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Sample records for microsecond polarized atomistic

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

    PubMed

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

    2016-01-16

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

  2. Laser-Driven Microsecond Temperature Cycles Analyzed by Fluorescence Polarization Microscopy

    PubMed Central

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

    2006-01-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    1992-06-01

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

  4. Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

    PubMed

    Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

    2014-10-14

    Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

  5. 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

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

    PubMed

    Calvo, Florent

    2015-03-01

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

  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. 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.

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

    DOE PAGES

    Lane, J. Matthew D.

    2015-07-22

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

  10. 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.

  11. Sub-microsecond-resolution probe microscopy

    DOEpatents

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

    2014-04-01

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

  12. 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

  13. Microsecond flares in gamma-ray bursts

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  14. 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.

  15. 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

  16. Atomistics of friction

    NASA Astrophysics Data System (ADS)

    Hirano, M.

    2006-03-01

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

  17. Efficient illumination for microsecond tracking microscopy.

    PubMed

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

    2014-01-01

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

  18. Microsecond subdomain folding in dihydrofolate reductase.

    PubMed

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

    2011-07-08

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

  19. 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.

  20. Atomistic k ṡ p theory

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  1. 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

  2. Microsecond Molecular Dynamics Simulations of Lipid Mixing

    PubMed Central

    2015-01-01

    Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na+ ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. PMID:25237736

  3. 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.

  4. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    DTIC Science & Technology

    2014-03-28

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

  5. 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

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

    DOE PAGES

    Khodadadi, Sheila; Sokolov, Alexei P.

    2016-05-04

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

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

    SciTech Connect

    Khodadadi, Sheila; Sokolov, Alexei P.

    2016-05-04

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

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

    SciTech Connect

    Khodadadi, Sheila; Sokolov, Alexei P.

    2016-05-04

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

  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.

  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

    2013-04-04

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

  11. Atomistic modeling at experimental strain rates and timescales

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

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

    PubMed

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

    2015-06-20

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

  13. 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.

  14. 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.

  15. 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.

  16. Atomistic properties of γ uranium.

    PubMed

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

    2012-02-22

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

  17. 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.

  18. 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.

  19. [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.

  20. Connecting Atomistic and Continuous Models of Elastodynamics

    NASA Astrophysics Data System (ADS)

    Braun, Julian

    2017-06-01

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

  1. Connecting Atomistic and Continuous Models of Elastodynamics

    NASA Astrophysics Data System (ADS)

    Braun, Julian

    2017-02-01

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

  2. 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.

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

    PubMed

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

    2003-01-01

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

  4. Atomistic Simulations of Bicelle Mixtures

    PubMed Central

    Jiang, Yong; Wang, Hao; Kindt, James T.

    2010-01-01

    Abstract Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C14 tails) and dihexanoylphosphatidylcholine (DHPC, di-C6 tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C10 tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of ∼3 nm−1. The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets. PMID:20550902

  5. 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.

  6. 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.

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

    PubMed

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Maláč, Kamil; Barvík, Ivan

    2013-04-01

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

  9. Plasma dynamics in microsecond megaampere plasma opening switches

    SciTech Connect

    Loginov, S. V.

    2011-10-15

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

  10. 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

  11. Atomistic simulations of bicelle mixtures.

    PubMed

    Jiang, Yong; Wang, Hao; Kindt, James T

    2010-06-16

    Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets. (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Atomistic modeling of dropwise condensation

    SciTech Connect

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

    2016-05-23

    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.

  13. 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.

  14. Atomistic simulation of graphene-based polymer nanocomposites

    SciTech Connect

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

    2016-05-18

    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.

  15. Homogeneous Nucleation of Methane Hydrate in Microsecond Molecular Dynamics Simulations.

    PubMed

    Sarupria, Sapna; Debenedetti, Pablo G

    2012-10-18

    We report atomistically detailed molecular dynamics simulations of homogeneous nucleation of methane hydrate in bulk aqueous phase in the absence of any interface. Subcritical clusters of water and methane molecules are formed in the initial segment of the simulations, which then aggregate to give the critical hydrate nucleus. This occurs over time scales of several hundred nanoseconds, indicating that the formation and aggregation of subcritical clusters can contribute significantly to the overall rate of hydrate nucleation. The clusters have elements of sI hydrate structure, such as 5(12) and 5(12)6(2) cages as well as other uncommon 5(12)6(3) and 5(12)6(4) cages, but do not possess long-range order. Clusters are dynamic in nature and undergo continuous structural rearrangements.

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

    NASA Astrophysics Data System (ADS)

    Bell, Curtis John

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

  17. Atomistic simulation of nanostructured materials

    NASA Astrophysics Data System (ADS)

    Zhu, Ronghua

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

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

    NASA Astrophysics Data System (ADS)

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

    1992-07-01

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

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2015-10-23

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

  3. 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

  4. 10 microsecond time resolution studies of Cygnus X-1

    SciTech Connect

    Wen, H. C.

    1997-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1998-12-01

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

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

    PubMed

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

    2016-10-06

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

  7. Seamless elastic boundaries for atomistic calculations

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  8. Atomistic molecular dynamics simulations of shock compressed quartz

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

  9. 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.

  10. 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

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

    SciTech Connect

    Hamilton, John C.

    2005-06-01

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

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

    DTIC Science & Technology

    2014-09-01

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

  13. Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions

    NASA Astrophysics Data System (ADS)

    Renevey, Annick; Riniker, Sereina

    2017-03-01

    Reducing the number of degrees of freedom in molecular models—so-called coarse-graining—is a popular approach to increase the accessible time scales and system sizes in molecular dynamics simulations. It involves, however, per se a loss of information. In order to retain a high accuracy in the region of interest, hybrid methods that combine two levels of resolution in a single system are an attractive trade-off. Hybrid atomistic (AT)/coarse-grained (CG) simulations have previously been shown to preserve the secondary structure elements of AT proteins in CG water but to cause an artificial increase in intramolecular hydrogen bonds, resulting in a reduced flexibility of the proteins. Recently, it was found that the AT-CG interactions employed in these simulations were too favourable for apolar solutes and not favourable enough for polar solutes. Here, the AT-CG interactions are reparametrised to reproduce the solvation free energy of a series of AT alkanes and side-chain analogues in CG water, while retaining the good mixing behaviour of AT water with CG water. The new AT-CG parameters are tested in hybrid simulations of four proteins in CG water. Structural and dynamic properties are compared to those obtained in fully AT simulations and, if applicable, to experimental data. The results show that the artificial increase of intramolecular hydrogen bonds is drastically reduced, leading to a better reproduction of the structural properties and flexibility of the proteins in atomistic water, without the need for an atomistic solvent layer.

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

    PubMed

    Sattelle, Benedict M; Almond, Andrew

    2014-05-07

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

  15. Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations.

    PubMed

    Rydzewski, J; Nowak, W

    2017-08-10

    Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.

  16. 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).

  17. Atomistic deformation mechanisms in twinned copper nanospheres.

    PubMed

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

    2014-01-01

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

  18. 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.

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

    DOE PAGES

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

    2014-08-21

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

  20. 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.

  1. Variations in vacuum gap location in a microsecond plasma opening switch

    SciTech Connect

    Lisitsyn, I.V.; Kohno, S.; Kawauchi, T.; Akiyama, H.

    1997-10-01

    The process of vacuum gap formation in a microsecond plasma opening switch has been studied using a He{endash}Ne laser interferometer. Time and spatially resolved density measurements are performed in the plasma opening switch, showing a density decrease during switch opening in almost the whole interelectrode gap. Despite fine triggering accuracy and generally good shot-to-shot reproducibility of voltage and current waveforms, measurements made with the same laser beam location indicated remarkable shot-to-shot variation. The unstable formation of the vacuum gap in the microsecond plasma opening switch may be a major limiting factor for efficient switch operation. {copyright} {ital 1997 American Institute of Physics.}

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

    DTIC Science & Technology

    2015-05-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  4. 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

  5. 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.

  6. Addressing uncertainty in atomistic machine learning.

    PubMed

    Peterson, Andrew A; Christensen, Rune; Khorshidi, Alireza

    2017-05-10

    Machine-learning regression has been demonstrated to precisely emulate the potential energy and forces that are output from more expensive electronic-structure calculations. However, to predict new regions of the potential energy surface, an assessment must be made of the credibility of the predictions. In this perspective, we address the types of errors that might arise in atomistic machine learning, the unique aspects of atomistic simulations that make machine-learning challenging, and highlight how uncertainty analysis can be used to assess the validity of machine-learning predictions. We suggest this will allow researchers to more fully use machine learning for the routine acceleration of large, high-accuracy, or extended-time simulations. In our demonstrations, we use a bootstrap ensemble of neural network-based calculators, and show that the width of the ensemble can provide an estimate of the uncertainty when the width is comparable to that in the training data. Intriguingly, we also show that the uncertainty can be localized to specific atoms in the simulation, which may offer hints for the generation of training data to strategically improve the machine-learned representation.

  7. Atomistic simulations of nanoscale electrokinetic transport

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  8. Atomistic to continuum modeling of solidification microstructures

    DOE PAGES

    Karma, Alain; Tourret, Damien

    2015-09-26

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

  9. 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

  10. Filters for Improvement of Multiscale Data from Atomistic Simulations

    DOE PAGES

    Gardner, David J.; Reynolds, Daniel R.

    2017-01-05

    Multiscale computational models strive to produce accurate and efficient numerical simulations of systems involving interactions across multiple spatial and temporal scales that typically differ by several orders of magnitude. Some such models utilize a hybrid continuum-atomistic approach combining continuum approximations with first-principles-based atomistic models to capture multiscale behavior. By following the heterogeneous multiscale method framework for developing multiscale computational models, unknown continuum scale data can be computed from an atomistic model. Concurrently coupling the two models requires performing numerous atomistic simulations which can dominate the computational cost of the method. Furthermore, when the resulting continuum data is noisy due tomore » sampling error, stochasticity in the model, or randomness in the initial conditions, filtering can result in significant accuracy gains in the computed multiscale data without increasing the size or duration of the atomistic simulations. In this work, we demonstrate the effectiveness of spectral filtering for increasing the accuracy of noisy multiscale data obtained from atomistic simulations. Moreover, we present a robust and automatic method for closely approximating the optimum level of filtering in the case of additive white noise. By improving the accuracy of this filtered simulation data, it leads to a dramatic computational savings by allowing for shorter and smaller atomistic simulations to achieve the same desired multiscale simulation precision.« less

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

    SciTech Connect

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

    2008-04-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

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

  13. 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.

  14. 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.

  15. Does quantum mechanics tell an atomistic spacetime?

    NASA Astrophysics Data System (ADS)

    Elze, Hans-Thomas

    2009-06-01

    The canonical answer to the question posed is "Yes." - tacitly assuming that quantum theory and the concept of spacetime are to be unified by 'quantizing' a theory of gravitation. Yet, instead, one may ponder: Could quantum mechanics arise as a coarse-grained reflection of the atomistic nature of spacetime? - We speculate that this may indeed be the case. We recall the similarity between evolution of classical and quantum mechanical ensembles, according to Liouville and von Neumann equation, respectively. The classical and quantum mechanical equations are indistinguishable for objects which are free or subject to spatially constant but possibly time dependent, or harmonic forces, if represented appropriately. This result suggests a way to incorporate anharmonic interactions, including fluctuations which are tentatively related to the underlying discreteness of spacetime. Being linear and local at the quantum mechanical level, the model offers a decoherence and natural localization mechanism. However, the relation to primordial deterministic degrees of freedom is nonlocal.

  16. 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.

  17. 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.

  18. Statistical 3D 'Atomistic' Simulation of Decanano MOSFETs

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

    A 3D statistical 'atomistic' simulation technique has been developed to study the effect of the random dopant induced parameter fluctuations in aggressively scaled MOSFETs. Efficient implementation of the 'atomistic' simulation approach has been used to investigate the threshold voltage standard deviation and lowering in the case of uniformly doped MOSFETs, and in fluctuation-resistant architectures utilising epitaxial-layers and delta-doping. The effect of the random doping in the polysilicon gate on the threshold voltage fluctuations has also been thoroughly investigated. The influence of a single-charge trapping on the channel conductivity in decanano MOSFETs is studied in the 'atomistic' framework as well. Quantum effects are taken into consideration in our 'atomistic' simulations using the density gradient formalism.

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

    PubMed

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

    2014-08-06

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

  20. Electrocaloric effect in ferroelectric alloys from atomistic simulations

    NASA Astrophysics Data System (ADS)

    Lisenkov, Sergey; Ponomareva, Inna

    2012-02-01

    Caloric effects, such as magnetocaloric and electrocaloric effects, have attracted a lot of attention recently in the context of increasing interest in energy conversion and renewable energy materials and devices. Here we develop and use accurate first-principles-based simulations to study electrocaloric effect (ECE) from an atomistic point of view. In particular, we develop a computational technique that allows both direct and indirect simulations of ECE within the same atomistic framework. We then use such a tool to provide first systematic comparison between ECE estimates obtained from direct and indirect approach which will allow us to bridge the macroscopic and atomistic description of ECE. The results of our direct atomistic simulations are then used to explore the intrinsic features of ECE in ferroelectrics with multiple transitions.

  1. 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.

  2. 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

  3. Reaching the protein folding speed limit with large, sub-microsecond pressure jumps.

    PubMed

    Dumont, Charles; Emilsson, Tryggvi; Gruebele, Martin

    2009-07-01

    Biomolecules are highly pressure-sensitive, but their dynamics upon return to ambient pressure are often too fast to observe with existing approaches. We describe a sample-efficient method capable of large and very fast pressure drops (<1 nanomole, >2,500 atmospheres and <0.7 microseconds). We validated the method by fluorescence-detected refolding of a genetically engineered lambda repressor mutant from its pressure-denatured state. We resolved barrierless structure formation upon return to ambient pressure; we observed a 2.1 +/- 0.7 microsecond refolding time, which is very close to the 'speed limit' for proteins and much faster than the corresponding temperature-jump refolding of the same protein. The ability to experimentally perform a large and very fast pressure drop opens up a new region of the biomolecular energy landscape for atomic-level simulation.

  4. Atomistic modeling of thermodynamic equilibrium of plutonium

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  5. Atomistic simulation on indented defects in silicon.

