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Sample records for fully atomistic model

  1. A fully atomistic model of the Cx32 connexon.

    Directory of Open Access Journals (Sweden)

    Sergio Pantano

    Full Text Available Connexins are plasma membrane proteins that associate in hexameric complexes to form channels named connexons. Two connexons in neighboring cells may dock to form a "gap junction" channel, i.e. an intercellular conduit that permits the direct exchange of solutes between the cytoplasm of adjacent cells and thus mediate cell-cell ion and metabolic signaling. The lack of high resolution data for connexon structures has hampered so far the study of the structure-function relationships that link molecular effects of disease-causing mutations with their observed phenotypes. Here we present a combination of modeling techniques and molecular dynamics (MD to infer side chain positions starting from low resolution structures containing only C alpha atoms. We validated this procedure on the structure of the KcsA potassium channel, which is solved at atomic resolution. We then produced a fully atomistic model of a homotypic Cx32 connexon starting from a published model of the C alpha carbons arrangement for the connexin transmembrane helices, to which we added extracellular and cytoplasmic loops. To achieve structural relaxation within a realistic environment, we used MD simulations inserted in an explicit solvent-membrane context and we subsequently checked predictions of putative side chain positions and interactions in the Cx32 connexon against a vast body of experimental reports. Our results provide new mechanistic insights into the effects of numerous spontaneous mutations and their implication in connexin-related pathologies. This model constitutes a step forward towards a structurally detailed description of the gap junction architecture and provides a structural platform to plan new biochemical and biophysical experiments aimed at elucidating the structure of connexin channels and hemichannels.

  2. Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation.

    Science.gov (United States)

    Zahariev, Tsvetan K; Slavchov, Radomir I; Tadjer, Alia V; Ivanova, Anela N

    2014-04-15

    Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems.

  3. Atomistic modeling of dropwise condensation

    Science.gov (United States)

    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.

  4. Filler reinforcement in cross-linked elastomer nanocomposites: insights from fully atomistic molecular dynamics simulation.

    Science.gov (United States)

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

    Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more

  5. Rotational viscosity of a liquid crystal mixture:a fully atomistic molecular dynamics study

    Institute of Scientific and Technical Information of China (English)

    Zhang Ran; Peng Zeng-Hui; Liu Yong-Gang; Zheng Zhi-Gang; Xuan Li

    2009-01-01

    Fully atomistic molecular dynamics(MD)simulations at 293, 303 and 313 K have been performed for the four. component liquid crystal mixture, E7, using the software package Material Studio. Order parameters and orientational time correlation functions(TCFs)were calculated from MD trajectories. The rotational viscosity coefficients(RVCs)of the mixture were ca]culated using the Nemtsov-Zakharov and Fialkowski methods based on statistical-mechanical approaches. Temperature dependences of RVC and density were discussed in detall. Reasonable agreement between the simulated and experimental values was found.

  6. Atomistic Modelling of Si Nanoparticles Synthesis

    Directory of Open Access Journals (Sweden)

    Giovanni Barcaro

    2017-02-01

    Full Text Available Silicon remains the most important material for electronic technology. Presently, some efforts are focused on the use of Si nanoparticles—not only for saving material, but also for improving the efficiency of optical and electronic devices, for instance, in the case of solar cells coated with a film of Si nanoparticles. The synthesis by a bottom-up approach based on condensation from low temperature plasma is a promising technique for the massive production of such nanoparticles, but the knowledge of the basic processes occurring at the atomistic level is still very limited. In this perspective, numerical simulations can provide fundamental information of the nucleation and growth mechanisms ruling the bottom-up formation of Si nanoclusters. We propose to model the low temperature plasma by classical molecular dynamics by using the reactive force field (ReaxFF proposed by van Duin, which can properly describe bond forming and breaking. In our approach, first-principles quantum calculations are used on a set of small Si clusters in order to collect all the necessary energetic and structural information to optimize the parameters of the reactive force-field for the present application. We describe in detail the procedure used for the determination of the force field and the following molecular dynamics simulations of model systems of Si gas at temperatures in the range 2000–3000 K. The results of the dynamics provide valuable information on nucleation rate, nanoparticle size distribution, and growth rate that are the basic quantities for developing a following mesoscale model.

  7. Adhesive contact:from atomistic model to continuum model

    Institute of Scientific and Technical Information of China (English)

    Fan Kang-Qi; Jia Jian-Yuan; Zhu Ying-Min; Zhang Xiu-Yan

    2011-01-01

    Two types of Lennard-Jones potential are widely used in modeling adhesive contacts. However, the relationships between the parameters of the two types of Lennard-Jones potential are not well defined. This paper employs a selfconsistent method to derive the Lennard-Jones surface force law from the interatomic Lennard-Jones potential with emphasis on the relationships between the parameters. The effect of using correct parameters in the adhesion models is demonstrated in single sphere-flat contact via continuum models and an atomistic model. Furthermore, the adhesion hysteresis behaviour is investigated, and the S-shaped force-distance relation is revealed by the atomistic model. It shows that the adhesion hysteresis loop is generated by the jump-to-contact and jump-off-contact, which are illustrated by the S-shaped force-distance curve.

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

    Energy Technology Data Exchange (ETDEWEB)

    Amani, Ehsan, E-mail: eamani@aut.ac.ir; Movahed, Saeid, E-mail: smovahed@aut.ac.ir

    2016-06-07

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

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

    Science.gov (United States)

    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

  10. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations

    Science.gov (United States)

    Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue

    2016-05-01

    Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.

  11. Predicting dislocation climb: Classical modeling versus atomistic simulations

    OpenAIRE

    Clouet, Emmanuel

    2011-01-01

    International audience; The classical modeling of dislocation climb based on a continuous description of vacancy diffusion is compared to recent atomistic simulations of dislocation climb in body-centered cubic iron under vacancy supersaturation [Phys. Rev. Lett. 105 095501 (2010)]. A quantitative agreement is obtained, showing the ability of the classical approach to describe dislocation climb. The analytical model is then used to extrapolate dislocation climb velocities to lower dislocation...

  12. Atomistic modeling of carbon Cottrell atmospheres in bcc iron

    Science.gov (United States)

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

    2013-01-01

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jinbo [ORNL; Zhang, Z F [Shenyang National Laboratory for Materials Science; Osetskiy, Yury N [ORNL; Stoller, Roger E [ORNL

    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.

  14. Atomistic modeling of dislocation-interface interactions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jian [Los Alamos National Laboratory; Valone, Steven M [Los Alamos National Laboratory; Beyerlein, Irene J [Los Alamos National Laboratory; Misra, Amit [Los Alamos National Laboratory; Germann, T. C. [Los Alamos National Laboratory

    2011-01-31

    Using atomic scale models and interface defect theory, we first classify interface structures into a few types with respect to geometrical factors, then study the interfacial shear response and further simulate the dislocation-interface interactions using molecular dynamics. The results show that the atomic scale structural characteristics of both heterophases and homophases interfaces play a crucial role in (i) their mechanical responses and (ii) the ability of incoming lattice dislocations to transmit across them.

  15. Quantum transport in RTD and atomistic modeling of nanostructures

    Science.gov (United States)

    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. Atomistic Method Applied to Computational Modeling of Surface Alloys

    Science.gov (United States)

    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

  17. Going Backward : A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

    NARCIS (Netherlands)

    Wassenaar, Tsjerk A.; Pluhackova, Kristyna; Böckmann, Rainer A.; Marrink, Siewert J.; Tieleman, D. Peter

    2014-01-01

    The conversion of coarse-grained to atomistic models is an important step in obtaining insight about atomistic scale processes from coarse-grained simulations. For this process, called backmapping or reverse transformation, several tools are available, but these commonly require libraries of molecul

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Christopher D. Taylor

    2012-01-01

    Full Text Available 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 of 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.

  20. Effective Transparency: A Test of Atomistic Laser-Cluster Models

    CERN Document Server

    Pandit, Rishi; Teague, Thomas; Hartwick, Zachary; Bigaouette, Nicolas; Ramunno, Lora; Ackad, Edward

    2016-01-01

    The effective transparency of rare-gas clusters, post-interaction with an extreme ultraviolet (XUV) pump pulse, is studied by using an atomistic hybrid quantum-classical molecular dynamics model. We find there is an intensity range in which an XUV probe pulse has no lasting effect on the average charge state of a cluster after being saturated by an XUV pump pulse: the cluster is effectively transparent to the probe pulse. The range of this phenomena increases with the size of the cluster and thus provides an excellent candidate for an experimental test of the effective transparency effect. We present predictions for the clusters at the peak of the laser pulse as well as the experimental time-of-flight signal expected along with trends which can be compared with. Significant deviations from these predictions would provide evidence for enhanced photoionization mechanism(s).

  1. Physically representative atomistic modeling of atomic-scale friction

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  3. Dislocation climb models from atomistic scheme to dislocation dynamics

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  5. Atomistic modeling of phonon transport in turbostratic graphitic structures

    Science.gov (United States)

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

    2016-05-01

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

  6. Predictive atomistic simulations of electronic properties of realistic nanoscale devices: A multiscale modeling approach

    Science.gov (United States)

    Vedula, Ravi Pramod Kumar

    profiles, inherent in strain-engineered Ge nanofins, on their transport properties. Fully atomistic simulations, involving a combination molecular dynamics simulations with first-principles based force-fields and semi-empirical tight binding calculations, coupled with linearized Boltzmann model are used to calculate the hole transport properties of realistic Ge nanofins (heights 5-15nm and widths 5nm-40nm). Our simulations predict the technological limit of phonon limited hole mobility improvement in Ge channel PMOS devices (Hengineer high performance uniaxial devices conducive to the existing top-down fabrication approaches. From these calculations, we demonstrate that realistic modeling of the devices requires a reduction in the empiricism of fitting parameters and incorporation of new multi-scale, multi-resolution approach spanning across various spatial and temporal scales. Such physics based predictive multiscale models facilitate an integrated approach for rapid development and pave the way for designing new advanced materials and devices.

