the motion is independent of the enzyme catalyzing the substrate. These results illustrate the principle of microscopic reversibility applied to a Brownian ratchet, with lysozyme tracing a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity.

  11. 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

  12. Domain reduction method for atomistic simulations

    SciTech Connect

    Medyanik, Sergey N. . E-mail: medyanik@northwestern.edu; Karpov, Eduard G. . E-mail: edkarpov@gmail.com; Liu, Wing Kam . E-mail: w-liu@northwestern.edu

    2006-11-01

    In this paper, a quasi-static formulation of the method of multi-scale boundary conditions (MSBCs) is derived and applied to atomistic simulations of carbon nano-structures, namely single graphene sheets and multi-layered graphite. This domain reduction method allows for the simulation of deformable boundaries in periodic atomic lattice structures, reduces the effective size of the computational domain, and consequently decreases the cost of computations. The size of the reduced domain is determined by the value of the domain reduction parameter. This parameter is related to the distance between the boundary of the reduced domain, where MSBCs are applied, and the boundary of the full domain, where the standard displacement boundary conditions are prescribed. Two types of multi-scale boundary conditions are derived: one for simulating in-layer multi-scale boundaries in a single graphene sheet and the other for simulating inter-layer multi-scale boundaries in multi-layered graphite. The method is tested on benchmark nano-indentation problems and the results are consistent with the full domain solutions.

  13. Atomistic Simulations of Fracture in Semiconductors

    NASA Astrophysics Data System (ADS)

    Bernstein, Noam

    Semiconductors are the materials that underlie nearly all modern electron ics. They include elemental solids, such as silicon and germanium, as well as compounds such as gallium arsenide and silicon carbide. Since their main use is in electronic applications, semiconductors are not usually thought of as structural materials. Nevertheless there are important reasons, both technological and scientific, for the study of mechanical properties of semiconductors. The developing field of micro-machines, from micro-electromechanical systems (MEMS) to nanotechnology, relies on fabrication techniques developed for electronic devices to make microscopic mechanical system. To a large extent it is the link between these fabrication techniques, including deposition, masking, and etching, and the materials that has driven the use of semiconductors as structural components. On a more fundamental level, the ability to fabricate extremely pure and nearly defect free samples makes semiconductors excellent model systems for studying the physics of fracture. In this section I will attempt to give an overview of the ways in which atomistic simulations have been applied to fracture in semiconductors using a number of illustrative examples.

  14. Robust atomistic calculation of dislocation line tension

    NASA Astrophysics Data System (ADS)

    Szajewski, B. A.; Pavia, F.; Curtin, W. A.

    2015-12-01

    The line tension Γ of a dislocation is an important and fundamental property ubiquitous to continuum scale models of metal plasticity. However, the precise value of Γ in a given material has proven difficult to assess, with literature values encompassing a wide range. Here results from a multiscale simulation and robust analysis of the dislocation line tension, for dislocation bow-out between pinning points, are presented for two widely-used interatomic potentials for Al. A central part of the analysis involves an effective Peierls stress applicable to curved dislocation structures that markedly differs from that of perfectly straight dislocations but is required to describe the bow-out both in loading and unloading. The line tensions for the two interatomic potentials are similar and provide robust numerical values for Al. Most importantly, the atomic results show notable differences with singular anisotropic elastic dislocation theory in that (i) the coefficient of the \\text{ln}(L) scaling with dislocation length L differs and (ii) the ratio of screw to edge line tension is smaller than predicted by anisotropic elasticity. These differences are attributed to local dislocation core interactions that remain beyond the scope of elasticity theory. The many differing literature values for Γ are attributed to various approximations and inaccuracies in previous approaches. The results here indicate that continuum line dislocation models, based on elasticity theory and various core-cut-off assumptions, may be fundamentally unable to reproduce full atomistic results, thus hampering the detailed predictive ability of such continuum models.

  15. Atomistic simulations of langmuir monolayer collapse.

    PubMed

    Lorenz, Christian D; Travesset, Alex

    2006-11-21

    Monolayers at the vapor/water interface collapse by exploring the third dimension at sufficient lateral compression, either by forming three-dimensional structures or by solubilization into the aqueous solution. In this paper, we provide an atomistic description of collapse from molecular dynamics (MD) simulations. More specifically, we investigate monolayers of arachidic acids spread on pure water and in an aqueous solution with Ca2+ ions in the subphase. In both cases, it is found that the collapsed systems generally lead to the formation of multilayer structures, which in the system with Ca2+ ions, proceeds by an intermediate regime where the monolayer exhibits significant roughness (of the order of 4 A). If no roughness is present, the system forms collapsed structures into the aqueous solution. The computational cost of atomic MD limits our simulations to relatively small system sizes, fast compression rates, and temporal scales on the order of a nanosecond. We discuss the issues caused by these limitations and present a detailed discussion of how the collapse regime proceeds at long time scales. We conclude with a summary of the implications of our results for further theoretical and experimental studies. PMID:17106994

  16. 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.

  17. 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.

  18. Modeling: The Role of Atomistic Simulations

    SciTech Connect

    Aga, Rachel S; Morris, James R

    2007-01-01

    A major advantage of atomistic simulations is that a detailed picture of the model under investigation is available, and so they have been very instrumental in explaining the connection of macroscopic properties to the atomic scale. Simulations play a significant role in the development and testing of theories. For example, simulations have been extensively used to test the mode-coupling theory (MCT). The theory predicts that at some critical temperature Tc, known as the mode-coupling temperature, the supercooled liquid undergoes a structural arrest, prohibiting the system from accessing all possible states, thus, essentially undergoing an ergodic to nonergodic transition. It gives definite predictions on various correlation functions that can be calculated directly in simulations. Simulations and MCT have played a tremendous role in elucidating a majority of what we now understand about the dynamics of glass-forming systems. Simulations can also be used to compare with experimental results to validate the model, so that one can use simulation results to measure properties not accessible to experiments. In many cases, as will be illustrated in the next sections, results of simulations motivate experimental investigations. Part of the goal of this chapter is to examine the contributions of atomic simulations to the current state of understanding of metallic glasses.

  19. 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.

  20. Atomistic theory of amyloid fibril nucleation

    NASA Astrophysics Data System (ADS)

    Cabriolu, Raffaela; Kashchiev, Dimo; Auer, Stefan

    2010-12-01

    We consider the nucleation of amyloid fibrils at the molecular level when the process takes place by a direct polymerization of peptides or protein segments into β-sheets. Employing the atomistic nucleation theory (ANT), we derive a general expression for the work to form a nanosized amyloid fibril (protofilament) composed of successively layered β-sheets. The application of this expression to a recently studied peptide system allows us to determine the size of the fibril nucleus, the fibril nucleation work, and the fibril nucleation rate as functions of the supersaturation of the protein solution. Our analysis illustrates the unique feature of ANT that the size of the fibril nucleus is a constant integer in a given supersaturation range. We obtain the ANT nucleation rate and compare it with the rates determined previously in the scope of the classical nucleation theory (CNT) and the corrected classical nucleation theory (CCNT). We find that while the CNT nucleation rate is orders of magnitude greater than the ANT one, the CCNT and ANT nucleation rates are in very good quantitative agreement. The results obtained are applicable to homogeneous nucleation, which occurs when the protein solution is sufficiently pure and/or strongly supersaturated.

  1. 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.

  2. Long Time-Scale Atomistic Simulations

    SciTech Connect

    Sadigh, B; Cai, W; de Koning, M; Oppelstrup, T; Bulatov, V; Kalos, M

    2005-02-11

    During the past two years, we have succeeded in implementing an efficient parallel Importance Sampling Monte-Carlo (ISMC) scheme with application towards rarely occurring transition events, of great abundance in materials science and chemistry. The inefficiency of the standard atomistic modeling techniques for these problems may be traced to the extremely low probability of sampling system trajectories, or paths, that lead to a successful transition event. Instead of following the conventional approach of developing smart algorithms for searching transition paths, we tackle this problem by explicitly enhancing the probability of sampling successful transition events by means of an importance function. By selecting it appropriately, one focuses predominantly on the successful transition paths while discarding most irrelevant ones. In this manner, the rare-event problem is reformulated into an optimization problem for finding the best-possible importance function. Utilizing efficient iterative minimization algorithms, our IS approach can now be used to calculate the rate of occurrence of low-probability transition phenomena of short duration (short successful paths), but which involve collective degrees of freedom of many atoms.

  3. Atomistic simulations of caloric effects in ferroelectrics

    NASA Astrophysics Data System (ADS)

    Lisenkov, Sergey; Ponomareva, Inna

    2013-03-01

    The materials that exhibit large caloric effects have emerged as promising candidates for solid-state refrigeration which is an energy-efficient and environmentally friendly alternative to the conventional refrigeration technology. However, despite recent ground breaking discoveries of giant caloric effects in some materials they appear to remain one of nature's rarities. Here we use atomistic simulations to study electrocaloric and elastocaloric effects in Ba0.5Sr0.5TiO3 and PbTiO3 ferroelectrics. Our study reveals the intrinsic features of such caloric effects in ferroelectrics and their potential to exhibit giant caloric effects. Some of the findings include the coexistence of negative and positive electrocaloric effects in one material and an unusual field-driven transition between them as well as the coexistence of multiple giant caloric effects in Ba0.5Sr0.5TiO3 alloys. These findings could potentially lead to new paradigms for cooling devices. This work is partially supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0005245.

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2008-01-01

    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 140mm and maximum current from 3.5to5MA. 700to800ns implosion Z-pinch experiments are performed on this driver essentially with aluminium. Best results obtained before the improvement described in this paper were 1-3TW radial total power, 100-300kJ total yield, and 20-30kJ energy above 1keV. 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 ˜10kA and 50μs. 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.

  6. 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.

  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 electrophoresis

    PubMed Central

    Plenert, Matthew L.; Shear, Jason B.

    2003-01-01

    Although analysis strategies exist for probing a diverse array of molecular properties, most of these approaches are not amenable to the study of reaction intermediates and other transient species. Separations in particular can provide detailed information on attributes not readily measured by spectroscopy but typically are performed over time scales much longer than the life span of highly unstable compounds. Here we report the development of an electrophoretic strategy that dramatically extends the practical speed limit for fractionations and demonstrate its utility in examining transient hydroxyindole photoproducts. Fluorescent reaction intermediates are optically generated in femtoliter volumes within a flowing reagent stream and are differentially transported at velocities as large as 1.3 m⋅s−1, thereby minimizing band variance and allowing multicomponent reaction mixtures to be resolved over separation paths as short as 9 μm. Analyte migration times and band variances do not deviate significantly from basic theory for separations performed with fields that exceed 0.1 MV⋅cm−1, indicating that effects from Joule heating are minor. We demonstrate the feasibility of achieving baseline resolution of a binary mixture in <10 μs, nearly 100-fold faster than previously possible. Application of this approach to the study of a range of short-lived molecules should be feasible. PMID:12629208

  10. An object oriented Python interface for atomistic simulations

    NASA Astrophysics Data System (ADS)

    Hynninen, T.; Himanen, L.; Parkkinen, V.; Musso, T.; Corander, J.; Foster, A. S.

    2016-01-01

    Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment.

  11. Atomistic Simulation of Carbon Nanotube Ropes and Hydrogen Absorption

    NASA Astrophysics Data System (ADS)

    Li, Ju; Yip, Sidney; Fujiwara, Joshua

    2001-06-01

    Atomistic Simulation of Carbon Nanotube Ropes and Hydrogen Absorption Ju Li, Sidney Yip, Massachusetts Institute of Technology, Department of Nuclear Engineering, Cambridge, MA 02139; Joshua Fujiwara, Honda R&D Co., Ltd., Wako Research Center, JAPAN. Using Brenner type Reactive Empirical Bond Order (REBO) interatomic potentials, we perform atomistic simulations to calculate the optimized structures, tensile and bending strengths, and thermal conductivities of both straight and twisted single-walled nanotube ropes (bundles) where results from direct simulation are checked against those from the Green-Kubo linear response theory. Preliminary calculations are performed to study hydrogen absorption by SWNTs at room temperature and 77K.

  12. Stability of polarized states for diamond valleytronics

    SciTech Connect

    Hammersberg, J.; Majdi, S.; Kovi, K. K.; Suntornwipat, N.; Gabrysch, M.; Isberg, J.; Twitchen, D. J.

    2014-06-09

    The stability of valley polarized electron states is crucial for the development of valleytronics. A long relaxation time of the valley polarization is required to enable operations to be performed on the polarized states. Here, we investigate the stability of valley polarized states in diamond, expressed as relaxation time. We have found that the stability of the states can be extremely long when we consider the electron-phonon scattering processes allowed by symmetry considerations. We determine electron-phonon coupling constants by Time-of-Flight measurements and Monte Carlo simulations and use these data to map out the relaxation time temperature dependency. The relaxation time for diamond can be microseconds or longer below 100 K and 100 V/cm due to the strong covalent bond, which is highly encouraging for future use in valleytronic applications.

  13. Magnetoacoustic imaging of magnetic iron oxide nanoparticles embedded in biological tissues with microsecond magnetic stimulation

    NASA Astrophysics Data System (ADS)

    Hu, Gang; He, Bin

    2012-01-01

    We present an experimental study on magnetoacoustic imaging of superparamagnetic iron oxide (SPIO) nanoparticles embedded in biological tissues. In experiments, a large-current-carrying coil is used to deliver microsecond pulsed magnetic stimulation to samples. The ultrasound signals induced by magnetic forces on SPIO nanoparticles are measured by a rotating transducer. The distribution of nanoparticles is reconstructed by a back-projection imaging algorithm. The results demonstrated the feasibility to obtain cross-sectional image of magnetic nanoparticle targets with faithful dimensional and positional information, which suggests a promising tool for tomographic reconstruction of magnetic nanoparticle-labeled diseased tissues (e.g., cancerous tumor) in molecular or clinic imaging.

  14. Temperature-Jump Fluorescence Provides Evidence for Fully Reversible Microsecond Dynamics in a Thermophilic Alcohol Dehydrogenase

    PubMed Central

    2015-01-01

    Protein dynamics on the microsecond (μs) time scale were investigated by temperature-jump fluorescence spectroscopy as a function of temperature in two variants of a thermophilic alcohol dehydrogenase: W87F and W87F:H43A. Both mutants exhibit a fast, temperature-independent μs decrease in fluorescence followed by a slower full recovery of the initial fluorescence. The results, which rule out an ionizing histidine as the origin of the fluorescence quenching, are discussed in the context of a Trp49-containing dimer interface that acts as a conduit for thermally activated structural change within the protein interior. PMID:26223665

  15. Experimental Study of Implosion Dynamics of Multi-Shell Z-Pinches at Microsecond Implosion Times

    NASA Astrophysics Data System (ADS)

    Shishlov, Alexander V.; Chaikovsky, Stanislav A.; Fedunin, Anatoly V.; Fursov, Fedor I.; Kokshenev, Vladimir A.; Kurmaev, Nikolai E.; Labetsky, Aleksey Yu.; Oreshkin, Vladimir I.; Rousskikh, Alexander G.; Zhidkova, Natalia A.

    2006-01-01

    A set of experiments has been conducted on the GIT-12 generator (4.7 MA, 1.7 μs) operating at microsecond mode. The experiments were carried out with multi-shell gas puffs. Dynamics of current-carrying plasma was registered by a set of B-dots monitors placed at different radii inside a multi-shell gas puff. The experimental data obtained with the help of B-dots monitors are compared with 0D snow-plow simulations of implosion dynamics and discussed taking into consideration the data from other Z-pinch diagnostics.

  16. Hybrid continuum-atomistic approach to model electrokinetics in nanofluidics.

    PubMed

    Amani, Ehsan; Movahed, Saeid

    2016-06-01

    In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. PMID:27155300

  17. Electrochemical phase formation: classical and atomistic theoretical models.

    PubMed

    Milchev, Alexander

    2016-08-01

    The process of electrochemical phase formation at constant thermodynamic supersaturation is considered in terms of classical and atomistic nucleation theories. General theoretical expressions are derived for important thermodynamic and kinetic quantities commenting also upon the correlation between the existing theoretical models and experimental results. Progressive and instantaneous nucleation and growth of multiple clusters of the new phase are briefly considered, too. PMID:27108683

  18. Statistically Reliable 'Atomistic' Simulation of Sub 100 nm MOSFETs

    NASA Technical Reports Server (NTRS)

    Asenov, Asen

    2000-01-01

    A 3D 'atomistic' simulation technique to study random impurity induced threshold voltage lowering and fluctuations in sub 0. 1 micron MOSFETs is presented. It allows statistical analysis of random impurity effects down to the individual impurity level-Efficient algorithms based on a single solution of Poisson's equation, followed by the solution of a simplified current continuity equation are used in the simulations.

  19. Cascade defect evolution processes: Comparison of atomistic methods

    NASA Astrophysics Data System (ADS)

    Xu, Haixuan; Stoller, Roger E.; Osetsky, Yury N.

    2013-11-01

    Determining defect evolution beyond the molecular dynamics (MD) time scale is critical to bridging the gap between atomistic simulations and experiments. The recently developed self-evolving atomistic kinetic Monte Carlo (SEAKMC) method provides new opportunities to simulate long-term defect evolution with MD-like fidelity to the atomistic processes involved. To demonstrate this capability, three examples are presented in which SEAKMC has been used to investigate the evolution of typical radiation-induced defects in bcc iron. Depending on the particular example, SEAKMC results are compared with those obtained using two other on-the-fly KMC techniques, object KMC, and MD. The three examples are: (1) evolution of a vacancy-rich region similar to the core of a displacement cascade, (2) the stability of recently reported interstitial clusters with a structure similar to the C15 Laves phase, and (3) long-term aging of atomic displacement cascade debris. In the various examples, the SEAKMC approach provides better agreement with MD simulations, highlights the importance of the underlying atomistic processes, and provides new information on long-term defect evolution in iron.

  20. 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. PMID:22680758

  1. Bridging the Macroscopic and Atomistic Descriptions of the Electrocaloric Effect

    NASA Astrophysics Data System (ADS)

    Ponomareva, I.; Lisenkov, S.

    2012-04-01

    First-principles-based simulations are used to simulate the electrocaloric effect (ECE) in Ba0.5Sr0.5TiO3 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.

  2. Grain boundary migration: Atomistic simulation studies

    NASA Astrophysics Data System (ADS)

    Upmanyu, Moneesh

    Control of microstructural evolution is the goal of much of materials processing. Properties of grain boundaries and associated higher order defects determine fundamental microstructural parameters such as grain size/shape and texture, which in turn control an amalgam of material properties and applications. Microstructural evolution theories are based on certain assumptions, and attempts to experimentally validate them have not been promising, predominantly due to the presence of impurities. In this thesis, classical molecular dynamics simulation techniques are used to investigate boundary kinetics. Validity of the assumptions inherent in the theory of grain boundary migration is first ascertained. The U-shaped half-loop geometry is employed in a two-dimensional (triangular lattice) Lennard-Jones system to observe steady-state, curvature driven boundary migration. The classical linear relation between the migration rate and the driving force is recovered at low driving forces. Three-dimensional, highly parallelized simulations of <111> tilt grain boundaries in aluminum (EAM potentials) also confirm this result. The boundary mobility is found to have an Arrhenius dependence on temperature. However, the extracted activation energies of migration are significantly lower than those extracted in experiments, confirming the presence of impurities in the latter. Structurally similar boundaries are found to exhibit the compensation effect. Both boundary mobility and energy vary non-monotonically with the boundary misorientation, exhibiting maxima and minima for high symmetry (low Sigma) special misorientations, respectively. Using these anisotropic boundary properties in a Potts model reveals that the evolution of two-dimensional random textures is mostly controlled by boundary energy anisotropy, not the mobility anisotropy. Atomistic migration mechanism studies suggest that while single hops across the boundary are frequent, migration occurs primarily due to correlated

  3. Dynamics of Lipids, Cholesterol, and Transmembrane α-Helices from Microsecond Molecular Dynamics Simulations

    PubMed Central

    2015-01-01

    Extensive all-atom molecular dynamics (∼24 μs total) allowed exploration of configurational space and calculation of lateral diffusion coefficients of the components of a protein-embedded, cholesterol-containing model bilayer. The three model membranes are composed of an ∼50/50 (by mole) dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayer and contained an α-helical transmembrane protein (HIV-1 gp41 TM). Despite the high concentration of cholesterol, normal Brownian motion was observed and the calculated diffusion coefficients (on the order of 10–9 cm2/s) are consistent with experiments. Diffusion is sensitive to a variety of parameters, and a temperature difference of ∼4 K from thermostat artifacts resulted in 2–10-fold differences in diffusion coefficients and significant differences in lipid order, membrane thickness, and unit cell area. Also, the specific peptide sequence likely underlies the consistently observed faster diffusion in one leaflet. Although the simulations here present molecular dynamics (MD) an order of magnitude longer than those from previous studies, the three systems did not approach ergodicity. The distributions of cholesterol and DPPC around the peptides changed on the microsecond time scale, but not significantly enough to thoroughly explore configurational space. These simulations support conclusions of other recent microsecond MD in that even longer time scales are needed for equilibration of model membranes and simulations of more realistic cellular or viral bilayers. PMID:25380392

  4. Aging Characteristics on Epoxy Resin Surface Under Repetitive Microsecond Pulses in Air at Atmospheric Pressure

    NASA Astrophysics Data System (ADS)

    Xie, Qing; Liu, Xiong; Zhang, Cheng; Wang, Ruixue; Rao, Zhangquan; Shao, Tao

    2016-03-01

    Research on aging characteristics of epoxy resin (EP) under repetitive microsecond pulses is important for the design of insulating materials in high power apparatus. It is because that very fast transient overvoltage always occurs in a power system, which causes flashover and is one of the main factors causing aging effects of EP materials. Therefore, it is essential to obtain a better understanding of the aging effect on an EP surface resulting from flashover. In this work, aging effects on an EP surface were investigated by surface flashover discharge under repetitive microsecond pulses in atmospheric pressure. The investigations of parameters such as the surface micro-morphology and chemical composition of the insulation material under different degrees of aging were conducted with the aid of measurement methods such as atomic force microscopy (AFM), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS). Results showed that with the accumulation of aging energy on the material surface, the particles formed on the material surface increased both in number and size, leading to the growth of surface roughness and a reduction in the water contact angle; the surface also became more absorbent. Furthermore, in the aging process, the molecular chains of EP on the surface were broken, resulting in oxidation and carbonisation. supported by the Natural Science Foundation of Hebei Province (No. E2015502081), National Natural Science Foundation of China (Nos. 51222701, 51307060), and the National Basic Research Program of China (No. 2014CB239505-3)

  5. 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

  6. Tuning Neuronal Hardware with Microsecond Precision: Sound Localization in the Barn Owl

    NASA Astrophysics Data System (ADS)

    van Hemmen, J. Leo

    1998-03-01

    In auditory and electrosensory neuronal systems, there seems to exist an unresolved paradox: They encode behaviorally relevant signals in the range of a few microseconds with neurons that are at least one order of magnitude slower. The barn owl's auditory system is a prominent example that may serve to provide a solution(W. Gerstner, R. Kempter, J.L. van Hemmen, and H. Wagner, Nature 383) (1996) 76--78 to the above paradox. First, neuronal output is much more accurate than the input, phprovided the presynaptic spikes arrive coherently on the average -- as they do in the adult animal. Second, this coherence in signal arrival times can be attained through unsupervised Hebbian learning (`tuning') during ontogenetic development. The learning rule governing the strength of a synapse is based on the precise timing of input as compared to output spikes. Third, the learning rule also selects the correct delays from two independent groups of input, for example, from the left and right ear and, thus, can explain the tuning to interaural time differences in the microsecond range that underlies sound localization. The relation to stochastic resonance is indicated.

  7. Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein

    SciTech Connect

    Wu, Ying; Kondrashkina, Elena; Kayatekin, Can; Matthews, C. Robert; Bilsel, Osman

    2008-09-29

    The earliest kinetic folding events for ({beta}{alpha}){sub 8} barrels reflect the appearance of off-pathway intermediates. Continuous-flow microchannel mixing methods interfaced to small-angle x-ray scattering (SAXS), circular dichroism (CD), time-resolved Foerster resonant energy transfer (trFRET), and time-resolved fluorescence anisotropy (trFLAN) have been used to directly monitor global and specific dimensional properties of the partially folded state in the microsecond time range for a representative ({beta}{alpha}){sub 8} barrel protein. Within 150 {micro}s, the {alpha}-subunit of Trp synthase ({alpha}TS) experiences a global collapse and the partial formation of secondary structure. The time resolution of the folding reaction was enhanced with trFRET and trFLAN to show that, within 30 {micro}s, a distinct and autonomous partially collapsed structure has already formed in the N-terminal and central regions but not in the C-terminal region. A distance distribution analysis of the trFRET data confirmed the presence of a heterogeneous ensemble that persists for several hundreds of microseconds. Ready access to locally folded, stable substructures may be a hallmark of repeat-module proteins and the source of early kinetic traps in these very common motifs. Their folding free-energy landscapes should be elaborated to capture this source of frustration.

  8. 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.

  9. 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

  10. Stimulation of secretion from bovine adrenal chromaffin cells by microsecond bursts of therapeutic levels of ultrasound.