    PubMed

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

    2013-12-01

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

  6. 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.

  7. 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.

  8. 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.

  9. NiTi superelasticity via atomistic simulations

    NASA Astrophysics Data System (ADS)

    Chowdhury, Piyas; Ren, Guowu; Sehitoglu, Huseyin

    2015-12-01

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

  10. Atomistic study of boron-doped silicon

    SciTech Connect

    Fearn, M.; Pettifor, D.G.; Jefferson, J.H.

    1996-12-31

    Atomistic simulations using both tight-binding and density-functional approaches have been performed to investigate boron-related defects in silicon. In agreement with experiment, the boron interstitial is shown to be a negative-U center in the sense that its neutral charge state, with an associated Jahn-Teller distortion off the ideal tetrahedral site, is never the ground state for any value of the chemical potential in the gap. The possible consequences for an electron-assisted migration of the interstitial are discussed. The authors also find the boron substitutional defect to be a next-nearest neighbor of a silicon vacancy in agreement with EPR spectra. A semi-empirical tight-binding model of the boron-silicon system is validated by direct comparison with the accurate density-functional results and is then used to perform molecular dynamics simulations of boron diffusion at high temperatures. The mobility of the interstitial is found to be strongly charge-state dependent. Termination of the boron interstitial migration path by recombination with a silicon vacancy is shown to be a very likely process with a number of configurations having no barrier to capture when the boron is a near-neighbor of the vacancy.

  11. 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.

  12. 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.

  13. 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

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

    SciTech Connect

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

    2003-10-31

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

  15. Atomistic simulation of Voronoi-based coated nanoporous metals

    NASA Astrophysics Data System (ADS)

    Onur Yildiz, Yunus; Kirca, Mesut

    2017-02-01

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

  16. 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

  17. Sub-microsecond x-ray imaging using hole-collecting Schottky type CdTe with charge-integrating pixel array detectors

    NASA Astrophysics Data System (ADS)

    Becker, J.; Tate, M. W.; Shanks, K. S.; Philipp, H. T.; Weiss, J. T.; Purohit, P.; Chamberlain, D.; Gruner, S. M.

    2017-06-01

    CdTe is increasingly being used as the x-ray sensing material in imaging pixel array detectors for x-rays, generally above 20 keV, where silicon sensors become unacceptably transparent. Unfortunately CdTe suffers from polarization, which can alter the response of the material over time and with accumulated dose. Most prior studies used long integration times or CdTe that was not of the hole-collecting Schottky type. We investigated the temporal response of hole-collecting Schottky type CdTe sensors on timescales ranging from tens of nanoseconds to several seconds. We found that the material shows signal persistence on the timescale of hundreds of milliseconds attributed to the detrapping of a shallow trap, and additional persistence on sub-microsecond timescales after polarization. The results show that this type of CdTe can be used for time resolved studies down to approximately 100 ns. However quantitative interpretation of the signal requires careful attention to bias voltages, polarization and exposure history.

  18. 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

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

    PubMed

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

    2013-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-11-01

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

  2. Atomistic and Coarse-grained Simulations of Hexabenzocoronene Crystals

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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

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

    PubMed

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

    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.

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

    PubMed

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

    2014-07-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    1980-09-01

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

  10. 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.

  11. 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

  12. A concurrent atomistic-continuum methodolody and its applications

    NASA Astrophysics Data System (ADS)

    Xiong, Liming

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

  13. 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.

  14. 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

  15. The development of a heterodyne velocimeter system for use in sub-microsecond time regimes

    NASA Astrophysics Data System (ADS)

    Bowden, M. D.; Maisey, M. P.

    2007-09-01

    Recent advances over the last five years in high-speed digitizing oscilloscopes and high-bandwidth photodiodes, driven primarily by the telecommunications industry, have enabled the development of a new type of interferometer for measuring high velocities, such as those found in detonics experiments. The heterodyne velocimeter can be visualized as a fiber-based Michelson interferometer. The beam from a single-mode fiber laser at 1550 nm is passed through a circulator, acting to separate bi-directional light. The beam is then reflected via free-space optics from the surface of interest, and then focused back into the same fiber. This reflected light is mixed with an approximately equal amount of non-reflected light, and the resulting interference is recorded using a high-bandwidth photodiode and oscilloscope. In contrast to more traditional velocimetry techniques such as VISAR, only a single data channel is required per probe. The uses of heterodyne velocimetry have, to date, been primarily in the multi-microsecond time regime, i.e. explosively driven metal plates. In this paper, we present a four-channel, ultra-high bandwidth system designed for use in the sub-microsecond time regime, and present the results obtained from laser-driven flyer plates traveling in excess of 3 km s -1. We have developed analysis software suited to use in this time regime, where a relatively small displacement is recorded. The original heterodyne velocimeter relied on back-reflectance from the probe to obtain the non-reflected light. This limits both the flexibility of the system and the efficiency of the probes. We have overcome this issue by introducing a beam splitter into the system prior to the circulator. This allows the probing system to be designed for maximum efficiency, and we are then able to tune the non-reflected light on a shot-to-shot basis.

  16. Photon-by-Photon Hidden Markov Model Analysis for Microsecond Single-Molecule FRET Kinetics.

    PubMed

    Pirchi, Menahem; Tsukanov, Roman; Khamis, Rashid; Tomov, Toma E; Berger, Yaron; Khara, Dinesh C; Volkov, Hadas; Haran, Gilad; Nir, Eyal

    2016-12-29

    The function of biological macromolecules involves large-scale conformational dynamics spanning multiple time scales, from microseconds to seconds. Such conformational motions, which may involve whole domains or subunits of a protein, play a key role in allosteric regulation. There is an urgent need for experimental methods to probe the fastest of these motions. Single-molecule fluorescence experiments can in principle be used for observing such dynamics, but there is a lack of analysis methods that can extract the maximum amount of information from the data, down to the microsecond time scale. To address this issue, we introduce H(2)MM, a maximum likelihood estimation algorithm for photon-by-photon analysis of single-molecule fluorescence resonance energy transfer (FRET) experiments. H(2)MM is based on analytical estimators for model parameters, derived using the Baum-Welch algorithm. An efficient and effective method for the calculation of these estimators is introduced. H(2)MM is shown to accurately retrieve the reaction times from ∼1 s to ∼10 μs and even faster when applied to simulations of freely diffusing molecules. We further apply this algorithm to single-molecule FRET data collected from Holliday junction molecules and show that at low magnesium concentrations their kinetics are as fast as ∼10(4) s(-1). The new algorithm is particularly suitable for experiments on freely diffusing individual molecules and is readily incorporated into existing analysis packages. It paves the way for the broad application of single-molecule fluorescence to study ultrafast functional dynamics of biomolecules.

  17. 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.

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

    PubMed

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

    2013-01-16

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

  19. Phase transformations at interfaces: Observations from atomistic modeling

    SciTech Connect

    Frolov, T.; Asta, M.; Mishin, Y.

    2016-10-01

    Here, we review the recent progress in theoretical understanding and atomistic computer simulations of phase transformations in materials interfaces, focusing on grain boundaries (GBs) in metallic systems. Recently developed simulation approaches enable the search and structural characterization of GB phases in single-component metals and binary alloys, calculation of thermodynamic properties of individual GB phases, and modeling of the effect of the GB phase transformations on GB kinetics. Atomistic simulations demonstrate that the GB transformations can be induced by varying the temperature, loading the GB with point defects, or varying the amount of solute segregation. The atomic-level understanding obtained from such simulations can provide input for further development of thermodynamics theories and continuous models of interface phase transformations while simultaneously serving as a testing ground for validation of theories and models. They can also help interpret and guide experimental work in this field.

  20. Phase transformations at interfaces: Observations from atomistic modeling

    DOE PAGES

    Frolov, T.; Asta, M.; Mishin, Y.

    2016-10-01

    Here, we review the recent progress in theoretical understanding and atomistic computer simulations of phase transformations in materials interfaces, focusing on grain boundaries (GBs) in metallic systems. Recently developed simulation approaches enable the search and structural characterization of GB phases in single-component metals and binary alloys, calculation of thermodynamic properties of individual GB phases, and modeling of the effect of the GB phase transformations on GB kinetics. Atomistic simulations demonstrate that the GB transformations can be induced by varying the temperature, loading the GB with point defects, or varying the amount of solute segregation. The atomic-level understanding obtained from suchmore » simulations can provide input for further development of thermodynamics theories and continuous models of interface phase transformations while simultaneously serving as a testing ground for validation of theories and models. They can also help interpret and guide experimental work in this field.« less

  1. Asymptotic analysis of microscopic impenetrability constraints for atomistic systems

    NASA Astrophysics Data System (ADS)

    Braides, A.; Gelli, M. S.

    2016-11-01

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

  2. 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.

  3. 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.

  4. Atomistic Modeling of Co Growth on Cu(111

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  6. Atomistic simulations of high strain rate loading of nanocrystals

    NASA Astrophysics Data System (ADS)

    Bringa, E. M.; Tramontina, D.; Ruestes, C. J.; Tang, Y.; Meyers, M. A.; Gunkelmann, N.; Urbassek, H. M.

    2013-03-01

    Materials loaded at high strain rates can reach extreme temperature and pressure conditions. Most experiments on loading of simple materials use poly crystals, while most atomistic simulations of shock wave loading deal with single crystals, due to the higher computational cost of running polycrystal samples. Of course, atomistic simulations of polycrystals with micron-sized grains are beyond the capabilities of current supercomputers. On the other hand, nanocrystals (nc) with grain sizes below 50 nm can be obtained experimentally and modeled reasonably well at high strain rates, opening the possibility of nearly direct comparison between atomistic molecular dynamics (MD) simulations and experiments using high power lasers. We will discuss MD simulations and links to experiments for nc Cu and Ni, as model f.c.c. solids, and nc Ta and Fe, as model b.c.c. solids. In all cases, the microstructure resulting from loading depends strongly on grain size, strain rate and peak applied pressure. We will also discuss effects related to target porosity in nc's. E.M.B. thanks funding from PICT2008-1325.

  7. 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

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

    PubMed

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

    1997-01-01

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

  9. Polarized cells, polar actions.

    PubMed

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

    1993-11-01

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

  10. 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.

  11. Ablation of dental hard tissues with a microsecond pulsed carbon dioxide laser operating at 9.3-μm with an integrated scanner

    NASA Astrophysics Data System (ADS)

    Assa, Shlomo; Meyer, Steve; Fried, Daniel

    2008-02-01

    Pulsed carbon dioxide lasers operating at the highly absorbed 9.3 and 9.6-μm wavelengths with pulse durations in the microsecond range are ideally suited for dental hard tissue modification and removal. The purpose of these studies was to demonstrate that a low cost 9.3-μm CO II laser system utilizing low-energy laser pulses (1-5 mJ /pulse) delivered at a high repetition rate (400-Hz) is feasible for removing dental hard tissues. The laser beam was focused to a small spot size to achieve ablative fluence and an integrated/programmable optical scanner was used to scan the laser beam over the desired area for tissue removal. Pulse durations of 35, 60 and 75-μs were employed and the enamel and dentin ablation rate and ablation efficiency was measured. Laser irradiated human and bovine samples were assessed for peripheral thermal and mechanical damage using polarized light microscopy. The heat accumulation during rapid scanning ablation with water-cooling at 400-Hz was monitored using micro-thermocouples. The laser was able to ablate both enamel and dentin without excessive peripheral thermal damage or heat accumulation. These preliminary studies suggest that a low-cost RF excited CO II laser used in conjunction with an integrated scanner has considerable potential for application to dental hard tissues.

  12. Microsecond-scale electric field pulses associated with lightning M-components

    NASA Astrophysics Data System (ADS)

    Tran, M. D.; Rakov, V. A.; Ngin, T.; Gamerota, W. R.; Pilkey, J. T.; Uman, M. A.; Jordan, D. M.

    2013-12-01

    Rakov et al. [2001, Fig. 7] reported on the M-component electric field recorded at a distance of 45 km from the triggered-lightning channel. The electric field signature appeared as a bipolar microsecond-scale pulse which began prior to the onset of the M-component current at the channel base. The pulse was inferred to be associated with establishing the contact between an in-cloud leader and the current-carrying channel to ground. This contact apparently initiated the downward moving M-wave, which subsequently reflected off ground. In the electric field records at distances ranging from 2.5 to 27 km, Rakov et al. [1992, 1996] found similar pulses, which were typically preceding the hook-shaped electric field waveforms characteristic of M components in that distance range. Shao et al. [1995], based on their electric field measurements in conjunction with VHF images of lightning channels, found that the microsecond-scale pulses similar to those studied by Rakov et al. [1992, 1996] were associated with the initiation of M-component charge transfer at the top of the channel to ground. This study is an extension of that of Rakov et al. [2001] who presented data only for one M-component. Here, we will use wideband electric field records acquired at the Lightning Observatory in Gainesville (LOG), Florida, and corresponding channel-base current records for negative lightning triggered using the rocket-and-wire technique at Camp Blanding (CB), Florida, in 2013. The LOG is located on the University of Florida campus (the same location where the electrical field reported by Rakov et al. [2001, Fig. 7] was recorded), at a distance of 45 km from CB. Our data set includes more than 50 M-components suitable for this analysis. It appears that the majority of M-components are preceded by detectable microsecond-scale electric field pulses. Acknowledgements This research was supported in part by NSF and DARPA. Reference: Rakov, V.A, R. Thottappillil, and M.A. Uman, Electric field

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  14. 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

  15. 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.

  16. Polarization measurement through combination polarizers

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    PubMed

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

    2002-07-23

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

  18. Agonist Dynamics and Conformational Selection during Microsecond Simulations of the A2A Adenosine Receptor

    PubMed Central

    Lee, Ji Young; Lyman, Edward

    2012-01-01

    The G-protein-coupled receptors (GPCRs) are a ubiquitous family of signaling proteins of exceptional pharmacological importance. The recent publication of structures of several GPCRs cocrystallized with ligands of differing activity offers a unique opportunity to gain insight into their function. To that end, we performed microsecond-timescale simulations of the A2A adenosine receptor bound to either of two agonists, adenosine or UK432097. Our data suggest that adenosine is highly dynamic when bound to A2A, in stark contrast to the case with UK432097. Remarkably, adenosine finds an alternate binding pose in which the ligand is inverted relative to the crystal structure, forming relatively stable interactions with helices I and II. Our observations suggest new experimental tests to validate our predictions and deepen our understanding of GPCR signaling. Overall, our data suggest an intriguing hypothesis: that the 100- to 1000-fold greater efficacy of UK432097 relative to adenosine arises because UK432097 stabilizes a much tighter neighborhood of active conformations, which manifests as a greater likelihood of G-protein activation per unit time. PMID:22824275

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  20. 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)

  1. 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.