  7. Atomistic modeling at experimental strain rates and timescales

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Salmani-Jelodar, M., E-mail: m.salmani@gmail.com; Klimeck, G. [Network for Computational Nanotechnology and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Kim, S. [Intel Corporation, 2501 Northwest 229th Avenue, Hillsboro, Oregon 97124 (United States); Ng, K. [Semiconductor Research Corporation (SRC), 1101 Slater Rd, Durham, North Carolina 27703 (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  11. An atomistic modelling of the porosity impact on UO{sub 2} matrix macroscopic properties

    Energy Technology Data Exchange (ETDEWEB)

    Jelea, A., E-mail: andrei.jelea@irsn.fr [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Institute of Physical Chemistry Ilie Murgulescu, Romanian Academy, 202 Spl Independentei St., 060021 Bucharest-12 (Romania); Colbert, M. [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Ribeiro, F. [Institut de Radioprotection et de Surete Nucleaire (IRSN), DPAM, SEMCA, LEC, Cadarache (France); Treglia, G. [Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Pellenq, R.J.-M. [Centre Interdisciplinaire des Nanosciences de Marseille, CNRS, Campus de Luminy, Marseille 13288 (France); Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States)

    2011-08-15

    Highlights: > The porosity impact on the UO{sub 2} matrix thermomechanical properties was investigated. > Atomistic simulation techniques were used in this study. > The UO{sub 2} thermal expansion coefficient is modified due to the pore surface effects. > The elastic moduli at 0 K and at finite temperature decrease linearly with porosity. - Abstract: The porosity impact on the UO{sub 2} matrix thermomechanical properties was investigated using atomistic simulation techniques. The porosity modifies the thermal expansion coefficient and this is attributed to pore surface effects. The elastic moduli at 0 K and at finite temperature decrease with porosity, this variation being well approximated using affine functions. These results agree with other mesoscale model predictions and experimental data, showing the ability of the semiempirical potential atomistic simulations to give an overall good description of the porous UO{sub 2}. However, the surface effects are incompletely described.

  12. Accelerating a hybrid continuum-atomistic fluidic model with on-the-fly machine learning

    CERN Document Server

    Stephenson, David; Lockerby, Duncan A

    2016-01-01

    We present a hybrid continuum-atomistic scheme which combines molecular dynamics (MD) simulations with on-the-fly machine learning techniques for the accurate and efficient prediction of multiscale fluidic systems. By using a Gaussian process as a surrogate model for the computationally expensive MD simulations, we use Bayesian inference to predict the system behaviour at the atomistic scale, purely by consideration of the macroscopic inputs and outputs. Whenever the uncertainty of this prediction is greater than a predetermined acceptable threshold, a new MD simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial enhancement to the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging-diverging channel, and make comparisons between the new s...

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

    Science.gov (United States)

    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.

  14. Transport properties of fully screened Kondo models

    NARCIS (Netherlands)

    Hörig, Christoph B M; Mora, Christophe; Schuricht, Dirk

    2014-01-01

    We study the nonequilibrium transport properties of fully (exactly) screened Kondo quantum dots subject to a finite bias voltage or a finite temperature. First, we calculate the Fermi-liquid coefficients of the conductance for models with arbitrary spin, i.e., its leading behavior for small bias vol

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Nanoscale finite element models for vibrations of single-walled carbon nanotubes:atomistic versus continuum

    Institute of Scientific and Technical Information of China (English)

    R ANSARI; S ROUHI; M ARYAYI

    2013-01-01

    By the atomistic and continuum finite element models, the free vibration behavior of single-walled carbon nanotubes (SWCNTs) is studied. In the atomistic finite element model, the bonds and atoms are modeled by the beam and point mass elements, respectively. The molecular mechanics is linked to structural mechanics to determine the elastic properties of the mentioned beam elements. In the continuum finite element approach, by neglecting the discrete nature of the atomic structure of the nanotubes, they are modeled with shell elements. By both models, the natural frequencies of SWCNTs are computed, and the effects of the geometrical parameters, the atomic structure, and the boundary conditions are investigated. The accuracy of the utilized methods is verified in comparison with molecular dynamic simulations. The molecular structural model leads to more reliable results, especially for lower aspect ratios. The present analysis provides valuable information about application of continuum models in the investigation of the mechanical behaviors of nanotubes.

  17. Atomistic modeling of H absorption in Pd nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Ruda, M., E-mail: ruda@cab.cnea.gov.a [Centro Atomico Bariloche, 8400 Bariloche (Argentina); Centro Regional Universitario Bariloche, U.N. Comahue (Argentina); Crespo, E.A., E-mail: crespo@uncoma.edu.a [Depto. de Fisica, Fac. de Ingenieria, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquen (Argentina); Debiaggi, S. Ramos de, E-mail: ramos@uncoma.edu.a [Depto. de Fisica, Fac. de Ingenieria, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquen (Argentina); CONICET (Argentina)

    2010-04-16

    Size affects the properties of absorption of H in Palladium nanoparticles. Because of their higher proportion of surface atoms compared to the bulk, the pressure-composition (P-C) isotherms of the nanoparticles are modified. We performed atomistic simulations for different-sized Pd nanoparticles and for the bulk at different H concentrations using the Monte Carlo technique in the TP{mu}N ensemble to calculate the P-C isotherms. The Pd-H interatomic potentials are of the Embedded Atom (EAM) type and have been recently developed by Zhou et al. . From the related van't Hoff equation we obtained |{Delta}H{sup o}| = (28 {+-} 7) kJ/0.5 mol of H{sub 2} and |{Delta}S{sup o}| = (71 {+-} 19) J/0.5 mol of H{sub 2}.K for the PdH formation in the bulk. For Pd nanoparticles previous simulations results based on a different set of EAM potentials showed that H was absorbed primarily in the surface before diffusing into the inside of small Pd clusters . Considering the better performance of Zhou's potentials for the bulk, in this work we analyzed the evolution of the equilibrium microstructure of Pd nanoparticles as a function of their size and H concentration. Our simulations predict enhanced hydrogen solubilities and vanishing plateaux when compared to the bulk and that H is absorbed in the subsurface of the nanoparticles.

  18. Fully Adaptive Radar Modeling and Simulation Development

    Science.gov (United States)

    2017-04-01

    Organization (NATO) Sensors Electronics Technology (SET)-227 Panel on Cognitive Radar. The FAR M&S architecture developed in Phase I allows for...Air Force’s previously developed radar M&S tools. This report is organized as follows. In Chapter 3, we provide an overview of the FAR framework...AFRL-RY-WP-TR-2017-0074 FULLY ADAPTIVE RADAR MODELING AND SIMULATION DEVELOPMENT Kristine L. Bell and Anthony Kellems Metron, Inc

  19. Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

    OpenAIRE

    Lipp, Vladimir

    2015-01-01

    In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First...

  20. Fully implicit kinetic modelling of collisional plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Mousseau, V.A.

    1996-05-01

    This dissertation describes a numerical technique, Matrix-Free Newton Krylov, for solving a simplified Vlasov-Fokker-Planck equation. This method is both deterministic and fully implicit, and may not have been a viable option before current developments in numerical methods. Results are presented that indicate the efficiency of the Matrix-Free Newton Krylov method for these fully-coupled, nonlinear integro-differential equations. The use and requirement for advanced differencing is also shown. To this end, implementations of Chang-Cooper differencing and flux limited Quadratic Upstream Interpolation for Convective Kinematics (QUICK) are presented. Results are given for a fully kinetic ion-electron problem with a self consistent electric field calculated from the ion and electron distribution functions. This numerical method, including advanced differencing, provides accurate solutions, which quickly converge on workstation class machines. It is demonstrated that efficient steady-state solutions can be achieved to the non-linear integro-differential equation, obtaining quadratic convergence, without incurring the large memory requirements of an integral operator. Model problems are presented which simulate plasma impinging on a plate with both high and low neutral particle recycling typical of a divertor in a Tokamak device. These model problems demonstrate the performance of the new solution method.

  1. Fully Equipped Dynamic Model of a Bus

    Directory of Open Access Journals (Sweden)

    I. Kowarska

    2014-01-01

    Full Text Available Nowadays, the time to market a new vehicle is crucial for every company as it is easier to meet the customers’ needs and expectations. However, designing a new vehicle is a long process which needs to take into account different performances. The most difficult is to predict a dynamic behavior of a vehicle especially when such a big vehicles as urban buses are considered. Therefore, there is a necessity to use a virtual model to investigate different performances. However, there is a lack of urban bus models that can fully reflect a dynamic behavior of the bus. This paper presents a fully equipped urban bus model which can be used to study a dynamic behavior of such vehicles. The model is based on innovative technique called cosimulation, which connects different modeling techniques (3D and 1D. Such a technique allows performing different analyses that require small deformations and large translations and rotations in shorter time and automatic way. The work has been carried out in a project EUREKA CHASING.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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. A study of conditions for dislocation nucleation in coarser-than-atomistic scale models

    Science.gov (United States)

    Garg, Akanksha; Acharya, Amit; Maloney, Craig E.

    2015-02-01

    We perform atomistic simulations of dislocation nucleation in defect free crystals in 2 and 3 dimensions during indentation with circular (2D) or spherical (3D) indenters. The kinematic structure of the theory of Field Dislocation Mechanics (FDM) is shown to allow the identification of a local feature of the atomistic velocity field in these simulations as indicative of dislocation nucleation. It predicts the precise location of the incipient spatially distributed dislocation field, as shown for the cases of the Embedded Atom Method potential for Al and the Lennard-Jones pair potential. We demonstrate the accuracy of this analysis for two crystallographic orientations in 2D and one in 3D. Apart from the accuracy in predicting the location of dislocation nucleation, the FDM based analysis also demonstrates superior performance than existing nucleation criteria in not persisting in time beyond the nucleation event, as well as differentiating between phase boundary/shear band and dislocation nucleation. Our analysis is meant to facilitate the modeling of dislocation nucleation in coarser-than-atomistic scale models of the mechanics of materials.

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

    Science.gov (United States)

    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.

  6. A fully quantum model of Big Bang

    CERN Document Server

    Maydanyuk, Sergei P; Olkhovsky, Vladislav S

    2013-01-01

    In the paper the closed Friedmann-Robertson-Walker model with quantization in the presence of the positive cosmological constant and radiation is studied. For analysis of tunneling probability for birth of an asymptotically deSitter, inflationary Universe as a function of the radiation energy a new definition of a "free" wave propagating inside strong fields is proposed. On such a basis, tunneling boundary condition is corrected, penetrability and reflection concerning to the barrier are calculated in fully quantum stationary approach. For the first time non-zero interference between the incident and reflected waves has been taken into account which turns out to play important role inside cosmological potentials and could be explained by non-locality of barriers in quantum mechanics. Inside whole region of energy of radiation the tunneling probability for the birth of the inflationary Universe is found to be close to its value obtained in semiclassical approach. The reflection from the barrier is determined f...

  7. Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling.

    Science.gov (United States)

    Lupala, Cecylia S; Rasaeifar, Bahareh; Gomez-Gutierrez, Patricia; Perez, Juan J

    2017-08-14

    Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.

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

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, B. [American Geophysical Union, Washington, DC (United States)

    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.