    PubMed Central

    Robinson, I M; Kinnick, R R; Greenleaf, J F; Fernandez, J M

    1996-01-01

    1. In this study the secretory response of individual bovine adrenal chromaffin cells was monitored using amperometric carbon-fibre microelectrodes. Cells were stimulated to secrete by exposure to 20-100 microseconds long tonebursts of ultrasound (2-4 x 10(5) Pa; peak pressure at 1 MHz). 2. Three types of secretory responses were observed: an almost instantaneous response, a delayed release of catecholamines, or a series of 'burst-like' secretory bouts. 3. Fura-2 measurements of intracellular Ca2+ concentrations showed that the release of catecholamines was accompanied by an increase in the intracellular Ca2+ concentration. In the absence of extracellular Ca2+, secretory responses were not evoked showing that Ca2+ entry was necessary to elicit catecholamine release. Images Figure 1 PMID:8730600

  11. 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.

  12. Analysis of the operating regimes of microsecond-conduction-time plasma opening switches

    NASA Astrophysics Data System (ADS)

    Cassany, B.; Grua, P.

    1995-07-01

    A theoretical model for the microsecond-conduction-time plasma opening switch (POS) based on magnetohydrodynamics is presented. The operating processes are associated with the magnetic field transport in the switch. The concept of the freezing-in of magnetic field in fluids is used to analyse the dynamics of this field in the plasma. One-dimensional and two-dimensional numerical simulations lead to the identification of two operating regimes, related to the Hall and the snowplow effects. The transition between these two regimes is determined by the plasma density. Scaling relations are developed from this model. In particular the electrical charge Q, conducted by the POS during the conduction time, provides a useful tool for comparisons between theory and experiments; it is shown to be the essential parameter for the switch design.

  13. Simulating the Thermal Response of High Explosives on Time Scales of Days to Microseconds

    SciTech Connect

    Yoh, J J; McClelland, M A

    2003-07-16

    We present an overview of computational techniques for simulating the thermal cookoff of high explosives using a multi-physics hydrodynamics code, ALE3D. Recent improvements to the code have aided our computational capability in modeling the response of energetic materials systems exposed to extreme thermal environments, such as fires. We consider an idealized model process for a confined explosive involving the transition from slow heating to rapid deflagration in which the time scale changes from days to hundreds of microseconds. The heating stage involves thermal expansion and decomposition according to an Arrhenius kinetics model while a pressure-dependent burn model is employed during the explosive phase. We describe and demonstrate the numerical strategies employed to make the transition from slow to fast dynamics.

  14. Progress toward a microsecond duration, repetitive, intense-ion beam for active spectroscopic measurements on ITER

    SciTech Connect

    Davis, H.A.; Bartsch, R.R.; Barnes, C.W.

    1996-06-01

    The authors describe the design of an intense, pulsed, repetitive, neutral beam based on magnetically insulated diode technology for injection into ITER for spectroscopic measurements of thermalizing alpha particle and thermal helium density profiles, ion temperature, plasma rotation, and low Z impurity concentrations in the confinement region. The beam is being developed to enhance low signal-to-noise ratios expected with conventional steady-state ion beams because of severe beam attenuation and intense bremstrahlung emission. A 5 GW (e.g., 100 keV, 50 kA) one-microsecond-duration beam would increase the signal by 10{sup 3} compared to a conventional 5 MW beam with signal-to-noise ratios comparable to those from a chopped conventional beam in one second.

  15. Atomistic aspects of crack propagation along high angle grain boundaries

    SciTech Connect

    Farkas, D.

    1997-12-31

    The author presents atomistic simulations of the crack tip configuration near a high angle {Sigma} = 5 [001](210) symmetrical tilt grain boundary in NiAl. The simulations were carried out using molecular statics and embedded atom (EAM) potentials. The cracks are stabilized near a Griffith condition involving the cohesive energy of the grain boundary. The atomistic configurations of the tip region are different in the presence of the high angle grain boundary than in the bulk. Three different configurations of the grain boundary were studied corresponding to different local compositions. It was found that in ordered NiAl, cracks along symmetrical tilt boundaries show a more brittle behavior for Al rich boundaries than for Ni-rich boundaries. Lattice trapping effects in grain boundary fracture were found to be more significant than in the bulk.

  16. Atomistic study on dithiolated oligo-phenylenevinylene gated device

    SciTech Connect

    Mahmoud, Ahmed Lugli, Paolo

    2014-11-28

    Thanks to their semiconducting behavior, conjugated molecules are considered as an attractive candidate for future electronic devices. Understanding the charge transport characteristics through such molecules for different device applications would accelerate the progress in the field of molecular electronics. In addition, it would become more feasible to introduce/enhance specific properties of molecular devices. This theoretical paper focuses on atomistic simulation and characterization of novel molecular FET employing dithiolated oligo-phenylenevinylene molecules. The simulation is validated by its agreement with the experimental measurements conducted on the same molecules. The employed molecule has oxygen linkers, which are responsible for the strongly nonlinear current characteristics on the molecular device. We perform a thorough atomistic device analysis to illustrate the principles behind the nonlinear current characteristics and the gating effect.

  17. Glide-Shuffle Competition in Silicon: An Atomistic Study

    NASA Astrophysics Data System (ADS)

    Li, Ju; Cai, Wei; Chang, Jinpeng; Yip, Sidney

    2001-06-01

    Glide-Shuffle Competition in Silicon: An Atomistic Study Ju Li, Wei Cai, Jinpeng Chang, Sidney Yip, Massachusetts Institute of Technology, Department of Nuclear Engineering, Cambridge, MA 02139 Recent experiments by Suzuki et al and Rabier et al suggest that low-T and high-T plasticity in Si and III-IV compounds may be governed by different mechanisms. We perform direct atomistic calculations to obtain the core energies, Peierls-Nabarro stresses, and kink formation and migration energies of full shuffle- and glide-set dislocations and glide-set partial dislocations in Si using the Stillinger-Weber potential. These results are compared with previous calculations, and their implications will be discussed. Dynamical simulations of some of the full dislocations in motion show qualitatively different behavior with their counterparts in bcc metals.

  18. From microseconds to seconds and minutes-time computation in insect hearing.

    PubMed

    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

  19. 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

  20. Histotripsy Produced by Hundred-Microsecond-Long Focused Ultrasonic Pulses: A Preliminary Study.

    PubMed

    Guan, Yubo; Lu, Mingzhu; Li, Yujiao; Liu, Fenfen; Gao, Ya; Dong, Tengju; Wan, Mingxi

    2016-09-01

    A new strategy is proposed in this study to rapidly generate mechanical homogenized lesions using hundred-microsecond-long pulses. The pulsing scheme was divided into two stages: generating sufficient bubble seed nuclei via acceleration by boiling bubbles and efficiently forming a mechanically homogenized and regularly shaped lesion with a homogenate inside via inertial cavitation. The duty cycle was set at 4.9%/3.9% in stage 1 and 1%/0.88% in stage 2 by changing the pulse duration (PD) and off-time independently. The pulse sequence was 500-μs/400-μs PD with a 100-Hz pulse repetition frequency (PRF) in stage 1, followed by 500-μs/400-μs PD with a 100-Hz PRF and 200-μs PD with a 200-Hz PRF in stage 2. Experiments were conducted on polyacrylamide phantoms with bovine serum albumin and on ex vivo porcine kidney tissues using a single-element 1.06-MHz transducer at an 8-MPa peak negative pressure with shock waves. The lesion evolution and dynamic elastic modulus variation in the phantoms and the histology in the tissue samples were investigated. The results indicate that the two-stage treatment using hundred-microsecond-long pulses can efficiently produce mechanically homogenized lesions with smooth borders, long tear shapes and the total homogenate inside. The time to generate a single mechanically homogenized lesion is shortened from >50 s to 17.1 s. PMID:27318864

  1. 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. PMID:19518394

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Atomistic molecular dynamic simulations of multiferroics.

    PubMed

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

    2012-08-10

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings. PMID:23006300

  4. Atomistic Molecular Dynamic Simulations of Multiferroics

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  5. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA

    PubMed Central

    Mitchell, J. S.; Laughton, C. A.; Harris, Sarah A.

    2011-01-01

    Although DNA is frequently bent and supercoiled in the cell, much of the available information on DNA structure at the atomistic level is restricted to short linear sequences. We report atomistic molecular dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we compare with a recent biochemical study of structural distortions in these tight DNA loops. We have observed a wealth of non-canonical DNA structures such as kinks, denaturation bubbles and wrinkled conformations that form in response to bending and torsional stress. The simulations show that bending alone is sufficient to induce the formation of kinks in circles containing only 65 bp, but we did not observe any defects in simulations of larger torsionally relaxed circles containing 110 bp over the same MD timescales. We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to the formation of single stranded bubbles and wrinkles. These calculations are used to assess the ability of atomistic MD simulations to determine the structure of bent and supercoiled DNA. PMID:21247872

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

    PubMed Central

    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

  7. 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. PMID:27082331

  8. 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

  9. Solid-state NMR approaches to internal dynamics of proteins: from picoseconds to microseconds and seconds.

    PubMed

    Krushelnitsky, Alexey; Reichert, Detlef; Saalwächter, Kay

    2013-09-17

    Solid-state nuclear magnetic resonance (NMR) spectroscopy has matured to the point that it is possible to determine the structure of proteins in immobilized states, such as within microcrystals or embedded in membranes. Currently, researchers continue to develop and apply NMR techniques that can deliver site-resolved dynamic information toward the goal of understanding protein function at the atomic scale. As a widely-used, natural approach, researchers have mostly measured longitudinal (T1) relaxation times, which, like in solution-state NMR, are sensitive to picosecond and nanosecond motions, and motionally averaged dipolar couplings, which provide an integral amplitude of all motions with a correlation time of up to a few microseconds. While overall Brownian tumbling in solution mostly precludes access to slower internal dynamics, dedicated solid-state NMR approaches are now emerging as powerful new options. In this Account, we give an overview of the classes of solid-state NMR experiments that have expanded the accessible range correlation times from microseconds to many milliseconds. The measurement of relaxation times in the rotating frame, T1ρ, now allows researchers to access the microsecond range. Using our recent theoretical work, researchers can now quantitatively analyze this data to distinguish relaxation due to chemical-shift anisotropy (CSA) from that due to dipole-dipole couplings. Off-resonance irradiation allows researchers to extend the frequency range of such experiments. We have built multidimensional analogues of T2-type or line shape experiments using variants of the dipolar-chemical shift correlation (DIPSHIFT) experiment that are particularly suited to extract intermediate time scale motions in the millisecond range. In addition, we have continuously improved variants of exchange experiments, mostly relying on the recoupling of anisotropic interactions to address ultraslow motions in the ms to s ranges. The NH dipolar coupling offers a

  10. 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. PMID:25819916

  11. Cascade Defect Evolution Processes: Comparison of Atomistic Methods

    SciTech Connect

    Xu, Haixuan; Stoller, Roger E; Osetskiy, Yury N

    2013-11-01

    Determining the defect evolution beyond the molecular dynamics (MD) time scale is critical in bridging the gap between atomistic simulations and experiments. The recently developed self-evolving atomistic kinetic Monte Carlo (SEAKMC) method provides new opportunities to simulate long-term defect evolution with MD-like fidelity. In this study, SEAKMC is applied to investigate the cascade defect evolution in bcc iron. First, the evolution of a vacancy rich region is simulated and compared with results obtained using autonomous basin climbing (ABC) +KMC and kinetic activation-relaxation technique (kART) simulations. Previously, it is found the results from kART are orders of magnitude faster than ABC+KMC. The results obtained from SEAKMC are similar to kART but the time predicted is about one order of magnitude faster than kART. The fidelity of SEAKMC is confirmed by statistically relevant MD simulations at multiple higher temperatures, which proves that the saddle point sampling is close to complete in SEAKMC. The second is the irradiation-induced formation of C15 Laves phase nano-size defect clusters. In contrast to previous studies, which claim the defects can grow by capturing self-interstitials, we found these highly stable clusters can transform to <111> glissile configuration on a much longer time scale. Finally, cascade-annealing simulations using SEAKMC is compared with traditional object KMC (OKMC) method. SEAKMC predicts substantially fewer surviving defects compared with OKMC. The possible origin of this difference is discussed and a possible way to improve the accuracy of OKMC based on SEAKMC results is outlined. These studies demonstrate the atomistic fidelity of SEAKMC in comparison with other on-the-fly KMC methods and provide new information on long-term defect evolution in iron.

  12. 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.

  13. The Landau-Lifshitz equation in atomistic models

    NASA Astrophysics Data System (ADS)

    Ellis, M. O. A.; Evans, R. F. L.; Ostler, T. A.; Barker, J.; Atxitia, U.; Chubykalo-Fesenko, O.; Chantrell, R. W.

    2015-09-01

    The Landau-Lifshitz (LL) equation, originally proposed at the macrospin level, is increasingly used in Atomistic Spin Dynamic (ASD) models. These models are based on a spin Hamiltonian featuring atomic spins of fixed length, with the exchange introduced using the Heisenberg formalism. ASD models are proving a powerful approach to the fundamental understanding of ultrafast magnetization dynamics, including the prediction of the thermally induced magnetization switching phenomenon in which the magnetization is reversed using an ultra-fast laser pulse in the absence of an externally applied field. This paper outlines the ASD model approach and considers the role and limitations of the LL equation in this context.

  14. Atomistic simulation of a superionic transition in UO2

    NASA Astrophysics Data System (ADS)

    Korneva, M. A.; Starikov, S. V.

    2016-01-01

    The results of the atomistic simulation of a superionic transition and melting of uranium dioxide are presented. The temperature dependences of the concentration of defects in the oxygen sublattice and changes in the heat capacity and isothermal compressibility upon the superionic transition are calculated. It is shown that the curve of the superionic transition in the PT diagram can be described by the Ehrenfest's equation. The possibility of describing the superionic transition within the framework of the theory of second- order phase transitions is discussed. Based on the results obtained, it is considered that this structural transformation can occur in other materials.

  15. Ergodicity, mixing, and time reversibility for atomistic nonequilibrium steady states

    SciTech Connect

    Hoover, W.G.; Kum, O.

    1997-11-01

    Ergodic mixing is prerequisite to any statistical-mechanical calculation of properties derived from atomistic dynamical simulations. Thus the time-reversible thermostats and ergostats used in simulating Gibbsian equilibrium dynamics or nonequilibrium steady-state dynamics should impose ergodicity and mixing. Though it is hard to visualize many-dimensional phase-space distributions, recent developments provide several practical numerical approaches to the problem of ergodic mixing. Here we apply three of these approaches to a useful nonequilibrium test problem, an oscillator in a temperature gradient. {copyright} {ital 1997} {ital The American Physical Society}

  16. Interfacial Phenomena: Linking Atomistic and Molecular Level Processes

    SciTech Connect

    Jay A Brandes

    2009-09-23

    This was a grant to support travel for scientists to present data and interact with others in their field. Specifically, speakers presented their data in a session entitled “Interfacial Phenomena: Linking Atomistic and Macroscopic Properties: Theoretical and Experimental Studies of the Structure and Reactivity of Mineral Surfaces”. The session ran across three ½ day periods, March 30-31 2004. The session’s organizers were David J. Wesolowski andGordon E. Brown Jr. There were a total of 30 talks presented.

  17. Structure identification methods for atomistic simulations of crystalline materials

    DOE PAGESBeta

    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.

  18. 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.

  19. Microsecond regime optical cross connect: 32 port to 32 port scalable device

    NASA Astrophysics Data System (ADS)

    Lynn, Brittany; Miles, Alexander; Blanche, Pierre-Alexandre; Wissinger, John; Carothers, Daniel; Norwood, Robert A.; Peyghambarian, N.

    2014-03-01

    Presented here is a 32 × 32 optical switch for telecommunications applications capable of reconfiguring at speeds of up to 12 microseconds. The free space switching mechanism in this interconnect is a digital micromirror device (DMD) consisting of a 2D array of 10.8μm mirrors optimized for implementation at 1.55μm. Hinged along one axis, each micromirror is capable of accessing one of two positions in binary fashion. In general reflection based applications this corresponds to the ability to manifest only two display states with each mirror, but by employing this binary state system to display a set of binary amplitude holograms, we are able to access hundreds of distinct locations in space. We previously demonstrated a 7 × 7 switch employing this technology, providing a proof of concept device validating our initial design principles but exhibiting high insertion and wavelength dependent losses. The current system employs 1920 × 1080 DMD, allowing us to increase the number of accessible ports to 32 × 32. Adjustments in imaging, coupling component design and wavelength control were also made in order to improve the overall loss of the switch. This optical switch performs in a bit-rate and protocol independent manner, enabling its use across various network fabrics and data rates. Additionally, by employing a diffractive switching mechanism, we are able to implement a variety of ancillary features such as dynamic beam pick-off for monitoring purposes, beam division for multicasting applications and in situ attenuation control.

  20. Ultrafast x-ray photoelectron spectroscopy in the microsecond time domain

    SciTech Connect

    Höfert, O.; Gleichweit, C.; Steinrück, H.-P.; Papp, C.

    2013-09-15

    We introduce a new approach for ultrafast in situ high-resolution X-ray photoelectron spectroscopy (XPS) to study surface processes and reaction kinetics on the microsecond timescale. The main idea is to follow the intensity at a fixed binding energy using a commercial 7 channeltron electron analyzer with a modified signal processing setup. This concept allows for flexible switching between measuring conventional XP spectra and ultrafast XPS. The experimental modifications are described in detail. As an example, we present measurements for the adsorption and desorption of CO on Pt(111), performed at the synchrotron radiation facility BESSY II, with a time resolution of 500 μs. Due to the ultrafast measurements, we are able to follow adsorption and desorption in situ at pressures of 2 × 10{sup −6} mbar and temperatures up to 500 K. The data are consistently analyzed using a simple model in line with data obtained with conventional fast XPS at temperatures below 460 K. Technically, our new approach allows measurement on even shorter timescales, down to 20 μs.

  1. Mechanisms of allosteric gene regulation by NMR quantification of microsecond-millisecond protein dynamics.

    PubMed

    Kleckner, Ian R; Gollnick, Paul; Foster, Mark P

    2012-01-13

    The trp RNA-binding attenuation protein (TRAP) is a paradigmatic allosteric protein that regulates the tryptophan biosynthetic genes associated with the trp operon in bacilli. The ring-shaped 11-mer TRAP is activated for recognition of a specific trp-mRNA target by binding up to 11 tryptophan molecules. To characterize the mechanisms of tryptophan-induced TRAP activation, we have performed methyl relaxation dispersion (MRD) nuclear magnetic resonance (NMR) experiments that probe the time-dependent structure of TRAP in the microsecond-to-millisecond "chemical exchange" time window. We find significant side chain flexibility localized to the RNA and tryptophan binding sites of the apo protein and that these dynamics are dramatically reduced upon ligand binding. Analysis of the MRD NMR data provides insights into the structural nature of transiently populated conformations sampled in solution by apo TRAP. The MRD data are inconsistent with global two-state exchange, indicating that conformational sampling in apo TRAP is asynchronous. These findings imply a temporally heterogeneous population of structures that are incompatible with RNA binding and substantiate the study of TRAP as a paradigm for probing and understanding essential dynamics in allosteric, regulatory proteins. PMID:22115774

  2. [Microsecond Pulsed Hollow Cathode Lamp as Enhanced Excitation Source of Hydride Generation Atomic Fluorescence Spectrometry].

    PubMed

    Zhang, Shuo

    2015-09-01

    The spectral, electrical and atomic fluorescence characteristics of As, Se, Sb and Pb hollow cathode lamps (HCLs) powered by a laboratory-built high current microsecond pulse (HCMP) power supply were studied, and the feasibility of using HCMP-HCLs as the excitation source of hydride generation atomic fluorescence spectrometry (HG-AFS) was evaluated. Under the HCMP power supply mode, the As, Se, Sb, Pb HCLs can maintain stable glow discharge at frequency of 100~1000 Hz, pulse width of 4.0~20 μs and pulse current up to 4.0 A. Relationship between the intensity of characteristic emission lines and HCMP power supply parameters, such as pulse current, power supply voltage, pulse width and frequency, was studied in detail. Compared with the conventional pulsed (CP) HCLs used in commercial AFS instruments, HCMP-HCLs have a narrower pulse width and much stronger pulse current. Under the optimized HCMP power supply parameters, the intensity of atomic emission lines of As, Se, Sb HCLs had sharp enhancement and that indicated their capacity of being a novel HG-AFS excitation source. However, the attenuation of atomic lines and enhancement of ionic lines negated such feasibility of HCMP-Pb HCL. Then the HG-AFS analytical capability of using the HCMP-As/Se/Sb HCLs excitation source was established and results showed that the HCMP-HCL is a promising excitation source for HG-AFS. PMID:26669140

  3. 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)

  4. 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.

  5. Microsecond protein dynamics measured by 13Calpha rotating-frame spin relaxation.

    PubMed

    Lundström, Patrik; Akke, Mikael

    2005-09-01

    NMR spin relaxation in the rotating frame (R1rho) is a unique method for atomic-resolution characterization of conformational (chemical) exchange processes occurring on the microsecond timescale. We present a rotating-frame 13C(alpha) relaxation dispersion experiment for measuring conformational dynamics in uniformly 13C-labeled proteins. The experiment was validated by using the E140Q mutant of the C-terminal fragment of calmodulin, which exhibits significant conformational exchange between two major conformations, as gauged from previous 15N and 1H relaxation studies. Consistent with previous work, the present 13C(alpha) R1rho experiment detects conformational-exchange dynamics throughout the protein. The average correlation time of =25+/-8 micros is in excellent agreement with those determined previously from 1H and 15N R1rho relaxation data: =19+/-7 and 21+/-3 micros, respectively. The extracted chemical-shift differences between the exchanging states reveal significant fluctuations in dihedral angles within single regions of Ramachandran phi-psi space, that were not identified from the 1H and 15N relaxation data. The present results underscore the advantage of using several types of nuclei to probe exchange dynamics in biomolecules. PMID:16028301

  6. 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. PMID:25382060

  7. Ultrafast x-ray photoelectron spectroscopy in the microsecond time domain

    NASA Astrophysics Data System (ADS)

    Höfert, O.; Gleichweit, C.; Steinrück, H.-P.; Papp, C.

    2013-09-01

    We introduce a new approach for ultrafast in situ high-resolution X-ray photoelectron spectroscopy (XPS) to study surface processes and reaction kinetics on the microsecond timescale. The main idea is to follow the intensity at a fixed binding energy using a commercial 7 channeltron electron analyzer with a modified signal processing setup. This concept allows for flexible switching between measuring conventional XP spectra and ultrafast XPS. The experimental modifications are described in detail. As an example, we present measurements for the adsorption and desorption of CO on Pt(111), performed at the synchrotron radiation facility BESSY II, with a time resolution of 500 μs. Due to the ultrafast measurements, we are able to follow adsorption and desorption in situ at pressures of 2 × 10-6 mbar and temperatures up to 500 K. The data are consistently analyzed using a simple model in line with data obtained with conventional fast XPS at temperatures below 460 K. Technically, our new approach allows measurement on even shorter timescales, down to 20 μs.

  8. Evaluating Letter Recognition, Flicker Fusion, and the Talbot-Plateau Law using Microsecond-Duration Flashes

    PubMed Central

    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. PMID:25875652

  9. Investigating the allosteric reverse signalling of PARP inhibitors with microsecond molecular dynamic simulations and fluorescence anisotropy.

    PubMed

    Marchand, Jean-Rémy; Carotti, Andrea; Passeri, Daniela; Filipponi, Paolo; Liscio, Paride; Camaioni, Emidio; Pellicciari, Roberto; Gioiello, Antimo; Macchiarulo, Antonio

    2014-10-01

    The inhibition of the poly(ADP-ribose) polymerase (PARP) family members is a strategy pursued for the development of novel therapeutic agents in a range of diseases, including stroke, cardiac ischemia, cancer, inflammation and diabetes. Even though some PARP-1 inhibitors have advanced to clinical setting for cancer therapy, a great deal of attention is being devoted to understand the polypharmacology of current PARP inhibitors. Besides blocking the catalytic activity, recent works have shown that some PARP inhibitors exhibit a poisoning activity, by trapping the enzyme at damaged sites of DNA and forming cytotoxic complexes. In this study we have used microsecond molecular dynamics to study the allosteric reverse signalling that is at the basis of such an effect. We show that Olaparib, but not Veliparib and HYDAMTIQ, is able to induce a specific conformational drift of the WGR domain of PARP-1, which stabilizes PARP-1/DNA complex through the locking of several salt bridge interactions. Fluorescence anisotropy assays support such a mechanism, providing the first experimental evidence that HYDAMTIQ, a potent PARP inhibitor with neuroprotective properties, is less potent than Olaparib to trap PARP-1/DNA complex. PMID:25062913

  10. Effects of diffusion on energy transfer in solution using a microsecond decay time rhenium metal ligand complex as the donor

    NASA Astrophysics Data System (ADS)

    Kuśba, Józef; Piszczek, Grzegorz; Gryczynski, Ignacy; Johnson, Michael L.; Lakowicz, Joseph R.

    2000-03-01

    We used resonance energy transfer and frequency-domain fluorometry to measure slow donor to acceptor diffusion in viscous media. The frequency-domain RET data were analyzed using a new numerical algorithm for predicting the donor intensity decay in the presence of diffusion occurring within the donor decay time. By the use of a rhenium metal-ligand complex as a microsecond decay time donor we were able to measure mutual donor-to-acceptor diffusion coefficients as low as 2×10 -8 cm 2/s. The availability of microsecond decay time luminophores and appropriate theory suggests the use of diffusion-enhanced energy transfer for measurement of diffusive processes and structural dynamics in biological systems.