  2. 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

  3. 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.

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

    PubMed

    Greene, Ernest

    2015-01-01

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

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

    PubMed

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

    2009-10-14

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

  7. 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.

  8. Evaluation of sub-microsecond recovery resonators for In Vivo Electron Paramagnetic Resonance Imaging

    PubMed Central

    F, Hyodo; S, Subramanian; N, Devasahayam; R, Murugesan; K, Matsumoto; JB, Mitchell; MC, Krishna

    2008-01-01

    Time-domain (TD) electron paramagnetic resonance (EPR) imaging at 300 MHz for in vivo applications requires resonators with recovery times less than 1 microsecond after pulsed excitation to reliably capture the rapidly decaying free induction decay (FID). In this study, we tested the suitability of the Litz foil coil resonator (LCR), commonly used in MRI, for in vivo EPR/EPRI applications in the TD mode and compared with parallel coil resonator (PCR). In TD mode, the sensitivity of LCR was lower than that of the PCR. However, in continuous wave (CW) mode, the LCR showed better sensitivity. The RF homogeneity was similar in both the resonators. The axis of the RF magnetic field is transverse to the cylindrical axis of the LCR, making the resonator and the magnet co-axial. Therefore, the loading of animals, and placing of the anesthesia nose cone and temperature monitors was more convenient in the LCR compared to the PCR whose axis is perpendicular to the magnet axis. PMID:18042414

  9. Structure identification methods for atomistic simulations of crystalline materials

    DOE PAGES

    Stukowski, Alexander

    2012-05-28

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

  10. Structure identification methods for atomistic simulations of crystalline materials

    NASA Astrophysics Data System (ADS)

    Stukowski, Alexander

    2012-06-01

    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.

  11. Atomistic simulations of grain and interphase boundary mobility

    NASA Astrophysics Data System (ADS)

    Hoyt, J. J.

    2014-04-01

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

  12. Atomistic Modeling of Mechanical Loss in Amorphous Oxides

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  13. Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

    PubMed Central

    2015-01-01

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

  14. 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.

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

    PubMed

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

    2010-08-27

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

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

    PubMed

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

    2014-05-06

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

  17. Electrocaloric effects in the lead-free Ba (Zr ,Ti )O3 relaxor ferroelectric from atomistic simulations

    NASA Astrophysics Data System (ADS)

    Jiang, Zhijun; Prokhorenko, Sergei; Prosandeev, Sergey; Nahas, Y.; Wang, D.; Íñiguez, Jorge; Defay, E.; Bellaiche, L.

    2017-07-01

    Atomistic effective Hamiltonian simulations are used to investigate electrocaloric (EC) effects in the lead-free Ba (Zr0.5Ti0.5)O3 (BZT) relaxor ferroelectric. We find that the EC coefficient varies nonmonotonically with the field at any temperature, presenting a maximum that can be traced back to the behavior of BZT's polar nanoregions. We also introduce a simple Landau-based model that reproduces the EC behavior of BZT as a function of field and temperature, and which is directly applicable to other compounds. Finally, we confirm that, for low temperatures (i.e., in nonergodic conditions), the usual indirect approach to measure the EC response provides an estimate that differs quantitatively from a direct evaluation of the field-induced temperature change.

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

    DOE PAGES

    Taylor, Christopher D.

    2012-01-01

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

  19. 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.

  20. Using Multiorder Time-Correlation Functions (TCFs) To Elucidate Biomolecular Reaction Pathways from Microsecond Single-Molecule Fluorescence Experiments.

    PubMed

    Phelps, Carey; Israels, Brett; Marsh, Morgan C; von Hippel, Peter H; Marcus, Andrew H

    2016-12-29

    Recent advances in single-molecule fluorescence imaging have made it possible to perform measurements on microsecond time scales. Such experiments have the potential to reveal detailed information about the conformational changes in biological macromolecules, including the reaction pathways and dynamics of the rearrangements involved in processes, such as sequence-specific DNA "breathing" and the assembly of protein-nucleic acid complexes. Because microsecond-resolved single-molecule trajectories often involve "sparse" data, that is, they contain relatively few data points per unit time, they cannot be easily analyzed using the standard protocols that were developed for single-molecule experiments carried out with tens-of-millisecond time resolution and high "data density." Here, we describe a generalized approach, based on time-correlation functions, to obtain kinetic information from microsecond-resolved single-molecule fluorescence measurements. This approach can be used to identify short-lived intermediates that lie on reaction pathways connecting relatively long-lived reactant and product states. As a concrete illustration of the potential of this methodology for analyzing specific macromolecular systems, we accompany the theoretical presentation with the description of a specific biologically relevant example drawn from studies of reaction mechanisms of the assembly of the single-stranded DNA binding protein of the T4 bacteriophage replication complex onto a model DNA replication fork.

  1. 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.

  2. Atomistic Simulation of High-Density Uranium Fuels

    DOE PAGES

    Garcés, Jorge Eduardo; Bozzolo, Guillermo

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  4. Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Zavadlav, Julija; Praprotnik, Matej

    2017-09-01

    Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.

  5. Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics.

    PubMed

    Zavadlav, Julija; Praprotnik, Matej

    2017-09-21

    Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.

  6. Concurrent atomistic-continuum simulation of polycrystalline strontium titanate

    NASA Astrophysics Data System (ADS)

    Yang, Shengfeng; Zhang, Ning; Chen, Youping

    2015-08-01

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

  7. Heterogeneous Atomistic-Continuum Methods for Dense Fluid Systems

    NASA Astrophysics Data System (ADS)

    Hadjiconstantinou, Nicolas; Patera, Anthony

    1997-08-01

    We present new results obtained using the formulation and numerical solution procedure for heterogeneous atomistic--continuum representations of fluid flows presented in [1]. The ingredients are, from the atomistic side, non-equilibrium molecular dynamics, and from the continuum side, finite element solution; the matching is provided by a classical procedure, the Schwarz alternating method with overlapping subdomains. The technique is applied to the flow of two immiscible fluids in a microscale channel. The problem "presents" a particular modelling challenge because of the stress singularity at the moving contact line which is usually relieved through ad hoc methods, the most popular of which is the assumption of slip close to the contact line. The Heterogeneous method properly addresses the problem by treating the region near the contact line with molecular dynamics. References 1. Hadjiconstantinou N., Patera, A.T., Proceedings of the Sixth International Conference on Discrete Models for Fluid Mechanics, To appear as a special edition of the International Journal of Modern Physics C.

  8. 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.

  9. Coarse graining atomistic simulations of plastically deforming amorphous solids

    NASA Astrophysics Data System (ADS)

    Hinkle, Adam R.; Rycroft, Chris H.; Shields, Michael D.; Falk, Michael L.

    2017-05-01

    The primary mode of failure in disordered solids results from the formation and persistence of highly localized regions of large plastic strains known as shear bands. Continuum-level field theories capable of predicting this mechanical response rely upon an accurate representation of the initial and evolving states of the amorphous structure. We perform molecular dynamics simulations of a metallic glass and propose a methodology for coarse graining discrete, atomistic quantities, such as the potential energies of the elemental constituents. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. A signal-to-noise ratio provides a means of evaluating the strength of the signal of the shear band as a function of the coarse graining. Finally, we investigate the effect of different coarse graining length scales by comparing a two-dimensional, numerical implementation of the effective-temperature description in the shear transformation zone (STZ) theory with direct molecular dynamics simulations. These comparisons indicate the coarse graining length scale has a lower bound, above which there is a high level of agreement between the atomistics and the STZ theory, and below which the concept of effective temperature breaks down.

  10. 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.

  11. Atomistic simulation of ion beam patterning with crater functions

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

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

    PubMed

    Konuk, Mine; Durukanoğlu, Sondan

    2016-01-21

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

  13. 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.

  14. 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.

  15. Quantum transport in RTD and atomistic modeling of nanostructures

    NASA Astrophysics Data System (ADS)

    Jiang, Zhengping

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

  16. 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

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

    PubMed

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

    2013-02-01

    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.

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

    PubMed

    Rajabi, Khadijeh

    2015-02-07

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

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

    PubMed

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

    2016-05-03

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

  20. 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.

  1. 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

  2. Time-resolved polarization study of anisotropy in bacteriorhodopsin

    SciTech Connect

    Wan, Chaozhi; Qian, Jun; Johnson, C.K. )

    1990-11-01

    Time-resolved polarization spectroscopy is sensitive to the orientational dynamics of chromophores, and as a result it can be applied to study internal motion in restrictive environments. This paper describes the application of polarization spectroscopy to the photoactive protein bacteriorhodopsin on time scales from picoseconds to hundreds of microseconds. Anisotropy persists in both the ground-state bacteriorhodopsin population and in the photocycle intermediates due to a population bottleneck in the bacteriorhodopsin photocycle. The time dependence of the polarization signal expected for a sequence of intermediates is described and is shown to be sensitive both to population kinetics and to internal motion. The observed time dependence of the polarization signal reveals internal motion in the purple membrane fragments on the time scale of the K {yields} L transition ({approximately} 1 {mu}s). The results are consistent with the known kinetics of the bacteriorhodopsin photocycle. Evidence is also presented and discussed for a decay component on a time scale of < 50 ps.

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

    NASA Astrophysics Data System (ADS)

    Khorshidi, Alireza; Peterson, Andrew A.

    2016-10-01

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

  4. A computational atomistic model of radiation damage to DNA

    NASA Astrophysics Data System (ADS)

    Aydogan, Bulent

    A review of past and current biophysical models of DNA damage reveals that current DNA damage models have become increasingly complex in their attempts to model the full 3D structure of the nucleosome and chromatin fiber. As such, many of the finer details of direct, quasi-direct, and indirect action on DNA become difficult to study in isolation. Also, experimental comparisons that seek to validate these models become increasingly difficult to make. A better approach may be to perform the atomistic modeling of direct, indirect, and quasi-direct effects in total isolation from considerations of the macroscopic conformation of the DNA target. This would permit the highly detailed atomistic modeling to be performed only once in order to produce a database of outcome probabilities that can then be used in radiation chemistry modeling of different and more complex conformations of double-stranded DNA. This work is performed to establish the groundwork to accomplish this goal. A system of Monte Carlo computer codes that model radiation damage to DNA at the atomistic level is developed and used to predict the radiation damage to a 167-bp DNA molecule. A database of the OOH attack outcomes is generated for a 167-bp DNA molecule and used in the prediction of radiation-induced damage to DNA. Do (the dose required to create, on average, one single strand break per 167-bp DNA molecule) is calculated to be 69.9 Gy. There are no experimental study found in the literature that studied small DNA molecules like the one used in this study. Nevertheless, the results from this computational study can be compared to experimental studies preformed with larger DNA molecules such as plasmids when DNA concentrations are scaled. The `concentration scaled D0 (ssb)' values from Klimczak et al. [1993] and Tomita et al. [1998] were approximately 65 and 80 Gy, respectively. These experimental results compare favorably with the computational value of 69.9 Gy calculated in this study. With the

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

    NASA Astrophysics Data System (ADS)

    McCash, Kevin

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

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

    DOE PAGES

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

    2015-11-16

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

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

    SciTech Connect

    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.

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

    NASA Astrophysics Data System (ADS)

    Dupuis, A.; Koumoutsakos, P.

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

  9. Atomistic simulation of ferroelectric-ferroelastic gadolinium molybdate

    NASA Astrophysics Data System (ADS)

    Dudnikova, V. B.; Zharikov, E. V.

    2017-05-01

    Gadolinium molybdate Gd2(MoO4)3 orthorhombic ferroelectric ferroelastic (β'-phase) is simulated by the method of interatomic potentials. The simulation is performed using the GULP 4.0.1 code (General Utility Lattice Program), which is based on the minimization of the energy of the crystal structure. Parameters of the gadolinium-oxygen interatomic interaction potentials are determined by fitting to the experimental structural data and elastic constants by a procedure available in the GULP code. Atomistic modeling using the effective atomic charges and the system of interatomic potentials made it possible to obtain reasonable estimates of structural parameters, atomic coordinates, and the most important physical, mechanical, and thermodynamic properties of these crystals. Temperature dependences of the heat capacity and vibrational entropy of the crystal are obtained. The calculated parameters of gadolinium-oxygen interaction potentials can be used to simulate more complex gadolinium-containing compounds.

  10. Atomistic design of semiconductor nanostructures with optimal thermoelectric properties

    NASA Astrophysics Data System (ADS)

    Galli, Giulia

    2008-03-01

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

  11. Diffusion in energy materials: Governing dynamics from atomistic modelling

    NASA Astrophysics Data System (ADS)

    Parfitt, D.; Kordatos, A.; Filippatos, P. P.; Chroneos, A.

    2017-09-01

    Understanding diffusion in energy materials is critical to optimising the performance of solid oxide fuel cells (SOFCs) and batteries both of which are of great technological interest as they offer high efficiency for cleaner energy conversion and storage. In the present review, we highlight the insights offered by atomistic modelling of the ionic diffusion mechanisms in SOFCs and batteries and how the growing predictive capability of high-throughput modelling, together with our new ability to control compositions and microstructures, will produce advanced materials that are designed rather than chosen for a given application. The first part of the review focuses on the oxygen diffusion mechanisms in cathode and electrolyte materials for SOFCs and in particular, doped ceria and perovskite-related phases with anisotropic structures. The second part focuses on disordered oxides and two-dimensional materials as these are very promising systems for battery applications.

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

    NASA Astrophysics Data System (ADS)

    Nakano, Aiichiro

    2007-02-01

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

  13. 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.

  14. Reaction pathways in atomistic models of thin film growth

    NASA Astrophysics Data System (ADS)

    Lloyd, Adam L.; Zhou, Ying; Yu, Miao; Scott, Chris; Smith, Roger; Kenny, Steven D.