  9. Ion beam processing of surfaces and interfaces. Modeling and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liedke, Bartosz

    2011-03-24

    Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In

  10. Density Functional Theory and Materials Modeling at Atomistic Length Scales

    Directory of Open Access Journals (Sweden)

    Swapan K. Ghosh

    2002-04-01

    Full Text Available Abstract: We discuss the basic concepts of density functional theory (DFT as applied to materials modeling in the microscopic, mesoscopic and macroscopic length scales. The picture that emerges is that of a single unified framework for the study of both quantum and classical systems. While for quantum DFT, the central equation is a one-particle Schrodinger-like Kohn-Sham equation, the classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential, the exact functional form of which is unknown. One therefore approximates the exchange-correlation potential for quantum systems and the excess free energy density functional or the direct correlation functions for classical systems. Illustrative applications of quantum DFT to microscopic modeling of molecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are highlighted.

  11. Atomistic modelling of residual stress at UO2 surfaces.

    Science.gov (United States)

    Arayro, Jack; Tréglia, Guy; Ribeiro, Fabienne

    2016-01-13

    Modelling oxide surface behaviour is of both technological and fundamental interest. In particular, in the case of the UO2 system, which is of major importance in the nuclear industry, it is essential to account for the link between microstructure and macroscopic mechanical properties. Indeed micromechanical models at the mesoscale need to be supplied by the energetic and stress data calculated at the nanoscale. In this framework, we present a theoretical study, coupling an analytical model and thermostatistical simulation to investigate the modifications induced by the presence of a surface regarding atomic relaxation and energetic and stress profiles. In particular, we show that the surface effective thickness as well as the stress profile, which are required by micromechanical approaches, are strongly anisotropic.

  12. Atomistic modeling of shock-induced void collapse in copper

    Energy Technology Data Exchange (ETDEWEB)

    Davila, L P; Erhart, P; Bringa, E M; Meyers, M A; Lubarda, V A; Schneider, M S; Becker, R; Kumar, M

    2005-03-09

    Nonequilibrium molecular dynamics (MD) simulations show that shock-induced void collapse in copper occurs by emission of shear loops. These loops carry away the vacancies which comprise the void. The growth of the loops continues even after they collide and form sessile junctions, creating a hardened region around the collapsing void. The scenario seen in our simulations differs from current models that assume that prismatic loop emission is responsible for void collapse. We propose a new dislocation-based model that gives excellent agreement with the stress threshold found in the MD simulations for void collapse as a function of void radius.

  13. Atomistic approach for modeling metal-semiconductor interfaces

    DEFF Research Database (Denmark)

    Stradi, Daniele; Martinez, Umberto; Blom, Anders

    2016-01-01

    realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via the I–V curve. In particular, it will be demonstrated how doping — and bias — modifies the Schottky barrier, and how finite size models (the slab approach) are unable to describe these interfaces...

  14. Molecular recognition effects in atomistic models of imprinted polymers.

    Science.gov (United States)

    Dourado, Eduardo M A; Herdes, Carmelo; van Tassel, Paul R; Sarkisov, Lev

    2011-01-01

    In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  15. Molecular Recognition Effects in Atomistic Models of Imprinted Polymers

    Directory of Open Access Journals (Sweden)

    Carmelo Herdes

    2011-07-01

    Full Text Available In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  16. Atomistic modelling of the Fe-Cr-C system

    Science.gov (United States)

    Wallenius, Janne; Sandberg, Nils; Henriksson, Krister

    2011-08-01

    For the purpose of modelling the impact of carbon on radiation damage phenomena in steels, we have performed an extensive set of first principle calculations on the Fe-Cr-C system. The calculated solution and diffusion enthalpies of carbon in iron and in chromium agree well with experimental data, as do the relative formation energies of mono-carbides, cementite, Hägg and M 23C 6 carbides. Our data further indicate that interstitial carbon is attracted to a solute iron atom in bcc chromium, while the reaction between carbon and a solute chromium atom in bcc iron is repulsive. An empirical potential fitted to data for iron carbides is capable of reproducing melting behaviour of cementite, while the predicted interaction with point defects agrees less well with DFT data than a potential recently published by Hepburn and Ackland.

  17. Use of atom probe techniques to support thermodynamic and atomistic modelling of phase transformations

    Energy Technology Data Exchange (ETDEWEB)

    Andren, Hans-Olof

    2003-07-25

    Atom probe field ion microscopy (APFIM) gives accurate data on phase composition for all elements and has a good sensitivity and excellent spatial resolution. APFIM data have therefore been used as support for thermodynamic modelling of phase equilibria and phase transformations. This paper describes a number of cases where atom probe data from Chalmers University have been used to judge the accuracy of modelling: the solubility of W and C in Co, the equilibrium volume fraction of VN in a complex chromium steel, the content of B in M{sub 23}C{sub 6} precipitates, the growth of Laves phase during ageing of a chromium steel, and the growth of secondary NbC precipitates in a stabilised austenitic stainless steel. Atomistic modelling is now emerging as a tool for materials science, in particular for modelling of interfacial structure and energies. The status of the activities in this field at Chalmers University is described, and the role of APFIM in atomistic modelling is discussed.

  18. Atomistic modeling of thermomechanical properties of SWNT/Epoxy nanocomposites

    Science.gov (United States)

    Fasanella, Nicholas; Sundararaghavan, Veera

    2015-09-01

    Molecular dynamics simulations are performed to compute thermomechanical properties of cured epoxy resins reinforced with pristine and covalently functionalized carbon nanotubes. A DGEBA-DDS epoxy network was built using the ‘dendrimer’ growth approach where 75% of available epoxy sites were cross-linked. The epoxy model is verified through comparisons to experiments, and simulations are performed on nanotube reinforced cross-linked epoxy matrix using the CVFF force field in LAMMPS. Full stiffness matrices and linear coefficient of thermal expansion vectors are obtained for the nanocomposite. Large increases in stiffness and large decreases in thermal expansion were seen along the direction of the nanotube for both nanocomposite systems when compared to neat epoxy. The direction transverse to nanotube saw a 40% increase in stiffness due to covalent functionalization over neat epoxy at 1 K whereas the pristine nanotube system only saw a 7% increase due to van der Waals effects. The functionalized SWNT/epoxy nanocomposite showed an additional 42% decrease in thermal expansion along the nanotube direction when compared to the pristine SWNT/epoxy nanocomposite. The stiffness matrices are rotated over every possible orientation to simulate the effects of an isotropic system of randomly oriented nanotubes in the epoxy. The randomly oriented covalently functionalized SWNT/Epoxy nanocomposites showed substantial improvements over the plain epoxy in terms of higher stiffness (200% increase) and lower thermal expansion (32% reduction). Through MD simulations, we develop means to build simulation cells, perform annealing to reach correct densities, compute thermomechanical properties and compare with experiments.

  19. Atomistic Modeling of Thermal Conductivity of Epoxy Nanotube Composites

    Science.gov (United States)

    Fasanella, Nicholas A.; Sundararaghavan, Veera

    2016-05-01

    The Green-Kubo method was used to investigate the thermal conductivity as a function of temperature for epoxy/single wall carbon nanotube (SWNT) nanocomposites. An epoxy network of DGEBA-DDS was built using the `dendrimer' growth approach, and conductivity was computed by taking into account long-range Coulombic forces via a k-space approach. Thermal conductivity was calculated in the direction perpendicular to, and along the SWNT axis for functionalized and pristine SWNT/epoxy nanocomposites. Inefficient phonon transport at the ends of nanotubes is an important factor in the thermal conductivity of the nanocomposites, and for this reason discontinuous nanotubes were modeled in addition to long nanotubes. The thermal conductivity of the long, pristine SWNT/epoxy system is equivalent to that of an isolated SWNT along its axis, but there was a 27% reduction perpendicular to the nanotube axis. The functionalized, long SWNT/epoxy system had a very large increase in thermal conductivity along the nanotube axis (~700%), as well as the directions perpendicular to the nanotube (64%). The discontinuous nanotubes displayed an increased thermal conductivity along the SWNT axis compared to neat epoxy (103-115% for the pristine SWNT/epoxy, and 91-103% for functionalized SWNT/epoxy system). The functionalized system also showed a 42% improvement perpendicular to the nanotube, while the pristine SWNT/epoxy system had no improvement over epoxy. The thermal conductivity tensor is averaged over all possible orientations to see the effects of randomly orientated nanotubes, and allow for experimental comparison. Excellent agreement is seen for the discontinuous, pristine SWNT/epoxy nanocomposite. These simulations demonstrate there exists a threshold of the SWNT length where the best improvement for a composite system with randomly oriented nanotubes would transition from pristine SWNTs to functionalized SWNTs.

  20. Modelling of gas-surface interactions using atomistic approaches

    Science.gov (United States)

    Violanda, M.

    2010-12-01

    The oxidation of Si is one the basic steps in the manufacture of microchips in electronic devices. With integrated circuits increasingly getting smaller, the controlled deposition of the thin insulating SiO layers becomes critical. During rf reactive magnetron sputter deposition of silicon suboxides, various relevant ionic and molecular Si- and O-containing species relevant are present in the reaction chamber. These species impinge on the deposition surface, i.e., the Si substrate, oxidizing it and then forms a thin insulating layer of SiOx material. Precise control of vapor deposition of Si and O containing species requires understanding of the deposition process at the atomic or molecular. Here ab-initio methods, mainly density functional theory based techniques, are used to theoretically investigate the ability of relevant molecules in gas phase to physically or chemically adsorb on the clean Si surface. The most stable (clean) Si surface model with p(2x2) reconstruction was utilized in this work. Relevant species for SiOx deposition are O2, SiO, SiO, as well as the Si and O atoms. O and O, the well-adsorbed species on the Si surface have adsorption energies up to -6.00 eV. The SiO molecule, which is abundant at the deposition chamber, is adsorbed on Si surface with adsorption energies up to -2.50 eV. While SiO molecule on Si surface has adsorption energies up to -4.90 eV. Various adsorption sites of both SiO and SiO on the Si surface were identified, showing negligible adsorption barrier, an indication that these molecules are readily adsorbed on the Si surface. Observed red-shifts in the vibrational frequencies of both the adsorbed SiO and SiO molecules, indicate weakening of the Si-O bonds. Simultaneous co-adsorption of O with a SiO molecule on the Si surface indicates an energy gain of -2.90 eV, higher than the energies gained when O and SiO are individually adsorbed, in case where O2 and SiO share the same Si surface atom to bond with. A SiO-precovered Si

  1. Modeling micelle-templated mesoporous material SBA-15: atomistic model and gas adsorption studies.

    Science.gov (United States)

    Bhattacharya, Supriyo; Coasne, Benoit; Hung, Francisco R; Gubbins, Keith E

    2009-05-19

    We report the development of a realistic molecular model for mesoporous silica SBA-15, which includes both the large cylindrical mesopores and the smaller micropores in the pore walls. The methodology for modeling the SBA-15 structure involves molecular and mesoscale simulations combined with geometrical interpolation techniques. First, a mesoscale model is prepared by mimicking the synthesis process using lattice Monte Carlo simulations. The main physical features of this mesoscale pore model are then carved out of an atomistic silica block; both the mesopores and the micropores are incorporated from the mimetic simulations. The calculated pore size distribution, surface area, and simulated TEM images of the model structure are in good agreement with those obtained from experimental samples of SBA-15. We then investigate the adsorption of argon in this structure using Grand Canonical Monte Carlo (GCMC) simulations. The adsorption results for our SBA-15 model are compared with those for a similar model that does not include the micropores; we also compare with results obtained in a regular cylindrical pore. The simulated adsorption isotherm for the SBA-15 model shows semiquantitative agreement with the experimental isotherm for a SBA-15 sample having a similar pore size. We observe that the presence of the micropores leads to increased adsorption at low pressure compared to the case of a model without micropores in the pore walls. At higher pressures, for all models, the filling proceeds via the monolayer-multilayer adsorption on the mesopore surface followed by capillary condensation, which is mainly controlled by the mesopore diameter and is not influenced by the presence of the micropores.