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

    DOE PAGESBeta

    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. Nuclear magnetic resonance inverse spectra of InGaAs quantum dots: Atomistic level structural information

    NASA Astrophysics Data System (ADS)

    Bulutay, Ceyhun; Chekhovich, E. A.; Tartakovskii, A. I.

    2014-11-01

    A wealth of atomistic information is contained within a self-assembled quantum dot (QD), associated with its chemical composition and the growth history. In the presence of quadrupolar nuclei, as in InGaAs QDs, much of this is inherited to nuclear spins via the coupling between the strain within the polar lattice and the electric quadrupole moments of the nuclei. Here, we present a computational study of the recently introduced inverse spectra nuclear magnetic resonance technique to assess its suitability for extracting such structural information. We observe marked spectral differences between the compound InAs and alloy InGaAs QDs. These are linked to the local biaxial and shear strains, and the local bonding configurations. The cation alloying plays a crucial role especially for the arsenic nuclei. The isotopic line profiles also largely differ among nuclear species: While the central transition of the gallium isotopes have a narrow linewidth, those of arsenic and indium are much broader and oppositely skewed with respect to each other. The statistical distributions of electric field gradient (EFG) parameters of the nuclei within the QD are analyzed. The consequences of various EFG axial orientation characteristics are discussed. Finally, the possibility of suppressing the first-order quadrupolar shifts is demonstrated by simply tilting the sample with respect to the static magnetic field.

  13. Analysis of the pH-dependent thermodynamic stability, local motions, and microsecond folding kinetics of carbonmonoxycytochrome c.

    PubMed

    Kumar, Rajesh

    2016-09-15

    This paper analyzes the effect of pH on thermodynamic stability, low-frequency local motions and microsecond folding kinetics of carbonmonoxycytochrome c (Cyt-CO) all across the alkaline pH-unfolding transition of protein. Thermodynamic analysis of urea-induced unfolding transitions of Cyt-CO measured between pH 6 and pH 11.9 reveals that Cyt-CO is maximally stable at pH∼9.5. Dilution of unfolded Cyt-CO into refolding medium forms a native-like compact state (NCO-state), where Fe(2+)-CO interaction persists. Kinetic and thermodynamic parameters measured for slow thermally-driven CO dissociation (NCO→N+CO) and association (N+CO→NCO) reactions between pH 6.5 and pH 13 reveal that the thermal-motions of M80-containing Ω-loop are decreased in subdenaturing limit of alkaline pH. Laser photolysis of Fe(2+)-CO bond in NCO-state triggers the microsecond folding (NCO→N). The microsecond kinetics measured all across the alkaline pH-unfolding transition of Cyt-CO produce rate rollover in the refolding limb of chevron plot, which suggests a glass transition of NCO en route to N. Between pH 7 and pH 11.9, the natural logarithm of the microsecond folding rate varies by < 1.5 units while the natural logarithm of apparent equilibrium constant varies by 11.8 units. This finding indicates that the pH-dependent ionic-interactions greatly affect the global stability of protein but have very small effect on folding kinetics. PMID:27424489

  14. A comparison between characteristics of atmospheric-pressure plasma jets sustained by nanosecond- and microsecond-pulse generators in helium

    SciTech Connect

    Zhang, Cheng; Shao, Tao Wang, Ruixue; Yan, Ping; Zhou, Zhongsheng; Zhou, Yixiao

    2014-10-15

    Power source is an important parameter that can affect the characteristics of atmospheric-pressure plasma jets (APPJs), because it can play a key role on the discharge characteristics and ionization process of APPJs. In this paper, the characteristics of helium APPJs sustained by both nanosecond-pulse and microsecond-pulse generators are compared from the aspects of plume length, discharge current, consumption power, energy, and optical emission spectrum. Experimental results showed that the pulsed APPJ was initiated near the high-voltage electrode with a small curvature radius, and then the stable helium APPJ could be observed when the applied voltage increased. Moreover, the discharge current of the nanosecond-pulse APPJ was larger than that of the microsecond-pulse APPJ. Furthermore, although the nanosecond-pulse generator consumed less energy than the microsecond-pulse generator, longer plume length, larger instantaneous power per pulse and stronger spectral line intensity could be obtained in the nanosecond-pulse excitation case. In addition, some discussion indicated that the rise time of the applied voltage could play a prominent role on the generation of APPJs.

  15. Modeling the atomistic growth behavior of gold nanoparticles in solution

    NASA Astrophysics Data System (ADS)

    Turner, C. Heath; Lei, Yu; Bao, Yuping

    2016-04-01

    The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions.

  16. Modeling the atomistic growth behavior of gold nanoparticles in solution.

    PubMed

    Turner, C Heath; Lei, Yu; Bao, Yuping

    2016-04-28

    The properties of gold nanoparticles strongly depend on their three-dimensional atomic structure, leading to an increased emphasis on controlling and predicting nanoparticle structural evolution during the synthesis process. In order to provide this atomistic-level insight and establish a link to the experimentally-observed growth behavior, a kinetic Monte Carlo simulation (KMC) approach is developed for capturing Au nanoparticle growth characteristics. The advantage of this approach is that, compared to traditional molecular dynamics simulations, the atomistic nanoparticle structural evolution can be tracked on time scales that approach the actual experiments. This has enabled several different comparisons against experimental benchmarks, and it has helped transition the KMC simulations from a hypothetical toy model into a more experimentally-relevant test-bed. The model is initially parameterized by performing a series of automated comparisons of Au nanoparticle growth curves versus the experimental observations, and then the refined model allows for detailed structural analysis of the nanoparticle growth behavior. Although the Au nanoparticles are roughly spherical, the maximum/minimum dimensions deviate from the average by approximately 12.5%, which is consistent with the corresponding experiments. Also, a surface texture analysis highlights the changes in the surface structure as a function of time. While the nanoparticles show similar surface structures throughout the growth process, there can be some significant differences during the initial growth at different synthesis conditions. PMID:27091290

  17. 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.

  18. Atomistic Simulation of High-Density Uranium Fuels

    DOE PAGESBeta

    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. 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.

  20. Atomistic simulations of surfactant adsorption kinetics at interfaces

    NASA Astrophysics Data System (ADS)

    Iskrenova, Eugeniya; Patnaik, Soumya

    2014-03-01

    Heat transfer control and enhancement is an important and challenging problem in a variety of industrial and technological applications including aircraft thermal management. The role of additives in nucleate boiling and phase change in general has long been recognized and studied experimentally and modeled theoretically but in-depth description and atomistic understanding of the multiscale processes involved are still needed for better prediction and control of the heat transfer efficiency. Surfactant additives have been experimentally observed to either enhance or inhibit the boiling heat transfer depending on the surfactant concentration and chemistry and, on a molecular level, their addition leads to dynamic surface tension and changes in interfacial and transfer properties, thus contributing to the complexity of the problem. We present our atomistic modeling study of the interfacial adsorption kinetics of aqueous surfactant (sodium dodecyl sulfate) systems at a range of concentrations at room and boiling temperatures. Classical molecular dynamics and Umbrella Sampling simulations were used to study the surfactant transport properties and estimate the adsorption and desorption rates at liquid-vacuum and liquid-solid interfaces. The authors gratefully acknowledge funding from AFOSR Thermal Science Program and the Air Force Research Laboratory DoD Supercomputing Resource Center for computing time and resources.

  1. Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

    PubMed Central

    Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

    2014-01-01

    Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

  2. Atomistic calculation of the thermoelectric properties of Si nanowires

    NASA Astrophysics Data System (ADS)

    Bejenari, I.; Kratzer, P.

    2014-07-01

    The thermoelectric properties of 1.6-nm-thick Si square nanowires with [100] crystalline orientation are calculated over a wide temperature range from 0 K to 1000 K, taking into account atomistic electron-phonon interaction. In our model, the [010] and [001] facets are passivated by hydrogen and there are Si-Si dimers on the nanowire surface. The electronic structure was calculated by using the sp3 spin-orbit-coupled atomistic second-nearest-neighbor tight-binding model. The phonon dispersion was calculated from a valence force field model of the Brenner type. A scheme for calculating electron-phonon matrix elements from a second-nearest-neighbor tight-binding model is presented. Based on Fermi's golden rule, the electron-phonon transition rate was obtained by combining the electron and phonon eigenstates. Both elastic and inelastic scattering processes are taken into consideration. The temperature dependence of transport characteristics was calculated by using a solution of the linearized Boltzmann transport equation obtained by means of the iterative orthomin method. At room temperature, the electron mobility is 195 cm2 V-1 s-1 and increases with temperature, while a figure of merit ZT =0.38 is reached for n-type doping with a concentration of n =1019 cm-3.

  3. Self-evolving atomistic kinetic Monte Carlo: fundamentals and applications

    NASA Astrophysics Data System (ADS)

    Xu, Haixuan; Osetsky, Yuri N.; Stoller, Roger E.

    2012-09-01

    The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed and applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.

  4. Void Coalescence Processes Quantified through Atomistic and Multiscale Simulation

    SciTech Connect

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2005-12-31

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process.

  5. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    SciTech Connect

    Rudd, R E; Seppala, E T; Dupuy, L M; Belak, J

    2007-01-12

    Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process. We also discuss a technique for optimizing the calculation of fine-scale information on the fly for use in a coarse-scale simulation, and discuss the specific case of a fine-scale model that calculates void growth explicitly feeding into a coarse-scale mechanics model to study damage localization.

  6. Hierarchical Approach to 'Atomistic' 3-D MOSFET Simulation

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Brown, Andrew R.; Davies, John H.; Saini, Subhash

    1999-01-01

    We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1 micron MOSFET's. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations.

  7. 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. PMID:27010399

  8. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale

    PubMed Central

    Islam, Barira; Sgobba, Miriam; Laughton, Charlie; Orozco, Modesto; Sponer, Jiri; Neidle, Stephen; Haider, Shozeb

    2013-01-01

    The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 μs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology. PMID:23293000

  9. Flexoelectricity and the polarity of complex ferroelastic twin patterns

    NASA Astrophysics Data System (ADS)

    Salje, Ekhard K. H.; Li, Suzhi; Stengel, Massimiliano; Gumbsch, Peter; Ding, Xiangdong

    2016-07-01

    We study, by means of an atomistic toy model, the interplay of ferroelastic twin patterns and electrical polarization. Our molecular dynamics simulations reproduce polarity in straight twin walls as observed experimentally. We show, by making contact with continuum theory, that the effect is governed by linear flexoelectricity. Complex twin patterns, with very high densities of kinks and/or junctions, produce winding structures in the dipolar field, which are reminiscent of polarization vortices. By means of a "cold shearing" technique, we produce patches with high vortex densities; these unexpectedly show a net macroscopic polarization even if neither the original sample nor the applied mechanical perturbation breaks inversion symmetry by itself. These results may explain some puzzling experimental observations of "parasitic" polarity in the paraelectric phase of BaTi O3 and LaAl O3 .

  10. Atomistic simulations to micro-mechanisms of adhesion in automotive applications

    NASA Astrophysics Data System (ADS)

    Sen, Fatih Gurcag

    This study aimed at depicting atomistic and microstructural aspects of adhesion and friction that appear in different automotive applications and manufacturing processes using atomistic simulations coupled with tribological tests and surface characterization experiments. Thin films that form at the contact interfaces due to chemical reactions and coatings that are developed to mitigate or enhance adhesion were studied in detail. The adhesion and friction experiments conducted on diamond-like carbon (DLC) coatings against Al indicated that F incorporation into DLC decreased the coefficient of friction (COF) by 30% -with respect to H-DLC that is known to have low COF and anti-adhesion properties against Al- to 0.14 owing to formation of repulsive F-F interactions at the sliding interface as shown by density functional theory (DFT) calculations. F atoms transferred to the Al surface with an increase in the contact pressure, and this F transfer led to the formation of a stable AlF3 compound at the Al surface as confirmed by XPS and cross-sectional FIB-TEM. The incorporation of Si and O in a F-containing DLC resulted in humidity independent low COF of 0.08 due to the hydration effect of the Si-O-Si chains in the carbonaceous tribolayers that resulted in repulsive OH-OH interactions at the contact interface. At high temperatures, adhesion of Al was found to be enhanced as a result of superplastic oxide fibers on the Al surface. Molecular dynamics (MD) simulations of tensile deformation of Al nanowires in oxygen carried out with ReaxFF showed that native oxide of Al has an oxygen deficient, low density structure and in O2, the oxygen diffusion in amorphous oxide healed the broken Al-O bonds during applied strain and resulted in the superplasticity. The oxide shell also provided nucleation sites for dislocations in Al crystal. In fuel cell applications, where low Pt/carbon adhesion is causing durability problems, spin-polarized DFT showed that metals with unfilled d

  11. Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS

    PubMed Central

    Kathuria, Sagar V.; Kayatekin, Can; Barrea, Raul; Kondrashkina, Elena; Graceffa, Rita; Guo, Liang; Nobrega, R. Paul; Chakravarthy, Srinivas; Matthews, C. Robert; Irving, Thomas C.; Bilsel, Osman

    2014-01-01

    It is generally held that random coil polypeptide chains undergo a barrier-less continuous collapse when the solvent conditions are changed to favor the fully-folded native conformation. We test this hypothesis by probing intramolecular distance distributions during folding in one of the paradigms of folding reactions, that of cytochrome c. The Trp59 to heme distance was probed by time-resolved Förster resonance energy transfer (trFRET) in the microsecond time range of refolding. Contrary to expectation, a state with a Trp59-heme distance close to that of the GdnHCl denatured state is present after ~27 µs of folding. A concomitant decrease in the population of this state and an increase in the population of a compact high-FRET state (efficiency > 90%) show that the collapse is barrier-limited. Small-angle x-ray scattering measurements over a similar time range show that the radius of gyration under native favoring conditions is comparable to that of the GdnHCl denatured unfolded state. An independent comprehensive global thermodynamic analysis reveals that marginally stable partially folded structures are also present in the nominally unfolded GdnHCl denatured state. These observations suggest that specifically collapsed intermediate structures with low stability in rapid equilibrium with the unfolded state may contribute to the apparent chain contraction observed in previous fluorescence studies using steady state detection. In the absence of significant dynamic averaging of marginally stable partially folded states and with use of probes sensitive to distance distributions, barrier-limited chain contraction is observed upon transfer of the GdnHCl denatured state ensemble to native like conditions. PMID:24607691

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

    PubMed

    Rajabi, Khadijeh

    2015-02-01

    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. PMID:25553956

  13. 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

    2016-05-01

    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. PMID:27055808

  14. Material fields in atomistics as pull-backs of spatial distributions

    NASA Astrophysics Data System (ADS)

    Chandra Admal, Nikhil; Tadmor, Ellad B.

    2016-04-01

    The various fields defined in continuum mechanics have both a material and a spatial description that are related through the deformation mapping. In contrast, continuum fields defined for atomistic systems using the Irving-Kirkwood or Murdoch-Hardy procedures correspond to a spatial description. It is uncommon to define atomistic fields in the reference configuration due to the lack of a unique definition for the deformation mapping in atomistic systems. In this paper, we construct referential atomistic distributions as pull-backs of the spatial distributions obtained in the Murdoch-Hardy procedure with respect to a postulated deformation mapping that tracks particles. We then show that some of these referential distributions are independent of the choice of the deformation mapping and only depend on the reference and current configuration of particles. Therefore, the fields obtained from these distributions can be calculated without explicitly constructing a deformation map, and by construction they satisfy the balance equations. In particular, we obtain definitions for the first and second atomistic Piola-Kirchhoff stress tensors. We demonstrate the validity of these definitions through a numerical example involving finite deformation of a slab containing a notch under tension. An interesting feature of the atomistic first Piola-Kirchhoff stress tensor is the absence of a kinetic part, which in the atomistic Cauchy stress tensor accounts for thermal fluctuations. We show that this effect is implicitly included in the atomistic first Piola-Kirchhoff stress tensor through the motion of the particles. An open source program to compute the atomistic Cauchy and first Piola-Kirchhoff stress fields called MDStressLab is available online at

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

    DOE PAGESBeta

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

    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.

  16. An Atomistic View on Human Hemoglobin Carbon Monoxide Migration Processes

    PubMed Central

    Lucas, M. Fátima; Guallar, Víctor

    2012-01-01

    A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing the ligand migration processes. First, the methodology was tested on myoglobin's CO migration, and the results were compared with the wealth of theoretical and experimental studies. Then, we explored both hemoglobin tense and relaxed states and identified the differences between the α-and β-subunits. Our results indicate that the proximal site, equivalent to the Xe1 cavity in myoglobin, is never visited. Furthermore, strategically positioned residues alter the diffusion processes within hemoglobin's subunits and suggest that multiple pathways exist, especially diversified in the α-globins. A significant dependency of the ligand dynamics on the tertiary structure is also observed. PMID:22385860

  17. Atomistic simulations of material damping in amorphous silicon nanoresonators

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sankha; Song, Jun; Vengallatore, Srikar

    2016-06-01

    Atomistic simulations using molecular dynamics (MD) are emerging as a valuable tool for exploring dissipation and material damping in nanomechanical resonators. In this study, we used isothermal MD to simulate the dynamics of the longitudinal-mode oscillations of an amorphous silicon nanoresonator as a function of frequency (2 GHz–50 GHz) and temperature (15 K–300 K). Damping was characterized by computing the loss tangent with an estimated uncertainty of 7%. The dissipation spectrum displays a sharp peak at 50 K and a broad peak at around 160 K. Damping is a weak function of frequency at room temperature, and the loss tangent has a remarkably high value of ~0.01. In contrast, at low temperatures (15 K), the loss tangent increases monotonically from 4× {{10}-4} to 4× {{10}-3} as the frequency increases from 2 GHz to 50 GHz. The mechanisms of dissipation are discussed.

  18. Protein displacements under external forces: An atomistic Langevin dynamics approach

    NASA Astrophysics Data System (ADS)

    Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten

    2009-02-01

    We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

  19. Atomistic Simulation of Dislocation-Defect Interactions in Cu

    SciTech Connect

    Wirth, B D; Bulatov, V V; Diaz de la Rubia, T

    2001-01-01

    The mechanisms of dislocation-defect interactions are of practical importance for developing quantitative structure-property relationships, mechanistic understanding of plastic flow localization and predictive models of mechanical behavior in metals under irradiation. In copper and other face centered cubic metals, high-energy particle irradiation produces hardening and shear localization. Post-irradiation microstructural examination in Cu reveals that irradiation has produced a high number density of nanometer sized stacking fault tetrahedra. Thus, the resultant irradiation hardening and shear localization is commonly attributed to the interaction between stacking fault tetrahedra and mobile dislocations, although the mechanism of this interaction is unknown. In this work, we present a comprehensive molecular dynamics simulation study that characterizes the interaction and fate of moving dislocations with stacking fault tetrahedra in Cu using an EAM interatomic potential. This work is intended to produce atomistic input into dislocation dynamics simulations of plastic flow localization in irradiated materials.

  20. Emergence of linear elasticity from the atomistic description of matter

    NASA Astrophysics Data System (ADS)

    Cakir, Abdullah; Pica Ciamarra, Massimo

    2016-08-01

    We investigate the emergence of the continuum elastic limit from the atomistic description of matter at zero temperature considering how locally defined elastic quantities depend on the coarse graining length scale. Results obtained numerically investigating different model systems are rationalized in a unifying picture according to which the continuum elastic limit emerges through a process determined by two system properties, the degree of disorder, and a length scale associated to the transverse low-frequency vibrational modes. The degree of disorder controls the emergence of long-range local shear stress and shear strain correlations, while the length scale influences the amplitude of the fluctuations of the local elastic constants close to the jamming transition.

  1. Atomistic simulation of static magnetic properties of bit patterned media

    NASA Astrophysics Data System (ADS)

    Arbeláez-Echeverri, O. D.; Agudelo-Giraldo, J. D.; Restrepo-Parra, E.

    2016-09-01

    In this work we present a new design of Co based bit pattern media with out-of-plane uni-axial anisotropy induced by interface effects. Our model features the inclusion of magnetic impurities in the non-magnetic matrix. After the material model was refined during three iterations using Monte Carlo simulations, further simulations were performed using an atomistic integrator of Landau-Lifshitz-Gilbert equation with Langevin dynamics to study the behavior of the system paying special attention to the super-paramagnetic limit. Our model system exhibits three magnetic phase transitions, one due to the magnetically doped matrix material and the weak magnetic interaction between the nano-structures in the system. The different magnetic phases of the system as well as the features of its phase diagram are explained.

  2. 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.

  3. 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.

  4. Atomistic Simulations of a Thermotropic Biaxial Liquid Crystal

    NASA Astrophysics Data System (ADS)

    Peláez, Jorge; Wilson, Mark R.

    2006-12-01

    We have performed molecular dynamics simulations of a 2,5-bis-(p-hydroxyphenyl)-1,3,4-oxadiazole mesogen (ODBP-Ph-C7) at a fully atomistic level for a range of temperatures within the region that has experimentally been assigned to a biaxial nematic phase. Analysis of the data shows that the simulated nematic phase is biaxial but that the degree of biaxiality is small. The simulations show also the formation of ferroelectric domains in the nematic where the molecular short axis is aligned with the oxadiazole dipoles parallel to each other. Removal of electrostatic interactions leads to destabilization of ferroelectric domains and destabilization of the biaxiality. An additional simulation shows the slow growth of a mesophase directly from the isotropic fluid over a period of approximately 50 ns. This is the first time this has been achieved within the framework of an all-atom model.

  5. Experimentally driven atomistic model of 1,2 polybutadiene

    NASA Astrophysics Data System (ADS)

    Gkourmpis, Thomas; Mitchell, Geoffrey R.

    2014-02-01

    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 CC and C  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.

  6. Inter-ribbon tunneling in graphene: An atomistic Bardeen approach

    NASA Astrophysics Data System (ADS)

    Van de Put, Maarten L.; Vandenberghe, William G.; Sorée, Bart; Magnus, Wim; Fischetti, Massimo V.

    2016-06-01

    A weakly coupled system of two crossed graphene nanoribbons exhibits direct tunneling due to the overlap of the wavefunctions of both ribbons. We apply the Bardeen transfer Hamiltonian formalism, using atomistic band structure calculations to account for the effect of the atomic structure on the tunneling process. The strong quantum-size confinement of the nanoribbons is mirrored by the one-dimensional character of the electronic structure, resulting in properties that differ significantly from the case of inter-layer tunneling, where tunneling occurs between bulk two-dimensional graphene sheets. The current-voltage characteristics of the inter-ribbon tunneling structures exhibit resonance, as well as stepwise increases in current. Both features are caused by the energetic alignment of one-dimensional peaks in the density-of-states of the ribbons. Resonant tunneling occurs if the sign of the curvature of the coupled energy bands is equal, whereas a step-like increase in the current occurs if the signs are opposite. Changing the doping modulates the onset-voltage of the effects as well as their magnitude. Doping through electrostatic gating makes these structures promising for application towards steep slope switching devices. Using the atomistic empirical pseudopotentials based Bardeen transfer Hamiltonian method, inter-ribbon tunneling can be studied for the whole range of two-dimensional materials, such as transition metal dichalcogenides. The effects of resonance and of step-like increases in the current we observe in graphene ribbons are also expected in ribbons made from these alternative two-dimensional materials, because these effects are manifestations of the one-dimensional character of the density-of-states.

  7. 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.

  8. An atomistic-continuum Cosserat rod model of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chandraseker, Karthick; Mukherjee, Subrata; Paci, Jeffrey T.; Schatz, George C.

    2009-06-01

    The focus of the present work is an atomistic-continuum model of single-walled carbon nanotubes (CNTs) based on an elastic rod theory which can exhibit geometric as well as material nonlinearity [Healey, T.J., 2002. Material symmetry and chirality in nonlinearly elastic rods. Mathematics and Mechanics of Solids 7, 405-420]. In particular, the single-walled carbon nanotube (SWNT) is modeled as a one-dimensional elastic continuum with some finite thickness bounded by the lateral surface. Exploitation of certain symmetries in the underlying atomic structure leads to suitable representations of the continuum elastic strain energy density in terms of strain measures that capture extension, twist, bending, and shear deformations [Healey, T.J., 2002. Material symmetry and chirality in nonlinearly elastic rods. Mathematics and Mechanics of Solids 7, 405-420]. Bridging between the atomic scale and the effective continuum is carried out by parameterization of the continuum elastic energy and determination of the parameters using unit cell atomistic simulations over a range of deformation magnitudes and types. Specifically, the proposed model takes into account (a) bending, (b) twist, (c) shear, (d) extension, (e) coupled extension and twist, and (f) coupled bending and shear deformations. The extracted parameters reveal benefits of accounting for important anisotropic and large-strain effects as improvements over employing traditional, linearly elastic, isotropic, small-strain, continuum models to simulate deformations of atomic systems such as SWNTs. It is envisioned that the proposed approach and the extracted model parameters can serve as a useful input to simulations of SWNT deformations using existing nonlinearly elastic continuum codes based, for example, on the finite element method (FEM).

  9. An Atomistic Statistically Effective Energy Function for Computational Protein Design.

    PubMed

    Topham, Christopher M; Barbe, Sophie; André, Isabelle

    2016-08-01

    Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical

  10. Polarization developments

    SciTech Connect

    Prescott, C.Y.

    1993-07-01

    Recent developments in laser-driven photoemission sources of polarized electrons have made prospects for highly polarized electron beams in a future linear collider very promising. This talk discusses the experiences with the SLC polarized electron source, the recent progress with research into gallium arsenide and strained gallium arsenide as a photocathode material, and the suitability of these cathode materials for a future linear collider based on the parameters of the several linear collider designs that exist.