    2017-10-01

    The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides.

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

    PubMed

    Chen, Jie; Zhang, Gang; Li, Baowen

    2012-06-13

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

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

    PubMed

    Dapp, Wolf B; Müser, Martin H

    2013-08-14

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

  17. Atomistic simulations of grain boundary migration in copper

    NASA Astrophysics Data System (ADS)

    Schönfelder, B.; Gottstein, G.; Shvindlerman, L. S.

    2006-06-01

    While the motion of twist boundaries can be readily studied by atomistic simulations with molecular dynamics (MD) under the action of an elastic driving force, the approach fails for tilt boundaries. This is due to the interaction of the elastic stress with the grain boundary (GB) structure, which causes plastic strain by GB sliding. A novel concept, the orientation correlated driving force, is introduced to circumvent this problem. It is shown that this concept can be successfully applied to the study of the migration of tilt boundaries. The migration behavior of several twist and tilt GBs was investigated. The transition from low-to high-angle boundaries can be captured, and a structural transition of tilt boundaries was found at high temperatures, which also affected the migration behavior. The results compare well with experimental results of the motion high-angle boundaries, but for low-angle boundaries, the agreement is poor.

  18. 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.

  19. Atomistic modeling of dislocation interactions with twin boundaries in Ti

    NASA Astrophysics Data System (ADS)

    Hooshmand, M. S.; Mills, M. J.; Ghazisaeidi, M.

    2017-06-01

    Dislocation/boundary interactions play a prominent role in mechanical properties and plastic deformation of materials. We study the interaction between prismatic screw < a> , prismatic edge < c> and pyramidal mixed < c+a> dislocations with (\\bar{1}011) and (\\bar{1}013) twin boundaries in titanium using atomistic simulations. Details of the dislocation reactions depend on the slip system, atomic structure of boundary and stress/strain states. All interactions lead to nucleation of twinning dislocations on both twin boundaries, confirming that the interaction with incoming dislocations is a twin growth mechanism. In addition, dissociation of < c> and < c+a> dislocations on the (\\bar{1}013) results in nucleation of a (\\bar{1}012) (tension twin) embryo in the second grain-a new twin nucleation mechanism for (\\bar{1}012) twins as a result of < c> and < c+a> slip.

  20. 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.

  1. Nanoscale structure and morphology of sulfonated polyphenylenes via atomistic simulations

    DOE PAGES

    Abbott, Lauren J.; Frischknecht, Amalie L.

    2017-01-23

    We performed atomistic simulations on a series of sulfonated polyphenylenes systematically varying the degree of sulfonation and water content to determine their effect on the nanoscale structure, particularly for the hydrophilic domains formed by the ionic groups and water molecules. We found that the local structure around the ionic groups depended on the sulfonation and hydration levels, with the sulfonate groups and hydronium ions less strongly coupled at higher water contents. In addition, we characterized the morphology of the ionic domains employing two complementary clustering algorithms. At low sulfonation and hydration levels, clusters were more elongated in shape and poorlymore » connected throughout the system. As the degree of sulfonation and water content were increased, the clusters became more spherical, and a fully percolated ionic domain was formed. As a result, these structural details have important implications for ion transport.« less

  2. Atomistic simulations for multiscale modeling in bcc metal

    SciTech Connect

    Belak, J.; Moriarty, J.A.; Soderlind, P.; Xu, W.; Yang, L.H.; Zhu

    1998-09-25

    Quantum-based atomistic simulations are being used to study fundamental deformation and defect properties relevant to the multiscale modeling of plasticity in bcc metals at both ambient and extreme conditions. Ab initio electronic-structure calculations on the elastic and ideal-strength properties of Ta and Mo help constrain and validate many-body interatomic potentials used to study grain boundaries and dislocations. The predicted C(capital Sigma)5 (310)[100] grain boundary structure for Mo has recently been confirmed in HREM measurements. The core structure, (small gamma) surfaces, Peierls stress, and kink-pair formation energies associated with the motion of a/2(111) screw dislocations in Ta and Mo have also been calculated. Dislocation mobility and dislocation junction formation and breaking are currently under investigation.

  3. 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.

  4. Atomistic molecular dynamics simulations of model C36 fullerite

    NASA Astrophysics Data System (ADS)

    Abramo, Maria C.; Caccamo, C.

    2008-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Mackenchery, Karoon; Dongare, Avinash

    2017-01-01

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

  6. Atomistic modeling of ion implantation technologies in silicon

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  7. Intrinsic electrocaloric effect in ferroelectric alloys from atomistic simulations

    NASA Astrophysics Data System (ADS)

    Lisenkov, S.; Ponomareva, I.

    2009-10-01

    Electrocaloric effect (ECE) in (Ba0.5Sr0.5)TiO3 ferroelectric alloys is calculated from first principles using a computational scheme that combines canonical and microcanonical Monte Carlo simulations. Our results are in very good agreement with the available experimental data and reveal many intriguing features of ECE including; (i) a significant enhancement of the ECE in paraelectric phase, (ii) nearly linear reversible temperature change associated with the electric field variation up to extremely large fields and, (iii) a possibility of achieving large ECE at room temperatures. Our atomistic insight suggests that in ferroelectrics ECE is caused by the redistribution of the entropy between the part associated with the dipoles’ order and the part associated with the order in the kinetic energies of atomic vibrations. This mechanism can also be viewed as a “conversion” of spatially inhomogeneous dipole distribution into spatially inhomogeneous temperature distribution.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  9. STROBE-X: X-Ray Timing Spectroscopy on Dynamical Timescales from Microseconds to Years

    NASA Technical Reports Server (NTRS)

    Wilson-Hodge, Colleen A.; Ray, P. S.; Gendreau, K.; Arzoumanian, Z.; Chakrabarty, D.; Remillard, R.; Feroci, M.; Maccarone, T.; Wood, K.; Jenke, P.

    2017-01-01

    We describe a probe-class mission concept that provides an unprecedented view of the X-ray sky, performing timing and 0.2-30 keV spectroscopy over timescales from microseconds to years. The Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X) comprises three primary instruments. The first uses an array of lightweight optics (3-m focal length) that concentrate incident photons onto solid state detectors with CCD-level (85-130 eV) energy resolution, 100 ns time resolution, and low background rates to cover the 0.2-12 keV band. This technology is scaled up from NICER, with enhanced optics to take advantage of the longer focal length of STROBE-X. The second uses large-area collimated silicon drift detectors, developed for ESA's LOFT, to cover the 2-30 keV band. These two instruments each provide an order of magnitude improvement in effective area compared with its predecessor (NICER and RXTE, respectively). Finally, a sensitive sky monitor triggers pointed observations, provides high duty cycle, high time resolution, high spectral resolution monitoring of the X-ray sky with approx. 20 times the sensitivity of the RXTE ASM, and enables multi-wavelength and multi-messenger studies on a continuous, rather than scanning basis.For the first time, the broad coverage provides simultaneous study of thermal components, non-thermal components, iron lines, and reflection features from a single platform for accreting black holes at all scales. The enormous collecting area allows detailed studies of the dense matter equation of state using both thermal emission from rotation-powered pulsars and harder emission from X-ray burst oscillations. The combination of the wide-field monitor and the sensitive pointed instruments enables observations of potential electromagnetic counterparts to LIGO and neutrino events. Additional extragalactic science, such as high quality spectroscopy of clusters of galaxies and unprecedented timing investigations of active

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

    NASA Astrophysics Data System (ADS)

    Wilson-Hodge, Colleen A.; Ray, Paul S.; Gendreau, Keith; Chakrabarty, Deepto; Feroci, Marco; Maccarone, Thomas J.; Arzoumanian, Zaven; Remillard, Ronald A.; Wood, Kent; Griffith, Christopher; Jenke, Peter

    2017-08-01

    We describe a probe-class mission concept that provides an unprecedented view of the X-ray sky, performing timing and 0.2-30 keV spectroscopy over timescales from microseconds to years. The Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X) comprises three primary instruments. The first uses an array of lightweight optics (3-m focal length) that concentrate incident photons onto solid state detectors with CCD-level (85-130 eV) energy resolution, 100 ns time resolution, and low background rates to cover the 0.2-12 keV band. This technology is scaled up from NICER, with enhanced optics to take advantage of the longer focal length of STROBE-X. The second uses large-area collimated silicon drift detectors, developed for ESA's LOFT, to cover the 2-30 keV band. These two instruments each provide an order of magnitude improvement in effective area compared with its predecessor (NICER and RXTE, respectively). Finally, a sensitive sky monitor triggers pointed observations, provides high duty cycle, high time resolution, high spectral resolution monitoring of the X-ray sky with ~20 times the sensitivity of the RXTE ASM, and enables multi-wavelength and multi-messenger studies on a continuous, rather than scanning basis.For the first time, the broad coverage provides simultaneous study of thermal components, non-thermal components, iron lines, and reflection features from a single platform for accreting black holes at all scales. The enormous collecting area allows detailed studies of the dense matter equation of state using both thermal emission from rotation-powered pulsars and harder emission from X-ray burst oscillations. The combination of the wide-field monitor and the sensitive pointed instruments enables observations of potential electromagnetic counterparts to LIGO and neutrino events. Additional extragalactic science, such as high quality spectroscopy of clusters of galaxies and unprecedented timing investigations of active galactic

  11. 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.

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

    SciTech Connect

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

    2016-06-07

    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.

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

    PubMed

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

    2016-08-09

    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

  14. Atomistic and multiscale analyses of brittle fracture in crystal lattices

    NASA Astrophysics Data System (ADS)

    Zhang, Sulin; Zhu, Ting; Belytschko, Ted

    2007-09-01

    Applicability of the Griffith criterion [A. A. Griffith, Philos. Trans. R. Soc. London, Ser. 221, 163 (1920); S. Zhang, S. L. Meilke, R. Khare, D. Troya, R. S. Ruoff, G. C. Schatz, and T. Belytschko, Phys. Rev. B 71, 115403 (2005)] for predicting the onset of crack extension in crystal lattices is systematically evaluated using atomistic and multiscale simulations with a focus on the effects of crack size and lattice discreteness. An atomistic scheme is developed to determine the true Griffith load defined by the thermodynamic energy balance of crack extension for both finite-sized and semi-infinite crack models. For a model monolayer lattice, we identify a characteristic crack length (about ten lattice spacings) below which the Griffith fracture stress markedly overestimates the true Griffith load. Through a stability analysis of crack-tip bond separation, the athermal (nonthermally activated) loads of instantaneous fracture are determined, thereby yielding the estimated lattice trapping range. Our simulations show that the strength of lattice trapping depends on the interaction range of the interatomic force fields. Using the reaction pathway exploration method, we determine the minimum energy paths of bond breaking and healing at a crack tip, giving a more precise estimate of the lattice trapping range. The activation energy barriers governing the rate of kinetic crack extension are extracted from the minimum energy paths. Implications concerning the distinction between the athermal and Griffith fracture loads are discussed. Based on these results, a general criterion is established to predict the onset of crack growth in crystal lattices. In addition to taking into account the lattice trapping effect, this criterion is applicable to a large spectrum of crack sizes.

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

    NASA Astrophysics Data System (ADS)

    Aghaei Anvigh, Samira

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

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

    NASA Astrophysics Data System (ADS)

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

    1995-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-07-01

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

  18. 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.

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

    PubMed

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

    2002-11-08

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

  20. 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.

  1. Sub-microsecond vapor plume dynamics under different keyhole penetration regimes in deep penetration laser welding

    NASA Astrophysics Data System (ADS)

    Chen, Xin; Pang, Shengyong; Shao, Xinyu; Wang, Chunming; Zhang, Xiaosi; Jiang, Ping; Xiao, Jianzhong

    2017-05-01

    It is well-known that distinct vapor plume dynamics occur during deep penetration laser welding under different keyhole penetration states. However, there is little knowledge about the physical characteristics of vapor plumes (velocity, pressure, flow patterns, etc) located inside transient keyholes of varying penetration regimes in laser welding. This lack of knowledge is primarily because mesoscale vapor plumes are highly dynamic and generally invisible. Based on a well-tested three-dimensional multiphase laser welding model, we conducted a computational study on vapor plume dynamics inside transient keyholes during the fiber laser welding of 304 austenite stainless steel as a function of keyhole penetration regimes. We observed three keyhole regimes of penetration: full penetration, partial penetration and no penetration. We then physically analyzed the vapor plumes in these regimes. We determined that the vapor plume velocities and pressures in all three regimes were uneven and oscillated following the dynamic keyhole with a characteristic timescale in sub-microseconds. Only when the keyhole approached the full penetration regime did vapor plumes begin to violently eject from the bottom of the keyhole opening, whereas in the partial penetration regime, even when the bottom part of the keyhole was open, most of the vapor plume ejected from the upper keyhole opening. This latter observation was similar to that in the no penetration mode. We studied the physical mechanism of this behavior by analyzing the keyhole temperature and vapor plume velocity distributions. We determined that the upward ejection of the vapor plume from the upper keyhole opening was the result of an uneven micro-meter scale boiling phenomenon of the transient keyhole governed by Fresnel absorptions dependent on the local inclination angle of the keyhole wall. Similarly, we determined that the ejection of the vapor plume from the bottom of the keyhole opening resulted from pressure

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

    DOE PAGES

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

    2015-08-11

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

  3. A new REBO potential based atomistic structural model for graphene sheets.

    PubMed

    Shakouri, A; Ng, T Y; Lin, R M

    2011-07-22

    A new atomistic structural model is developed here for graphene sheets based on the stiffnesses from the REBO potential. Using this model, the flexural vibration natural frequencies and buckling loads of rectangular single-layer graphene sheets of different sizes, chiralities and boundary conditions are calculated. The newly developed atomistic structural model is verified by comparing the calculated fundamental natural frequencies for small-sized graphene sheets with those obtained from ab initio density functional theory (DFT) frequency analysis. The vibration and buckling analysis results are also compared with those of an earlier atomistic structural model based on the AMBER potential as well as the equivalent continuum model for graphene sheets. Through this study, it is observed that graphene sheets display very slight anisotropic characteristics in flexural vibration and buckling. Also, it is shown that the atomistic structural model cannot be replaced by a classical equivalent continuum model such as a plate model. Most significantly, we verify that the new atomistic structural model based on the REBO potential predicts more accurate natural frequencies and buckling loads for graphene sheets, which are considerably lower than those predicted by the earlier atomistic structural model based on the AMBER potential.