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

    Science.gov (United States)

    Warczok, Piotr; Ženíšek, Jaroslav; Kozeschnik, Ernst

    2012-07-01

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

  3. A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems

    Energy Technology Data Exchange (ETDEWEB)

    Farrell, Kathryn, E-mail: kfarrell@ices.utexas.edu; Oden, J. Tinsley, E-mail: oden@ices.utexas.edu; Faghihi, Danial, E-mail: danial@ices.utexas.edu

    2015-08-15

    A general adaptive modeling algorithm for selection and validation of coarse-grained models of atomistic systems is presented. A Bayesian framework is developed to address uncertainties in parameters, data, and model selection. Algorithms for computing output sensitivities to parameter variances, model evidence and posterior model plausibilities for given data, and for computing what are referred to as Occam Categories in reference to a rough measure of model simplicity, make up components of the overall approach. Computational results are provided for representative applications.

  4. Theoretical modeling of zircon's crystal morphology according to data of atomistic calculations

    Science.gov (United States)

    Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

    2017-04-01

    Zircon is an essential mineral that is used in the U-Pb dating. Moreover, zircon is highly resistant to radioactive exposure. It is of great interest in solving both fundamental and applied problems associated with the isolation of high-level radioactive waste. There is significant progress in forecasting of the most energetically favorable crystal structures at the present time. Unfortunately, the theoretical forecast of crystal morphology at high technological level is under-explored nowadays, though the estimation of crystal equilibrium habit is extremely important in studying the physical and chemical properties of new materials. For the first time, the thesis about relation of the equilibrium shape of a crystal with its crystal structure was put forward in the works by O.Brave. According to it, the idealized habit is determined in the simplest case by a correspondence with the reticular densities Rhkl of individual faces. This approach, along with all subsequent corrections, does not take into account the nature of atoms and the specific features of the chemical bond in crystals. The atomistic calculations of crystal surfaces are commonly performed using the energetic characteristics of faces, namely, the surface energy (Esurf), which is a measure of the thermodynamic stability of the crystal face. The stable crystal faces are characterized by small positive values of Esurf. As we know from our previous research (Gromalova et al.,2015) one of the constitutive factors affecting the value of the surface energy in calculations is a choice of potentials model. In this regard, we studied several sets of parameters of atomistic interatomic potentials optimized previously. As the first test model («Zircon 1») were used sets of interatomic potentials of interaction Zr-O, Si-O and O-O in the form of Buckingham potentials. To improve playback properties of zircon additionally used Morse potential for a couple of Zr-Si, as well as the three-particle angular harmonic

  5. Matching conditions in the quasicontinuum method: Removal of the error introduced at the interface between the coarse-grained and fully atomistic region

    DEFF Research Database (Denmark)

    Shimokawa, T.; Mortensen, Jens Jørgen; Schiøtz, Jakob

    2004-01-01

    The quasicontinuum method is a way of reducing the number of degrees of freedom in an atomistic simulation by removing the majority of the atoms in regions of slowly varying strain fields. Due to the different ways the energy of the atoms is calculated in the coarse-grained regions and the regions...... where all the atoms are present, unphysical forces called "ghost forces" arise at the interfaces. Corrections may be used to almost remove the ghost forces, but the correction forces are nonconservative, ruining energy conservation in dynamic simulations. We show that it is possible to formulate...

  6. Collective dynamics in atomistic models with coupled translational and spin degrees of freedom

    Science.gov (United States)

    Perera, Dilina; Nicholson, Don M.; Eisenbach, Markus; Stocks, G. Malcolm; Landau, David P.

    2017-01-01

    Using an atomistic model that simultaneously treats the dynamics of translational and spin degrees of freedom, we perform combined molecular and spin dynamics simulations to investigate the mutual influence of the phonons and magnons on their respective frequency spectra and lifetimes in ferromagnetic bcc iron. By calculating the Fourier transforms of the space- and time-displaced correlation functions, the characteristic frequencies and the linewidths of the vibrational and magnetic excitation modes were determined. Comparison of the results with that of the stand-alone molecular dynamics and spin dynamics simulations reveals that the dynamic interplay between the phonons and magnons leads to a shift in the respective frequency spectra and a decrease in the lifetimes. Moreover, in the presence of lattice vibrations, additional longitudinal magnetic excitations were observed with the same frequencies as the longitudinal phonons.

  7. Development and assessment of atomistic models for predicting static friction coefficients

    Science.gov (United States)

    Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

    2016-08-01

    The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

  8. Atomistic simulations of nanoindentation

    Directory of Open Access Journals (Sweden)

    Izabela Szlufarska

    2006-05-01

    Full Text Available Our understanding of mechanics is pushed to its limit when the functionality of devices is controlled at the nanometer scale. A fundamental understanding of nanomechanics is needed to design materials with optimum properties. Atomistic simulations can bring an important insight into nanostructure-property relations and, when combined with experiments, they become a powerful tool to move nanomechanics from basic science to the application area. Nanoindentation is a well-established technique for studying mechanical response. We review recent advances in modeling (atomistic and beyond of nanoindentation and discuss how they have contributed to our current state of knowledge.

  9. Viscosity model for fully liquid silicate melt

    Directory of Open Access Journals (Sweden)

    Zhang Guo-Hua

    2012-01-01

    Full Text Available A model for estimating the viscosity of silicate melt as derived in our previous paper is extended to the system containing MgO, CaO, SrO, BaO, Li2O, Na2O, K2O, which can express the nonlinear variation of activation energy of viscosity with the composition. It is found that the optimized parameters of model which characterize the deforming ability of bonds around non-bridging oxygen decrease with increasing the bond strength of M-O bond expressed by I=2Q/RMz+ + rO2-2 (where Q is the valence of cation M; r is the radius. It is pointed out that viscosity is not only determined by the bond strength, but also by the radius of cation which is defined as the size effect. The radius of cation plays paradox roles in the two factors: smaller radius leads to a stronger bond, thus a higher viscosity; while cations with smaller radius are easier to diffuse when neglecting the interaction force, thus a lower viscosity will be.

  10. Prediction of TF target sites based on atomistic models of protein-DNA complexes

    Directory of Open Access Journals (Sweden)

    Collado-Vides Julio

    2008-10-01

    Full Text Available Abstract Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.

  11. Atomistic modeling of nanowires, small-scale fatigue damage in cast magnesium, and materials for MEMS

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Martin L. [Univ. of Colorado, Boulder, CO (United States); Talmage, Mellisa J. [Univ. of Colorado, Boulder, CO (United States); McDowell, David L. [Georgia Inst. of Technology, Atlanta, GA (United States); West, Neil [Univ. of Colorado, Boulder, CO (United States); Gullett, Philip Michael [Mississippi State Univ., Mississippi State, MS (United States); Miller, David C. [Univ. of Colorado, Boulder, CO (United States); Spark, Kevin [Univ. of Colorado, Boulder, CO (United States); Diao, Jiankuai [Univ. of Colorado, Boulder, CO (United States); Horstemeyer, Mark F. [Mississippi State Univ., Mississippi State, MS (United States); Zimmerman, Jonathan A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gall, K. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2006-10-01

    Lightweight and miniaturized weapon systems are driving the use of new materials in design such as microscale materials and ultra low-density metallic materials. Reliable design of future weapon components and systems demands a thorough understanding of the deformation modes in these materials that comprise the components and a robust methodology to predict their performance during service or storage. Traditional continuum models of material deformation and failure are not easily extended to these new materials unless microstructural characteristics are included in the formulation. For example, in LIGA Ni and Al-Si thin films, the physical size is on the order of microns, a scale approaching key microstructural features. For a new potential structural material, cast Mg offers a high stiffness-to-weight ratio, but the microstructural heterogeneity at various scales requires a structure-property continuum model. Processes occurring at the nanoscale and microscale develop certain structures that drive material behavior. The objective of the work presented in this report was to understand material characteristics in relation to mechanical properties at the nanoscale and microscale in these promising new material systems. Research was conducted primarily at the University of Colorado at Boulder to employ tightly coupled experimentation and simulation to study damage at various material size scales under monotonic and cyclic loading conditions. Experimental characterization of nano/micro damage will be accomplished by novel techniques such as in-situ environmental scanning electron microscopy (ESEM), 1 MeV transmission electron microscopy (TEM), and atomic force microscopy (AFM). New simulations to support experimental efforts will include modified embedded atom method (MEAM) atomistic simulations at the nanoscale and single crystal micromechanical finite element simulations. This report summarizes the major research and development accomplishments for the LDRD project

  12. Continuum Plate Theory and Atomistic Modeling to Find the Flexural Rigidity of a Graphene Sheet Interacting with a Substrate

    Directory of Open Access Journals (Sweden)

    M. W. Roberts

    2010-01-01

    Full Text Available Using a combination of continuum modeling, atomistic simulations, and numerical optimization, we estimate the flexural rigidity of a graphene sheet. We consider a rectangular sheet that is initially parallel to a rigid substrate. The sheet interacts with the substrate by van der Waals forces and deflects in response to loading on a pair of opposite edges. To estimate the flexural rigidity, we model the graphene sheet as a continuum and numerically solve an appropriate differential equation for the transverse deflection. This solution depends on the flexural rigidity. We then use an optimization procedure to find the value of the flexural rigidity that minimizes the difference between the numerical solutions and the deflections predicted by atomistic simulations. This procedure predicts a flexural rigidity of 0.26 nN nm=1.62 eV.