  11. Neuronal polarization.

    PubMed

    Takano, Tetsuya; Xu, Chundi; Funahashi, Yasuhiro; Namba, Takashi; Kaibuchi, Kozo

    2015-06-15

    Neurons are highly polarized cells with structurally and functionally distinct processes called axons and dendrites. This polarization underlies the directional flow of information in the central nervous system, so the establishment and maintenance of neuronal polarization is crucial for correct development and function. Great progress in our understanding of how neurons establish their polarity has been made through the use of cultured hippocampal neurons, while recent technological advances have enabled in vivo analysis of axon specification and elongation. This short review and accompanying poster highlight recent advances in this fascinating field, with an emphasis on the signaling mechanisms underlying axon and dendrite specification in vitro and in vivo. PMID:26081570

  12. 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.

  13. Evaluation of number concentration quantification by single-particle inductively coupled plasma mass spectrometry: microsecond vs. millisecond dwell times.

    PubMed

    Abad-Álvaro, Isabel; Peña-Vázquez, Elena; Bolea, Eduardo; Bermejo-Barrera, Pilar; Castillo, Juan R; Laborda, Francisco

    2016-07-01

    The quality of the quantitative information in single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS) depends directly on the number concentration of the nanoparticles in the sample analyzed, which is proportional to the flux of nanoparticles through the plasma. Particle number concentrations must be selected in accordance with the data acquisition frequency, to control the precision from counting statistics and the bias, which is produced by the occurrence of multiple-particle events recorded as single-particle events. With quadrupole mass spectrometers, the frequency of data acquisition is directly controlled by the dwell time. The effect of dwell times from milli- to microseconds (10 ms, 5 ms, 100 μs, and 50 μs) on the quality of the quantitative data has been studied. Working with dwell times in the millisecond range, precision figures about 5 % were achieved, whereas using microsecond dwell times, the suitable fluxes of nanoparticles are higher and precision was reduced down to 1 %; this was independent of the dwell time selected. Moreover, due to the lower occurrence of multiple-nanoparticle events, linear ranges are wider when dwell times equal to or shorter than 100 μs are used. A calculation tool is provided to determine the optimal concentration for any instrument or experimental conditions selected. On the other hand, the use of dwell times in the microsecond range reduces significantly the contribution of the background and/or the presence of dissolved species, in comparison with the use of millisecond dwell times. Although the use of dwell times equal to or shorter than 100 μs offers improved performance working in single-particle mode, the use of conventional dwell times (3-10 ms) should not be discarded, once their limitations are known. PMID:27086011

  14. Protein rotational motion in solution measured by polarized fluorescence depletion.

    PubMed Central

    Yoshida, T M; Barisas, B G

    1986-01-01

    A microscope-based system is described for directly measuring protein rotational motion in viscous environments such as cell membranes by polarized fluorescence depletion (PFD). Proteins labeled with fluorophores having a high quantum yield for triplet formation, such as eosin isothiocyanate (EITC), are examined anaerobically in a fluorescence microscope. An acousto-optic modulator generates a several-microsecond pulse of linearly polarized light which produces an orientationally-asymmetric depletion of ground state fluorescence in the sample. When the sample is then probed with light polarized parallel to the excitation pulse, fluorescence recovers over 0-1,000 microseconds as the sum of two exponentials. One exponential corresponds to triplet decay and the other to the rotational relaxation. An exciting pulse perpendicular to the probe beam is then applied. Fluorescence recovery following this pulse is the difference of the same two exponentials. Equations for fluorescence recovery kinetics to be expected in various experimentally significant cases are derived. Least-squares analysis using these equations then permits the triplet lifetime and rotational correlation time to be determined directly from PFD data. Instrumentation for PFD measurements is discussed that permits photobleaching recovery measurements of lateral diffusion coefficients using the same microscope system. With this apparatus, both rotational and translational diffusion coefficients (Dr, Dt) were measured for EITC-labeled bovine serum albumin in glycerol solutions. Values obtained for Dr and Dt are discussed in light of both the PFD models and the experimental system. PMID:3730506

  15. Atomistic-continuum coupling for solid mechanics enforcing momentum balance and continuity

    NASA Astrophysics Data System (ADS)

    Kraczek, B.; Johnson, D. D.; Xia, C.; Haber, R. B.

    2004-03-01

    We investigate an atomistic-continuum coupling strategy for solid mechanics based on the theoretical framework of Spacetime Discontinuous Galerkin (SDG) finite element methods. SDG methods weakly enforce momentum balance and continuity over computational cells that directly discretize a spacetime analysis domain. The explicit incorporation of spacetime momentum flux within this formulation supports a straightforward exchange of stress and force between the continuum and atomistic regions with no ad hoc coupling assumptions. We employ a simple MD model for the atomistics and only consider problems in 1d øtimes time. However, this coupling strategy should be applicable to other O(N) atomistic methods and extensible to higher spatial dimensions. We focus on the effects of continuum basis truncation and unresolved length-scales in the present investigation.

  16. Tracking Microstructure of Crystalline Materials: A Post-Processing Algorithm for Atomistic Simulations

    NASA Astrophysics Data System (ADS)

    Panzarino, Jason F.; Rupert, Timothy J.

    2014-03-01

    Atomistic simulations have become a powerful tool in materials research due to the extremely fine spatial and temporal resolution provided by such techniques. To understand the fundamental principles that govern material behavior at the atomic scale and directly connect to experimental works, it is necessary to quantify the microstructure of materials simulated with atomistics. Specifically, quantitative tools for identifying crystallites, their crystallographic orientation, and overall sample texture do not currently exist. Here, we develop a post-processing algorithm capable of characterizing such features, while also documenting their evolution during a simulation. In addition, the data is presented in a way that parallels the visualization methods used in traditional experimental techniques. The utility of this algorithm is illustrated by analyzing several types of simulation cells that are commonly found in the atomistic modeling literature but could also be applied to a variety of other atomistic studies that require precise identification and tracking of microstructure.

  17. 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. PMID:17677596

  18. Polar Bear

    USGS Publications Warehouse

    Amstrup, S.D.; DeMaster

    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.

  19. Polarization control at spin-driven ferroelectric domain walls

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  20. Polarized rainbow.

    PubMed

    Können, G P; de Boer, J H

    1979-06-15

    The Airy theory of the rainbow is extended to polarized light. For both polarization directions a simple analytic expression is obtained for the intensity distribution as a function of the scattering angle in terms of the Airy function and its derivative. This approach is valid at least down to droplet diameters of 0.3 mm in visible light. The degree of polarization of the rainbow is less than expected from geometrical optics; it increases with droplet size. For a droplet diameter >1 mm the locations of the supernumerary rainbows are equal for both polarization directions, but for a diameter <1 mm the supernumerary rainbows of the weaker polarization component are located between those in the strong component. PMID:20212586

  1. Nanosculpt: A methodology for generating complex realistic configurations for atomistic simulations

    PubMed Central

    Prakash, A.; Hummel, M.; Schmauder, S.; Bitzek, E.

    2016-01-01

    Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nanosculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data. PMID:27054098

  2. Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics

    SciTech Connect

    Wijesinghe, S; Hornung, R; Garcia, A; Hadjiconstantinou, N

    2004-04-15

    We present an adaptive mesh and algorithmic refinement (AMAR) scheme for modeling multi-scale hydrodynamics. The AMAR approach extends standard conservative adaptive mesh refinement (AMR) algorithms by providing a robust flux-based method for coupling an atomistic fluid representation to a continuum model. The atomistic model is applied locally in regions where the continuum description is invalid or inaccurate, such as near strong flow gradients and at fluid interfaces, or when the continuum grid is refined to the molecular scale. The need for such ''hybrid'' methods arises from the fact that hydrodynamics modeled by continuum representations are often under-resolved or inaccurate while solutions generated using molecular resolution globally are not feasible. In the implementation described herein, Direct Simulation Monte Carlo (DSMC) provides an atomistic description of the flow and the compressible two-fluid Euler equations serve as our continuum-scale model. The AMR methodology provides local grid refinement while the algorithm refinement feature allows the transition to DSMC where needed. The continuum and atomistic representations are coupled by matching fluxes at the continuum-atomistic interfaces and by proper averaging and interpolation of data between scales. Our AMAR application code is implemented in C++ and is built upon the SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure) framework developed at Lawrence Livermore National Laboratory. SAMRAI provides the parallel adaptive gridding algorithm and enables the coupling between the continuum and atomistic methods.

  3. Nano sculpt: A methodology for generating complex realistic configurations for atomistic simulations.

    PubMed

    Prakash, A; Hummel, M; Schmauder, S; Bitzek, E

    2016-01-01

    Atomistic simulations have now become commonplace in the study of the deformation and failure of materials. Increase in computing power in recent years has made large-scale simulations with billions, or even trillions, of atoms a possibility. Most simulations to-date, however, are still performed with quasi-2D geometries or rather simplistic 3D setups. Although controlled studies on such well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative studies focusing on e.g. the identification of mechanisms, researchers would greatly benefit from a methodology that helps realize more realistic configurations. The ideal scenario would be a one-on-one reconstruction of experimentally observed structures. To this end, we propose a new method and software tool called nano sculpt with the following features:•The method allows for easy sample generation for atomistic simulations from any arbitrarily shaped 3D enclosed volume.•The tool can be used to build atomistic samples from artificial geometries, including CAD geometries and structures obtained from simulation methods other than atomistic simulations.•The tool enables the generation of experimentally informed atomistic samples, by e.g. digitization of micrographs or usage of tomography data. PMID:27054098

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

    DOE PAGESBeta

    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 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

  5. 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.

  6. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    PubMed

    Petrov, Drazen; Zagrovic, Bojan

    2014-05-01

    The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the

  7. Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

    PubMed Central

    Petrov, Drazen; Zagrovic, Bojan

    2014-01-01

    The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the

  8. 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

  9. 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.

  10. 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. PMID:26106288

  11. 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

  12. 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

  13. 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.

  14. 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

  15. The non-uniqueness of the atomistic stress tensor and its relationship to the generalized Beltrami representation

    NASA Astrophysics Data System (ADS)

    Admal, Nikhil Chandra; Tadmor, E. B.

    2016-08-01

    The non-uniqueness of the atomistic stress tensor is a well-known issue when defining continuum fields for atomistic systems. In this paper, we study the non-uniqueness of the atomistic stress tensor stemming from the non-uniqueness of the potential energy representation. In particular, we show using rigidity theory that the distribution associated with the potential part of the atomistic stress tensor can be decomposed into an irrotational part that is independent of the potential energy representation, and a traction-free solenoidal part. Therefore, we have identified for the atomistic stress tensor a discrete analog of the continuum generalized Beltrami representation (a version of the vector Helmholtz decomposition for symmetric tensors). We demonstrate the validity of these analogies using a numerical test. A program for performing the decomposition of the atomistic stress tensor called MDStressLab is available online at

  16. 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. PMID:22400143

  17. Polar motion

    NASA Technical Reports Server (NTRS)

    Kolenkiewicz, R.

    1973-01-01

    Tracking of the Beacon Explorer-C satellite by a precision laser system was used to measure the polar motion and solid earth tide. The tidal perturbation of satellite latitude is plotted as variation in maximum latitude in seconds of arc on earth's surface as a function of the date, and polar motion is shown by plotting the variation in latitude of the laser in seconds of arc along the earth's surface as a function of date

  18. 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.

  19. AtomEye: an efficient atomistic configuration viewer

    NASA Astrophysics Data System (ADS)

    Li, Ju

    2003-03-01

    AtomEye is free atomistic visualization software for all major UNIX platforms. It is based on a newly developed graphics core library of higher quality than the X-window standard, with area-weighted anti-aliasing. An order-N neighbourlist algorithm is used to compute the bond connectivity. The functionalities of AtomEye include: parallel and perspective projections with full three-dimensional navigation; customizable bond and coordination number calculation; colour-encoding of arbitrary user-defined quantities; local atomic strain invariant; coloured atom tiling and tracing; up to 16 cutting planes; periodic boundary condition translations; high-quality JPEG, PNG and EPS screenshots; and animation scripting. The program is efficient compared to OpenGL hardware acceleration by employing special algorithms to treat spheres (atoms) and cylinders (bonds), in which they are rendered as primitive objects rather than as composites of polygons. AtomEye can handle more than one million atoms on a PC with 1 GB memory. It is a robust, low-cost tool for surveying nanostructures and following their evolutions.

  20. Atomistic modeling of phonon transport in turbostratic graphitic structures

    NASA Astrophysics Data System (ADS)

    Mao, Rui; Chen, Yifeng; Kim, Ki Wook

    2016-05-01

    Thermal transport in turbostratic graphitic systems is investigated by using an atomistic analytical model based on the 4th-nearest-neighbor force constant approximation and a registry-dependent interlayer potential. The developed model is shown to produce an excellent agreement with the experimental data and ab initio results in the calculation of bulk properties. Subsequent analysis of phonon transport in combination with the Green's function method illustrates the significant dependence of key characteristics on the misorientation angle, clearly indicating the importance of this degree of freedom in multi-stacked structures. Selecting three angles with the smallest commensurate unit cells, the thermal resistance is evaluated at the twisted interface between two AB stacked graphite. The resulting values in the range of 35 × 10-10 K m2/W to 116 × 10-10 K m2/W are as large as those between two dissimilar material systems such as a metal and graphene. The strong rotational effect on the cross-plane thermal transport may offer an effective means of phonon engineering for applications such as thermoelectric materials.

  1. 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.

  2. 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.

  3. 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. PMID:27195441

  4. 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.

  5. Atomistic processes of dislocation generation and plastic deformation during nanoindentation

    SciTech Connect

    Begau, C.; Hartmaier, A.; George, Easo P; Pharr, George M

    2011-01-01

    To enable plastic deformation during nanoindentation of an initially defect-free crystal, it is necessary first to produce dislocations. While it is now widely accepted that the nucleation of the first dislocations occurs at the start of the pop-in event frequently observed in experiments, it is unclear how these initial dislocations multiply during the early stages of plastic deformation and produce pop-in displacements that are typically much larger than the magnitude of the Burgers vector. This uncertainty about the complex interplay between dislocation multiplication and strain hardening during nanoindentation makes a direct correlation between force-displacement curves and macroscopic material properties difficult. In this paper, we study the early phase of plastic deformation during nanoindentation with the help of large-scale molecular dynamics simulations. A skeletonization method to simplify defect structures in atomistic simulations enables the direct observation and quantitative analysis of dislocation nucleation and multiplication processes occurring in the bulk as well as at the surface.

  6. 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. PMID:26930135

  7. Micromechanical tests of ion irradiated materials: Atomistic simulations and experiments

    SciTech Connect

    Shin, C.; Jin, H. H.; Kwon, J.

    2012-07-01

    We investigated irradiation effects on Fe-Cr binary alloys by using a nano-indentation combined with a continuous stiffness measurement (CSM) technique. We modeled the nano-indentation test by using a finite element method. We could extract the intrinsic hardness and the yield stress of an irradiation hardened region by using a so-called inverse method. SiC micro-pillars of various sizes were fabricated by mask and inductively coupled plasma etching technique and compressed by using flat punch nano-indentation. Compressive fracture strength showed a clear specimen size effect. Brittle-to-Ductile transition at room temperature was observed as the specimen size decreases. The effect of irradiation on the fracture strength of SiC micro-pillars was evaluated by performing ion irradiation with Si ions. We have performed molecular dynamics simulations of nano-indentation and nano-pillar compression tests. Radiation effect was observed which is found to be due to the interaction of dislocations nucleated by spherical indenter with pre-existing radiation defects (voids). These atomistic simulations are expected to significantly contribute to the investigation of the fundamental deformation mechanism of small scale irradiated materials. (authors)

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    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.

  9. 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. PMID:21391633

  10. 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.

  11. 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.

  12. Atomistic modelling of the hydration of CaSO 4

    NASA Astrophysics Data System (ADS)

    Adam, Craig D.

    2003-08-01

    Atomistic modelling techniques, using empirical potentials, have been used to simulate a range of structures formed by the hydration of γ-CaSO 4 and described as CaSO 4· nH 2O (0< n<1). The hemihydrate phase ( n=0.5) is of commercial importance and has been subjected to much experimental study. These simulation studies demonstrate significant water-matrix interactions that influence the crystallography of the hydrated phase. The existence of two types of hydration site has been predicted, including one within the Ca 2+coordination sphere. Close correlation between water molecule bonding energy, Ca 2+-O w bond length and unit-cell volume have been established. This shows that as the number of water molecules within the unit cell increases, the bonding energy increases and the unit cell contracts. However around n=0.5, this process reaches a turning point with the incorporation of further waters resulting in reduced binding energy and an expanding unit cell.

  13. Atomistic Hydrodynamics and the Dynamical Hydrophobic Effect in Porous Graphene.

    PubMed

    Strong, Steven E; Eaves, Joel D

    2016-05-19

    Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For numerical simulation to play a predictive and descriptive role, one must have theoretically sound methods that span orders of magnitude in physical scales, from the atomistic motions of particles inside the channels to the large-scale hydrodynamic gradients that drive transport. Here, we use constraint dynamics to derive a nonequilibrium molecular dynamics method for simulating steady-state mass flow of a fluid moving through the nanoscopic spaces of a porous solid. After validating our method on a model system, we use it to study the hydrophobic effect of water moving through pores of electrically doped single-layer graphene. The trend in permeability that we calculate does not follow the hydrophobicity of the membrane but is instead governed by a crossover between two competing molecular transport mechanisms. PMID:27139634

  14. 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

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

    PubMed

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

    2012-09-18

    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

  16. An Atomistic study of Helium Resolution in bcc Iron

    SciTech Connect

    Stoller, Roger E; Stewart, David M

    2011-01-01

    The evolution of gas-stabilized bubbles in irradiated materials can be a significant factor in the microstructural processes that lead to mechanical property and dimensional changes in structural materials exposed to high-energy neutrons. Helium generation and accumulation is particularly important under DT fusion irradiation conditions. Although the process of ballistic resolutioning of gas from bubbles has been long-discussed in the literature, there have been few computational studies of this mechanism. Resolutioning could limit bubble growth by ejecting gas atoms back into the metal matrix. A detailed atomistic study of ballistic He resolutioning from bubbles in bcc iron has been carried out using molecular dynamics. A newly-developed Fe-He interatomic potential was employed, with the iron matrix described by the potential of Ackland and co-workers from 1997. The primary variables examined were: irradiation temperature (100 and 600K), iron knock-on atom energy (5 and 20 keV), bubble radius (~0.5 and 1.0 nm), and He-to-vacancy ratio in the bubble (0.25, 0.5 and 1.0) in order to obtain an assessment of this dynamic resolutioning mechanism. The results presented here focus on the 5 keV cascades which indicate a modest, but potentially significant level of He removal by this process.

  17. 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.

  18. Atomistic modeling of diffusional phasetransformations with elastic strain

    SciTech Connect

    Mason, D R; Rudd, R E; Sutton, A P

    2003-10-31

    Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Atomic interactions are modelled by Finnis-Sinclair potentials constructed for these simulations. Vacancy diffusion is modelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of kBT. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r{sup 3} , it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice.

  19. 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.

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

    DOE PAGESBeta

    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,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

  1. Atomistic Mechanism of Surface-Oxide Formation on Ru(0001)

    NASA Astrophysics Data System (ADS)

    Reuter, K.; Ganduglia-Pirovano, M. V.; Scheffler, M.; Stampfl, C.

    2001-03-01

    CO-oxidation catalysis on Ruthenium is a prime example of the pressure and materials gap in the sense, that a very low activity under UHV conditions is contrasted with very high turnover rates at high pressures. A recent experimental study has connected this change in activity with the formation of RuO_2(110) patches on the surface (H. Over et al., Science 287, 1474 (2000)). In order to analyze the atomistic mechanism behind this surface oxide formation, we perform density functional theory calculations for more and more O loaded Ru(0001) surfaces. After a full monolayer coverage on the surface has been reached, O starts to penetrate into the sample. Instead of diffusing further into the bulk, oxygen agglomerates in subsurface islands between the first and second substrate layers. These islands can be characterized as a O-Ru-O trilayer ``floating'' on top of the Ru(0001) substrate. Further O incorporation leads to a successive formation of such O-Ru-O trilayers, which at first remain in a CaF2 type stacking sequence. After a critical thickness has been exceeded, we finally observe a phase transition into the experimentally seen rutile RuO_2(110) structure.

  2. 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.

  3. A spacetime, balance-law formulation of coupled atomistic and continuum dynamics for solids

    NASA Astrophysics Data System (ADS)

    Kraczek, Brent

    Coupled dynamic atomistic and continuum computational methods for solids have received much interest recently, because many problems are not addressed well by either model alone. In most coupled methods more emphasis has been placed on damping spurious reflections than on balancing momentum and energy. I present a new method for concurrent coupling of dynamic atomistic and continuum simulations of solids that enforces these balance laws on the atom/element level while minimizing spurious reflections. The coupled formulation is composed of the continuum spacetime discontinuous Galerkin (SDG) method and the mathematically consistent, time finite element, atomistic discontinuous Galerkin (ADG) method. On the continuum side I develop a two- and three-field SDG formulations for linearized elastodynamics to illuminate the mathematical structure of the original one-field SDG formulation and to assist in making connections to the atomistic formulation. On the atomistic side I examine connections between the SDG and ADG methods, and then extend this to relationships with the Velocity Verlet integrator. The component SDG and ADG methods are coupled using the same Godunov flux solution as is used by the SDG method, to enforce weakly the jump conditions on momentum balance and kinematic compatibility. To obtain compatible fluxes on the atomistic side of the coupling boundary I define a boundary atomistic trace that can be optimized to minimize boundary reflections. The coupled SDG--ADG formulation preserves the characteristic structure of the hyperbolic problem, guarantees element/atom-wise momentum balance to machine precision and yields energy error that is small, dissipative and controllable. The flux-based coupling can also be used with the Velocity Verlet method in place of the ADG, although the SDG--VV method suffers from uncontrolled energy error for long-time simulations due to the mismatch in the mathematical models. I present the formulations in spacetime, with one

  4. 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

  5. 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

  6. Microsecond X-ray Absorption Spectroscopy Identification of Co(I) Intermediates in Cobaloxime-Catalyzed Hydrogen Evolution.

    PubMed

    Smolentsev, Grigory; Cecconi, Bianca; Guda, Alexander; Chavarot-Kerlidou, Murielle; van Bokhoven, Jeroen A; Nachtegaal, Maarten; Artero, Vincent

    2015-10-19

    Rational development of efficient photocatalytic systems for hydrogen production requires understanding the catalytic mechanism and detailed information about the structure of intermediates in the catalytic cycle. We demonstrate how time-resolved X-ray absorption spectroscopy in the microsecond time range can be used to identify such intermediates and to determine their local geometric structure. This method was used to obtain the solution structure of the Co(I) intermediate of cobaloxime, which is a non-noble metal catalyst for solar hydrogen production from water. Distances between cobalt and the nearest ligands including two solvent molecules and displacement of the cobalt atom out of plane formed by the planar ligands have been determined. Combining in situ X-ray absorption and UV/Vis data, we demonstrate how slight modification of the catalyst structure can lead to the formation of a catalytically inactive Co(I) state under similar conditions. Possible deactivation mechanisms are discussed. PMID:26388205

  7. Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants

    PubMed Central

    2016-01-01

    Deletions in the stalk of the influenza neuraminidase (NA) surface protein are associated with increased virulence, but the mechanisms responsible for this enhanced virulence are unclear. Here we use microsecond molecular dynamics simulations to explore the effect of stalk deletion on enzymatic activity, contrasting NA proteins from the A/swine/Shandong/N1/2009 strain both with and without a stalk deletion. By modeling and simulating neuraminidase apo glycoproteins embedded in complex-mixture lipid bilayers, we show that the geometry and dynamics of the neuraminidase enzymatic pocket may differ depending on stalk length, with possible repercussions on the binding of the endogenous sialylated-oligosaccharide receptors. We also use these simulations to predict previously unrecognized druggable “hotspots” on the neuraminidase surface that may prove useful for future efforts aimed at structure-based drug design. PMID:27141956

  8. 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.

  9. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

    PubMed Central

    Pasi, Marco; Maddocks, John H.; Beveridge, David; Bishop, Thomas C.; Case, David A.; Cheatham, Thomas; Dans, Pablo D.; Jayaram, B.; Lankas, Filip; Laughton, Charles; Mitchell, Jonathan; Osman, Roman; Orozco, Modesto; Pérez, Alberto; Petkevičiūtė, Daiva; Spackova, Nada; Sponer, Jiri; Zakrzewska, Krystyna; Lavery, Richard

    2014-01-01

    We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters. PMID:25260586

  10. Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants.

    PubMed

    Durrant, Jacob D; Bush, Robin M; Amaro, Rommie E

    2016-08-25

    Deletions in the stalk of the influenza neuraminidase (NA) surface protein are associated with increased virulence, but the mechanisms responsible for this enhanced virulence are unclear. Here we use microsecond molecular dynamics simulations to explore the effect of stalk deletion on enzymatic activity, contrasting NA proteins from the A/swine/Shandong/N1/2009 strain both with and without a stalk deletion. By modeling and simulating neuraminidase apo glycoproteins embedded in complex-mixture lipid bilayers, we show that the geometry and dynamics of the neuraminidase enzymatic pocket may differ depending on stalk length, with possible repercussions on the binding of the endogenous sialylated-oligosaccharide receptors. We also use these simulations to predict previously unrecognized druggable "hotspots" on the neuraminidase surface that may prove useful for future efforts aimed at structure-based drug design. PMID:27141956

  11. 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

  12. 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.