  4. 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.

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

    PubMed Central

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

    2014-01-01

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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. The use of the 300 microsecond 1064 nm Nd:YAG laser in the treatment of keloids.

    PubMed

    Rossi, Anthony; Lu, Rebecca; Frey, Melissa K; Kubota, Takako; Smith, Lauren A; Perez, Maritza

    2013-11-01

    Keloids can be quite resistant to conventional methods of treatment. A wide range of treatment modalities exists, often with suboptimal results, recurrences, and adverse events occurring. Laser therapy with the carbon dioxide, erbium:YAG, Q switched frequency doubled neodymium-doped yttrium aluminium garnet (Nd:YAG), and 585/595 nm pulsed dye lasers have all be purported as potential treatment modalities however with limited efficacy and data especially in the skin of color population is limited. We report the successful use of the 300 microsecond 1064 nm Nd:YAG laser in treating keloids in patients with skin types ranging from Fitzpatrick I through VI with special attention in treating skin of color patients. We examined the use of the 300 microsecond 1064 nanometer (nm) Nd:YAG laser for the treatment keloids in patients with skin types ranging from Fitzpatrick I through VI. A retrospective analysis of treatment efficacy was conducted on 44 patients with keloids. Three separate treatment groups were compared. The groups consisted of: a "control group" in which the whole keloid was only treated with intralesional corticosteroid (triamcinolone 10 mg/cc) (16 patients); a "laser only" group in which the patient's keloid was only treated with the 1064 nm Nd:YAG laser at a fluency of 13 to 18 Joules / centimeter2 (J/cm2), a fixed pulse duration of 300 microseconds, 5 mm spot size, and a total of 2000 pulses (14 patients); and a "combination group" that received both the aforementioned laser therapy and adjuvant intralesional triamcinolone (14 patients). Patients in the "combination group" treated with the 300 microsecond 1064 nm Nd:YAG laser therapy plus intralesional corticosteroid and the "laser only" group both were observed to have durable clinical reduction in the thickness and erythema of the keloids. These results were shown to be superior to the "control group" whom were only treated with intralesional corticosteroids. Only mild and transient post treatment

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

    PubMed

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

    2015-04-14

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

  14. 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. Polar Bear

    USGS Publications Warehouse

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

    1988-01-01

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

  16. Macrophage Polarization.

    PubMed

    Murray, Peter J

    2017-02-10

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

  17. 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.

  18. 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.

  19. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

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

    2017-02-16

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

  20. 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.

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

    DOE PAGES

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

    2015-01-08

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

  2. Compression deformation of WC - atomistic description of hard ceramic material.

    PubMed

    Feng, Qing; Song, Xiaoyan; Liu, Xuemei; Liang, Shuhua; Wang, Haibin; Nie, Zuoren

    2017-10-10

    The deformation characteristics of WC, as a typical hard ceramic material, were studied on the nanoscale by atomistic simulations for both single-crystal and polycrystalline under uniaxial compression. The effects of crystallographic orientation, grain boundary coordination and grain size on the origin of deformation were particularly investigated. The single-crystal and polycrystalline WC exhibit strong orientation dependence of the deformation behavior. The grain boundaries play a significant role in deformation coordination and potential high fracture toughness of the nanocrystalline WC. In contrast to conventional knowledge of ceramics, a maximum strength has been obtained at a critical grain size corresponding to the turn point from Hall-Petch to inverse Hall-Petch relationship. For this the mechanisms of a combined effect of dislocations motion within grains and coordination of stress concentration at grain boundaries were proposed. The present work moved forward understanding of the plastic deformability and possibility to achieve high strength of the nanocrystalline ceramic materials. © 2017 IOP Publishing Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Baetzold, Roger C.

    1987-12-01

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

  5. 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.

  6. 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.

  7. 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

    2015-03-01

    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 multi-scale 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 island size beyond which nucleation of the second layer will take place. Intriguingly, the critical size exhibits an effective inverse ``Ehrlich-Schwoebel barrier'' effect. These findings allow us to propose a novel alternating growth scheme to realize mass production of bilayer graphene. Supported by USNSF, USDOE, and NNSF of China.

  8. Dislocation climb models from atomistic scheme to dislocation dynamics

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  9. Atomistic calculations of dislocation core energy in aluminium

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  10. 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

  11. 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.

  12. Atomistic modeling of phonon transport in turbostratic graphitic structures

    SciTech Connect

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

    2016-05-28

    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{sup −10} K m{sup 2}/W to 116 × 10{sup −10} K m{sup 2}/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.

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

    PubMed

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

    2013-05-09

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

  14. 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.

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

    PubMed

    Plattner, Nuria; Meuwly, Markus

    2008-06-23

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

  16. 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.

  17. Quantifying grain boundary damage tolerance with atomistic simulations

    NASA Astrophysics Data System (ADS)

    Foley, Daniel; Tucker, Garritt J.

    2016-10-01

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

  18. 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.

  19. 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.

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

    PubMed

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

    2008-08-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  2. Atomistic calculations of dislocation core energy in aluminium

    DOE PAGES

    Zhou, Xiaowang W.; Sills, Ryan B.; Ward, Donald K.; ...

    2017-02-16

    A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy:more » Ec = Asin2β + Bcos2β, and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. As a result, with our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.« less

  3. 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.

  4. 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.

  5. Polar Bears

    USGS Publications Warehouse

    Amstrup, Steven C.; Douglas, David C.; Reynolds, Patricia E.; Rhode, E.B.

    2002-01-01

    Polar bears (Ursus maritimus) are hunted throughout most of their range. In addition to hunting polar bears of the Beaufort Sea region are exposed to mineral and petroleum extraction and related human activities such as shipping road-building, and seismic testing (Stirling 1990).Little was known at the start of this project about how polar bears move about in their environment, and although it was understood that many bears travel across political borders, the boundaries of populations had not been delineated (Amstrup 1986, Amstrup et al. 1986, Amstrup and DeMaster 1988, Garner et al. 1994, Amstrup 1995, Amstrup et al. 1995, Amstrup 2000).As human populations increase and demands for polar bears and other arctic resources escalate, managers must know the sizes and distributions of the polar bear populations. Resource managers also need reliable estimates of breeding rates, reproductive intervals, litter sizes, and survival of young and adults.Our objectives for this research were 1) to determine the seasonal and annual movements of polar bears in the Beaufort Sea, 2) to define the boundaries of the population(s) using this region, 3) to determine the size and status of the Beaufort Sea polar bear population, and 4) to establish reproduction and survival rates (Amstrup 2000).

  6. 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.

  7. 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

  8. Cross-relaxation in nuclear polarization. A flash-CIDNP study

    NASA Astrophysics Data System (ADS)

    Yurkovskaya, A. V.; Tsentalovich, Yu. P.; Sagdeev, R. Z.

    1990-08-01

    CIDNP with microsecond time resolution was used to study the kinetics of nuclear polarization formation during the photolysis of acetone in isopropanol over a wide temperature range. The coincidence of signs of multiplet effects of CIDNP (A/E) for cage and escape reaction products as well as the presence of net polarization (E) changing its sign with decreasing temperature have been revealed. The account of scalar electron-nuclear cross-relaxation has been shown to be necessary for the interpretation of the results obtained.

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

    PubMed

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

    2015-04-23

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

  10. Polar Plumage

    NASA Image and Video Library

    2006-05-08

    This Mars MOC image shows dunes in the north polar region of Mars covered by a layer of carbon dioxide frost that accumulated during the winter in 2005. Dark spots indicate areas where frost has begun to sublime away

  11. Polar Dunes

    NASA Image and Video Library

    2010-09-27

    By high summer, the extensive dune fields of the north polar region are completely defrosted and the number and variety of dunes are readily visible. This image was captured by NASA Mars Odyssey on August 31, 2010.

  12. Polar Cone

    NASA Image and Video Library

    2006-07-10

    This MOC image shows a cone-shaped hill, perhaps a remnant of a material that was once more laterally extensive across the area, on a textured plain in the Hyperboreus Labyrinthus region in the north polar region of Mars

  13. 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.

  14. Polar Clouds

    NASA Image and Video Library

    2012-02-27

    With the changing of seasons comes changes in weather. This image from NASA 2001 Mars Odyssey spacecraft shows clouds in the north polar region. The surface is just barely visible in part of the image.

  15. Accessing ultrashort reaction times in particle formation with SAXS experiments: ZnS precipitation on the microsecond time scale.

    PubMed

    Schmidt, Wolfgang; Bussian, Patrick; Lindén, Mika; Amenitsch, Heinz; Agren, Patrik; Tiemann, Michael; Schüth, Ferdi

    2010-05-19

    Precipitation of zinc sulfide particles is a very rapid process, and monitoring of the particle growth is experimentally very demanding. Applying a liquid jet flow cell, we were able to follow zinc sulfide particle formation on time scales down to 10(-5) s. The flow cell was designed in such a way that data acquisition on the microsecond time scale was possible under steady-state conditions along a liquid jet (tubular reactor concept), allowing SAXS data accumulation over a time scale of minutes. We were able to monitor the growth of zinc sulfide particles and found experimental evidence for very rapid particle aggregation processes within the liquid jet. Under the experimental conditions the particle growth is controlled by mass transfer: i.e., the diffusion of the hydrogen sulfide into the liquid jet.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  19. High average power and energy microsecond pulse generation from an erbium-doped fluoride fiber MOPA system.

    PubMed

    Luo, Hongyu; Li, Jianfneg; Xie, Jitao; Zhai, Bo; Wei, Chen; Liu, Yong

    2016-12-12

    We reported a high average power and energy microsecond pulse erbium-doped fluoride fiber MOPA system centered at 2786.8 nm. The master oscillator was a passively Q-switched erbium-doped fluoride fiber laser based on SESAM in a linear cavity. Then a one-stage erbium-doped fluoride fiber amplifier was used to boost its average output power to 4.2 W and pulse energy to 58.87 μJ. The pulse duration and repetition rate were 2.29 µs and 71.73 kHz, respectively. To the best of our knowledge, the achieved average output power and pulse energy are the recorded levels for the passively Q-switched fiber lasers at 3 μm wavelength region.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1995-08-01

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

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

    SciTech Connect

    Sheftman, D.; Krasik, Ya. E.

    2011-09-15

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

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

    NASA Astrophysics Data System (ADS)

    Sheftman, D.; Krasik, Ya. E.

    2011-09-01

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  6. 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

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

    PubMed

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

    2014-04-09

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

  8. Thermal effects on 3D crater shape during IR laser ablation of monocrystalline silicon: From femtoseconds to microseconds

    NASA Astrophysics Data System (ADS)

    Buratin, Stefano; Bashtova, Kateryna; Kong, Ming Chu

    2017-07-01

    Analyzing the thermal effects (e.g., heat affected zone and debris analysis) on a laser-ablated crater using electron or atomic force microscopy is a time-consuming process while optical microscopy is limited to providing 2D information. The current work details an alternative method to identify and quantify the thermal effects based on an analysis of the 3D shape of craters. Starting from a thermal diffusion model, an iso-thermal function was developed and an iso-energetic function was defined based on the energy beam distribution. A systematic study of the 3D craters ablated on silicon was carried out at the four temporal regimes that are applicable in the industry: the femtosecond regime at 330 fs, the picosecond regime at 10 ps, the nanosecond regime in the range of 25-220 ns, and the microsecond regime in the range of 2-20 μs. It was shown that the defined Percentage Difference (PD) between the residual sum of squares (RSS) of the ellipsoid function and the RSS of the paraboloid function against the experimental crater, respectively, can be used to evaluate the presence of thermal effects. This corresponded with the results obtained using scanning electron microscope analysis. The analysis of the PD indicated how the crater shape was affected by the pulse duration while the non-thermal/thermal cutoff starting from the ps regime was studied. In addition, the crater shape was found to be affected by the laser beam fluence: for time regimes below the microsecond level, the thermal effects were seen to increase with higher laser beam fluence.

  9. Atomistic Mechanisms for Viscoelastic Damping in Inorganic Solids

    NASA Astrophysics Data System (ADS)

    Ranganathan, Raghavan

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

  10. 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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  13. Hepatocyte Polarity

    PubMed Central

    Treyer, Aleksandr; Müsch, Anne

    2013-01-01

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

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

    PubMed

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

    2015-12-03

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

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

    NASA Astrophysics Data System (ADS)

    Ko, Won-Seok; Lee, Byeong-Joo

    2014-06-01

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

  16. Atomistic simulation of the growth of defect-free carbon nanotubes.

    PubMed

    Xu, Ziwei; Yan, Tianying; Ding, Feng

    2015-08-01

    Atomistic simulation of defect-free single-walled carbon nanotube (SWCNT) growth is essential for the insightful understanding of the SWCNT's growth mechanism. Despite the extensive effort paid in the past two decades, the goal has not been completely achieved, due to the huge timescale discrepancy between atomistic simulation and the experimental synthesis of SWCNTs, as well as the lack of an accurate classical potential energy surface for large scale simulation. Here, we report atomistic simulations of defect-free SWCNT growth by using a new generation of carbon-metal potential and a hybrid method, in which a basin-hopping strategy is applied to facilitate the defect healing during the simulation. The simulations reveal a narrow diameter distribution and an even chiral angle distribution of the growth of SWCNTs from liquid catalyst, which is in agreement with most known experimental observations.

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

    PubMed

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

    2005-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-06-01

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

  19. Directional melting of alumina via polarized microwave heating

    NASA Astrophysics Data System (ADS)

    Hu, Yuan; Nakano, Aiichiro; Wang, Joseph

    2017-01-01

    Dynamical instabilities and melting of crystals upon heating are fundamental problems in physics and materials science. Using molecular dynamics simulations, we found that drastically different melting temperatures and behaviors can be achieved in α-alumina using microwave heating, where the electric field is aligned with different crystallographic orientations. Namely, alumina melts much earlier at lower temperatures when the electric field is parallel to the c-axis. The atomistic mechanism was identified as selective liberation of the Al sublattice due to the shear instability along the c-axis. This directional melting concept may be used for triggering distinct dynamical instabilities and melting of dielectric crystals using polarized microwave fields.