  13. Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

    Directory of Open Access Journals (Sweden)

    Helgi Adalsteinsson

    2008-01-01

    Full Text Available Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-level dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.

  14. An atomistically informed mesoscale model for growth and coarsening during discharge in lithium-oxygen batteries

    Energy Technology Data Exchange (ETDEWEB)

    Welland, Michael J.; Lau, Kah Chun; Redfern, Paul C.; Wolf, Dieter; Curtiss, Larry A., E-mail: curtiss@anl.gov [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Liang, Linyun [Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Zhai, Denyun [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2015-12-14

    An atomistically informed mesoscale model is developed for the deposition of a discharge product in a Li-O{sub 2} battery. This mescocale model includes particle growth and coarsening as well as a simplified nucleation model. The model involves LiO{sub 2} formation through reaction of O{sub 2}{sup −} and Li{sup +} in the electrolyte, which deposits on the cathode surface when the LiO{sub 2} concentration reaches supersaturation in the electrolyte. A reaction-diffusion (rate-equation) model is used to describe the processes occurring in the electrolyte and a phase-field model is used to capture microstructural evolution. This model predicts that coarsening, in which large particles grow and small ones disappear, has a substantial effect on the size distribution of the LiO{sub 2} particles during the discharge process. The size evolution during discharge is the result of the interplay between this coarsening process and particle growth. The growth through continued deposition of LiO{sub 2} has the effect of causing large particles to grow ever faster while delaying the dissolution of small particles. The predicted size evolution is consistent with experimental results for a previously reported cathode material based on activated carbon during discharge and when it is at rest, although kinetic factors need to be included. The approach described in this paper synergistically combines models on different length scales with experimental observations and should have applications in studying other related discharge processes, such as Li{sub 2}O{sub 2} deposition, in Li-O{sub 2} batteries and nucleation and growth in Li-S batteries.

  15. An atomistically informed mesoscale model for growth and coarsening during discharge in lithium-oxygen batteries

    Energy Technology Data Exchange (ETDEWEB)

    Welland, Michael J. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Lau, Kah Chun [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Redfern, Paul C. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Liang, Linyun [Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois 60439, USA; Zhai, Denyun [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Wolf, Dieter [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA; Curtiss, Larry A. [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA

    2015-12-14

    An atomistically informed mesoscale model is developed for the deposition of a discharge product in a Li-O-2 battery. This mescocale model includes particle growth and coarsening as well as a simplified nucleation model. The model involves LiO2 formation through reaction of O-2(-) and Li+ in the electrolyte, which deposits on the cathode surface when the LiO2 concentration reaches supersaturation in the electrolyte. A reaction-diffusion (rate-equation) model is used to describe the processes occurring in the electrolyte and a phase-field model is used to capture microstructural evolution. This model predicts that coarsening, in which large particles grow and small ones disappear, has a substantial effect on the size distribution of the LiO2 particles during the discharge process. The size evolution during discharge is the result of the interplay between this coarsening process and particle growth. The growth through continued deposition of LiO2 has the effect of causing large particles to grow ever faster while delaying the dissolution of small particles. The predicted size evolution is consistent with experimental results for a previously reported cathode material based on activated carbon during discharge and when it is at rest, although kinetic factors need to be included. The approach described in this paper synergistically combines models on different length scales with experimental observations and should have applications in studying other related discharge processes, such as Li2O2 deposition, in Li-O-2 batteries and nucleation and growth in Li-S batteries.

  16. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Directory of Open Access Journals (Sweden)

    Thomas M. Vlasic

    2016-08-01

    Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  17. Atomistic modelling and prediction of glass forming ability in bulk metallic glasses

    Science.gov (United States)

    Sedighi, Sina

    Atomistic modeling (via molecular dynamics with EAM interaction potentials) was conducted for the detailed investigation of kinetics, thermodynamics, structure, and bonding in Ni-Al and Cu-Zr metallic glasses. This work correlates GFA with the nature of atomic-level bonding and vibrational properties, with results potentially extensible to the Transition Metal -- Transition Metal and Transition Metal -- Metalloid alloy classes in general. As a first step in the development of a liquid-only GFA tuning approach, an automated tool has also been created for the broad compositional sampling of liquid and glassy phase properties in multicomponent (binary, ternary, quaternary) alloy systems. Its application to the Cu-Zr alloy system shows promising results, including the successful identification of the two highest GFA compositions, Cu50Zr50 and Cu64Zr 36. Combined, the findings of this work highlight the critical importance of incorporating more complex alloy-specific information regarding the nature of bonding and ordering at the atomic level into such an approach.

  18. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Science.gov (United States)

    Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

    2016-08-01

    This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  19. Atomistic Model for the Polyamide Formation from β-Lactam Catalyzed by Candida Antarctica Lipase B

    Energy Technology Data Exchange (ETDEWEB)

    Baum, Iris; Elsasser, Brigitta M.; Schwab, Leendert; Loos, Katja; Fels, Gregor

    2011-04-01

    Candida antarctica lipase B (CALB) is an established biocatalyst for a variety of transesterification, amidation, and polymerization reactions. In contrast to polyesters, polyamides are not yet generally accessible via enzymatic polymerization. In this regard, an enzyme-catalyzed ring-opening polymerization of {beta}-lactam (2-azetidinone) using CALB is the first example of an enzymatic polyamide formation yielding unbranched poly({beta}-alanine), nylon 3. The performance of this polymerization, however, is poor, considering the maximum chain length of 18 monomer units with an average length of 8, and the molecular basis of the reaction so far is not understood. We have employed molecular modeling techniques using docking tools, molecular dynamics, and QM/MM procedures to gain insight into the mechanistic details of the various reaction steps involved. As a result, we propose a catalytic cycle for the oligomerization of {beta}-lactam that rationalizes the activation of the monomer, the chain elongation by additional {beta}-lactam molecules, and the termination of the polymer chain. In addition, the processes leading to a premature chain termination are studied. Particularly, the QM/MM calculation enables an atomistic description of all eight steps involved in the catalytic cycle, which features an in situ-generated {beta}-alanine as the elongating monomer and which is compatible with the experimental findings.

  20. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

    Science.gov (United States)

    Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

    2016-08-25

    The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

  1. Degenerate Ising model for atomistic simulation of crystal-melt interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Schebarchov, D., E-mail: Dmitri.Schebarchov@gmail.com [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Schulze, T. P., E-mail: schulze@math.utk.edu [Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996-1300 (United States); Hendy, S. C. [The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140 (New Zealand); Department of Physics, University of Auckland, Auckland 1010 (New Zealand)

    2014-02-21

    One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level.

  2. Degenerate Ising model for atomistic simulation of crystal-melt interfaces

    Science.gov (United States)

    Schebarchov, D.; Schulze, T. P.; Hendy, S. C.

    2014-02-01

    One of the simplest microscopic models for a thermally driven first-order phase transition is an Ising-type lattice system with nearest-neighbour interactions, an external field, and a degeneracy parameter. The underlying lattice and the interaction coupling constant control the anisotropic energy of the phase boundary, the field strength represents the bulk latent heat, and the degeneracy quantifies the difference in communal entropy between the two phases. We simulate the (stochastic) evolution of this minimal model by applying rejection-free canonical and microcanonical Monte Carlo algorithms, and we obtain caloric curves and heat capacity plots for square (2D) and face-centred cubic (3D) lattices with periodic boundary conditions. Since the model admits precise adjustment of bulk latent heat and communal entropy, neither of which affect the interface properties, we are able to tune the crystal nucleation barriers at a fixed degree of undercooling and verify a dimension-dependent scaling expected from classical nucleation theory. We also analyse the equilibrium crystal-melt coexistence in the microcanonical ensemble, where we detect negative heat capacities and find that this phenomenon is more pronounced when the interface is the dominant contributor to the total entropy. The negative branch of the heat capacity appears smooth only when the equilibrium interface-area-to-volume ratio is not constant but varies smoothly with the excitation energy. Finally, we simulate microcanonical crystal nucleation and subsequent relaxation to an equilibrium Wulff shape, demonstrating the model's utility in tracking crystal-melt interfaces at the atomistic level.

  3. A fully-implicit model of the global ocean circulation

    NARCIS (Netherlands)

    Weijer, Wilbert; Dijkstra, Henk A.; Öksüzoğlu, Hakan; Wubs, Fred W.; Niet, Arie C. de

    2003-01-01

    With the recent developments in the solution methods for large-dimensional nonlinear algebraic systems, fully-implicit ocean circulation models are now becoming feasible. In this paper, the formulation of such a three-dimensional global ocean model is presented. With this implicit model, the

  4. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

    Science.gov (United States)

    Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

    2016-12-01

    The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

  5. General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium Green's function

    DEFF Research Database (Denmark)

    Stradi, Daniele; Martinez, Umberto; Blom, Anders

    2016-01-01

    this method to characterize an Ag/Si interface relevant for photovoltaic applications and study the rectifying-to-Ohmic transition as a function of the semiconductor doping. We also demonstrate that the standard “activation energy” method for the analysis of I-Vbias data might be inaccurate for nonideal...... interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid...

  6. Evaluation of Alternative Atomistic Models for the Incipient Growth of ZnO by Atomic Layer Deposition

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca

    2017-03-20

    ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural and chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.

  7. Evaluation of Alternative Atomistic Models for the Incipient Growth of ZnO by Atomic Layer Deposition

    Science.gov (United States)

    Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca

    2017-03-01

    ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural and chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.

  8. An Atomistic-Based Continuum Modeling for Evaluation of Effective Elastic Properties of Single-Walled Carbon Nanotubes

    Directory of Open Access Journals (Sweden)

    M. S. M. Al-Kharusi

    2016-01-01

    Full Text Available The mechanical behavior of SWCNTs is characterized using an atomistic-based continuum method. At nanoscale, interatomic energy among carbon atoms and the corresponding force constants are defined. Subsequently, we used an atomistic finite element analysis to calculate the energy stored in the SWCNT model, which forms a basis for calculating effective elastic moduli. In the finite element model, the force interaction among carbon atoms in a SWCNT is modeled using load-carrying structural beams. At macroscale, the SWCNT is taken as cylindrical continuum solid with transversely isotropic mechanical properties. Equivalence of energies of both models establishes a framework to calculate effective elastic moduli of armchair and zigzag nanotubes. This is achieved by solving five boundary value problems under distinct essential-controlled boundary conditions, which generates a prescribed uniform strain field in both models. Elastic constants are extracted from the calculated elastic moduli. While results of Young’s modulus obtained in this study generally concur with the published theoretical and numerical predictions, values of Poisson’s ratio are on the high side.