  13. Atomistic and model description of nanotube electromechanical devices

    NASA Astrophysics Data System (ADS)

    Rotkin, Slava V.

    2003-03-01

    Nanotubes (NTs), which are natural objects on the size scale compatible with nanodevices and bio-molecules, exhibit several unique properties by themselves and in specific environments such as electronic, bio-chemical or electromechanical nanodevices. A compact continuum model has been developed [1] for the multi-scale calculation of NT behavior in various devices, ranging from Nano-Electromechanical Systems (NEMS)[2] to Light-Controlled Molecular Switches [3]. The continuum model parameterization is based on Molecular Dynamics and microscopic modeling. For example, elements of quantum mechanical consideration were introduced through the calculation of the nanotube polarizability, atomistic capacitance [4], and van der Waals interaction [5]. Quantum-chemistry approach was used for computation of an equilibrium structure of chemically modified NTs. An analytical expression will be discussed for quantum capacitance of metallic NTs with arbitrary lateral deformation. Compact model and a quantum mechanical simulation will be compared for the NT charge density calculation. A scattering probability for a potential of charged impurity and ballistic conductance of NT channel have been computed for a light controlled electronic NT switch. Analytical expression for the pull-in voltage for NT NEMS will be presented with quantum corrections and van der Waals interactions taken into account. This calculation will demonstrate that a principal physical limit exists for fabricating NEMS [6]. 1. N.R.Aluru, et.al., in Handbook of Nanoscience, Engineering and Technology, Eds: W.Goddard, et.al.; CRC Press, 2002 2. M.Dequesnes, S.V.Rotkin, N.R.Aluru, Nanotechnology 13, 2002 3. S.V.Rotkin, I.Zharov, Int.J.of Nanoscience 1(3/4) 2002 4. K.A.Bulashevich, S.V.Rotkin, JETPL 75(4) 2002 5. S.V.Rotkin, K.Hess, J.of Comp.Electronics 1(3) 2002 6. S.V.Rotkin, in Microfabr. Syst. and MEMS, Eds: P. J. Hesketh, et.al. ECS Inc., Pennington, NJ, USA 2002

  14. 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.

  15. Growth energetics of germanium quantum dots by atomistic simulation

    NASA Astrophysics Data System (ADS)

    Wagner, Richard Joseph

    Strained epitaxial growth of Ge on Si(001) produces self-assembled, nanometer scale islands, or quantum dots. We study this growth by atomistic simulation, computing the energy of island structures to determine when and how islanding occurs. We also describe experimental methods of island growth and characterization in order to understand the relevant physical processes and to interpret experimental observations for comparison with simulation. We show that pyramidal Ge islands with rebonded step {105} facets are energetically favorable compared to growth of planar Ge (2 x 8) on Si(001). We determine how the chemical potential of these islands varies with size, lateral spacing, and wetting layer thickness. We also illustrate the atomic-level structure of these islands with favorable formation energy. Intermixing can occur between the growing Ge film and the Si substrate. We show that although Ge prefers to wet the surface, entropy drives some fraction into the underlying layers. We present a simple model of intermixing by equilibration of the top crystal layers. The equilibration is performed with a flexible lattice Monte Carlo simulation. Ultimately, intermixing produces a temperature-dependent graded Ge concentration. The resulting chemical potential leads to the onset of islanding after 3-4 monolayers of deposition, consistent with experimental observations. The distribution of island sizes on a surface is determined by the relation of island energy to size. We find that there exists a minimum-energy island size due to the interaction of surface energy and bulk relaxation. Applying the calculated chemical potential to the Boltzmann-Gibbs distribution, we predict size distributions as functions of coverage and temperature. The distributions, with peak populations around 86 000 atoms, compare favorably with experiment. This work explores the driving force in growth of Ge on Si(001). The knowledge derived here explains why islanding occurs and provides guidance for

  16. 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

    2014-04-01

    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. PMID:24654882

  17. Upgrade of the inverted source of polarized electrons at ELSA

    NASA Astrophysics Data System (ADS)

    Heiliger, D.; Hillert, W.; Neff, B.

    2011-05-01

    Since 2000 an inverted source of polarized electrons at the electron stretcher accelerator ELSA routinely provides a pulsed beam with a polarization degree of about 80%. One micro-second long pulses with 100 nC charge are produced by irradiating a strained-layer superlattice photocathode with laser light from a flashlamp-pumped Ti:Sa laser. A rectangular pulse shape is achieved by operating the source in space charge limitation. The proposed hadron physics program requires an intensity upgrade to 200 mA which can be achieved by enlarging the emission area or by improving the quantum efficiency (QE). The resulting changes of the beam parameters (like emittance and space charge) and of the optics of the transfer line were investigated in numerical simulations. In order to enhance the source performance a new load lock system with crystal storage and atomic hydrogen cleaning will be installed in the near future.

  18. Linear scaling approach for atomistic calculation of excitonic properties of 10-million-atom nanostructures

    NASA Astrophysics Data System (ADS)

    RóŻański, Piotr T.; Zieliński, Michał

    2016-07-01

    Numerical calculations of excitonic properties of novel nanostructures, such as nanowire and crystal phase quantum dots, must combine atomistic accuracy with an approachable computational complexity. The key difficulty comes from the fact that excitonic spectra details arise from atomic-scale contributions that must be integrated over a large spatial domain containing a million and more atoms. In this work we present a step-by-step solution to this problem: a combined empirical tight-binding and configuration interaction scheme that unites linearly scaling computational time with the essentials of the atomistic modeling. We benchmark our method on the example of well-studied self-assembled InAs/GaAs quantum dots. Next, we apply our atomistic approach to crystal phase quantum dots containing more than 10 million atoms.

  19. Limitations of reactive atomistic potentials in describing defect structures in oxides

    NASA Astrophysics Data System (ADS)

    Hynninen, Teemu; Musso, Tiziana; Foster, Adam S.

    2016-03-01

    It is difficult to achieve low expense and high accuracy in computational methods, yet it remains a key objective in atomistic approaches. In solid state physics, advanced atomistic potentials using reactive force fields have shown promise in delivering both. However, these methods have not been applied widely beyond their development environment and thus their strengths and weaknesses are not fully understood. In this work we present benchmark calculations on silica (SiO2) and hafnia (HfO2) structures, comparing a leading charge optimized many-body potential to a more advanced density functional calculation. We find that although the atomistic potential gives excellent results for bulk structures, it has severe shortcomings when applied to small systems with low coordinated atoms. We also establish clearly the components of the many-body potential and how these relate to predicted physical properties.

  20. Local stress and heat flux in atomistic systems involving three-body forces.

    PubMed

    Chen, Youping

    2006-02-01

    Local densities of fundamental physical quantities, including stress and heat flux fields, are formulated for atomistic systems involving three-body forces. The obtained formulas are calculable within an atomistic simulation, in consistent with the conservation equations of thermodynamics of continuum, and can be applied to systems with general two- and three-body interaction forces. It is hoped that this work may correct some misuse of inappropriate formulas of stress and heat flux in the literature, may clarify the definition of site energy of many-body potentials, and may serve as an analytical link between an atomistic model and a continuum theory. Physical meanings of the obtained formulas, their relation with virial theorem and heat theorem, and the applicability are discussed. PMID:16468857

  1. Polar Stratigraphy

    NASA Technical Reports Server (NTRS)

    1999-01-01

    These three images were taken on three different orbits over the north polar cap in April 1999. Each shows a different part of the same ice-free trough. The left and right images are separated by a distance of more than 100 kilometers (62 miles). Note the similar layers in each image.

  2. Political polarization

    PubMed Central

    Dixit, Avinash K.; Weibull, Jörgen W.

    2007-01-01

    Failures of government policies often provoke opposite reactions from citizens; some call for a reversal of the policy, whereas others favor its continuation in stronger form. We offer an explanation of such polarization, based on a natural bimodality of preferences in political and economic contexts and consistent with Bayesian rationality. PMID:17452633

  3. Atomistic Simulation of Electronic and Optical Properties of (100), (110) and (111) Oriented InAs/GaAs Quantum Dots

    NASA Astrophysics Data System (ADS)

    Chimalgi, Vinay; Ahmed, Shaikh

    2014-03-01

    Recent advances in growth techniques and increasing number of experimental studies have made semiconducting InAs/GaAs quantum dots (QDs) grown along different crystallographic directions a reality and promising systems for applications in infrared detection, optical memories, laser, and in quantum cryptography as single photon sources and quantum computation. However, only few theoretical investigations have been performed on these QDs due to the complex nature of the coupling of atomicity, structural fields, polarization, and quantum size-quantization, all strong function of the crystallographic direction. The objective of this paper is to integrate a computational framework employing a combination of fully atomistic valence force-field molecular mechanics and 20-band sp3 s *d5 -SO tight-binding based electronic bandstructure models, and numerically investigate the effects of internal fields on the electronic and optical properties of InAs/GaAs quantum dots grown on (100), (110), and (111) orientated substrates. It is found that, while piezoelectricity has largest effects on lowering the symmetry of (100) oriented QDs, its effect is minimum in (111) orientated QDs. Supported by the U.S. National Science Foundation Grant No. 1102192.

  4. A triangulation-based method to identify dislocations in atomistic models

    NASA Astrophysics Data System (ADS)

    Stukowski, Alexander

    2014-10-01

    A simple, efficient, and fully automated computer algorithm is described that identifies dislocations in atomistic crystal models and determines their Burgers vectors. To achieve this, the algorithm maps the edges of a Delaunay tessellation to corresponding vectors in an ideal crystal. Dislocations are identified by detecting incompatibilities in this discrete elastic mapping using triangular Burgers circuits. While the presented method is limited to single crystals, it stands out due to its simplicity, straightforward implementation, and computational efficiency. It can provide a bridge from atomistic descriptions of crystals to mesoscale models based on discrete dislocation lines.

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

    PubMed

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

    2016-07-22

    The experimental determination of atomistic mechanisms linking crystal structures during a compression-driven solid-solid phase transformation is a long-standing and challenging scientific objective. 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. The approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes. PMID:27494481

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    The experimental determination of atomistic mechanisms linking crystal structures during a compression-driven solid-solid phase transformation is a long-standing and challenging scientific objective. 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. The approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Polar Textures

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03646 Polar Textures

    This VIS image shows part of the south polar region. The ejecta from the relatively young crater covers the rougher textured polar surface.

    Image information: VIS instrument. Latitude 81S, Longitude 54.5E. 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.

  14. 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.

  15. 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.

  16. 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.

  17. An atomistically validated continuum model for strain relaxation and misfit dislocation formation

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Ward, D. K.; Zimmerman, J. A.; Cruz-Campa, J. L.; Zubia, D.; Martin, J. E.; van Swol, F.

    2016-06-01

    In this paper, molecular dynamics (MD) calculations have been used to examine the physics behind continuum models of misfit dislocation formation and to assess the limitations and consequences of approximations made within these models. Without compromising the physics of misfit dislocations below a surface, our MD calculations consider arrays of dislocation dipoles constituting a mirror imaged "surface". This allows use of periodic boundary conditions to create a direct correspondence between atomistic and continuum representations of dislocations, which would be difficult to achieve with free surfaces. Additionally, by using long-time averages of system properties, we have essentially reduced the errors of atomistic simulations of large systems to "zero". This enables us to deterministically compare atomistic and continuum calculations. Our work results in a robust approach that uses atomistic simulation to accurately calculate dislocation core radius and energy without the continuum boundary conditions typically assumed in the past, and the novel insight that continuum misfit dislocation models can be inaccurate when incorrect definitions of dislocation spacing and Burgers vector in lattice-mismatched systems are used. We show that when these insights are properly incorporated into the continuum model, the resulting energy density expression of the lattice-mismatched systems is essentially indistinguishable from the MD results.

  18. Hybrid Atomistic and Coarse-Grained Molecular Dynamics Simulations of Polyethylene Glycol (PEG) in Explicit Water.

    PubMed

    Stanzione, Francesca; Jayaraman, Arthi

    2016-05-01

    In-silico design of polymeric biomaterials requires molecular dynamics (MD) simulations that retain essential atomistic/molecular details (e.g., explicit water around the biofunctional macromolecule) while simultaneously achieving large length and time scales pertinent to macroscale function. Such large-scale atomistically detailed macromolecular MD simulations with explicit solvent representation are computationally expensive. One way to overcome this limitation is to use an adaptive resolution scheme (AdResS) in which the explicit solvent molecules dynamically adopt either atomistic or coarse-grained resolution depending on their location (e.g., near or far from the macromolecule) in the system. In this study we present the feasibility and the limitations of AdResS methodology for studying polyethylene glycol (PEG) in adaptive resolution water, for varying PEG length and architecture. We first validate the AdResS methodology for such systems, by comparing PEG and solvent structure with that from all-atom simulations. We elucidate the role of the atomistic zone size and the need for calculating thermodynamic force correction within this AdResS approach to correctly reproduce the structure of PEG and water. Lastly, by varying the PEG length and architecture, we study the hydration of PEG, and the effect of PEG architectures on the structural properties of water. Changing the architecture of PEG from linear to multiarm star, we observe reduction in the solvent accessible surface area of the PEG, and an increase in the order of water molecules in the hydration shells. PMID:27108869

  19. Atomistic and electronic structure calculation of defects at the surfaces of oxides

    NASA Astrophysics Data System (ADS)

    Watson, G. W.

    We present the results of simulations using both atomistic and density functional theory (DFT) approaches that illustrate the uses of these techniques for investigating the structure and electronic structure of defects at the surfaces of oxides. Atomistic simulation studies of the low index surfaces of spinel (MgAl2O4) will show the role of vacancy configuration and surface rearrangement. Atomistic and DFT studies on Li doped MgO illustrate the importance of both the defect structure and its effect of morphology. We will also illustrate using DFT electronic defects at the surface of CeO2 , which are of great importance in redox reactions and catalytic activity. Finally we will present a novel atomistic approach for predicting the structure of supported oxide nanoclusters giving rise to a wide range of defects including a range of surface terminations, grain formation, mixed screw edge dislocations and misfit dislocations. We will illustrate this using the structure of a BaO supported MgO nanocluster.

  20. 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

  1. Polar Landforms

    NASA Technical Reports Server (NTRS)

    2005-01-01

    10 August 2005 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows eroded remnants of carbon dioxide ice in the south polar residual cap of Mars. The scarps that outline each small mesa have retreated about 3 meters (10 feet) per Mars year since MGS began orbiting the red planet in 1997.

    Location near: 87.0oS, 31.9oW Image width: width: 3 km (1.9 mi) Illumination from: upper left Season: Southern Spring

  2. 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.

  3. Aryl-Decorated Ru(II) Polypyridyl-type Photosensitizer Approaching NIR Emission with Microsecond Excited State Lifetimes.

    PubMed

    Schlotthauer, Tina; Suchland, Benedikt; Görls, Helmar; Parada, Giovanny A; Hammarström, Leif; Schubert, Ulrich S; Jäger, Michael

    2016-06-01

    Bis-tridentate Ru(II) complexes based on the dqp scaffold (dqp is 2,6-di(quinolin-8-yl)pyridine) with multiple aryl substituents were explored to tailor the absorption and emission properties. A synthetic methodology was developed for the facile synthesis and purification of homo- and heteroleptic bis-tridentate Ru complexes. The effect of the aryl substituents in the para positions of the pyridine and quinoline subunits was detailed by X-ray crystallography, steady state and time-resolved spectroscopy, electrochemistry, and computational methods. The attachment of the aryl groups results in enhanced molar extinction coefficients with the largest effect in the pyridine position, whereas the quinoline substituent leads to red-shifted emission tailing into the NIR region (up to 800 nm). Notably, the excited state lifetimes remain in the microsecond time scale even in the presence of O2, whereas the emission quantum yields are slightly increased with respect to the parental complex [Ru(dqp)2](2+). The peripheral functional groups (Br, Me, OMe) have only a minor impact on the optical properties and are attractive to utilize such complexes as functional building blocks. PMID:27228222

  4. Microsecond atomic force sensing of protein conformational dynamics: Implications for the primary light-induced events in bacteriorhodopsin

    PubMed Central

    Rousso, Itay; Khachatryan, Edward; Gat, Yahaloma; Brodsky, Igor; Ottolenghi, Michael; Sheves, Mordechai; Lewis, Aaron

    1997-01-01

    In this paper a new atomic force sensing technique is presented for dynamically probing conformational changes in proteins. The method is applied to the light-induced changes in the membrane-bound proton pump bacteriorhodopsin (bR). The microsecond time-resolution of the method, as presently implemented, covers many of the intermediates of the bR photocycle which is well characterized by spectroscopical methods. In addition to the native pigment, we have studied bR proteins substituted with chemically modified retinal chromophores. These synthetic chromophores were designed to restrict their ability to isomerize, while maintaining the basic characteristic of a large light-induced charge redistribution in the vertically excited Franck–Condon state. An analysis of the atomic force sensing signals lead us to conclude that protein conformational changes in bR can be initiated as a result of a light-triggered redistribution of electronic charge in the retinal chromophore, even when isomerization cannot take place. Although the coupling mechanism of such changes to the light-induced proton pump is still not established, our data question the current working hypothesis which attributes all primary events in retinal proteins to an initial trans⇔cis isomerization. PMID:9223291

  5. Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations

    PubMed Central

    Ulmschneider, Jakob P.; Smith, Jeremy C.; Ulmschneider, Martin B.; Ulrich, Anne S.; Strandberg, Erik

    2012-01-01

    The membrane-active antimicrobial peptide PGLa from Xenopus laevis is known from solid-state 2H-, 15N-, and 19F-NMR spectroscopy to occupy two distinct α-helical surface adsorbed states in membranes: a surface-bound S-state with a tilt angle of ∼95° at low peptide/lipid molar ratio (P/L = 1:200), and an obliquely tilted T-state with a tilt angle of 127° at higher peptide concentration (P/L = 1:50). Using a rapid molecular-dynamics insertion protocol in combination with microsecond-scale simulation, we have characterized the structure of both states in detail. As expected, the amphiphilic peptide resides horizontally on the membrane surface in a monomeric form at a low P/L, whereas the T-state is seen in the simulations to be a symmetric antiparallel dimer, with close contacts between small glycine and alanine residues at the interface. The computed tilt angles and azimuthal rotations, as well as the quadrupolar splittings predicted from the simulations agree with the experimental NMR data. The simulations reveal many structural details previously inaccessible, such as the immersion depth of the peptide in the membrane and the packing of the dimerization interface. The study highlights the ability and limitations of current state-of-the-art multimicrosecond all-atom simulations of membrane-active peptides to complement experimental data from solid-state NMR. PMID:22947863

  6. 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

  7. 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.

  8. Polar Markings

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Context image for PIA02155 Polar Markings

    These bright and dark markings occurred near the end of summer in the south polar region. The dark material is likely dust that has been freed of frost cover.

    Image information: VIS instrument. Latitude -76.3N, Longitude 84.9E. 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.

  9. Polar Layers

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Context image for PIA02153 Polar Layers

    This image of the south polar region shows layered material. It is not known if the layers are formed yearly or if they form over the period of 10s to 100s of years or more.

    Image information: VIS instrument. Latitude -80.3N, Longitude 296.2E. 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.

  10. Polar Ridges

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Context image for PIA03662 Polar Ridges

    This ridge system is located in the south polar region.

    Image information: VIS instrument. Latitude -81.7N, Longitude 296.5E. 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.

  11. Polar Textures

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03638 Polar Textures

    This image illustrates the variety of textures that appear in the south polar region during late summer.

    Image information: VIS instrument. Latitude 80.5S, Longitude 57.9E. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Polar Polygons

    NASA Technical Reports Server (NTRS)

    2004-01-01

    26 December 2003 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) picture displays polygons outlined by cracks in the martian south polar region. This southern summer view was acquired in October 2003 and is located near 86.9oS, 170.6oW. Polygons similar in size and shape to these are common in the arctic and antarctic regions of Earth. On Earth, they indicate the presence (or the past presence) of ground ice and the freeze-thaw cycles that accompany this ice. On Mars, whether ground ice was responsible for these landforms is uncertain, but their presence is suggestive that ground ice may exist or may once have existed in this region. The picture covers an area 3 km (1.9 mi) wide. Sunlight illuminates the scene from the upper left.

  17. Polarized fluorescence photobleaching recovery for measuring rotational diffusion in solutions and membranes.

    PubMed Central

    Velez, M; Axelrod, D

    1988-01-01

    A variation of fluorescence photobleaching recovery (FPR) suitable for measuring the rate of rotational molecular diffusion in solution and cell membranes is presented in theory and experimental practice for epi-illumination microscopy. In this technique, a brief flash of polarized laser light creates an anisotropic distribution of unbleached fluorophores which relaxes by rotational diffusion, leading to a time-dependent postbleach fluorescence. Polarized FPR (PFPR) is applicable to any time scales from seconds to microseconds. However, at fast (microsecond) time scales, a partial recovery independent of molecular orientation tends to obscure rotational effects. The theory here presents a method for overcoming this reversible photobleaching, and includes explicit results for practical geometries, fast wobble of fluorophores, and arbitrary bleaching depth. This variation of a polarized luminescence "pump-and-probe" technique is compared with prior ones and with "pump-only" time-resolved luminescence anisotropy decay methods. The technique is experimentally verified on small latex beads with a variety of diameters, common fluorophore labels, and solvent viscosities. Preliminary measurements on a protein (acetylcholine receptor) in the membrane of nondeoxygenated cells in live culture (rat myotubes) show a difference in rotational diffusion between clustered and nonclustered receptors. In most experiments, signal averaging, high laser power, and automated sample translation must be employed to achieve adequate statistical accuracy. PMID:3382712

  18. Structural Diversity of Ligand-Binding Androgen Receptors Revealed by Microsecond Long Molecular Dynamics Simulations and Enhanced Sampling.

    PubMed

    Duan, Mojie; Liu, Na; Zhou, Wenfang; Li, Dan; Yang, Minghui; Hou, Tingjun

    2016-09-13

    Androgen receptor (AR) plays important roles in the development of prostate cancer (PCa). The antagonistic drugs, which suppress the activity of AR, are widely used in the treatment of PCa. However, the molecular mechanism of antagonism about how ligands affect the structures of AR remains elusive. To better understand the conformational variability of ARs bound with agonists or antagonists, we performed long time unbiased molecular dynamics (MD) simulations and enhanced sampling simulations for the ligand binding domain of AR (AR-LBD) in complex with various ligands. Based on the simulation results, we proposed an allosteric pathway linking ligands and helix 12 (H12) of AR-LBD, which involves the interactions among the ligands and the residues W741, H874, and I899. The interaction pathway provides an atomistic explanation of how ligands affect the structure of AR-LBD. A repositioning of H12 was observed, but it is facilitated by the C-terminal of H12, instead of by the loop between helix 11 (H11) and H12. The bias-exchange metadynamics simulations further demonstrated the above observations. More importantly, the free energy profiles constructed by the enhanced sampling simulations revealed the transition process between the antagonistic form and agonistic form of AR-LBD. Our results would be helpful for the design of more efficient antagonists of AR to combat PCa. PMID:27560203

  19. Atomistic mechanism leading to complex antiferroelectric and incommensurate perovskites

    NASA Astrophysics Data System (ADS)

    Patel, Kinnary; Prosandeev, Sergey; Yang, Yurong; Xu, Bin; Íñiguez, Jorge; Bellaiche, L.

    2016-08-01

    An atomic interaction is identified in all perovskite compounds, such as A B O3 oxides, that can potentially result in unconventional structures. The term is harmonic in nature and couples the motions of the A cations with the rotations of the oxygen octahedra in the perovskite lattice. When strong enough, this coupling leads to hybrid normal modes that present both (anti)polar and rotational characters, which are keys to understand a variety of exotic phases. For example, we show that not only does this new coupling explain the long-period soft phonons characterizing prototype antiferroelectric PbZrO3, but it also provides us with an unified description of the complex antipolar structures of a variety of perovskites, including the possible occurrence of incommensurate phases. This coupling is further demonstrated to result, in the continuum limit, in an energy invariant adopting an analytical form that has been previously overlooked, to the best of our knowledge.

  20. Analysis of the polarity effects in the electrical breakdown of liquids.

    SciTech Connect

    Woodworth, Joseph Ray; Qian, J.; Joshi, Ravindra P.; Schamiloglu, Edl; Gaudet, John A.; Lehr, Jane Marie

    2005-03-01

    Electrical breakdown simulations are carried out for liquids in response to a sub-microsecond ({approx}100-200 ns) voltage pulse. This model builds on our previous analysis and focuses particularly on the polarity effect seen experimentally in point-plane geometries. The flux-corrected transport approach is used for the numerical implementation. Our model adequately explains experimental observations of pre-breakdown current fluctuations, streamer propagation and branching as well as disparities in hold-off voltage and breakdown initiation times between the anode and cathode polarities. It is demonstrated that polarity effects basically arise from the large mobility difference between electrons and ions. The higher electron mobility leads to greater charge smearing and diffusion that impacts the local electric field distributions. Non-linear couplings between the number density, electric field and charge generation rates then collectively affect the formation of ionized channels and their temporal dynamics.

  1. Temporal and spatial profiles of emission intensities in atmospheric pressure helium plasma jet driven by microsecond pulse: Experiment and simulation

    SciTech Connect

    Wang, Ruixue; Zhang, Cheng; Yan, Ping; Shao, Tao; Shen, Yuan; Zhu, Weidong; Babaeva, Natalia Yu.; Naidis, George V.