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

    DOE PAGES

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

    2016-07-20

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

  1. 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.

  2. 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.

  3. Anisotropic solid-liquid interface kinetics in silicon: an atomistically informed phase-field model

    NASA Astrophysics Data System (ADS)

    Bergmann, S.; Albe, K.; Flegel, E.; Barragan-Yani, D. A.; Wagner, B.

    2017-09-01

    We present an atomistically informed parametrization of a phase-field model for describing the anisotropic mobility of liquid-solid interfaces in silicon. The model is derived from a consistent set of atomistic data and thus allows to directly link molecular dynamics and phase field simulations. Expressions for the free energy density, the interfacial energy and the temperature and orientation dependent interface mobility are systematically fitted to data from molecular dynamics simulations based on the Stillinger-Weber interatomic potential. The temperature-dependent interface velocity follows a Vogel-Fulcher type behavior and allows to properly account for the dynamics in the undercooled melt.

  4. Effects of atomistic defects on coherent electron transmission in Si nanowires: Full band calculations

    NASA Astrophysics Data System (ADS)

    Ko, Young-Jo; Shin, Mincheol; Lee, Seongjae; Park, Kyoung Wan

    2001-01-01

    The effects of atomistic imperfections on coherent electron transmission in Si[100] quantum wires a few nanometers wide are investigated using a tight-binding Green function approach. We find a significant suppression in the electron transmission by atomistic imperfections in these extremely narrow wires. Multiple conductance peaks or oscillations can be easily developed by the presence of only several vacancy defects, which can lead to a finite zero-conductance region around the subband edge. Several substitutional defects and surface dangling bonds generally result in decreased, oscillatory conductances with more significant effects found in narrower wires.

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

    NASA Astrophysics Data System (ADS)

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

    2005-02-01

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

  6. A multiscale approach to triglycerides simulations: from atomistic to coarse-grained models and back.

    PubMed

    Brasiello, Antonio; Crescitelli, Silvestro; Milano, Giuseppe

    2012-01-01

    The aim of this paper is to provide a simulation strategy to study the liquid-solid transition of triglycerides. The strategy is based on a multiscale approach. A coarse-grained model, parameterized on the basis of reference atomistic simulations, has been used to model the liquid-solid transition. A reverse mapping procedure has been proposed to reconstruct atomistic models from coarse-grained configurations and validated against experimental structural properties. The nucleation and growth of the crystalline order have been analysed in terms of several properties.

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

    SciTech Connect

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

    1990-05-22

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

  8. Glycan flexibility: insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect.

    PubMed

    Landström, Jens; Widmalm, Göran

    2010-01-26

    An atomistic all-atom molecular dynamics simulation of the trisaccharide beta-D-ManpNAc-(1-->4)[alpha-D-Glcp-(1-->3)]-alpha-L-Rhap-OMe with explicit solvent molecules has been carried out. The trisaccharide represents a model for the branching region of the O-chain polysaccharide of a strain from Aeromonas salmonicida. The extensive MD simulations having a 1-micros duration revealed a conformational dynamics process on the nanosecond time scale, that is, a 'time window' not extensively investigated for carbohydrates to date. The results obtained from the MD simulation underscore the predictive power of molecular simulations in studies of biomolecular systems and also explain an unusual nuclear Overhauser effect originating from conformational exchange. 2009 Elsevier Ltd. All rights reserved.

  9. 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.

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

    PubMed Central

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

    1998-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Norman, Paul Erik

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

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

    NASA Astrophysics Data System (ADS)

    Chopra, Irinder Singh

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

  13. 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

  14. Polarized Campuses.

    ERIC Educational Resources Information Center

    Parr, Susan Resneck

    1991-01-01

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

  15. 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.

  16. Polar Dune

    NASA Image and Video Library

    2009-07-01

    A large sand sheet with surface dune forms is located on the floor of this crater near the south pole. The polar cap rests against the southern part of the sand sheet. The dune appears bright in this daytime 2001 Mars Odyssey THEMIS IR image.

  17. 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

  18. 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.

  19. 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.

  20. Crystalline cellulose elastic modulus predicted by atomistic models of uniform deformation and nanoscale indentation

    Treesearch

    Xiawa Wu; Robert J. Moon; Ashlie Martini

    2013-01-01

    The elastic modulus of cellulose Iß in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive...

  1. 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.

  2. Literature review report on atomistic modeling tools for FeCrAl alloys

    SciTech Connect

    Yongfeng Zhang; Daniel Schwen; Enrique Martinez

    2015-12-01

    This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing for better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.

  3. 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.

  4. The microsecond 1064 nm Nd:YAG laser as an adjunct to improving surgical scars following Mohs micrographic surgery.

    PubMed

    Ezra, Navid; Arshanapalli, Ashish; Bednarek, Robert; Akaishi, Satoshi; Somani, Ally-Khan

    2016-08-01

    Scarring following skin surgery is an unavoidable certainty. Scars resulting from Mohs Micrographic Surgery (MMS) can cause both cosmetic and functional problems. Various lasers have been used to treat scars, but the role of the microsecond pulsed 1064 nanometer neodymium-doped yttrium aluminum garnet (1064 nm Nd:YAG) in treating surgical scars is not well-defined. We aim to examine the clinical application of the 1064 nm Nd:YAG laser in improving surgical scars. Ten patients who were unhappy with cosmetic or functional outcomes of their surgical scars following MMS were treated with 1-3 sessions of the 1064 nm Nd:YAG laser to improve their scars. Therapy completion was determined by patient satisfaction with the appearance of their scars and/or resolution of any contractures that formed following surgery. All ten patients were pleased with the improved appearance of their scars. Four patients saw complete resolution of an ectropion or eclabium that formed secondary to scar contractures from MMS. The side effects of laser treatments were limited to 1-2 hours of erythema, and there were no incidences of adverse effects or recurrence of contractures. Our clinical experience with the 1064 nm Nd:YAG laser provides promising data on improving appearance of and functionality from post-surgical scars.

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

    NASA Astrophysics Data System (ADS)

    Dobrynin, Danil

    2013-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    Ultra-small gadolinium oxide (Gd2O3) can be used as T1-weighted Magnetic Resonance Imaging (MRI) contrast agent own to its high longitudinal relaxivity (r1) and has attracted intensive attention in these years. In this paper, ultra-small Gd2O3 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 Gd2O3 by laser ablation in DEG. The r1 value and T1-weighted MR images are measured by a 3.0 T MRI spectroscope. The results show these nanoparticles with a high r1 value of 9.76 s-1 mM-1 to be good MRI contrast agents. We propose an explanation for the high r1 value of ultra-small Gd2O3 by considering the decreasing factor (surface to volume ratio of the nanoparticles, S/V) and the increasing factor (water hydration number of the Gd3+ on Gd2O3 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 Gd2O3 of high r1 value by laser ablation in DEG and develops the understanding of high relaxivity of ultra-small Gd2O3 MRI contrast agents.

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

    PubMed

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

    2017-02-09

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

  8. Microsecond Unfolding Kinetics of Sheep Prion Protein Reveals an Intermediate that Correlates with Susceptibility to Classical Scrapie

    PubMed Central

    Chen, Kai-Chun; Xu, Ming; Wedemeyer, William J.; Roder, Heinrich

    2011-01-01

    The microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94–233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfolding kinetics of ovPrP provides evidence for an intermediate species. However, in contrast to previous results for human PrP, there is no evidence for an intermediate under refolding conditions. Global analysis of the kinetic data, based on a sequential three-state mechanism, quantitatively accounts for all folding and unfolding data as a function of denaturant concentration. The simulations predict that an intermediate accumulates under both folding and unfolding conditions, but is observable only in unfolding experiments because the intermediate is optically indistinguishable from the native state. The relative population of intermediates in two ovPrP variants, both transiently and under destabilizing equilibrium conditions, correlates with their propensities for classical scrapie. The variant susceptible to classical scrapie has a larger population of the intermediate state than the resistant variant. Thus, the susceptible variant should be favored to undergo the PrPC to PrPSc conversion and oligomerization. PMID:21889460

  9. Broadband ultraviolet-visible transient absorption spectroscopy in the nanosecond to microsecond time domain with sub-nanosecond time resolution.

    PubMed

    Lang, Bernhard; Mosquera-Vázquez, Sandra; Lovy, Dominique; Sherin, Peter; Markovic, Vesna; Vauthey, Eric

    2013-07-01

    A combination of sub-nanosecond photoexcitation and femtosecond supercontinuum probing is used to extend femtosecond transient absorption spectroscopy into the nanosecond to microsecond time domain. Employing a passively Q-switched frequency tripled Nd:YAG laser and determining the jitter of the time delay between excitation and probe pulses with a high resolution time delay counter on a single-shot basis leads to a time resolution of 350 ps in picosecond excitation mode. The time overlap of almost an order of magnitude between fs and sub-ns excitation mode permits to extend ultrafast transient absorption (TA) experiments seamlessly into time ranges traditionally covered by laser flash photolysis. The broadband detection scheme eases the identification of intermediate reaction products which may remain undetected in single-wavelength detection flash photolysis arrangements. Single-shot referencing of the supercontinuum probe with two identical spectrometer/CCD arrangements yields an excellent signal-to-noise ratio for the so far investigated chromophores in short to moderate accumulation times.

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

    PubMed

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

    2012-10-28

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

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

    PubMed

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

    2014-04-05

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

  12. 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.

  13. 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

  14. Polar Diving

    NASA Technical Reports Server (NTRS)

    2006-01-01

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

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

  15. Polar Diving

    NASA Technical Reports Server (NTRS)

    2006-01-01

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

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

  16. Polar Textures

    NASA Image and Video Library

    2017-06-08

    This VIS image of the south pole was taken at the end of summer. Frost will soon start to form as the season transitions into fall. Fall in the southern hemisphere means spring in the northern, so the north polar cap is just starting to thaw. Orbit Number: 67893 Latitude: -87.0251 Longitude: 275.679 Instrument: VIS Captured: 2017-04-04 06:19 https://photojournal.jpl.nasa.gov/catalog/PIA21679

  17. 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

  18. 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.

  19. Electrocaloric effect in ferroelectric nanowires from atomistic simulations

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  20. 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

  1. Electrocaloric effect in ferroelectric nanowires from atomistic simulations.

    PubMed

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

    2015-11-27

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

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

    NASA Astrophysics Data System (ADS)

    Yinkai Lei

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

  3. 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.

  4. 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

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

    PubMed Central

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

    2014-01-01

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Photo absorption enhancement in strained silicon nanowires: An atomistic study

    NASA Astrophysics Data System (ADS)

    Shiri, Daryoush; Golam Rabbani, M.; Qi, Jianqing; Buin, Andrei K.; Anantram, M. P.

    2017-07-01

    The absorption spectra of silicon nanowires are calculated using semi-empirical sp3d5s* tight binding and Density Functional Theory methods. The roles of diameter, wave function symmetry, strain, and crystallographic direction in determining the absorption are discussed. We find that compressive strain can change the band edge absorption by more than one order of magnitude due to the change in wave function symmetry. In addition, photon polarization with respect to the nanowire axis significantly alters the band edge absorption. Overall, the band edge absorption of [110] and [100] silicon nanowires can differ by as much as three orders of magnitude. We find that compared to bulk Silicon, a strained Silicon nanowire array can absorb infrared photons (1.1 eV) approximately one hundred times better. Finally, we compare a fully numerical and a computationally efficient semi-analytical method, and find that they both yield satisfactory values of the band edge absorption.

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

    PubMed

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

    2001-08-20

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

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

    NASA Astrophysics Data System (ADS)

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

    2001-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2001-08-01

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

  15. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

    PubMed Central

    2016-01-01

    Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460

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

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

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

  17. 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.

  18. Polar Layers

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03581 Polar Layers

    This image shows just one example of the bright and dark markings that appear during summer time. The marks are related to the polar layers. If you happen to see a wild-eyed guy sticking his tongue out at you, you'll know why this image qualifies for the old 'art' category of THEMIS releases.

    Image information: VIS instrument. Latitude 80.6S, Longitude 34.1E. 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.

  19. Darcy-Weisbach friction factor at the nanoscale: From atomistic calculations to continuum models

    NASA Astrophysics Data System (ADS)

    Liakopoulos, A.; Sofos, F.; Karakasidis, T. E.

    2017-05-01

    A modification of the Darcy-Weisbach friction factor applicable to nanoscale liquid transport processes is proposed. Non-equilibrium molecular dynamics simulations allow us to access the atomic behaviour of liquids moving in nanochannels, and by comparing atomistic simulation results with continuum Navier-Stokes solutions, we extend the applicability of continuum theory to nanoscale liquid flows. We find that classical continuum theory predictions of power dissipation do not apply in the case of nanochannels and have to be modified accordingly with input from atomistic simulations such as slip velocity and profiles of variable viscosity. The mathematical form of the friction factor expression persists for quite small nanochannel widths, i.e., the form of the relation for the friction factor f Re = const. is practically maintained even at the nanoscale, but the value of the constant significantly increases with increasing hydrophilicity.

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

    PubMed

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

    2015-11-10

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

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

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    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.

  3. 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.

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Buerkle, Marius; Asai, Yoshihiro

    2017-02-01

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

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

    PubMed Central

    Buerkle, Marius; Asai, Yoshihiro

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  8. Modified NEGF method for atomistic modeling of field emission from carbon nanotube

    NASA Astrophysics Data System (ADS)

    Monshipouri, Mahta; Behrooz, Milad; Abdi, Yaser

    2017-09-01

    A model to simulate the atomistic properties of the field emission (FE) from a zigzag-single walled carbon nanotube (Z-SWCNT) is presented. By a modification of the self-energy in non-equilibrium Green's function (NEGF) method, we simulated the field emission current, considering the quantum transport of electrons within the CNT. The paper involves investigation on the effect of the n index of the (n , 0) Z-SWCNT and the number of carbon dimers in the length direction as well as the anode-cathode separation on the FE current. Effect of additional gate voltage and substitutional impurities on the FE current is also studied. A comparison between the experimental data and simulation results are also included in the paper. The model can be used to consider different quantum effects of the atomistic emitter structure on the FE current.

  9. Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.

    PubMed

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

    2015-05-01

    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. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. 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.