  9. Schwinger boson approach to the fully screened Kondo model.

    Science.gov (United States)

    Rech, J; Coleman, P; Zarand, G; Parcollet, O

    2006-01-13

    We apply the Schwinger boson scheme to the fully screened Kondo model and generalize the method to include antiferromagnetic interactions between ions. Our approach captures the Kondo crossover from local moment behavior to a Fermi liquid with a nontrivial Wilson ratio. When applied to the two-impurity model, the mean-field theory describes the "Varma-Jones" quantum phase transition between a valence bond state and a heavy Fermi liquid.

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

    Science.gov (United States)

    Zhang, W.; Mi, J.

    2016-03-01

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

  11. Asteroseismology of pulsating DA white dwarfs with fully evolutionary models

    Directory of Open Access Journals (Sweden)

    Althaus L.G.

    2013-03-01

    Full Text Available We present a new approach for asteroseismology of DA white dwarfs that consists in the employment of a large set of non-static, physically sound, fully evolutionary models representative of these stars. We already have applied this approach with success to pulsating PG1159 stars (GW Vir variables. Our white dwarf models, which cover a wide range of stellar masses, effective temperatures, and envelope thicknesses, are the result of fully evolutionary computations that take into account the complete history of the progenitor stars from the ZAMS. In particular, the models are characterized by self-consistent chemical structures from the centre to the surface, a crucial aspect of white dwarf asteroseismology. We apply this approach to an ensemble of 44 bright DAV (ZZ Ceti stars.

  12. Molecular and intermolecular effects in collagen fibril mechanics: a multiscale analytical model compared with atomistic and experimental studies.

    Science.gov (United States)

    Marino, Michele

    2016-02-01

    Both atomistic and experimental studies reveal the dependence of collagen fibril mechanics on biochemical and biophysical features such as, for instance, cross-link density, water content and protein sequence. In order to move toward a multiscale structural description of biological tissues, a novel analytical model for collagen fibril mechanics is herein presented. The model is based on a multiscale approach that incorporates and couples: thermal fluctuations in collagen molecules; the uncoiling of collagen triple helix; the stretching of molecular backbone; the straightening of the telopeptide in which covalent cross-links form; slip-pulse mechanisms due to the rupture of intermolecular weak bonds; molecular interstrand delamination due to the rupture of intramolecular weak bonds; the rupture of covalent bonds within molecular strands. The effectiveness of the proposed approach is verified by comparison with available atomistic results and experimental data, highlighting the importance of cross-link density in tuning collagen fibril mechanics. The typical three-region shape and hysteresis behavior of fibril constitutive response, as well as the transition from a yielding-like to a brittle-like behavior, are recovered with a special insight on the underlying nanoscale mechanisms. The model is based on parameters with a clear biophysical and biochemical meaning, resulting in a promising tool for analyzing the effect of pathological or pharmacological-induced histochemical alterations on the functional mechanical response of collagenous tissues.

  13. A Fully Gradient Model for Euler-Bernoulli Nanobeams

    Directory of Open Access Journals (Sweden)

    Raffaele Barretta

    2015-01-01

    Full Text Available A fully gradient elasticity model for bending of nanobeams is proposed by using a nonlocal thermodynamic approach. As a basic theoretical novelty, the proposed constitutive law is assumed to depend on the axial strain gradient, while existing gradient elasticity formulations for nanobeams contemplate only the derivative of the axial strain with respect to the axis of the structure. Variational equations governing the elastic equilibrium problem of bending of a fully gradient nanobeam and the corresponding differential and boundary conditions are thus provided. Analytical solutions for a nanocantilever are given and the results are compared with those predicted by other theories. As a relevant implication of applicative interest in the research field of nanobeams used in nanoelectromechanical systems (NEMS, it is shown that displacements obtained by the present model are quite different from those predicted by the known gradient elasticity treatments.

  14. Double transitions in the fully frustrated XY model

    Science.gov (United States)

    Jeon, Gun Sang; Park, Sung Yong; Choi, M. Y.

    1997-06-01

    The fully frustrated XY model is studied via the position-space renormalization group approach. The model is mapped into two coupled XY models, for which the scaling equations are derived. By integrating directly the scaling equations, we observe that there exists a narrow temperature range in which both the vortex and coupling charge fugacities grow large, suggesting double transitions in the system. While the transition at lower temperature is identified to be of the Kosterlitz-Thouless type, the higher-temperature one appears not to be of the Ising universality class.

  15. A self-consistent dynamo model for fully convective stars

    Science.gov (United States)

    Yadav, Rakesh Kumar; Christensen, Ulrich; Morin, Julien; Gastine, Thomas; Reiners, Ansgar; Poppenhaeger, Katja; Wolk, Scott J.

    2016-01-01

    The tachocline region inside the Sun, where the rigidly rotating radiative core meets the differentially rotating convection zone, is thought to be crucial for generating the Sun's magnetic field. Low-mass fully convective stars do not possess a tachocline and were originally expected to generate only weak small-scale magnetic fields. Observations, however, have painted a different picture of magnetism in rapidly-rotating fully convective stars: (1) Zeeman broadening measurements revealed average surface field of several kiloGauss (kG), which is similar to the typical field strength found in sunspots. (2) Zeeman-Doppler-Imaging (ZDI) technique discovered large-scale magnetic fields with a morphology often similar to the Earth's dipole-dominated field. (3) Comparison of Zeeman broadening and ZDI results showed that more than 80% of the magnetic flux resides at small scales. So far, theoretical and computer simulation efforts have not been able to reproduce these features simultaneously. Here we present a self-consistent global model of magnetic field generation in low-mass fully convective stars. A distributed dynamo working in the model spontaneously produces a dipole-dominated surface magnetic field of the observed strength. The interaction of this field with the turbulent convection in outer layers shreds it, producing small-scale fields that carry most of the magnetic flux. The ZDI technique applied to synthetic spectropolarimetric data based on our model recovers most of the large-scale field. Our model simultaneously reproduces the morphology and magnitude of the large-scale field as well as the magnitude of the small-scale field observed on low-mass fully convective stars.

  16. Atomistic Modeling of the Negative Thermal Expansion in δ- Plutonium  Based on the Two-State Description

    Directory of Open Access Journals (Sweden)

    Steven M. Valone

    2012-06-01

    Full Text Available The δ phase  of plutonium with the fcc structure exhibits an unusual negative thermal expansion (NTE over its narrow  temperature range of stability, 593–736 K. An accurate description  of the anomalous high-temperature volume effect of plutonium  goes beyond the current capability  of electronic-structure  calculations.  We propose an atomistic scheme to model the thermodynamic properties of δ-Pu based on the two-state model of Weiss for the Invar alloys, inspired by the simple free-energy analysis previously conducted by Lawson et al. The two-state mechanism is incorporated into the atomistic description of a many-body  interacting  system.  Two modified  embedded atom method potentials are employed to represent the binding energies of two competing  electronic  states in δ-Pu. We demonstrate how the NTE takes place in δ-Pu by means of Monte Carlo simulations implemented with the two-state mechanism.

  17. Revised Atomistic Models of the Crystal Structure of C-S-H with high C/S Ratio

    Science.gov (United States)

    Kovačević, Goran; Nicoleau, Luc; Nonat, André; Veryazov, Valera

    2016-09-01

    The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been studied. Atomistic C-S-H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C-S-H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C-S-H. The new geometries of C-S-H, reported in this paper, show lower relative energy with respect to the geometries from the original definition of C-S-H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values.

  18. Atomistic simulation of laser-pulse surface modification: Predictions of models with various length and time scales

    Energy Technology Data Exchange (ETDEWEB)

    Starikov, Sergey V., E-mail: starikov@ihed.ras.ru; Pisarev, Vasily V. [Moscow Institute of Physics and Technology, Dolgoprudny 141700 (Russian Federation); Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412 (Russian Federation)

    2015-04-07

    In this work, the femtosecond laser pulse modification of surface is studied for aluminium (Al) and gold (Au) by use of two-temperature atomistic simulation. The results are obtained for various atomistic models with different scales: from pseudo-one-dimensional to full-scale three-dimensional simulation. The surface modification after laser irradiation can be caused by ablation and melting. For low energy laser pulses, the nanoscale ripples may be induced on a surface by melting without laser ablation. In this case, nanoscale changes of the surface are due to a splash of molten metal under temperature gradient. Laser ablation occurs at a higher pulse energy when a crater is formed on the surface. There are essential differences between Al ablation and Au ablation. In the first step of shock-wave induced ablation, swelling and void formation occur for both metals. However, the simulation of ablation in gold shows an additional athermal type of ablation that is associated with electron pressure relaxation. This type of ablation takes place at the surface layer, at a depth of several nanometers, and does not induce swelling.

  19. Shock Particle Interaction - Fully Resolved Simulations and Modeling

    Science.gov (United States)

    Mehta, Yash; Neal, Chris; Jackson, Thomas L.; Balachandar, S. "Bala"; Thakur, Siddharth

    2016-11-01

    Currently there is a substantial lack of fully resolved data for shock interacting with multiple particles. In this talk we will fill this gap by presenting results of shock interaction with 1-D array and 3-D structured arrays of particles. Objectives of performing fully resolved simulations of shock propagation through packs of multiple particles are twofold, 1) To understand the complicated physical phenomena occurring during shock particle interaction, and 2) To translate the knowledge from microscale simulations in building next generation point-particle models for macroscale simulations that can better predict the motion (forces) and heat transfer for particles. We compare results from multiple particle simulations against the single particle simulations and make relevant observations. The drag history and flow field for multiple particle simulations are markedly different from those of single particle simluations, highlighting the effect of neighboring particles. We propose new models which capture this effect of neighboring particles. These models are called Pair-wise Interaction Extended Point Particle models (PIEP). Effect of multiple neighboring particles is broken down into pair-wise interactions, and these pair-wise interactions are superimposed to get the final model U.S. Department of Energy, National Nuclear Security Administration, Advanced Simulation and Computing Program, as a Cooperative Agreement under the Predictive Science Academic Alliance Program, under Contract No. DE-NA0002378.