    2015-09-28

    A needle-circular electrode structure helium plasma jet driven by microsecond pulsed power is studied. Spatially resolved emission results show that the emission intensity of He(3{sup 3}S{sub 1}) line decreases monotonically along the axial direction, while those of N{sub 2}(C{sup 3}Π{sub u}), N{sub 2}{sup +}(B{sup 2}∑{sup +}{sub u}), and O(3p{sup 5}P) reach their maxima at 3 cm, 2.6 cm, and 1.4 cm, respectively. The plasma plume of the four species shows different characteristics: The N{sub 2} emission plume travels at a fast speed along the entire plasma jet; the N{sub 2}{sup +} emission plume is composed of a bright head and relatively weak tail and travels a shorter distance than the N{sub 2} emission plume; the He emission plume travels at a slower speed for only a very short distance; propagation of the O emission plume is not observed. Results of calculation of radiation fluxes emitted by positive streamers propagating along helium plasma jets are presented. It is shown, in agreement with the results of the present experiment and with other available experimental data, that the intensities of radiation of N{sub 2}(C{sup 3}Π{sub u}) molecules and He(3{sup 3}S{sub 1}) atoms vary with time (along the plasma jet) quite differently. The factors resulting in this difference are discussed.

  2. 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.

  3. 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.

  4. Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

    NASA Astrophysics Data System (ADS)

    Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

    2016-07-01

    Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

  5. Electronic states in an atomistic carbon quantum dot patterned in graphene

    NASA Astrophysics Data System (ADS)

    Craco, L.; Carara, S. S.; da Silva Pereira, T. A.; Milošević, M. V.

    2016-04-01

    We reveal the emergence of metallic Kondo clouds in an atomistic carbon quantum dot, realized as a single-atom junction in a suitably patterned graphene nanoflake. Using density functional dynamical mean-field theory (DFDMFT) we show how correlation effects lead to striking features in the electronic structure of our device, and how those are enhanced by the electron-electron interactions when graphene is patterned at the atomistic scale. Our setup provides a well-controlled environment to understand the principles behind the orbital-selective Kondo physics and the interplay between orbital and spin degrees of freedom in carbon-based nanomaterials, which indicate new pathways for spintronics in atomically patterned graphene.

  6. 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

  7. Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

    SciTech Connect

    Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

    2014-10-21

    We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example.

  8. 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.

  9. Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

    2000-01-01

    We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

  10. 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. PMID:27071488

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

    PubMed

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

    2015-01-01

    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. PMID:26555179

  12. Atomistic simulation and XAS investigation of Mn induced defects in Bi12TiO20

    NASA Astrophysics Data System (ADS)

    Rezende, Marcos V. dos S.; Santos, Denise J.; Jackson, Robert A.; Valerio, Mário E. G.; Macedo, Zélia S.

    2016-06-01

    This work reports an investigation of the valence and site occupancy of Mn dopants in Bi12TiO20 (BTO: Mn) host using X-ray Absorption (XAS) and atomistic simulation techniques based on energy minimisation. X-ray Absorption Near Edge Structure (XANES) at the Mn K-edges gave typical results for Mn ions with mixed valences of 3+ and 4+. Extended X-ray Absorption Fine Structure (EXAFS) results indicated that Mn ions are probably substituted at Ti sites. Atomistic simulation was performed assuming the incorporation of Mn2+, Mn3+ and Mn4+ ions at either Bi3+ or Ti4+ sites, and the results were compared to XANES and EXAFS measurements. Electrical conductivity for pure and doped samples was used to evaluate the consistency of the proposed model.

  13. A numerical method for the time coarsening of transport processes at the atomistic scale

    NASA Astrophysics Data System (ADS)

    Gonzalez-Ferreiro, B.; Romero, I.; Ortiz, M.

    2016-05-01

    We propose a novel numerical scheme for the simulation of slow transport processes at the atomistic scale. The scheme is based on a model for non-equilibrium statistical thermodynamics recently proposed by the authors, and extends it by formulating a variational integrator, i.e. a discrete functional whose optimality conditions provide all the governing equations of the problem. The method is employed to study surface segregation of AuAg alloys and its convergence is confirmed numerically.

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

    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 1d×time 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

  15. 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. PMID:26809025

  16. 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.

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

    PubMed

    Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F J; Javanainen, Matti; Kanduč, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S; Monticelli, Luca; Määttä, Jukka; Ollila, O H Samuli; Retegan, Marius; Róg, Tomasz; Santuz, Hubert; Tynkkynen, Joona

    2015-12-10

    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

  18. 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

  19. Membrane pore formation in atomistic and coarse-grained simulations.

    PubMed

    Kirsch, Sonja A; Böckmann, Rainer A

    2016-10-01

    Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26748016

  20. Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks.

    PubMed

    Zhang, Haiyang; Lv, Yongqin; Tan, Tianwei; van der Spoel, David

    2016-01-28

    Fabrication of metal-organic frameworks (MOFs) with large apertures triggers a brand-new research area for selective encapsulation of biomolecules within MOF nanopores. The underlying inclusion mechanism is yet to be clarified however. Here we report a molecular dynamics study on the mechanism of protein encapsulation in MOFs. Evaluation for the binding of amino acid side chain analogues reveals that van der Waals interaction is the main driving force for the binding and that guest size acts as a key factor predicting protein binding with MOFs. Analysis on the conformation and thermodynamic stability of the miniprotein Trp-cage encapsulated in a series of MOFs with varying pore apertures and surface chemistries indicates that protein encapsulation can be achieved via maintaining a polar/nonpolar balance in the MOF surface through tunable modification of organic linkers and Mg-O chelating moieties. Such modifications endow MOFs with a more biocompatible confinement. This work provides guidelines for selective inclusion of biomolecules within MOFs and facilitates MOF functions as a new class of host materials and molecular chaperones. PMID:26730607

  1. A Computational Algorithm to Produce Virtual X-ray and Electron Diffraction Patterns from Atomistic Simulations

    NASA Astrophysics Data System (ADS)

    Coleman, Shawn P.; Sichani, Mehrdad M.; Spearot, Douglas E.

    2014-03-01

    Electron and x-ray diffraction are well-established experimental methods used to explore the atomic scale structure of materials. In this work, a computational algorithm is developed to produce virtual electron and x-ray diffraction patterns directly from atomistic simulations. This algorithm advances beyond previous virtual diffraction methods by using a high-resolution mesh of reciprocal space that eliminates the need for a priori knowledge of the crystal structure being modeled or other assumptions concerning the diffraction conditions. At each point on the reciprocal space mesh, the diffraction intensity is computed via explicit computation of the structure factor equation. To construct virtual selected-area electron diffraction patterns, a hemispherical slice of the reciprocal lattice mesh lying on the surface of the Ewald sphere is isolated and viewed along a specified zone axis. X-ray diffraction line profiles are created by binning the intensity of each reciprocal lattice point by its associated scattering angle, effectively mimicking powder diffraction conditions. The virtual diffraction algorithm is sufficiently generic to be applied to atomistic simulations of any atomic species. In this article, the capability and versatility of the virtual diffraction algorithm is exhibited by presenting findings from atomistic simulations of <100> symmetric tilt Ni grain boundaries, nanocrystalline Cu models, and a heterogeneous interface formed between α-Al2O3 (0001) and γ-Al2O3 (111).

  2. Hybrid Simulation Strategy for Simulating Self-Assembled Morphologies at the Atomistic Length Scales

    NASA Astrophysics Data System (ADS)

    Sethuraman, Vaidyanathan; Ganesan, Venkat

    In the context of Lithium-ion batteries, an enhancement in both ionic conductivity and mechanical properties, were observed for block copolymer electrolytes with increasing MW. On the contrary, when homopolymers were used as electrolytes, the ionic conductivity decreased with increasing MW. However, the origins of such increase in conductivity are unclear and are speculated to be tied to both the morphology and the atomistic details of the copolymer themselves. Motivated by such issues, we present a strategy to create ordered morphologies of block copolymers at the atomistic level using a combination of coarse-graining and inverse coarse-graining techniques. A mapping which is developed using the long-ranged structural mapping in the disordered phases will be utilized to generate self-assembled morphologies. In particular we focus on generating self-assembled morphologies of PS-PEO at the atomistic length scales. Statics and dynamics of such self-assembled morphologies will be presented and the effect of self assembly on the transport properties of ions will also be explored. Funded by NSF.

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

    DOE PAGESBeta

    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 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

  4. 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.

  5. Atomistic modeling of the dislocation dynamics and evaluation of static yield stress

    NASA Astrophysics Data System (ADS)

    Karavaev, A. V.; Dremov, V. V.; Ionov, G. V.

    2015-09-01

    Static strength characteristics of structural materials are of great importance for the analysis of the materials behaviour under mechanical loadings. Mechanical characteristics of structural materials such as elastic limit, strength limit, ultimate tensile strength, plasticity are, unlike elastic moduli, very sensitive to the presence of impurities and defects of crystal structure. Direct atomistic modeling of the static mechanical strength characteristics of real materials is an extremely difficult task since the typical time scales available for the direct modeling in the frames of classical molecular dynamics do not exceed a hundred of nanoseconds. This means that the direct atomistic modeling of the material deformation can be done for the regimes with rather high strain rates at which the yield stress and other mechanical strength characteristics are controlled by microscopic mechanisms different from those at low (quasi-static) strain rates. In essence, the plastic properties of structural materials are determined by the dynamics of the extended defects of crystal structure (edge and screw dislocations) and by interactions between them and with the other defects in the crystal. In the present work we propose a method that is capable to model the dynamics of edge dislocations in the fcc and hcp materials at dynamic deformations and to estimate the material static yield stress in the states of interest in the frames of the atomistic approach. The method is based on the numerical characterization of the stress relaxation processes in specially generated samples containing solitary edge dislocations.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  7. Moisture-assisted cracking and atomistic crack path meandering in oxidized hydrogenated amorphous silicon carbide films

    NASA Astrophysics Data System (ADS)

    Matsuda, Yusuke; King, Sean W.; Oliver, Mark; Dauskardt, Reinhold H.

    2013-02-01

    Moisture-assisted cracking of silica-derived materials results from a stress-enhanced reaction between water molecules and moisture-sensitive SiOSi bonds at the crack tip. We report the moisture-assisted cracking of oxidized hydrogenated amorphous silicon carbide films (a-SiCO:H) consisting of both moisture-sensitive SiOSi bonds and moisture-insensitive bonds. The sensitivity of the films to moisture-assisted cracking was observed to increase with the SiOSi bond density, ρSiOSi. This sensitivity was correlated with the number of SiOSi bonds ruptured, NSiOSi, through an atomistic kinetic fracture model. By comparing these correlated NSiOSi values with those estimated by a planar crack model, we demonstrated that at the atomistic scale the crack path meanders three-dimensionally so as to intercept the most SiOSi bonds. This atomistic crack path meandering was verified by a computational method based on graph theory and molecular dynamics. Our findings could provide a basis for better understanding of moisture-assisted cracking in materials consisting of other types of moisture-sensitive and moisture-insensitive bonds.

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

    SciTech Connect

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

    2013-11-21

    The determination of an atomistic graphene oxide (GO) model has been challenging due to the structural dependence on different synthesis methods. In this work we combine temperature-programmed molecular dynamics simulation techniques and the ReaxFF reactive force field to generate realistic atomistic GO structures. By grafting a mixture of epoxy and hydroxyl groups to the basal graphene surface and fine-tuning their initial concentrations, we produce in a controllable manner the GO structures with different functional groups and defects. The models agree with structural experimental data and with other ab initio quantum calculations. Using the generated atomistic models, we perform reactive adsorption calculations for H{sub 2}S and H{sub 2}O/H{sub 2}S mixtures on GO materials and compare the results with experiment. We find that H{sub 2}S molecules dissociate on the carbonyl functional groups, and H{sub 2}O, CO{sub 2}, and CO molecules are released as reaction products from the GO surface. The calculation reveals that for the H{sub 2}O/H{sub 2}S mixtures, H{sub 2}O molecules are preferentially adsorbed to the carbonyl sites and block the potential active sites for H{sub 2}S decomposition. The calculation agrees well with the experiments. The methodology and the procedure applied in this work open a new door to the theoretical studies of GO and can be extended to the research on other amorphous materials.

  9. 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.

  10. Bridging the Gap between Quantum Mechanics and Large-Scale Atomistic Simulation

    SciTech Connect

    Moriarty, J A

    2004-08-16

    The prospect of modeling across disparate length and time scales to achieve a predictive multiscale description of real materials properties has attracted widespread research interest in the last decade. To be sure, the challenges in such multiscale modeling are many, and in demanding cases, such as mechanical properties or dynamic phase transitions, multiple bridges extending from the atomic level all the way to the continuum level must be built. Although often overlooked in this process, one of the most fundamental and important problems in multiscale modeling is that of bridging the gap between first-principles quantum mechanics, from which true predictive power for real materials emanates, and the large-scale atomistic simulation of thousands or millions of atoms, which is usually essential to describe the complex atomic processes that link to higher length and time scales. For example, to model single-crystal plasticity at micron length scales via dislocation-dynamics simulations that evolve the detailed dislocation microstructure requires accurate large-scale atomistic information on the mobility and interaction of individual dislocations. Similarly, modeling the kinetics of structural phase transitions requires linking accurate large-scale atomistic information on nucleation processes with higher length and time scale growth processes.

  11. Phase field crystal modelling of the order-to-disordered atomistic structure transition of metallic glasses

    NASA Astrophysics Data System (ADS)

    Zhang, W.; Mi, J.

    2016-03-01

    Bulk metallic glass composites are a new class of metallic alloy systems that have very high tensile strength, ductility and fracture toughness. This unique combination of mechanical properties is largely determined by the presence of crystalline phases uniformly distributed within the glassy matrix. However, there have been very limited reports on how the crystalline phases are nucleated in the super-cooled liquid and their growth dynamics, especially lack of information on the order-to-disordered atomistic structure transition across the crystalline-amorphous interface. In this paper, we use phase field crystal (PFC) method to study the nucleation and growth of the crystalline phases and the glass formation of the super cooled liquid of a binary alloy. The study is focused on understanding the order-to-disordered transition of atomistic configuration across the interface between the crystalline phases and amorphous matrix of different chemical compositions at different thermal conditions. The capability of using PFC to simulate the order-to-disorder atomistic transition in the bulk material or across the interface is discussed in details.

  12. 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.

  13. 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.

  14. 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

  15. Microsecond Time-Resolved Absorption Spectroscopy Used to Study CO Compounds of Cytochrome bd from Escherichia coli

    PubMed Central

    Siletsky, Sergey A.; Zaspa, Andrey A.; Poole, Robert K.; Borisov, Vitaliy B.

    2014-01-01

    Cytochrome bd is a tri-heme (b558, b595, d) respiratory oxygen reductase that is found in many bacteria including pathogenic species. It couples the electron transfer from quinol to O2 with generation of an electrochemical proton gradient. We examined photolysis and subsequent recombination of CO with isolated cytochrome bd from Escherichia coli in one-electron reduced (MV) and fully reduced (R) states by microsecond time-resolved absorption spectroscopy at 532-nm excitation. Both Soret and visible band regions were examined. CO photodissociation from MV enzyme possibly causes fast (τ<1.5 µs) electron transfer from heme d to heme b595 in a small fraction of the protein, not reported earlier. Then the electron migrates to heme b558 (τ∼16 µs). It returns from the b-hemes to heme d with τ∼180 µs. Unlike cytochrome bd in the R state, in MV enzyme the apparent contribution of absorbance changes associated with CO dissociation from heme d is small, if any. Photodissociation of CO from heme d in MV enzyme is suggested to be accompanied by the binding of an internal ligand (L) at the opposite side of the heme. CO recombines with heme d (τ∼16 µs) yielding a transient hexacoordinate state (CO-Fe2+-L). Then the ligand slowly (τ∼30 ms) dissociates from heme d. Recombination of CO with a reduced heme b in a fraction of the MV sample may also contribute to the 30-ms phase. In R enzyme, CO recombines to heme d (τ∼20 µs), some heme b558 (τ∼0.2–3 ms), and finally migrates from heme d to heme b595 (τ∼24 ms) in ∼5% of the enzyme population. Data are consistent with the recent nanosecond study of Rappaport et al. conducted on the membranes at 640-nm excitation but limited to the Soret band. The additional phases were revealed due to differences in excitation and other experimental conditions. PMID:24755641

  16. 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

  17. Penta prism laser polarizer.

    PubMed

    Lotem, H; Rabinovitch, K

    1993-04-20

    A novel type of laser prism polarizer is proposed. The polarizer is characterized by a high transmission efficiency, a high optical damage threshold, and a high extinction ratio. The polarizer is shaped like a regular penta prism and, thus, it is a constant deviation angle device. Polarization effects occur upon the two internal cascade reflections in the prism. Anisotropic and Isotropic types of the polarizer are discussed. The isotropic polarizer is a prism made of a high refractive-index glass coated by multilayer polarization-type dielectric coatings. Efficient s-state polarization is obtained because of p-state leakage upon the two internal cascade reflections. The anisotropic polarizer is made of a birefringent crystal in which angular polarization splitting is obtained by the bireflectance (double-reflection) effect. Fanning of a laser beam into up to eight polarized beams is possible in a prism made of a biaxial crystal. PMID:20820335

  18. A microsecond time resolved x-ray absorption near edge structure synchrotron study of phase transitions in Fe undergoing ramp heating at high pressure

    SciTech Connect

    Marini, C.; Mathon, O.; Pascarelli, S.; Occelli, F.; Torchio, R.; Recoules, V.; Loubeyre, P.

    2014-03-07

    We report a microsecond time-resolved x-ray absorption near edge structure study using synchrotron radiation to dynamically detect structural phase transitions in Fe undergoing rapid heating along a quasi-isochoric path. Within a few ms, we observed two structural phase transitions, which transform the ambient bcc phase of Fe into the fcc phase, and then into the liquid phase. This example illustrates the opportunities offered by energy dispersive x-ray absorption spectroscopy in the study of matter under extreme dynamic conditions. Advanced simulations are compared to these data.

  19. Polarized Light in Astronomy.

    ERIC Educational Resources Information Center

    King, D. J.

    1983-01-01

    The application of very sensitive electronic detecting devices during the last decade has revolutionized and revitalized the study of polarization in celestial objects. The nature of polarization, how polaroids work, interstellar polarization, dichroic filters, polarization by scattering, and modern polarimetry are among the topics discussed. (JN)

  20. Linearly polarized fiber amplifier

    DOEpatents

    Kliner, Dahv A.; Koplow, Jeffery P.

    2004-11-30

    Optically pumped rare-earth-doped polarizing fibers exhibit significantly higher gain for one linear polarization state than for the orthogonal state. Such a fiber can be used to construct a single-polarization fiber laser, amplifier, or amplified-spontaneous-emission (ASE) source without the need for additional optical components to obtain stable, linearly polarized operation.

  1. Nondiffracting transversally polarized beam.

    PubMed

    Yuan, G H; Wei, S B; Yuan, X-C

    2011-09-01

    Generation of a nondiffracting transversally polarized beam by means of transmitting an azimuthally polarized beam through a multibelt spiral phase hologram and then highly focusing by a high-NA lens is presented. A relatively long depth of focus (∼4.84λ) of the electric field with only radial and azimuthal components is achieved. The polarization of the wavefront near the focal plane is analyzed in detail by calculating the Stokes polarization parameters. It is found that the polarization is spatially varying and entirely transversally polarized, and the polarization singularity disappears at the beam center, which makes the central bright channel possible. PMID:21886250

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

    PubMed

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

    2015-01-01

    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. PMID:25868608

  3. 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.

  4. 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.

  5. 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.

  6. Neutron polarizers based on polarized ^3He

    NASA Astrophysics Data System (ADS)

    Gentile, T. R.; Jones, G. L.; Thompson, A. K.; Fei, X.; Keith, C. D.; Rich, D.; Snow, W. M.; Penttila, S.

    1997-10-01

    Research is underway at NIST, Indiana Univ., and LANL to develop neutron polarizers and analyzers based on polarized ^3He. Such devices, which rely on the strong spin dependence of the neutron capture cross section by polarized ^3He, have applications in weak interaction physics and materials science. In addition, the technology for polarized ^3He production is directly applicable to polarized gas MRI of lungs, and polarized targets. Our program, which includes both the spin-exchange and metastability-exchange optical pumping methods, will be reviewed. Spin-exchange has been used to analyze a polarized cold neutron beam at NIST, and also for lung imaging in collaboration with the Univ. of Pennsylvania. In the metastable method, the ^3He is polarized at low pressure, and must be substantially compressed. A piston compressor has been designed for this goal at Indiana Univ. and is under construction. At NIST we have compressed polarized gas using an apparatus that is based on a modified commercial diaphragm pump.

  7. 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. PMID:19256521

  8. Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.

    PubMed

    Ithuralde, Raúl Esteban; Roitberg, Adrián Enrique; Turjanski, Adrián Gustavo

    2016-07-20

    Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs. PMID:27348048

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

    PubMed Central

    Wright, David W.; Perkins, Stephen J.

    2015-01-01

    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. PMID:26089768

  10. 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. PMID:27154600

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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.

  12. 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.

  13. Atomistic spin dynamic method with both damping and moment of inertia effects included from first principles.

    PubMed

    Bhattacharjee, Satadeep; Nordström, Lars; Fransson, Jonas

    2012-02-01

    We consider spin dynamics for implementation in an atomistic framework and we address the feasibility of capturing processes in the femtosecond regime by inclusion of moment of inertia. In the spirit of an s-d-like interaction between the magnetization and electron spin, we derive a generalized equation of motion for the magnetization dynamics in the semiclassical limit, which is nonlocal in both space and time. Using this result we retain a generalized Landau-Lifshitz-Gilbert equation, also including the moment of inertia, and demonstrate how the exchange interaction, damping, and moment of inertia, all can be calculated from first principles. PMID:22400957

  14. 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.

  15. 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.

  16. Gilbert-like damping caused by time retardation in atomistic magnetization dynamics

    NASA Astrophysics Data System (ADS)

    Thonig, Danny; Henk, Jürgen; Eriksson, Olle

    2015-09-01

    Gilbert-like damping in magnetization dynamics is commonly attributed to the interplay of the spin, the electron, and the phonon reservoirs. Spatial correlations within the spin reservoir itself, for example magnons, mediate damping as well. We show theoretically that temporal correlations within the spin reservoir cause a similar effect. We investigate the role of time retardation in the atomistic Landau-Lifshitz-Gilbert equation using two different retardation kernels. Although viscous damping is explicitly excluded, we find both analytically and numerically that damping and higher-order effects emerge due to time retardation. Thus, our results establish a mechanism for damping and inertia in magnetic systems.

  17. Directional pair distribution function for diffraction line profile analysis of atomistic models

    PubMed Central

    Leonardi, Alberto; Leoni, Matteo; Scardi, Paolo

    2013-01-01

    The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren–Averbach method. PMID:23396818

  18. 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.

  19. Heterogeneous plastic deformation and Bauschinger effect in ultrafine-grained metals: atomistic simulations

    NASA Astrophysics Data System (ADS)

    Tsuru, Tomohito; Aoyagi, Yoshiteru; Kaji, Yoshiyuki; Shimokawa, Tomotsugu

    2016-03-01

    The effect of the dislocation density on yield strength and subsequent plastic deformation of ultrafine-grained metals was investigated in large-scale atomistic simulations. Polycrystalline models were constructed and uniaxial tension and compression were applied to elucidate the heterogeneous plastic deformation and the Bauschinger effect. The initial yield becomes heterogeneous as the dislocation density decreases owing to a wide range of Schmid factors of activated slip systems in each grain. A different mechanism of the Bauschinger effect was proposed, where the Bauschinger effect of ultrafine-grained metals is caused by the change in dislocation density in the process of forward and backward loadings.

  20. 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.

  1. Heat flux expressions that satisfy the conservation laws in atomistic system involving multibody potentials

    NASA Astrophysics Data System (ADS)

    Fu, Yao; Song, Jeong-Hoon

    2015-08-01

    Heat flux expressions are derived for multibody potential systems by extending the original Hardy's methodology and modifying Admal & Tadmor's formulas. The continuum thermomechanical quantities obtained from these two approaches are easy to compute from molecular dynamics (MD) results, and have been tested for a constant heat flux model in two distinctive systems: crystalline iron and polyethylene (PE) polymer. The convergence criteria and affecting parameters, i.e. spatial and temporal window size, and specific forms of localization function are found to be different between the two systems. The conservation of mass, momentum, and energy are discussed and validated within this atomistic-continuum bridging.

  2. 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.

  3. Reflection-free atomistic-continuum coupling for solid mechanics employing spacetime discontinuous finite element method

    NASA Astrophysics Data System (ADS)

    Kraczek, B.

    2005-03-01

    We present a means for coupling dynamic atomistic and continuum simulations via a spacetime discontinuous Galerkin (SDG) finite element method. Our scheme allows the SDG method to couple a general MD simulation using Verlet time-stepping through the flux conditions on the element boundaries at the interface. These flux conditions ensure weak balance of momentum and energy to achieve reflection-free transfer of disturbance across the interface. Our work is supported by the National Science Foundation (ITR grant DMR-0121695) on Process Simulation and Design and, in part, by the Materials Computation Center (FRG grant DMR-99-76550)

  4. 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.

  5. 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.

  6. 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.