  11. Bipolar quantum corrections in resolving individual dopants in `atomistic' device simulation

    NASA Astrophysics Data System (ADS)

    Roy, Gareth; Brown, Andrew R.; Asenov, Asen; Roy, Scott

    2003-09-01

    In 'atomistic' device simulation the resolving of discrete charges onto a fine-grained simulation mesh can lead to problems. The sharply resolved Coloumb potential can cause simulation artefacts to appear in classical simulation environments using Boltzmann or Fermi-Dirac statistics. Various methods have been proposed in an effort to reduce or eliminate such artefacts as the localisation of mobile carriers by sharply resolved Coulomb wells, however they have met with limited success. In this paper we present an alternative approach for handling discrete charges in drift diffusion 'atomistic' simulations by properly introducing the related quantum mechanical effects using the density gradient formalism for both electrons and holes. This eliminates the trapping of mobile charge in heavily doped regions of the device and the related artefacts in the simulated device characteristics.

  12. 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.

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

    PubMed

    Pourali, Meisam; Meloni, Simone; Magaletti, Francesco; Maghari, Ali; 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.

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

    SciTech Connect

    Duchemin, Ivan; Donadio, Davide

    2011-09-15

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

  15. Atomistic insight into the non-classical nucleation mechanism during solidification in Ni

    NASA Astrophysics Data System (ADS)

    Díaz Leines, Grisell; Drautz, Ralf; Rogal, Jutta

    2017-04-01

    Nucleation is a key step during crystallization, but a complete understanding of the fundamental atomistic processes remains elusive. We investigate the mechanism of nucleation during solidification in nickel for various undercoolings using transition path sampling simulations. The temperature dependence of the free energy barriers and rate constants that we obtain is consistent with the predictions of classical nucleation theory and experiments. However, our analysis of the transition path ensemble reveals a mechanism that deviates from the classical picture of nucleation: the growing solid clusters have predominantly non-spherical shapes and consist of face-centered-cubic and random hexagonal-close-packed coordinated atoms surrounded by a cloud of prestructured liquid. The nucleation initiates in regions of supercooled liquid that are characterized by a high orientational order with structural features that predetermine the polymorph selection. These results provide atomistic insight not only into the nucleation mechanism of nickel but also into the role of the preordered liquid regions as precursors for crystallization.

  16. 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.

  17. Atomistic evaluation of the stress concentration factor of graphene sheets having circular holes

    NASA Astrophysics Data System (ADS)

    Jalali, S. K.; Beigrezaee, M. J.; Pugno, N. M.

    2017-09-01

    Stress concentration factor concept has been developed for single-layered graphene sheets (SLGSs) with circular holes through an atomistic point of view by the application of molecular structural mechanics (MSM) approach. In this approach the response of SLGSs against unidirectional tensile loading is matched to the response of a frame-like macro structure containing beam elements by making an equivalence between strain energies of beam elements in MSM and potential energies of chemical bonds of SLGSs. Both chirality and size effects are considered and the atomistic evaluation of stress concentration factor is performed for different sizes of circular holes. Also, molecular dynamics simulations are implemented to verify the existence and location of the predicted stress concentration. The results reveal that size effects and the diameters of circular holes have a significant influence on the stress concentration factor of SLGSs and armchair SLGSs show a larger value of stress concentration than zigzag ones.

  18. Atomistic Modeling of the Electrode–Electrolyte Interface in Li-Ion Energy Storage Systems: Electrolyte Structuring

    SciTech Connect

    Jorn, Ryan P.; Kumar, Revati; Abraham, Daniel P; Voth, Gregory A.

    2013-01-01

    The solid electrolyte interface (SEI) forms as a result of side reactions between the electrolyte and electrode surfaces in Li-ion batteries and can adversely impact performance by impeding Li-ion transport and diminishing the storage capacity of the battery. To gain a detailed understanding of the impact of the SEI on electrolyte structure, atomistic molecular dynamics simulations of the electrode/electrolyte interface were performed in the presence and absence of the SEI under applied voltages. The composition of the SEI was guided by a wealth of data from experiments and allowed to vary across the simulations. A novel computational approach was implemented that showed significant computational speedup compared to fully polarizable electrode simulations, yet, retained the correct qualitative physics for the electrolyte. A force-matching algorithm was used to construct a new force field for the pure electrolyte, LiPF6 in ethylene carbonate, which was developed from ab initio molecular dynamics simulations. The electrode/electrolyte interface was included using a simple, physically motivated model, which includes the polarization of the conducting graphitic electrode by the electrolyte and the application of an external voltage. Changes in the structure of the electrolyte at the interface as a function of applied voltage, the thickness of the SEI layer, and composition of the SEI provide molecular level insight into the species present at these interfaces and potential clues to the effect of the SEI on transport. It is noted that, with increasing SEI thickness and LiF content, lithium ions are drawn closer to the SEI surface, which implies that these interfaces favor desolvation and promote more rapid lithium transport.

  19. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. 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.

  1. Atomistic simulation of tunneling magnetoresistance using extended Hückel theory

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

  2. Piezoelectric effects in boron nitride nanotubes predicted by the atomistic finite element method and molecular mechanics

    NASA Astrophysics Data System (ADS)

    Tolladay, Mat; Ivanov, Dmitry; Allan, Neil L.; Scarpa, Fabrizio

    2017-09-01

    We calculate the tensile and shear moduli of a series of boron nitride nanotubes and their piezoelectric response to applied loads. We compare in detail results from a simple molecular mechanics (MM) potential, the universal force field, with those from the atomistic finite element method (AFEM) using both Euler-Bernoulli and Timoshenko beam formulations. The MM energy minimisations are much more successful than those using the AFEM, and we analyse the failure of the latter approach both qualitatively and quantitatively.

  3. Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

    DTIC Science & Technology

    2014-10-01

    Atomistic Molecular Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Robert M Elder, Timothy W Sirk, and...Antechamber program in Assisted Model Building with Energy Refinement (AMBER) Tools to assign partial charges (using the Austin Model 1 [AM1]-bond charge...differences in .mol2 file formatting between various molecule building programs (e.g., field width, number format), Antechamber may fail to read

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

    SciTech Connect

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

    2010-03-20

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

  5. Piezoelectric effects in boron nitride nanotubes predicted by the atomistic finite element method and molecular mechanics.

    PubMed

    Tolladay, Mat; Ivanov, Dmitry; Allan, Neil L; Scarpa, Fabrizio

    2017-09-01

    We calculate the tensile and shear moduli of a series of boron nitride nanotubes and their piezoelectric response to applied loads. We compare in detail results from a simple molecular mechanics (MM) potential, the universal force field, with those from the atomistic finite element method (AFEM) using both Euler-Bernoulli and Timoshenko beam formulations. The MM energy minimisations are much more successful than those using the AFEM, and we analyse the failure of the latter approach both qualitatively and quantitatively.

  6. Idealized vs. Realistic Microstructures: An Atomistic Simulation Case Study on γ/γ′ Microstructures

    PubMed Central

    Prakash, Aruna; Bitzek, Erik

    2017-01-01

    Single-crystal Ni-base superalloys, consisting of a two-phase γ/γ′ microstructure, retain high strengths at elevated temperatures and are key materials for high temperature applications, like, e.g., turbine blades of aircraft engines. The lattice misfit between the γ and γ′ phases results in internal stresses, which significantly influence the deformation and creep behavior of the material. Large-scale atomistic simulations that are often used to enhance our understanding of the deformation mechanisms in such materials must accurately account for such misfit stresses. In this work, we compare the internal stresses in both idealized and experimentally-informed, i.e., more realistic, γ/γ′ microstructures. The idealized samples are generated by assuming, as is frequently done, a periodic arrangement of cube-shaped γ′ particles with planar γ/γ′ interfaces. The experimentally-informed samples are generated from two different sources to produce three different samples—the scanning electron microscopy micrograph-informed quasi-2D atomistic sample and atom probe tomography-informed stoichiometric and non-stoichiometric atomistic samples. Additionally, we compare the stress state of an idealized embedded cube microstructure with finite element simulations incorporating 3D periodic boundary conditions. Subsequently, we study the influence of the resulting stress state on the evolution of dislocation loops in the different samples. The results show that the stresses in the atomistic and finite element simulations are almost identical. Furthermore, quasi-2D boundary conditions lead to a significantly different stress state and, consequently, different evolution of the dislocation loop, when compared to samples with fully 3D boundary conditions. PMID:28772453

  7. 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

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

    PubMed

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

    2004-11-01

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

  9. Validation of the Concurrent Atomistic-Continuum Method on Screw Dislocation/Stacking Fault Interactions

    DOE PAGES

    Xu, Shuozhi; Xiong, Liming; Chen, Youping; ...

    2017-04-26

    Dislocation/stacking fault interactions play an important role in the plastic deformation of metallic nanocrystals and polycrystals. These interactions have been explored in atomistic models, which are limited in scale length by high computational cost. In contrast, multiscale material modeling approaches have the potential to simulate the same systems at a fraction of the computational cost. In this paper, we validate the concurrent atomistic-continuum (CAC) method on the interactions between a lattice screw dislocation and a stacking fault (SF) in three face-centered cubic metallic materials—Ni, Al, and Ag. Two types of SFs are considered: intrinsic SF (ISF) and extrinsic SF (ESF).more » For the three materials at different strain levels, two screw dislocation/ISF interaction modes (annihilation of the ISF and transmission of the dislocation across the ISF) and three screw dislocation/ESF interaction modes (transformation of the ESF into a three-layer twin, transformation of the ESF into an ISF, and transmission of the dislocation across the ESF) are identified. Here, our results show that CAC is capable of accurately predicting the dislocation/SF interaction modes with greatly reduced DOFs compared to fully-resolved atomistic simulations.« less

  10. 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.

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

    PubMed

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

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

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

    DOE PAGES

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

    2015-01-29

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

  14. 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.

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

    PubMed

    Zelovich, Tamar; Kronik, Leeor; Hod, Oded

    2014-08-12

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

  16. 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.

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

    PubMed

    Yang, Shengfeng; Chen, Youping

    2015-03-08

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

  18. 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

  19. Atomistic insight into lipid translocation by a TMEM16 scramblase

    PubMed Central

    Bethel, Neville P.; Grabe, Michael

    2016-01-01

    The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood coagulation. The crystal structure of the fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase suggested a putative mechanism of lipid transport, whereby polar and charged lipid headgroups move through the low-dielectric environment of the membrane by traversing a hydrophilic groove on the membrane-spanning surface of the protein. Here, we use computational methods to explore the membrane–protein interactions involved in lipid scrambling. Fast, continuum membrane-bending calculations reveal a global pattern of charged and hydrophobic surface residues that bends the membrane in a large-amplitude sinusoidal wave, resulting in bilayer thinning across the hydrophilic groove. Atomic simulations uncover two lipid headgroup-interaction sites flanking the groove. The cytoplasmic site nucleates headgroup–dipole stacking interactions that form a chain of lipid molecules that penetrate into the groove. In two instances, a cytoplasmic lipid interdigitates into this chain, crosses the bilayer, and enters the extracellular leaflet, and the reverse process happens twice as well. Continuum membrane-bending analysis carried out on homology models of mammalian homologs shows that these family members also bend the membrane—even those that lack scramblase activity. Sequence alignments show that the lipid-interaction sites are conserved in many family members but less so in those with reduced scrambling ability. Our analysis provides insight into how large-scale membrane bending and protein chemistry facilitate lipid permeation in the TMEM16 family, and we hypothesize that membrane interactions also affect ion permeation. PMID:27872308

  20. Atomistic insight into lipid translocation by a TMEM16 scramblase.

    PubMed

    Bethel, Neville P; Grabe, Michael

    2016-12-06

    The transmembrane protein 16 (TMEM16) family of membrane proteins includes both lipid scramblases and ion channels involved in olfaction, nociception, and blood coagulation. The crystal structure of the fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase suggested a putative mechanism of lipid transport, whereby polar and charged lipid headgroups move through the low-dielectric environment of the membrane by traversing a hydrophilic groove on the membrane-spanning surface of the protein. Here, we use computational methods to explore the membrane-protein interactions involved in lipid scrambling. Fast, continuum membrane-bending calculations reveal a global pattern of charged and hydrophobic surface residues that bends the membrane in a large-amplitude sinusoidal wave, resulting in bilayer thinning across the hydrophilic groove. Atomic simulations uncover two lipid headgroup-interaction sites flanking the groove. The cytoplasmic site nucleates headgroup-dipole stacking interactions that form a chain of lipid molecules that penetrate into the groove. In two instances, a cytoplasmic lipid interdigitates into this chain, crosses the bilayer, and enters the extracellular leaflet, and the reverse process happens twice as well. Continuum membrane-bending analysis carried out on homology models of mammalian homologs shows that these family members also bend the membrane-even those that lack scramblase activity. Sequence alignments show that the lipid-interaction sites are conserved in many family members but less so in those with reduced scrambling ability. Our analysis provides insight into how large-scale membrane bending and protein chemistry facilitate lipid permeation in the TMEM16 family, and we hypothesize that membrane interactions also affect ion permeation.

  1. The polarization properties of a tilted polarizer.

    PubMed

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

    2013-11-04

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

  2. Polarization in Scattering

    DTIC Science & Technology

    2010-09-01

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

  3. 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.

  4. 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.

  5. Discovery of Optical Circular Polarization of the Crab Pulsar

    NASA Astrophysics Data System (ADS)

    Wiktorowicz, Sloane; Ramirez-Ruiz, Enrico; Illing, Rainer M. E.; Nofi, Larissa

    2015-01-01

    Nearly 50 years ago at the Lick 3-m Shane telescope, Wampler et al. (1969) discovered optical linear depolarization of the Crab pulsar's main pulse and interpulse regions, which led to the interpretation of synchrotron radiation as the source of pulsed emission. We present phase-resolved, simultaneous linear and circular polarization of the Crab pulsar using the POLISH2 aperture-integrated, optical polarimeter at the Lick 3-m telescope. The two photoelastic modulators in this instrument, used instead of waveplates, AC couple incident Stokes Q, U, and V to unique, independent frequencies between 10 and 200 kHz. Stokes I is measured from the time-averaged intensity of the beam. Thus, this instrument is capable of simultaneous measurement of Q/I, U/I, and V/I in 20 microsecond temporal bins with part-per-million nightly sensitivity on naked eye stars. From just one hour of observations, we confirm linear depolarization of the main pulse and interpulse regions, and we also discover significant optical circular polarization at all pulsar phases. Furthermore, we observe circular depolarization of the main pulse and interpulse regions with respect to the off-pulse region. Observations of strongly polarized calibration stars, as well as lamp observations with a linear polarizer inserted upstream of the modulators, demonstrate that circular polarization results obtained on the Crab pulsar are not due to spurious, instrumental conversion of linear to circular polarization. Therefore, using novel instrumentation, our observations shed new light on this enigmatic object, and we demonstrate that the Lick 3-m Shane telescope still remains at the cutting edge for optical polarimetry.