  20. Atomistic modeling of metal surfaces under electric fields: direct coupling of electric fields to a molecular dynamics algorithm

    CERN Document Server

    Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

    2011-01-01

    The effect of electric fields on metal surfaces is fairly well studied, resulting in numerous analytical models developed to understand the mechanisms of ionization of surface atoms observed at very high electric fields, as well as the general behavior of a metal surface in this condition. However, the derivation of analytical models does not include explicitly the structural properties of metals, missing the link between the instantaneous effects owing to the applied field and the consequent response observed in the metal surface as a result of an extended application of an electric field. In the present work, we have developed a concurrent electrodynamic–molecular dynamic model for the dynamical simulation of an electric-field effect and subsequent modification of a metal surface in the framework of an atomistic molecular dynamics (MD) approach. The partial charge induced on the surface atoms by the electric field is assessed by applying the classical Gauss law. The electric forces acting on the partially...

  1. Fully Coupled Electromechanical Elastodynamic Model for Guided Wave Propagation Analysis

    CERN Document Server

    Borkowski, Luke; Chattopadhyay, Aditi

    2013-01-01

    Physics-based computational models play a key role in the study of wave propagation for structural health monitoring (SHM) and the development of improved damage detection methodologies. Due to the complex nature of guided waves, accurate and efficient computation tools are necessary to investigate the mechanisms responsible for dispersion, coupling, and interaction with damage. In this paper, a fully coupled electromechanical elastodynamic model for wave propagation in a heterogeneous, anisotropic material system is developed. The final framework provides the full three dimensional displacement and electrical potential fields for arbitrary plate and transducer geometries and excitation waveform and frequency. The model is validated theoretically and proven computationally efficient. Studies are performed with surface bonded piezoelectric sensors to gain insight into the physics of experimental techniques used for SHM. Collocated actuation of the fundamental Lamb wave modes is modeled over a range of frequenc...

  2. Modelling the dynamo in fully convective M-stars

    Science.gov (United States)

    Yadav, Rakesh Kumar; Christensen, Ulrich; Morin, Julien; Wolk, Scott; Poppenhaeger, Katja; Reiners, Ansgar; gastine, Thomas

    2017-05-01

    M-stars are among the most active and numerous stars in our galaxy. Their activity plays a fundamentally important role in shaping the exoplanetary biosphere since the habitable zones are very close to these stars. Therefore, modeling M-star activity has become a focal point in habitability studies. The fully convective members of the M-star population demand more immediate attention due to the discovery of Earth-like exoplanets around our stellar neighbors Proxima Centauri and TRAPPIST-1 which are both fully convective. The activity of these stars is driven by their convective dynamo, which may be fundamentally different from the solar dynamo due the absence of radiative cores. We model this dynamo mechanism using high-resolution 3D anelastic MHD simulations. To understand the evolution of the dynamo mechanism we simulate two cases, one with a fast enough rotation period to model a star in the `saturated' regime of the rotation-activity realtionship and the other with a slower period to represent cases in the `unsaturated' regime. We find the rotation period fundamentally controls the behavior of the dynamo solution: faster rotation promotes strong magnetic fields (of order kG) on both small and large length scales and the dipolar component of the magnetic field is dominant and stable, however, slower rotation leads to weaker magnetic fields which exhibit cyclic behavior. In this talk, I will present the simulation results and discuss how we can use them to interpret several observed features of the M-star activity.

  3. Adaptive modeling of shallow fully nonlinear gravity waves

    CERN Document Server

    Dutykh, Denys; Mitsotakis, Dimitrios

    2014-01-01

    This paper presents an extended version of the celebrated Serre-Green-Naghdi (SGN) system. This extension is based on the well-known Bona-Smith-Nwogu trick which aims to improve the linear dispersion properties. We show that in the fully nonlinear setting it results in modifying the vertical acceleration. Even if this technique is well-known, the effect of this modification on the nonlinear properties of the model is not clear. The first goal of this study is to shed some light on the properties of solitary waves, as the most important class of nonlinear permanent solutions. Then, we propose a simple adaptive strategy to choose the optimal value of the free parameter at every instance of time. This strategy is validated by comparing the model prediction with the reference solutions of the full Euler equations and its classical counterpart. Numerical simulations show that the new adaptive model provides a much better accuracy for the same computational complexity.

  4. Steepest-entropy-ascent nonequilibrium quantum thermodynamic framework to model chemical reaction rates at an atomistic level

    Science.gov (United States)

    Beretta, G. P.; Al-Abbasi, Omar; von Spakovsky, M. R.

    2017-04-01

    The steepest entropy ascent (SEA) dynamical principle provides a general framework for modeling the dynamics of nonequilibrium (NE) phenomena at any level of description, including the atomistic one. It has recently been shown to provide a precise implementation and meaning to the maximum entropy production principle and to encompass many well-established theories of nonequilibrium thermodynamics into a single unifying geometrical framework. Its original formulation in the framework of quantum thermodynamics (QT) assumes the simplest and most natural Fisher-Rao metric to geometrize from a dynamical standpoint the manifold of density operators, which represent the thermodynamic NE states of the system. This simplest SEAQT formulation is used here to develop a general mathematical framework for modeling the NE time evolution of the quantum state of a chemically reactive mixture at an atomistic level. The method is illustrated for a simple two-reaction kinetic scheme of the overall reaction F +H2⇔HF +F in an isolated tank of fixed volume. However, the general formalism is developed for a reactive system subject to multiple reaction mechanisms. To explicitly implement the SEAQT nonlinear law of evolution for the density operator, both the energy and the particle number eigenvalue problems are set up and solved analytically under the dilute gas approximation. The system-level energy and particle number eigenvalues and eigenstates are used in the SEAQT equation of motion to determine the time evolution of the density operator, thus effectively describing the overall kinetics of the reacting system as it relaxes toward stable chemical equilibrium. The predicted time evolution in the near-equilibrium limit is compared to the reaction rates given by a standard detailed kinetic model so as to extract the single time constant needed by the present SEA model.

  5. Steepest-entropy-ascent nonequilibrium quantum thermodynamic framework to model chemical reaction rates at an atomistic level.

    Science.gov (United States)

    Beretta, G P; Al-Abbasi, Omar; von Spakovsky, M R

    2017-04-01

    The steepest entropy ascent (SEA) dynamical principle provides a general framework for modeling the dynamics of nonequilibrium (NE) phenomena at any level of description, including the atomistic one. It has recently been shown to provide a precise implementation and meaning to the maximum entropy production principle and to encompass many well-established theories of nonequilibrium thermodynamics into a single unifying geometrical framework. Its original formulation in the framework of quantum thermodynamics (QT) assumes the simplest and most natural Fisher-Rao metric to geometrize from a dynamical standpoint the manifold of density operators, which represent the thermodynamic NE states of the system. This simplest SEAQT formulation is used here to develop a general mathematical framework for modeling the NE time evolution of the quantum state of a chemically reactive mixture at an atomistic level. The method is illustrated for a simple two-reaction kinetic scheme of the overall reaction F+H_{2}⇔HF+F in an isolated tank of fixed volume. However, the general formalism is developed for a reactive system subject to multiple reaction mechanisms. To explicitly implement the SEAQT nonlinear law of evolution for the density operator, both the energy and the particle number eigenvalue problems are set up and solved analytically under the dilute gas approximation. The system-level energy and particle number eigenvalues and eigenstates are used in the SEAQT equation of motion to determine the time evolution of the density operator, thus effectively describing the overall kinetics of the reacting system as it relaxes toward stable chemical equilibrium. The predicted time evolution in the near-equilibrium limit is compared to the reaction rates given by a standard detailed kinetic model so as to extract the single time constant needed by the present SEA model.

  6. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

    Science.gov (United States)

    Rzepiela, Andrzej J; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J

    2011-06-14

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1:1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein

  7. Atomistic simulations of anionic Au-144(SR)(60) nanoparticles interacting with asymmetric model lipid membranes

    DEFF Research Database (Denmark)

    Heikkila, E.; Martinez-Seara, H.; Gurtovenko, A. A.

    2014-01-01

    Experimental observations indicate that the interaction between nanoparticles and lipid membranes varies according to the nanoparticle charge and the chemical nature of their protecting side groups. We report atomistic simulations of an anionic Au nanoparticle (AuNP-) interacting with membranes...... clearly show that AuNP- attaches to the extracellular membrane surface within a few tens of nanoseconds, while it avoids contact with the membrane on the cytosolic side. This behavior stems from several factors. In essence, when the nanoparticle interacts with lipids in the extracellular compartment......, it forms relatively weak contacts with the zwitterionic head groups (in particular choline) of the phosphatidylcholine lipids. Consequently, AuNP- does not immerse deeply in the leaflet, enabling, e.g., lateral diffusion of the nanoparticle along the surface. On the cytosolic side, AuNP- remains...

  8. Hybrid Methods and Atomistic Models to Explore Free Energies, Rates and Pathways of Protein Shape Changes

    DEFF Research Database (Denmark)

    Wang, Yong

    revisited the problem of accurately quantifying the thermodynamics and kinetics, by following a novel route. In this route both of the forward and backward rates are calculated directly from MD simulations using a recently developed enhanced sampling method, called \\infrequent metadynamics......When I just joined the Lindor-Larsen group as a fresh PhD student, the Nobel Prize in Chemistry that year was awarded for the development of multiscale models for complex chemical systems" to prize the pioneering works of Martin Karplus, Michael Levitt and Arieh Warshel. As a computational...... an irreplaceable role rather than supporting role of wet-lab experiments, to obtain a complete understanding of complex biomolecules. Some of the progress in the eld has been introduced in the rst Chapter of this thesis. Despite its enormous success, this eld has not yet been fully developed. In some respects...

  9. 19-vertex version of the fully frustrated XY model

    Science.gov (United States)

    Knops, Yolanda M. M.; Nienhuis, Bernard; Knops, Hubert J. F.; Blöte, Henk W. J.

    1994-07-01

    We investigate a 19-vertex version of the two-dimensional fully frustrated XY (FFXY) model. We construct Yang-Baxter equations for this model and show that there is no solution. Therefore we have chosen a numerical approach based on the transfer matrix. The results show that a coupled XY Ising model is in the same universality class as the FFXY model. We find that the phase coupling over an Ising wall is irrelevant at criticality. This leads to a correction of earlier determinations of the dimension x*h,Is of the Ising disorder operator. We find x*h,Is=0.123(5) and a conformal anomaly c=1.55(5). These results are consistent with the hypothesis that the FFXY model behaves as a superposition of an Ising model and an XY model. However, the dimensions associated with the energy, xt=0.77(3), and with the XY magnetization xh,XY~=0.17, refute this hypothesis.