  7. Atomistic mechanisms of moisture-induced fracture at copper-silica interfaces

    NASA Astrophysics Data System (ADS)

    Vijayashankar, Dandapani; Zhu, Hong; Garg, Saurabh; Teki, Ranganath; Ramprasad, R.; Lane, Michael W.; Ramanath, Ganpati

    2011-09-01

    Tailoring the chemo-mechanical properties of metal-dielectric interfaces is crucial for many applications including nanodevice wiring, packaging, composites, and catalysis. Here, we combine moisture-induced fracture tests, electron spectroscopy, and density functional theory calculations to reveal fracture toughness partitioning and atomistic delamination mechanisms at copper-silica interfaces. Copper plasticity is supported above a threshold work of adhesion and delamination occurs by moisture-induced Cu-O bond scission in Cu-O-Si bridges. These results provide insights into the effects of the nature of metal-oxygen bonding on moisture-induced delamination of metal-dielectric interfaces.

  8. 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.

  9. Investigation on Sintering Mechanism of Nanoscale Tungsten Powder Based on Atomistic Simulation

    NASA Astrophysics Data System (ADS)

    Moitra, Amitava; Kim, Sungho; Kim, Seong-Gon; Park, Seong Jin; German, Randall M.; Horstemeyer, Mark F.

    2010-06-01

    Atomistic simulations focusing on sintering of crystalline tungsten powders at the submicroscopic level are performed to shed light on the processing on the nanoscale powders. The neck growth and shrinkage were calculated during these sintering simulations, so it is possible to extend these results to the global physical property evolution via sintering. The densification and grain growth during sintering were calculated with variations in temperature, pressure, particle configuration, additives, and crystalline misalignment between particles. These findings lay a foundation for a virtual approach to setting the processing cycles and materials design applicable to nanoscale powders.

  10. 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.

  11. Applications of single-layered graphene sheets as mass sensors and atomistic dust detectors

    NASA Astrophysics Data System (ADS)

    Sakhaee-Pour, A.; Ahmadian, M. T.; Vafai, A.

    2008-01-01

    Molecular structural mechanics is implemented to model the vibrational behavior of defect-free single-layered graphene sheets (SLGSs) at constant temperature. To mimic these two-dimensional layers, zigzag and armchair models with cantilever and bridge boundary conditions are adopted. Fundamental frequencies of these nanostructures are calculated, and it is perceived that they are independent of the chirality and aspect ratio. The effects of point mass and atomistic dust on the fundamental frequencies are also considered in order to investigate the possibility of using SLGSs as sensors. The results show that the principal frequencies are highly sensitive to an added mass of the order of 10-6 fg.

  12. Mechanism of Void Nucleation and Growth in bcc Fe: Atomistic Simulations at Experimental Time Scales

    SciTech Connect

    Fan Yue; Kushima, Akihiro; Yip, Sidney; Yildiz, Bilge

    2011-03-25

    Evolution of small-vacancy clusters in bcc Fe is simulated using a multiscale approach coupling an atomistic activation-relaxation method for sampling transition-state pathways with environment-dependent reaction coordinate calculations and a kinetic Monte Carlo simulation to reach time scales on the order of {approx}10{sup 4} s. Under vacancy-supersaturated condition, di- and trivacancy clusters form and grow by coalescence (Ostwald ripening). For cluster size greater than four we find a transition temperature of 150 deg. C for accelerated cluster growth, as observed in positron annihilation spectroscopy experiments. Implications for the mechanism of stage-IV radiation-damage-recovery kinetics are discussed.

  13. 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.

  14. Atomistic simulation based prediction of the solvent effect on the molecular mobility and glass transition of poly (methyl methacrylate)

    NASA Astrophysics Data System (ADS)

    Mishra, Shawn; Keten, Sinan

    2013-01-01

    We present an investigation of the retained solvent effect on the glass transition temperature (Tg) of poly(methyl methacrylate) (PMMA) through all-atom molecular dynamics simulations. Addition of a weakly interactive solvent, tetrahydrofuran (THF), causes a depression of the PMMA Tg that can be identified through an analysis of the mean squared displacement of the polymer chains from atomistic trajectories. Our results are in very good agreement with an atomistically informed theoretical model based on free volume theory and demonstrate the applicability of molecular simulation to discern solvent effects on polymer thermomechanical behavior in silico.

  15. Analysis of microsecond relaxation dynamics of proteins and viscous media by recording relaxation shifts of phosphorescence spectra

    NASA Astrophysics Data System (ADS)

    Barinov, A. V.; Goryachev, N. S.; Kotel'nikov, A. I.

    2011-05-01

    We studied the low-temperature dynamics of the Stokes shift of instantaneous phosphorescence spectra of eosin and eosin maleimide covalently bound to hemoglobin in a 66% v/v aqueous solution of glycerol under conditions of pulsed excitation. The kinetics of the Stokes shifts are described using the Cole-Davidson distribution function. From the experimental data, we obtain the parameters τ0 and β, which describe the Cole-Davidson distribution. Values of τ0 and β agree well with data obtained by other methods, and these parameters can be used to describe electron transfer reactions in polar solutions and proteins.

  16. 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)

  17. 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.

  18. 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.

  19. A systematic procedure to build a relaxed dense-phase atomistic representation of a complex amorphous polymer using a coarse-grained modeling approach

    PubMed Central

    Li, Xianfeng; Latour, Robert A.

    2009-01-01

    A systematic procedure has been developed to construct a relaxed dense-phase atomistic structure of a complex amorphous polymer. The numerical procedure consists of (1) coarse graining the atomistic model of the polymer into a mesoscopic model based on an iterative algorithm for potential inversion from distribution functions of the atomistic model, (2) relaxation of the coarse grained chain using a molecular dynamics scheme, and (3) recovery of the atomistic structure by reverse mapping based on the superposition of atomistic counterparts on the corresponding coarse grained coordinates. These methods are demonstrated by their application to construct a relaxed, dense-phase model of poly(DTB succinate), which is an amorphous tyrosine-derived biodegradable polymer that is being developed for biomedical applications. Both static and dynamic properties from the coarse-grained and atomistic simulations are analyzed and compared. The coarse-grained model, which contains the essential features of the DTB succinate structure, successfully described both local and global structural properties of the atomistic chain. The effective speedup compared to the corresponding atomistic simulation is substantially above 102, thus enabling simulation times to reach well into the characteristic experimental regime. The computational approach for reversibly bridging between coarse-grained and atomistic models provides an efficient method to produce relaxed dense-phase all-atom molecular models of complex amorphous polymers that can subsequently be used to study and predict the atomistic-level behavior of the polymer under different environmental conditions in order to optimally design polymers for targeted applications. PMID:20161121

  20. 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. PMID:27050675

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

    PubMed Central

    Neilson, James R.; McQueen, Tyrel M.

    2015-01-01

    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. 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. PMID:26500465

  2. Atomistic nature in band-to-band tunneling in two-dimensional silicon pn tunnel diodes

    NASA Astrophysics Data System (ADS)

    Tabe, Michiharu; Tan, Hoang Nhat; Mizuno, Takeshi; Muruganathan, Manoharan; Anh, Le The; Mizuta, Hiroshi; Nuryadi, Ratno; Moraru, Daniel

    2016-02-01

    We study low-temperature transport properties of two-dimensional (2D) Si tunnel diodes, or Si Esaki diodes, with a lateral layout. In ordinary Si Esaki diodes, interband tunneling current is severely limited because of the law of momentum conservation, while nanoscale Esaki diodes may behave differently due to the dopants in the narrow depletion region, by atomistic effects which release such current limitation. In thin-Si lateral highly doped pn diodes, we find clear signatures of interband tunneling between 2D-subbands involving phonon assistance. More importantly, the tunneling current is sharply enhanced in a narrow voltage range by resonance via a pair of a donor- and an acceptor-atom in the pn junction region. Such atomistic behavior is recognized as a general feature showing up only in nanoscale tunnel diodes. In particular, a donor-acceptor pair with deeper ground-state energies is likely to be responsible for such a sharply enhanced current peak, tunable by external biases.

  3. Atomistic Design of Favored Compositions for Synthesizing the Al-Ni-Y Metallic Glasses.

    PubMed

    Wang, Q; Li, J H; Liu, J B; Liu, B X

    2015-01-01

    For a ternary alloy system promising for obtaining the so-called bulk metallic glasses (BMGs), the first priority issue is to predict the favored compositions, which could then serve as guidance for the appropriate alloy design. Taking the Al-Ni-Y system as an example, here we show an atomistic approach, which is developed based on a recently constructed and proven realistic interatomic potential of the system. Applying the Al-Ni-Y potential, series simulations not only clarify the glass formation mechanism, but also predict in the composition triangle, a hexagonal region, in which a disordered state, i.e., the glassy phase, is favored energetically. The predicted region is defined as glass formation region (GFR) for the ternary alloy system. Moreover, the approach is able to calculate an amorphization driving force (ADF) for each possible glassy alloy located within the GFR. The calculations predict an optimized sub-region nearby a stoichiometry of Al80Ni5Y15, implying that the Al-Ni-Y metallic glasses designed in the sub-region could be the most stable. Interestingly, the atomistic predictions are supported by experimental results observed in the Al-Ni-Y system. In addition, structural origin underlying the stability of the Al-Ni-Y metallic glasses is also discussed in terms of a hybrid packing mode in the medium-range scale. PMID:26592568

  4. 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. PMID:25020237

  5. Atomistic Design of Favored Compositions for Synthesizing the Al-Ni-Y Metallic Glasses

    NASA Astrophysics Data System (ADS)

    Wang, Q.; Li, J. H.; Liu, J. B.; Liu, B. X.

    2015-11-01

    For a ternary alloy system promising for obtaining the so-called bulk metallic glasses (BMGs), the first priority issue is to predict the favored compositions, which could then serve as guidance for the appropriate alloy design. Taking the Al-Ni-Y system as an example, here we show an atomistic approach, which is developed based on a recently constructed and proven realistic interatomic potential of the system. Applying the Al-Ni-Y potential, series simulations not only clarify the glass formation mechanism, but also predict in the composition triangle, a hexagonal region, in which a disordered state, i.e., the glassy phase, is favored energetically. The predicted region is defined as glass formation region (GFR) for the ternary alloy system. Moreover, the approach is able to calculate an amorphization driving force (ADF) for each possible glassy alloy located within the GFR. The calculations predict an optimized sub-region nearby a stoichiometry of Al80Ni5Y15, implying that the Al-Ni-Y metallic glasses designed in the sub-region could be the most stable. Interestingly, the atomistic predictions are supported by experimental results observed in the Al-Ni-Y system. In addition, structural origin underlying the stability of the Al-Ni-Y metallic glasses is also discussed in terms of a hybrid packing mode in the medium-range scale.

  6. Intergranular fracture in UO{sub 2}: derivation of traction-separation law from atomistic simulations

    SciTech Connect

    Zhang, Yongfeng; Millett, P.C.; Tonks, M.R.; Bai, Xian-Ming; Biner, S.B.

    2013-07-01

    In this study, the intergranular fracture behavior of UO{sub 2} 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 Σ5 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. (authors)

  7. Atomistic Design of Favored Compositions for Synthesizing the Al-Ni-Y Metallic Glasses

    PubMed Central

    Wang, Q.; Li, J. H.; Liu, J. B.; Liu, B. X.

    2015-01-01

    For a ternary alloy system promising for obtaining the so-called bulk metallic glasses (BMGs), the first priority issue is to predict the favored compositions, which could then serve as guidance for the appropriate alloy design. Taking the Al-Ni-Y system as an example, here we show an atomistic approach, which is developed based on a recently constructed and proven realistic interatomic potential of the system. Applying the Al-Ni-Y potential, series simulations not only clarify the glass formation mechanism, but also predict in the composition triangle, a hexagonal region, in which a disordered state, i.e., the glassy phase, is favored energetically. The predicted region is defined as glass formation region (GFR) for the ternary alloy system. Moreover, the approach is able to calculate an amorphization driving force (ADF) for each possible glassy alloy located within the GFR. The calculations predict an optimized sub-region nearby a stoichiometry of Al80Ni5Y15, implying that the Al-Ni-Y metallic glasses designed in the sub-region could be the most stable. Interestingly, the atomistic predictions are supported by experimental results observed in the Al-Ni-Y system. In addition, structural origin underlying the stability of the Al-Ni-Y metallic glasses is also discussed in terms of a hybrid packing mode in the medium-range scale. PMID:26592568

  8. 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

  9. Fracture toughness from atomistic simulations: Brittleness induced by emission of sessile dislocations

    SciTech Connect

    Farkas, D.

    1998-08-04

    Using atomistic simulations of crack response for intermetallic materials the author shows that when the emitted dislocations are sessile and stay in the immediate vicinity of the crack tip the emitted dislocations can actually lead to brittle failure. She present the results of an atomistic simulation study of the simultaneous dislocation emission and crack propagation process in this class of materials. She used a molecular statics technique with embedded atom (EAM) potentials developed for NiAl. The crystal structure of NiAl is the CsCl type (B2) with a lattice parameter of 0.287 nm, which is reproduced by the potential together with the cohesive energy and elastic constants. The compound stays ordered up to the melting point, indicating a strong tendency towards chemical ordering with a relatively high energy of the antiphase boundary (APB). As a result of this relatively large energy the dislocations of 1/2<111> type Burgers vectors imply a high energy and the deformation process occurs via the larger <100> type dislocations.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Hybrid polarization control

    NASA Astrophysics Data System (ADS)

    Gray, George R.; Ibragimov, Edem; Sluz, Joseph; Sova, Raymond

    2005-05-01

    We demonstrate a novel method of polarization control that combines rotatable waveplates (angle control) and variable retarders (retardance control). Such a "hybrid" polarization controller performs far better than conventional controllers, allowing nearly perfect arbitrary-to-arbitrary polarization transformations. We show theoretically that the two control parameters augment one another because they tend to result in orthogonal movements on the Poincaré sphere.

  18. 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…

  19. 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)

  20. 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…

  1. 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)

  2. Bumblebees Learn Polarization Patterns

    PubMed Central

    Foster, James J.; Sharkey, Camilla R.; Gaworska, Alicia V.A.; Roberts, Nicholas W.; Whitney, Heather M.; Partridge, Julian C.

    2014-01-01

    Summary Foraging insect pollinators such as bees must find and identify flowers in a complex visual environment. Bees use skylight polarization patterns for navigation [1–3], a capacity mediated by the polarization-sensitive dorsal rim area (DRA) of their eye [4, 5]. While other insects use polarization sensitivity to identify appropriate habitats [6], oviposition sites, and food sources [7], to date no nonnavigational functions of polarization vision have been identified in bees. Here we investigated the ability of bumblebees (Bombus terrestris) to learn polarization patterns on artificial “flowers” in order to obtain a food reward. We show that foraging bumblebees can learn to discriminate between two differently polarized targets, but only when the target artificial “flower” is viewed from below. A context for these results is provided by polarization imaging of bee-pollinated flowers, revealing the potential for polarization patterns in real flowers. Bees may therefore have the ability to use polarization vision, possibly mediated by their polarization-sensitive DRA, both for navigation and to learn polarization patterns on flowers, the latter being the first nonnavigational function for bee polarization vision to be identified. PMID:24909321

  3. 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.

  4. 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.

  5. 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

  6. Effect of polar solvents on beta-carotene radical precursor.

    PubMed

    Tian, Yu-Xi; Han, Rui-Min; Zhang, Jian-Ping; Skibsted, Leif H

    2008-03-01

    Beta-carotene forms radicals in chloroform upon photo-excitation (i) in the femtosecond time-scale by direct electron ejection into chloroform and (ii) in the microsecond time-scale by secondary reactions with chloroform radicals formed in the faster reactions. The precursor for beta-carotene radical cation decays in a second-order reaction in the mixed solvents, with a rate decreasing for increasing dielectric constant of cosolvent (acetic acid < ethanol < acetonitrile approximately methanol). The precursor is assigned as an ion pair from which the beta-carotene radical cation is formed in neat chloroform, but in more polar solvents it reacts at least partly through disproportionation in a bimolecular reaction promoted by the presence of ions. The stabilization of the radical precursor by increased solvent polarity, allowing for deactivation of the precursor by an alternative reaction channel, is discussed in relation to the balance of pro- and antioxidative properties of beta-carotene at lipid/water interfaces. PMID:18344123

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

    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.

  10. Scanning Single-Molecule Fluorescence Correlation Spectroscopy Enables Kinetics Study of DNA Hairpin Folding with a Time Window from Microseconds to Seconds.

    PubMed

    Bi, Huimin; Yin, Yandong; Pan, Bailong; Li, Geng; Zhao, Xin Sheng

    2016-05-19

    Single-molecule fluorescence measurements have been widely used to explore kinetics and dynamics of biological systems. Among them, single-molecule imaging (SMI) is good at tracking processes slower than tens of milliseconds, whereas fluorescence correlation spectroscopy (FCS) is good at probing processes faster than submilliseconds. However, there is still shortage of simple yet effective single-molecule fluorescence method to cover the time-scale between submilliseconds and tens of milliseconds. To effectively bridge this millisecond gap, we developed a single-molecule fluorescence correlation spectroscopy (smFCS) method that works on surface-immobilized single molecules through surface scanning. We validated it by monitoring the classical DNA hairpin folding process. With a wide time window from microseconds to seconds, the experimental data are well fitted to the two-state folding model. All relevant molecular parameters, including the relative fluorescence brightness, equilibrium constant, and reaction rate constants, were uniquely determined. PMID:27140004

  11. [Atomic/ionic fluorescence in microwave plasma torch discharge with excitation of high current and microsecond pulsed hollow cathode lamp: Ca atomic/ionic fluorescence spectrometry].

    PubMed

    Gong, Zhen-bin; Liang, Feng; Yang, Peng-yuan; Jin, Qin-han; Huang, Ben-li

    2002-02-01

    A system of atomic and ionic fluorescence spectrometry in microwave plasma torch (MPT) discharge excited by high current microsecond pulsed hollow cathode lamp (HCMP HCL) has been developed. The operation conditions for Ca atomic and ionic fluorescence spectrometry have been optimized. Compared with atomic fluorescence spectrometry (AFS) in argon microwave induced plasma (MIP) and MPT with the excitation of direct current and conventional pulsed HCL, the system with HCMP HCL excitation can improve AFS and ionic fluorescence spectrometry (IFS) detection limits in MPT atomizer and ionizer. Detection limits (3 sigma) with HCMP HCL-MPT-AFS/IFS are 10.1 ng.mL-1 for Ca I 422.7 nm, 14.6 ng.mL-1 for Ca II 393.4 nm, and 37.4 ng.mL-1 for Ca II 396.8 nm, respectively. PMID:12940030

  12. Composition law for polarizers

    NASA Astrophysics Data System (ADS)

    Lages, J.; Giust, R.; Vigoureux, J.-M.

    2008-09-01

    The polarization process when polarizers act on an optical field is studied. We give examples for two kinds of polarizers. The first kind presents an anisotropic absorption—as in a Polaroid film—and the second one is based on total reflection at the interface with a birefringent medium. Using the Stokes vector representation, we determine explicitly the trajectories of the wave light polarization during the polarization process. We find that such trajectories are not always geodesics of the Poincaré sphere as is usually thought. Using the analogy between light polarization and special relativity, we find that the action of successive polarizers on the light wave polarization is equivalent to the action of a single resulting polarizer followed by a rotation achieved, for example, by a device with optical activity. We find a composition law for polarizers similar to the composition law for noncollinear velocities in special relativity. We define an angle equivalent to the relativistic Wigner angle which can be used to quantify the quality of two composed polarizers.

  13. 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. PMID:27557271

  14. The Physics of Polarization

    NASA Astrophysics Data System (ADS)

    Degl'Innocenti, Egidio Landi

    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.

  15. Constrained dynamics of localized excitations causes a non-equilibrium phase transition in an atomistic model of glass formers.

    PubMed

    Speck, Thomas; Chandler, David

    2012-05-14

    Recent progress has demonstrated that trajectory space for both kinetically constrained lattice models and atomistic models can be partitioned into a liquid-like and an inactive basin with a non-equilibrium phase transition separating these behaviors. Recent work has also established that excitations in atomistic models have statistics and dynamics like those in a specific class of kinetically constrained models. But it has not been known whether the non-equilibrium phase transitions occurring in the two classes of models have similar origins. Here, we show that the origin is indeed similar. In particular, we show that the number of excitations identified in an atomistic model serves as the order parameter for the inactive-active phase transition for that model. In this way, we show that the mechanism by which excitations are correlated in an atomistic model - by dynamical facilitation - is the mechanism from which the active-inactive phase transition emerges. We study properties of the inactive phase and show that it is amorphous lacking long-range order. We also discuss the choice of dynamical order parameters. PMID:22583302

  16. Multiple site optical recording of transmembrane voltage (MSORTV) in patterned growth heart cell cultures: assessing electrical behavior, with microsecond resolution, on a cellular and subcellular scale.

    PubMed Central

    Rohr, S; Salzberg, B M

    1994-01-01

    We have applied multiple site optical recording of transmembrane voltage (MSORTV) to patterned growth cultures of heart cells to analyze the effect of geometry per se on impulse propagation in excitable tissue, with cellular and subcellular resolution. Extensive dye screening led to the choice of di-8-ANEPPS as the most suitable voltage-sensitive dye for this application; it is internalized slowly and permits optical recording with signal-to-noise ratios as high as 40:1 (measured peak-to-peak) and average fractional fluorescence changes of 15% per 100 mV. Using a x 100 objective and a fast data acquisition system, we could resolve impulse propagation on a microscopic scale (15 microns) with high temporal resolution (uncertainty of +/- 5 microseconds). We could observe the decrease in conduction velocity of an impulse propagating along a narrow cell strand as it enters a region of abrupt expansion, and we could explain this phenomenon in terms of the micro-architecture of the tissue. In contrast with the elongated and aligned cells forming the narrow strands, the cells forming the expansions were aligned at random and presented 2.5 times as many cell-to-cell appositions per unit length. If the decrease in conduction velocity results entirely from this increased number of cell-to-cell boundaries per unit length, the mean activation delay introduced by each boundary can be estimated to be 70 microseconds. Using this novel experimental system, we could also demonstrate the electrical coupling of fibroblasts and endotheloid cells to myocytes in culture. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 FIGURE 7 FIGURE 8 PMID:7811945

  17. 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

  18. Device For Viewing Polarized Light

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1995-01-01

    Technique for detection of polarized light based on observation of scene through two stacked polarizing disks. No need to rotate polarizers to create flicker indicative of polarization. Implemented by relatively simple, lightweight apparatus. Polarization seen as bow-tie rainbow pattern. Advantageous for detecting polarization in variety of meteorological, geological, astronomical, and related applications.

  19. Consecutive polarizers arrangement producing maximum polarized light intensity

    NASA Astrophysics Data System (ADS)

    Wirjawan, Johannes V. D.

    2016-03-01

    Polarizer mainly functions as a specific filter that blocks or transmits lights of certain polarization. Malus' law predicts the average intensity of polarized light passing a polarizer that transmits certain polarization direction will be proportional to the squared cosine of angle between the two polarization directions. Arranging several polarizers consecutively with various transmission directions will produce various final intensity as well as final polarized direction. Specific arrangement of an arbitrary number (N > 3) of polarizers producing maximum intensity of polarized light will be discussed in this paper. In addition, interesting pattern of maximum values of some trigonometric functions that are difficult to be solved analytically can be obtained from this discussion.

  20. 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

  1. 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.

  2. The bridging scale for two-dimensional atomistic/continuum coupling

    NASA Astrophysics Data System (ADS)

    Park, Harold S.; Karpov, Eduard G.; Liu, Wing Kam; Klein, Patrick A.

    2005-01-01

    In this paper, we present all necessary generalisations to extend the bridging scale, a finite-temperature multiple scale method which couples molecular dynamics (MD) and finite element (FE) simulations, to two dimensions. The crucial development is a numerical treatment of the boundary condition acting upon the reduced atomistic system, as such boundary conditions are analytically intractable beyond simple one-dimension systems. The approach presented in this paper offers distinct advantages compared to previous works, specifically the compact size of the resulting time history kernel, and the fact that the time history kernel can be calculated using an automated numerical procedure for arbitrary multi-dimensional lattice structures and interatomic potentials. We demonstrate the truly two-way nature of the coupled FE and reduced MD equations of motion via two example problems, wave propagation and dynamic crack propagation. Finally, we compare both problems to benchmark full MD simulations to validate the accuracy and efficiency of the proposed method.

  3. Changes in portlandite morphology with solvent composition: Atomistic simulations and experiment

    SciTech Connect

    Galmarini, Sandra Aimable, Anne; Ruffray, Nicolas; Bowen, Paul

    2011-12-15

    Experimental work has been done to determine changes in the particle shape of portlandite grown in the presence of different ions. To quantify the experimentally observed changes in morphology a new analysis tool was developed, allowing the calculation of the relative surface energies of the crystal facets. The observed morphology in the presence of chlorides and nitrates was facetted particles of a similar shape, the addition of sulfates leads to hexagonal platelet morphology and the addition of silicates leads to the formation of large irregular aggregates. In addition to the experimental work, the surfaces of portlandite were studied with atomistic simulation techniques. The empirical force field used has first been validated. The equilibrium morphology of portlandite in vacuum and in water was then calculated. The results indicate that the presence of water stabilizes the [20.3] surface and changes the morphology. This is consistent with the experimental observation of [20.3] surfaces.

  4. 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.

  5. 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.