  6. Broadband graphene polarizer

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

  7. 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

  8. 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.

  9. 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)

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

    PubMed

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

    2016-12-13

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

  11. Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

    PubMed

    May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

    2014-02-01

    To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

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

    PubMed Central

    Molugu, Trivikram R.

    2017-01-01

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

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

    PubMed

    Wright, David W; Perkins, Stephen J

    2015-06-01

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

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

    PubMed

    Molugu, Trivikram R; Brown, Michael F

    2016-09-01

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

  15. Polarized maser growth

    SciTech Connect

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

    2004-11-01

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

  16. Polarized electron sources

    SciTech Connect

    Prepost, R.

    1994-12-01

    The fundamentals of polarized electron sources are described with particular application to the Stanford Linear Accelerator Center. The SLAC polarized electron source is based on the principle of polarized photoemission from Gallium Arsenide. Recent developments using epitaxially grown, strained Gallium Arsenide cathodes have made it possible to obtain electron polarization significantly in excess of the conventional 50% polarization limit. The basic principles for Gallium and Arsenide polarized photoemitters are reviewed, and the extension of the basic technique to strained cathode structures is described. Results from laboratory measurements of strained photocathodes as well as operational results from the SLAC polarized source are presented.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Dai, Fu-Zhi; Zhang, Wen-Zheng

    2015-03-01

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

  19. Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

    NASA Astrophysics Data System (ADS)

    Stukowski, Alexander

    2010-01-01

    The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/.

  20. 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.

  1. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

    PubMed Central

    2017-01-01

    The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments. PMID:28666087

  2. 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.

  3. 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.

  4. 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.

  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. Atomistic theory and simulation of the morphology and structure of ionic nanoparticles.

    PubMed

    Spagnoli, Dino; Gale, Julian D

    2012-02-21

    Computational techniques are widely used to explore the structure and properties of nanomaterials. This review surveys the application of both quantum mechanical and force field based atomistic simulation methods to nanoparticles, with a particular focus on the methodologies available and the ways in which they can be utilised to study structure, phase stability and morphology. The main focus of this article is on partially ionic materials, from binary semiconductors through to mineral nanoparticles, with more detailed considered of three examples, namely titania, zinc sulphide and calcium carbonate. This journal is © The Royal Society of Chemistry 2012

  7. Atomistic theory and simulation of the morphology and structure of ionic nanoparticles

    NASA Astrophysics Data System (ADS)

    Spagnoli, Dino; Gale, Julian D.

    2012-02-01

    Computational techniques are widely used to explore the structure and properties of nanomaterials. This review surveys the application of both quantum mechanical and force field based atomistic simulation methods to nanoparticles, with a particular focus on the methodologies available and the ways in which they can be utilised to study structure, phase stability and morphology. The main focus of this article is on partially ionic materials, from binary semiconductors through to mineral nanoparticles, with more detailed considered of three examples, namely titania, zinc sulphide and calcium carbonate.

  8. Atomistic simulation of heat-assisted linear reversal mode in nanodots with perpendicular anisotropy

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Tanaka, T.; Matsuyama, K.

    2017-05-01

    The spin dynamics of nanodots in the thermally induced linear reversal mode have been studied by atomistic simulation. A systematic investigation was conducted of the dependence of the properties of heat-assisted magnetization reversal on the thermal pulse width and the elevated peak temperature. An order-of-magnitude decrease in the reversal field was demonstrated for a sub-nanosecond thermal-pulse width and a peak temperature just above the Curie point. The required reversal field was found to increase with atomic uniaxial anisotropy even in the non-equilibrium field cooling process.

  9. First-principles atomistic thermodynamics for oxidation catalysis: surface phase diagrams and catalytically interesting regions.

    PubMed

    Reuter, Karsten; Scheffler, Matthias

    2003-01-31

    Present knowledge of the function of materials is largely based on studies (experimental and theoretical) that are performed at low temperatures and ultralow pressures. However, the majority of everyday applications, like, e.g., catalysis, operate at atmospheric pressures and temperatures at or higher than 300 K. Here we employ ab initio, atomistic thermodynamics to construct a phase diagram of surface structures in the (T,p) space from ultrahigh vacuum to technically relevant pressures and temperatures. We emphasize the value of such phase diagrams as well as the importance of the reaction kinetics that may be crucial, e.g., close to phase boundaries.

  10. 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.

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

    PubMed Central

    Zhai, Ming-Xing; Wang, Xue-Feng

    2016-01-01

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

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    Das, Suvankar; Dutta, Amlan

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Hardy, Robert J.

    2016-11-01

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhai, Ming-Xing; Wang, Xue-Feng

    2016-11-01

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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  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. Evidence from infrared dichroism, x-ray diffraction, and atomistic computer simulation for a ``zigzag'' molecular shape in tilted smectic liquid crystal phases

    NASA Astrophysics Data System (ADS)

    Jang, W. G.; Glaser, M. A.; Park, C. S.; Kim, K. H.; Lansac, Y.; Clark, N. A.

    2001-11-01

    Infrared dichroism (IR) and atomistic computer simulation are employed to probe molecular shape in smectic liquid crystal phases where the optic axis is tilted relative to the layer normal. Polar plots of absorption profiles due to core (phenyl, C-C) and tail (alkyl or methylene, CH2) vibrations in the tilted synclinic (smectic-C) phase of a variety of materials show the phenyl (core) IR absorbance symmetry axes to be consistently tilted at larger angle from the layer normal than the alkyl or methylene (tail). This suggests that, on average, the tails are less tilted than the cores. Furthermore, we find that optic axis tilt angle is close to the core tilt angle measured by IR dichroism, as expected, since liquid crystal birefringence arises primarily from the cores. These results are in accord with the ``zigzag'' model of Bartolino, Doucet, and Durand. However, we find that only a small fraction of the tail, the part nearest the core, is tilted, and only this part contributes significantly to layer contraction upon molecular tilt.

  5. Metasurface polarization splitter

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  6. Metasurface polarization splitter.

    PubMed

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

    2017-03-28

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

  7. Metasurface polarization splitter

    DOE PAGES

    Slovick, Brian A.; Zhou, You; Yu, Zhi Gang; ...

    2017-02-20

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

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

    PubMed

    Li, Xianfeng; Latour, Robert A

    2009-07-31

    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 10(2), 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.

  9. 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

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

    PubMed

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

    2015-06-09

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

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

    SciTech Connect

    Srolovitz, D.J.

    1995-11-01

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

  12. 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.

  13. Quantum treatment of phonon scattering for modeling of three-dimensional atomistic transport

    NASA Astrophysics Data System (ADS)

    Lee, Y.; Bescond, M.; Cavassilas, N.; Logoteta, D.; Raymond, L.; Lannoo, M.; Luisier, M.

    2017-05-01

    Based on the nonequilibrium Green's function formalism, we show a numerically efficient method to treat inelastic scattering in multidimensional atomistic codes. Using a simple rescaling approach, we detail the calculations of the lowest-order approximation (LOA) [Y. Lee et al., Phys. Rev. B 93, 205411 (2016), 10.1103/PhysRevB.93.205411] series to the usual, computationally intensive, self-consistent Born approximation (SCBA). This, combined with the analytic continuation technique of Padé approximants, is applied to an atomistic code based on a tight-binding s p3d5s* model for electrons and holes, and a modified valence-force-field method for phonons. Currents in Si and Ge gate-all-around nanowire transistors are then computed considering the main crystallographic transport directions (<100 > , <110 > , <111 > ) for both n -type and p -type devices. Our results show that in most configurations, third-order LOA currents are enough to achieve a high agreement with SCBA results, while reducing the calculation time by about one order. In addition, we propose a criterion to determine the validity of such expansion techniques.

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

    NASA Technical Reports Server (NTRS)

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

    2008-01-01

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

  15. Comparisons Between Integral Equation Theory and Molecular Dynamics Simulations for Atomistic Models of Polyethylene Liquids

    SciTech Connect

    Curro, John G.; Webb III, Edmund B.; Grest, Gary S.; Weinhold, Jeffrey D.; Putz, Mathias; McCoy, John D.

    1999-07-21

    Molecular dynamics (MD) simulations were performed on dense liquids of polyethylene chains of 24 and 66 united atom CH{sub 2} units. A series of models was studied ranging in atomistic detail from coarse-grained, freely-jointed, tangent site chains to realistic, overlapping site models subjected to bond angle restrictions and torsional potentials. These same models were also treated with the self-consistent, polymer reference interaction site model (PRISM) theory. The intramolecular and total structure factors, as well as, the intermolecular radial distribution functions g(r) and direct correlation functions C(r) were obtained from theory and simulation. Angular correlation functions were also simulation obtained from the MD simulations. Comparisons between theory and reveal that PRISM theory works well for computing the intermolecular structure of coarse-grained chain models, but systematically underpredicts the extent of intermolecular packing as more atomistic details are introduced into the model. A consequence of g(r) having insufficient structure is that the theory yields an isothermal compressibility that progressively becomes larger, relative to the simulations, as overlapping the PRISM sites and angular restrictions are introduced into the model. We found that theory could be considerably improved by adding a tail function to C(r) beyond the effective hard core diameter. The range of this tail function was determined by requiring the theory to yield the correct compressibility.

  16. 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.

  17. 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.

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

    PubMed

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

    2017-03-01

    Atomistic simulations of binary amorphous systems with over 4 million atoms are performed. Systems of two interatomic potentials of the Lennard-Jones type, LJ12-6 and LJ9-6, are simulated. The athermal quasistatic shearing protocol is adopted, where the shear strain is applied in a stepwise fashion with each step followed by energy minimization. For each avalanche event, the shear stress drop (Δσ), the hydrostatic pressure drop (Δσ_{h}), and the potential energy drop (ΔE) are computed. It is found that, with the avalanche size increasing, the three become proportional to each other asymptotically. The probability distributions of avalanche sizes are obtained and values of scaling exponents fitted. In particular, the distributions follow a power law, P(ΔU)∼ΔU^{-τ}, where ΔU is a measure of avalanche sizes defined based on shear stress drops. The exponent τ is 1.25±0.1 for the LJ12-6 systems, and 1.15±0.1 for the LJ9-6 systems. The value of τ for the LJ12-6 systems is consistent with that from an earlier atomistic simulation study by Robbins et al. [Phys. Rev. Lett. 109, 105703 (2012)]PRLTAO0031-900710.1103/PhysRevLett.109.105703, but the fitted values of other scaling exponents differ, which may be because the shearing protocol used here differs from that in their study.

  19. 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.

  20. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DOE PAGES

    Neilson, James R.; McQueen, Tyrel M.

    2015-09-20

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

  2. Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces

    NASA Astrophysics Data System (ADS)

    Ardham, Vikram Reddy; Leroy, Frédéric

    2017-08-01

    In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics.

  3. 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

  4. 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)

  5. 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.

  6. 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

  7. Atomistic near-field nanoplasmonics: reaching atomic-scale resolution in nanooptics.

    PubMed

    Barbry, M; Koval, P; Marchesin, F; Esteban, R; Borisov, A G; Aizpurua, J; Sánchez-Portal, D

    2015-05-13

    Electromagnetic field localization in nanoantennas is one of the leitmotivs that drives the development of plasmonics. The near-fields in these plasmonic nanoantennas are commonly addressed theoretically within classical frameworks that neglect atomic-scale features. This approach is often appropriate since the irregularities produced at the atomic scale are typically hidden in far-field optical spectroscopies. However, a variety of physical and chemical processes rely on the fine distribution of the local fields at this ultraconfined scale. We use time-dependent density functional theory and perform atomistic quantum mechanical calculations of the optical response of plasmonic nanoparticles, and their dimers, characterized by the presence of crystallographic planes, facets, vertices, and steps. Using sodium clusters as an example, we show that the atomistic details of the nanoparticles morphologies determine the presence of subnanometric near-field hot spots that are further enhanced by the action of the underlying nanometric plasmonic fields. This situation is analogue to a self-similar nanoantenna cascade effect, scaled down to atomic dimensions, and it provides new insights into the limits of field enhancement and confinement, with important implications in the optical resolution of field-enhanced spectroscopies and microscopies.

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

    SciTech Connect

    Neilson, James R.; McQueen, Tyrel M.

    2015-09-20

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

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

    SciTech Connect

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

    2016-02-29

    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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Świderski, M.; Zieliński, M.

    2017-03-01

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

  13. PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.

    PubMed

    Graham, James A; Essex, Jonathan W; Khalid, Syma

    2017-04-24

    Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of internal coordinates directly from atomistic molecular dynamics simulation trajectories. The derivation of bespoke parameters from atomistic simulations improves the quality of the CG model compared to the use of generic parameters derived from other molecules, while automation greatly reduces the time required. The ease of configuration of PyCGTOOL enables the rapid investigation of multiple atom-to-bead mappings and topologies. Although we present PyCGTOOL used in combination with the GROMACS molecular dynamics engine its use of standard trajectory input libraries means that it is in principle compatible with other software. The software is available from the URL https://github.com/jag1g13/pycgtool as the following doi: 10.5281/zenodo.259330 .

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  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. 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.

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

    NASA Astrophysics Data System (ADS)

    Xu, Yun; Chen, Jun

    2015-02-01

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

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

    PubMed Central

    Plattner, Nuria; Noé, Frank

    2015-01-01

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

  19. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy.

    PubMed

    Tollinger, Martin; Sivertsen, Astrid C; Meier, Beat H; Ernst, Matthias; Schanda, Paul

    2012-09-12

    We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr-Purcell-Meiboom-Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers.

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

    NASA Astrophysics Data System (ADS)

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

    1998-08-01

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