  6. Difference in aggregation between functional and toxic amyloids studied by atomistic simulations

    NASA Astrophysics Data System (ADS)

    Carballo Pacheco, Martin; Ismail, Ahmed E.; Strodel, Birgit

    Amyloids are highly structured protein aggregates, normally associated with neurodegenerative diseases such as Alzheimer's disease. In recent years, a number of nontoxic amyloids with physiologically normal functions, called functional amyloids, have been found. It is known that soluble small oligomers are more toxic than large fibrils. Thus, we study with atomistic explicit-solvent molecular dynamics simulations the oligomer formation of the amyloid- β peptide Aβ25 - 35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Our simulations show that monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations. In addition, we observe faster aggregation by functional amyloids than toxic amyloids, which could explain their lack of toxicity.

  7. 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.

  8. Mapping between atomistic simulations and Eshelby inclusions in the shear deformation of an amorphous silicon model.

    PubMed

    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. PMID:27300968

  9. 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.

  10. Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.

    PubMed

    Fenley, Andrew T; Muddana, Hari S; Gilson, Michael K

    2014-01-01

    Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications. PMID:25503996

  11. 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.

  12. Peculiarities of sliding friction in graphene, graphene fluoride, graphite: Comparison of experiment with atomistic simulations

    NASA Astrophysics Data System (ADS)

    Barabanova, Liudmyla; McCausland, Jeffrey; Buldum, Alper; Lyuksyutov, Sergei

    Friction is the major source of energy dissipation at the nanoscale. We use atomic force microscopy (AFM) to study slide friction based on analysis of trace-minus-retrace (TMR) signals. To obtain the signals a directional dependence of the sliding friction using a rotational technique was used at the edges and interiors of the samples graphene (G), graphene fluoride (GF), and graphite. The friction coefficient experimental results were based on a methodology assuming orthotropic friction and found to be in the range of 10-3 to 10-1 over all samples. Supplementing experimental measurements, we also performed atomistic modeling and simulations to investigate tribological properties of G including the edges. Molecular dynamics simulations and geometry optimization calculations were carried and compared with experimental measurements. It is suggested that the atoms at the apex of the asperities and at the graphene edges have important effect on friction.

  13. Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules

    PubMed Central

    Gilson, Michael K.

    2014-01-01

    Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications. PMID:25503996

  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. Permutation invariant potential energy surfaces for polyatomic reactions using atomistic neural networks.

    PubMed

    Kolb, Brian; Zhao, Bin; Li, Jun; Jiang, Bin; Guo, Hua

    2016-06-14

    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. PMID:27305992

  16. Atomistic effects on friction and contact area in single and multi asperity contacts

    NASA Astrophysics Data System (ADS)

    Luan, Binquan; Robbins, Mark

    2008-03-01

    Contact and friction are universal phenomena in our daily life. Theoretical studies of macroscopic contact and friction are usually based on continuum theories such as Hertz theory and Amontons's laws. Recent advances in nanotechnology have stimulated research into friction at the nanometer scale where new phenomena emerge. Contact and friction in single- and multi-asperity contacts with nanometer dimensions were studied using molecular dynamics simulations (MD) and a hybrid method. The hybrid method retains a full atomistic treatment near contacts and replaces more distant regions with a more efficient finite element description. Our results demonstrate that atomic-scale changes in surface structure produce huge changes in friction and contact area and substantial deviations from the predictions of continuum theories. Unanticipated surface plasticity is observed near peaks on crystalline surfaces. In the case of multiasperity amorphous systems, the rate of local plastic deformation near the surface is directly related to the frictional dissipation of energy.

  17. A fully atomistic computer simulation study of cold denaturation of a β-hairpin

    NASA Astrophysics Data System (ADS)

    Yang, Changwon; Jang, Soonmin; Pak, Youngshang

    2014-12-01

    Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in molecular details can provide a new insight into the detailed natures of hydrophobic forces governing the stability of proteins in water. We show that the cold-denaturation-like phenomenon can be directly observed at low temperatures using a fully atomistic molecular dynamics simulation method. Using a highly optimized protein force field in conjunction with three different explicit water models, a replica exchange molecular dynamics simulation scheme at constant pressures allows for the computation of the melting profile of an experimentally well-characterized β-hairpin peptide. For all three water models tested, the simulated melting profiles are indicative of possible cold denaturation. From the analysis of simulation ensembles, we find that the most probable cold-denatured structure is structurally compact, with its hydrogen bonds and native hydrophobic packing substantially disrupted.

  18. Crystal Structures of Precise Functional Copolymers: Atomistic Molecular Dynamics Simulations and Comparisons with Experiments

    NASA Astrophysics Data System (ADS)

    Trigg, Edward B.; Stevens, Mark J.; Winey, Karen I.

    Layered crystal structures have been observed in linear poly(ethylene-co-acrylic acid) in which the carboxylic acid groups are placed precisely every 21 carbon atoms along the backbone. The alkane segments form structures resembling orthorhombic polyethylene crystals, while the acid groups form continuous domains that may act as pathways for ion conduction. Further details of the crystal structure have been difficult to elucidate experimentally, but could be important for understanding structure-property relationships. Here, two classes of crystal structures are evaluated via atomistic molecular dynamics: extended chain structures, wherein the polymer backbones are highly extended in near-trans conformations, and adjacent reentry structures, wherein the polymer backbones conform in adjacent reentry loops near the site of each covalently-bonded acid group. Energies of relaxed structures and hydrogen bonding states are compared, and X-ray scattering and other experimental data is compared with the simulation results.

  19. Atomistic simulation of the deformation of nanocrystalline palladium: the effect of voids

    NASA Astrophysics Data System (ADS)

    Bachurin, D. V.; Gumbsch, P.

    2014-03-01

    Atomistic simulations of uniaxial deformation of porous nanocrystalline palladium were performed at room temperature. The porosity was varied from 1% to 3%. The diameter of the pores was varied from 1 to 4 nm. It is found that a significant part of the void volume fraction is lost during sample preparation at high temperature. During deformation, the presence of voids does not lead to an earlier onset of dislocation activity compared to the void-free sample. Poisson's ratio is found to be almost insensitive to porosity, while Young's modulus and the stress for the initiation of grain boundary mediated plastic flow moderately decrease with increasing porosity. The total strain for the onset of plastic deformation, however, is unaffected by the porosity.

  20. Frozen-density embedding theory with average solvent charge densities from explicit atomistic simulations.

    PubMed

    Laktionov, Andrey; Chemineau-Chalaye, Emilie; Wesolowski, Tomasz A

    2016-08-21

    Besides molecular electron densities obtained within the Born-Oppenheimer approximation (ρB(r)) to represent the environment, the ensemble averaged density (〈ρB〉(r)) is also admissible in frozen-density embedding theory (FDET) [Wesolowski, Phys. Rev. A, 2008, 77, 11444]. This makes it possible to introduce an approximation in the evaluation of the solvent effect on quantum mechanical observables consisting of replacing the ensemble averaged observable by the observable evaluated at ensemble averaged ρB(r). This approximation is shown to affect negligibly the solvatochromic shift in the absorption of hydrated acetone. The proposed model provides a continuum type of representation of the solvent, which reflects nevertheless its local structure, and it is to be applied as a post-simulation analysis tool in atomistic level simulations. PMID:26984532

  1. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

    PubMed

    Raffaini, Giuseppina; Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  2. Structured water in polyelectrolyte dendrimers: Understanding small angle neutron scattering results through atomistic simulation

    SciTech Connect

    Chen, Wei-Ren; Do, Changwoo; Hong, Kunlun; Liu, Emily; Liu, Yun; Porcar, L.; Smith, Gregory Scott; Wu, Bin; Egami, T; Smith, Sean C

    2012-01-01

    Based on atomistic molecular dynamics (MD) simulations, the small angle neutron scattering (SANS) intensity behavior of a single generation-4 (G4) polyelectrolyte polyamidoamine (PAMAM) starburst dendrimer is investigated at different levels of molecular protonation. The SANS form factor, P(Q), and Debye autocorrelation function, (r), are calculated from the equilibrium MD trajectory based on a mathematical approach proposed in this work which provides a link between the neutron scattering experiment and MD computation. The simulations enable scattering calculations of not only the hydrocarbons, but also the contribution to the scattering length density fluctuations caused by structured, confined water within the dendrimer. Based on our computational results, we question the validity of using radius of gyration RG for microstructure characterization of a polyelectrolyte dendrimer from the scattering perspective.

  3. Atomistic modeling of the interaction of cladding elements (Fe, Ni, Cr) with U-Zr fuel

    NASA Astrophysics Data System (ADS)

    Bozzolo, G.; Mosca, H. O.; Yacout, A. M.; Hofman, G. L.

    2011-07-01

    Atomistic simulations of U-Zr fuel and its interaction with Fe, Ni, and Cr using the BFS method for alloys are presented. Results for the γU-βZr solid solution are discussed, including the behavior of the lattice parameter and coefficient of thermal expansion as a function of concentration and temperature. Output from these calculations is used to study the surface structure of γU-βZr for different crystallographic orientations, determining the concentration profiles, surface energy, and segregation behavior. The analysis is completed with simulations of the deposition of Fe, Ni and Cr on U-Zr substrates with varying Zr concentration. All results are discussed and interpreted by means of the concepts of strain and chemical energy underlying the BFS method, thus obtaining a simple explanation for the observed Zr segregation and its influence in allowing for cladding elements diffusion into the U-Zr fuel.

  4. 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.

  5. 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.

  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. Diffusive-to-ballistic transition in grain boundary motion studied by atomistic simulations

    SciTech Connect

    Deng Chuang; Schuh, Christopher A.

    2011-12-01

    An adapted simulation method is used to systematically study grain boundary motion at velocities and driving forces across more than five orders of magnitude. This analysis reveals that grain boundary migration can occur in two modes, depending upon the temperature (T) and applied driving force (P). At low P and T, grain boundary motion is diffusional, exhibiting the kinetics of a thermally activated system controlled by grain boundary self-diffusion. At high P and T, grain boundary migration exhibits the characteristic kinetic scaling behavior of a ballistic process. A rather broad transition range in both P and T lies between the regimes of diffusive and ballistic grain boundary motion, and is charted here in detail. The recognition and delineation of these two distinct modes of grain boundary migration also leads to the suggestion that many prior atomistic simulations might have probed a different kinetic regime of grain boundary motion (ballistic) as compared to that revealed in most experimental studies (diffusional).

  8. Atomistic origin of an ordered superstructure induced superconductivity in layered chalcogenides

    NASA Astrophysics Data System (ADS)

    Ang, R.; Wang, Z. C.; Chen, C. L.; Tang, J.; Liu, N.; Liu, Y.; Lu, W. J.; Sun, Y. P.; Mori, T.; Ikuhara, Y.

    2015-01-01

    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.

  9. Emergence of step flow from an atomistic scheme of epitaxial growth in 1+1 dimensions.

    PubMed

    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. PMID:25871119

  10. 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.

  11. 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.

  12. 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.

  13. The first atomistic modelling-aided reproduction of morphologically defective single walled carbon nanohorns.

    PubMed

    Furmaniak, Sylwester; Terzyk, Artur P; Kaneko, Katsumi; Gauden, Piotr A; Kowlaczyk, Piotr; Itoh, Tsutomu

    2013-01-28

    A new modelling-aided approach for the atomistic model of single walled carbon nanohorn (SWNH) creation is presented, based on experimental evidence, on realistic potential of carbon-carbon interactions and on molecular simulations. A new model of SWNHs is next used to predict Ar adsorption properties and to check the molecular fundamentals of the adsorption mechanism. The influence of the apex angle value, nanohorn diameter and nanohorn length on the shapes of isotherms, enthalpy, high resolution α(s)-plots and adsorption potential distribution curves is checked. Finally the comparison with new experimental Ar adsorption results is shown and the conclusions on the porosity of real SWNH aggregates are given. PMID:23229231

  14. Atomistic and continuums modeling of cluster migration and coagulation in precipitation reactions

    PubMed Central

    Warczok, Piotr; Ženíšek, Jaroslav; Kozeschnik, Ernst

    2012-01-01

    The influence of vacancy preference towards one of the constituents in a binary system on the formation of precipitates was investigated by atomistic and continuums modeling techniques. In case of vacancy preference towards the solute atoms, we find that the mobility of individual clusters as well as entire atom clusters is significantly altered compared to the case of vacancy preference towards the solvent atoms. The increased cluster mobility leads to pronounced cluster collisions, providing a precipitate growth and coarsening mechanism competitive to that of pure solute evaporation and adsorption considered in conventional diffusional growth and Ostwald ripening. A modification of a numerical Kampmann–Wagner type continuum model for precipitate growth is proposed, which incorporates the influence of both mechanisms. The prognoses of the modified model are validated against the growth laws obtained with lattice Monte Carlo simulations and a growth simulation considering solely the coalescence mechanism.

  15. Atomistic force field for pyridinium-based ionic liquids: reliable transport properties.

    PubMed

    Voroshylova, Iuliia V; Chaban, Vitaly V

    2014-09-11

    Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cation-anion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove that three parameters per interaction site (atom diameter, depth of potential well, point electrostatic charge) provide a sufficient basis to predict thermodynamics (heat of vaporization, density), structure (radial distributions), and transport (diffusion, viscosity, conductivity) of ILs at room conditions and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia Lopes-Pádua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids. PMID:25144141

  16. Formalism for the calculation of local elastic constants at grain boundaries by means of atomistic simulation

    NASA Astrophysics Data System (ADS)

    Kluge, M. D.; Wolf, D.; Lutsko, J. F.; Phillpot, S. R.

    1990-03-01

    A new formalism for use in atomistic simulations to calculate the full local elastic-constant tensor in terms of local stresses and strains is presented. Results of simulations on a high-angle (001) twist grain boundary are illustrated, using both a Lennard-Jones potential for Cu and an embedded-atom potential for Au. The two conceptionally rather different potentials show similar anomalies in all elastic constants, confined to within a few lattice planes of the grain boundary, with an especially dramatic reduction in the resistance to shear parallel to the grain-boundary plane. It is found that the primary cause of the anomalies is the atomic disorder near the grain boundary, as evidenced by the slice-by-slice radial distribution functions for the inhomogeneous interface system.

  17. Atomistic modeling of the self-diffusion in γ-U and γ-U-Mo

    NASA Astrophysics Data System (ADS)

    Smirnova, D. E.; Kuksin, A. Yu.; Starikov, S. V.; Stegailov, V. V.

    2015-05-01

    Results of investigations of the self-diffusion in gamma-uranium and metallic U-Mo alloys are presented. Calculations are performed using the method of atomistic modeling with the help of interatomic potentials based on the embedded-atom model and its modifications. Proposed potentials are verified by calculating thermodynamic and mechanical properties of uranium and U-Mo alloys. The formation energies of point defects and atomic diffusivities due to the diffusion of defects are calculated for gamma-uranium and alloy containing 9 wt % molybdenum. Self-diffusion coefficients of uranium and molybdenum are evaluated. Based on the data obtained, it has been concluded that the experimentally observed features of the self-diffusion in gamma-uranium can be explained by the prevalence of the interstitial mechanism.

  18. 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.

  19. Influence of calcium substitution on defect disorder in barium titanate by atomistic simulation

    NASA Astrophysics Data System (ADS)

    Sampaio, D. V.; Santos, J. C. A.; Rezende, M. V. dos S.; Valerio, M. E. G.; Silva, R. S.

    2016-01-01

    In this work, classical atomistic simulation was employed to study the intrinsic disorder influenced by calcium substitution in BaTiO3 structure. The defects were modeled using the Mott-Littleton approximation, in which: a spherical region of the lattice surrounding the defect is treated explicitly, all interactions are considered, and more distant parts of the lattice are treated using a continuum approach. Frenkel, Schottky, pseudo-Schottky and anti-Schottky defects in Ba1-x Ca x TiO3 (x  =  0-1) were investigated. It was found that the most probable defects to occur in this system are CaO pseudo-Schottky defect and the incorporation of \\text{Ca}\\text{Ti}\\prime \\prime with compensation by oxygen vacancy.

  20. 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.

  1. Stabilization of Model Membrane Systems by Disaccharides. Quasielastic Neutron Scattering Experiments and Atomistic Simulations

    NASA Astrophysics Data System (ADS)

    Doxastakis, Emmanouil; Garcia Sakai, Victoria; Ohtake, Satoshi; Maranas, Janna K.; de Pablo, Juan J.

    2006-03-01

    Trehalose, a disaccharide of glucose, is often used for the stabilization of cell membranes in the absence of water. This work studies the effects of trehalose on model membrane systems as they undergo a melting transition using a combination of experimental methods and atomistic molecular simulations. Quasielastic neutron scattering experiments on selectively deuterated samples provide the incoherent dynamic structure over a wide time range. Elastic scans probing the lipid tail dynamics display clear evidence of a main melting transition that is significantly lowered in the presence of trehalose. Lipid headgroup mobility is considerably restricted at high temperatures and directly associated with the dynamics of the sugar in the mixture. Molecular simulations provide a detailed overview of the dynamics and their spatial and time dependence. The combined simulation and experimental methodology offers a unique, molecular view of the physics of systems commonly employed in cryopreservation and lyophilization processes.

  2. Atomistic mechanisms of amorphization during nanoindentation of SiC: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Szlufarska, Izabela; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2005-05-01

    Atomistic mechanisms underlying the nanoindentation-induced amorphization in SiC crystal has been studied by molecular dynamics simulations on parallel computers. The calculated load-displacement curve consists of a series of load drops, corresponding to plastic deformation, in addition to a shoulder at a smaller displacement, which is fully reversible upon unloading. The peaks in the load-displacement curve are shown to reflect the crystalline structure and dislocation activities under the surface. The evolution of indentation damage and defect accumulation are also discussed in terms of bond angles, local pressure, local shear stress, and spatial rearrangements of atoms. These structural analyses reveal that the defect-stimulated growth and coalescence of dislocation loops are responsible for the crystalline-to-amorphous transition. The shortest-path-ring analysis is effectively employed to characterize nanoindentation-induced structural transformations and dislocation activities.

  3. 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.

  4. Atomistic full-band simulations of monolayer MoS2 transistors

    NASA Astrophysics Data System (ADS)

    Chang, Jiwon; Register, Leonard F.; Banerjee, Sanjay K.

    2013-11-01

    We study the transport properties of deeply scaled monolayer MoS2 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 MoS2 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 MoS2.

  5. The role of halide ions in the anisotropic growth of gold nanoparticles: a microscopic, atomistic perspective.

    PubMed

    Meena, Santosh Kumar; Celiksoy, Sirin; Schäfer, Philipp; Henkel, Andreas; Sönnichsen, Carsten; Sulpizi, Marialore

    2016-05-21

    We provide a microscopic view of the role of halides in controlling the anisotropic growth of gold nanorods through a combined computational and experimental study. Atomistic molecular dynamics simulations unveil that Br(-) adsorption is not only responsible for surface passivation, but also acts as the driving force for CTAB micelle adsorption and stabilization on the gold surface in a facet-dependent way. The partial replacement of Br(-) by Cl(-) decreases the difference between facets and the surfactant density. Finally, in the CTAC solution, no halides or micellar structures protect the gold surface and further gold reduction should be uniformly possible. Experimentally observed nanoparticle's growth in different CTAB/CTAC mixtures is more uniform and faster as the amount of Cl(-) increases, confirming the picture from the simulations. In addition, the surfactant layer thickness measured on nanorods exposed to CTAB and CTAC quantitatively agrees with the simulation results. PMID:27118188

  6. Atomistic study of dynamics for metallic filament growth in conductive-bridge random access memory.

    PubMed

    Qin, Shengjun; Liu, Zhan; Zhang, Guo; Zhang, Jinyu; Sun, Yaping; Wu, Huaqiang; Qian, He; Yu, Zhiping

    2015-04-14

    The growth dynamics for metallic filaments in conductive-bridge resistive-switching random access memory (CBRAM) are studied using the kinetic Monte Carlo (KMC) method. The physical process at the atomistic level is revealed in explaining the experimental observation that filament growth can originate at either the cathode or the anode. The statistical nature of the filament growth is best shown by the random topography of dendrite-like conductive paths obtained. Critical material properties, such as charged-particle mobility in the switching layer of a solid electrolyte or a dielectric, are mapped to KMC model parameters through activation energy, etc. The accuracy of the simulator is established by the good agreement between the simulated forming time and the measured data. PMID:25750983

  7. 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.

  8. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    PubMed Central

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Summary Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  9. 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.

  10. Automatic Bayesian polarity determination

    NASA Astrophysics Data System (ADS)

    Pugh, D. J.; White, R. S.; Christie, P. A. F.

    2016-04-01

    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 mechanims, and are better constrained than source mechanisms determined using a uniform probability of an incorrect polarity pick.

  11. On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations.

    PubMed

    Kuhn, Alexander B; Gopal, Srinivasa M; Schäfer, Lars V

    2015-09-01

    Hybrid all-atom/coarse-grained (AA-CG) simulations in which AA solutes are embedded in a CG environment can provide a significant computational speed-up over conventional fully atomistic simulations and thus alleviate the current length and time scale limitations of molecular dynamics (MD) simulations of large biomolecular systems. On one hand, coarse graining the solvent is particularly appealing, since it typically constitutes the largest part of the simulation system and thus dominates computational cost. On the other hand, retaining atomic-level solvent layers around the solute is desirable for a realistic description of hydrogen bonds and other local solvation effects. Here, we devise and systematically validate fixed resolution AA-CG schemes, both with and without atomistic water layers. To quantify the accuracy and diagnose possible pitfalls, Gibbs free energies of solvation of amino acid side chain analogues were calculated, and the influence of the nature of the CG solvent surrounding (polarizable vs nonpolarizable CG water) and the size of the AA solvent region was investigated. We show that distance restraints to keep the AA solvent around the solute lead to too high of a density in the inner shell. Together with a long-ranged effect due to orientational ordering of water molecules at the AA-CG boundary, this affects solvation free energies. Shifting the onset of the distance restraints slightly away from the central solute significantly improves solvation free energies, down to mean unsigned errors with respect to experiment of 2.3 and 2.6 kJ/mol for the polarizable and nonpolarizable CG water surrounding, respectively. The speed-up of the nonpolarizable model renders it computationally more attractive. The present work thus highlights challenges, and outlines possible solutions, involved with modeling the boundary between different levels of resolution in hybrid AA-CG simulations. PMID:26575936

  12. 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.

  13. 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.

  14. Atomistic study of diffusion-mediated plasticity and creep using phase field crystal methods

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    The nonequilibrium dynamics of diffusion-mediated plasticity and creep in materials subjected to constant load at high homologous temperatures is studied atomistically using phase field crystal (PFC) methods. Creep stress and grain size exponents obtained for nanopolycrystalline systems, m ≃1.02 and p ≃1.98 , respectively, closely match those expected for idealized diffusional Nabarro-Herring creep. These exponents are observed in the presence of significant stress-assisted diffusive grain boundary migration, indicating that Nabarro-Herring creep and stress-assisted boundary migration contribute in the same manner to the macroscopic constitutive relation. When plastic response is dislocation-mediated, power-law stress exponents inferred from dislocation climb rates are found to increase monotonically from m ≃3 , as expected for generic climb-mediated natural creep, to m ≃5.8 as the dislocation density ρd is increased beyond typical experimental values. Stress exponents m ≳3 directly measured from simulations that include dislocation nucleation, climb, glide, and annihilation are attributed primarily to these large ρd effects. Extrapolation to lower ρd suggests that m ≃4 -4.5 should be obtained from our PFC description at typical experimental ρd values, which is consistent with expectations for power-law creep via mixed climb and glide. The anomalously large stress exponents observed in our atomistic simulations at large ρd may nonetheless be relevant to systems in which comparable densities are obtained locally within heterogeneous defect domains such as dislocation cell walls or tangles.

  15. Atomistic simulation studies of size effects in plasticity and dislocation patterning

    NASA Astrophysics Data System (ADS)

    Weingarten, Neil Scott

    Experimental studies of deformation of crystalline solids have demonstrated that the hardness of a material in the plastic, or inelastic, regime is inversely related to the size of the sample, for samples up to a few hundred microns in size. It has also been observed that a material's mechanical response to deformation depends on the structure and patterning of dislocations, or defects, in the material. The underlying mechanisms behind dislocation patterning and size effects in plasticity are not well understood. To study these effects, atomistic Monte Carlo simulations of bending a Lennard-Jones single crystal in two dimensions are performed. In these simulations, when dislocations reach sufficient density, they coalesce to form grain boundaries. A reverse-size effect is demonstrated, which can be attributed to a shortage of dislocation sources and high effective strain rate. The effects of crystal orientation, temperature, and strain rate are explored, and a scaling relationship between size- and rate-effects is proposed. In one simulation, an instability in grain boundary evolution suggests a novel mechanism for hillock formation on metal surfaces. Simulations of pure compression are also performed on both single crystal and polycrystalline samples, and the results are compared to those involving bending. An effective means of expanding the capabilities of simulation techniques is through multiscale algorithms. The performance of a coupled atomistics-continuum formulation has been tested on surface relaxation simulations of gold, as well as 2-d and 3-d simulations of gold nanowire under applied compression. The coupling algorithm involves communication between the coarse and fine scales via ghost atoms, and the energy contribution from bonds between real and ghost atoms is weighted such that the energy is minimized based on a consistency condition of homogeneous deformation. The algorithm was updated to allow the use of Embedded Atom Method (EAM) potentials

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Asymptotes in Polar Coordinates.

    ERIC Educational Resources Information Center

    Fay, Temple H.

    1986-01-01

    An old way to determine asymptotes for curves described in polar coordinates is presented. Practice in solving trigonometric equations, in differentiation, and in calculating limits is involved. (MNS)