  10. Insight into the influence of liquid paraffin for methanol synthesis on Cu(110) surface using continuum and atomistic models

    Energy Technology Data Exchange (ETDEWEB)

    Jiao, Wei-Hong [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Liu, Shi-Zhong [Department of Chemistry, Stony Brook University, Stony Brook, NY 11794 (United States); Zuo, Zhi-Jun, E-mail: zuozhijun@tyut.edu.cn [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Ren, Rui-Peng; Gao, Zhi-Hua [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Huang, Wei, E-mail: huangwei@tyut.edu.cn [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China)

    2016-11-30

    Highlights: • The influence of liquid paraffin is studied using continuum and atomistic models. • Liquid paraffin does not alter the reaction pathways of CO hydrogenation and WGS. • Liquid paraffin alters the reaction pathways of CO{sub 2} hydrogenation. - Abstract: Methanol synthesis from CO/CO{sub 2} hydrogenation and water-gas shift (WGS) reaction on Cu(110) in liquid paraffin and vacuum have been systematically researched with density functional theory calculation (DFT). For methanol synthesis from CO hydrogenation, the reaction pathways in liquid paraffin and vacuum are CO + H → HCO → H{sub 2}CO → H{sub 3}CO → H{sub 3}COH; in the case of WGS, the reaction pathways in liquid paraffin and vacuum are CO + 2H{sub 2}O → CO + 2OH + 2H → CO + H{sub 2}O + O + H{sub 2} → CO{sub 2} + H{sub 2}O + H{sub 2}; the reaction pathways of methanol synthesis from CO{sub 2} hydrogenation in liquid paraffin and vacuum are CO{sub 2} + H → HCOO → H{sub 2}COO → H{sub 2}CO → H{sub 3}CO → H{sub 3}COH and CO{sub 2} + H → HCOO → HCOOH → H{sub 2}COOH → H{sub 3}CO → H{sub 3}COH, respectively. The result shows that liquid paraffin does not affect the reaction mechanisms of methanol synthesis from CO and WGS, but it changes the reaction mechanisms of methanol synthesis from CO{sub 2} hydrogenation. Hirshfeld charge and the d-band centers indicate that the catalytic activity of Cu(110) in liquid paraffin is smaller than that in vacuum. Our results also show that it is necessary to consider both continuum and atomistic models in the slurry bed.

  11. Parallel implementation of approximate atomistic models of the AMOEBA polarizable model

    Science.gov (United States)

    Demerdash, Omar; Head-Gordon, Teresa

    2016-11-01

    In this work we present a replicated data hybrid OpenMP/MPI implementation of a hierarchical progression of approximate classical polarizable models that yields speedups of up to ∼10 compared to the standard OpenMP implementation of the exact parent AMOEBA polarizable model. In addition, our parallel implementation exhibits reasonable weak and strong scaling. The resulting parallel software will prove useful for those who are interested in how molecular properties converge in the condensed phase with respect to the MBE, it provides a fruitful test bed for exploring different electrostatic embedding schemes, and offers an interesting possibility for future exascale computing paradigms.

  12. Modeling supersonic combustion using a fully-implicit numerical method

    Science.gov (United States)

    Maccormack, Robert W.; Wilson, Gregory J.

    1990-01-01

    A fully-implicit finite-volume algorithm for two-dimensional axisymmetric flows has been coupled to a detailed hydrogen-air reaction mechanism (13 species and 33 reactions) so that supersonic combustion phenomena may be investigated. Numerical computations are compared with ballistic-range shadowgraphs of Lehr (1972) that exhibit two discontinuities caused by a blunt body as it passes through a premixed stoichiometric hydrogen-air mixture. The suitability of the numerical procedure for simulating these double-front flows is shown. The requirements for the physical formulation and the numerical modeling of these flowfields are discussed. Finally, the sensitivity of these external flowfields to changes in certain key reaction rate constants is examined.

  13. A fully dynamic magneto-rheological fluid damper model

    Science.gov (United States)

    Jiang, Z.; Christenson, R. E.

    2012-06-01

    Control devices can be used to dissipate the energy of a civil structure subjected to dynamic loading, thus reducing structural damage and preventing failure. Semiactive control devices have received significant attention in recent years. The magneto-rheological (MR) fluid damper is a promising type of semiactive device for civil structures due to its mechanical simplicity, inherent stability, high dynamic range, large temperature operating range, robust performance, and low power requirements. The MR damper is intrinsically nonlinear and rate-dependent, both as a function of the displacement across the MR damper and the command current being supplied to the MR damper. As such, to develop control algorithms that take maximum advantage of the unique features of the MR damper, accurate models must be developed to describe its behavior for both displacement and current. In this paper, a new MR damper model that includes a model of the pulse-width modulated (PWM) power amplifier providing current to the damper, a proposed model of the time varying inductance of the large-scale 200 kN MR dampers coils and surrounding MR fluid—a dynamic behavior that is not typically modeled—and a hyperbolic tangent model of the controllable force behavior of the MR damper is presented. Validation experimental tests are conducted with two 200 kN large-scale MR dampers located at the Smart Structures Technology Laboratory (SSTL) at the University of Illinois at Urbana-Champaign and the Lehigh University Network for Earthquake Engineering Simulation (NEES) facility. Comparison with experimental test results for both prescribed motion and current and real-time hybrid simulation of semiactive control of the MR damper shows that the proposed MR damper model can accurately predict the fully dynamic behavior of the large-scale 200 kN MR damper.

  14. A fully polarimetric scattering model for a coniferous forest

    Science.gov (United States)

    Karam, M. A.; Fung, A. K.; Lopes, A.; Mougin, E.

    1991-01-01

    For an elliptically polarized plane wave exciting a coniferous forested canopy a fully polarimetric scattering model has been developed to account for the size and orientation distributions of each forest constituent. A canopy is divided into three layers over a rough interface. The upper two layers represent the crown with its constituents (leaves, stems, and branches). The lower layer stands for the trunks and the rough interface is the canopy-ground interface. For a plane wave exciting the canopy, the explicit expressions for the bistatic scattering coefficient associated with each scattering mechanism are given. For an elliptically polarized incidence wave, the present model can be recast in a form suitable for polarimetric wave synthesis. The model validation is justified by comparing the measured and the calculated values of the backscattering coefficients for a linearly polarized incident wave. The comparison is made over a wide range of frequencies and incident angles. Numerical simulations are conducted to calculate the radar polarization signature of the canopy for different incident frequencies and angles.

  15. Ovine ear model for fully endoscopic stapedectomy training.

    Science.gov (United States)

    Cordero, A; Benítez, S; Reyes, P; Vaca, M; Polo, R; Pérez, C; Alonso, A; Cobeta, I

    2015-09-01

    Endoscopic surgery of the middle ear is progressively gaining the interest of otologists, as technological advances have overcome some of its main drawbacks. The long learning curve required to master this technique, urges the search for models to practice it. After the validation of sheep's ear as a proper training model for microscopic stapedectomy, our objective is to demonstrate its adequacy for practicing stapes surgery but performed through a fully endoscopic approach. Endoscopic stapedectomy was performed by two surgeons in 40 sheep ears (20 specimens each). To analyze the effects of the learning curve on surgical success, complication rates and surgical time reduction, the sample was divided in two groups: group 1 being the first ten procedures of each surgeon, and group 2 the second set of stapedectomies. The impact of the operated side and the resection of the chordal spine were also studied. No statistically significant differences were found considering the operated side. A statistically significant improvement in some of the surgical steps was demonstrated comparing both groups and also after the resection of the chordal spine. Mean surgical time declined from 38 to 31.5 min (p sheep ear is an optimal model for endoscopic middle ear surgery, as it allows for the acquisition of the skills required to master this technique.

  16. Exploring the structure-solubility relationship of asphaltene models in toluene, heptane, and amphiphiles using a molecular dynamic atomistic methodology.

    Science.gov (United States)

    Aray, Yosslen; Hernández-Bravo, Raiza; Parra, José G; Rodríguez, Jesús; Coll, David S

    2011-10-27

    The solubility parameters, δ, of several asphaltene models were calculated by mean of an atomistic NPT ensemble. Continental and archipelago models were explored. A relationship between the solubility parameter and the molecule structure was determined. In general, increase of the fused-rings number forming the aromatic core and the numbers of heteroatoms such as oxygen, nitrogen, and sulfur produces an increase of the solubility parameter, while increases of the numbers and length of the aliphatic chains yield a systematic decrease of this parameter. Molecules with large total carbon atom number at the tails, n(c), and small aromatic ring number, n(r), exhibit the biggest values of δ, while molecules with small n(c) and large n(r) show the smallest δ values. A good polynomial correlation δ = 5.967(n(r)/n(c)) - 3.062(n(r)/n(c))(2) + 0.507(n(r)/n(c))(3) + 16.593 with R(2) = 0.965 was found. The solubilities of the asphaltene models in toluene, heptane, and amphiphiles were studied using the Scatchard-Hildebrand and the Hansen sphere methodologies. Generally, there is a large affinity between the archipelago model and amphiphiles containing large aliphatic tails and no aromatic rings, while continental models show high affinity for amphiphiles containing an aromatic ring and small aliphatic chains.

  17. Shape evolution of nanostructures by thermal and ion beam processing. Modeling and atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Roentzsch, L.

    2007-07-01

    Single-crystalline nanostructures often exhibit gradients of surface (and/or interface) curvature that emerge from fabrication and growth processes or from thermal fluctuations. Thus, the system-inherent capillary force can initiate morphological transformations during further processing steps or during operation at elevated temperature. Therefore and because of the ongoing miniaturization of functional structures which causes a general rise in surface-to-volume ratios, solid-state capillary phenomena will become increasingly important: On the one hand diffusion-mediated capillary processes can be of practical use in view of non-conventional nanostructure fabrication methods based on self-organization mechanisms, on the other hand they can destroy the integrity of nanostructures which can go along with the failure of functionality. Additionally, capillarity-induced shape transformations are effected and can thereby be controlled by applied fields and forces (guided or driven evolution). With these prospects and challenges at hand, formation and shape transformation of single-crystalline nanostructures due to the system-inherent capillary force in combination with external fields or forces are investigated in the frame of this dissertation by means of atomistic computer simulations. For the exploration (search, description, and prediction) of reaction pathways of nanostructure shape transformations, kinetic Monte Carlo (KMC) simulations are the method of choice. Since the employed KMC code is founded on a cellular automaton principle, the spatio-temporal development of lattice-based N-particle systems (N up to several million) can be followed for time spans of several orders of magnitude, while considering local phenomena due to atomic-scale effects like diffusion, nucleation, dissociation, or ballistic displacements. In this work, the main emphasis is put on nanostructures which have a cylindrical geometry, for example, nanowires (NWs), nanorods, nanotubes etc

  18. Atomistic modeling of oil shale kerogens and asphaltenes along with their interactions with the inorganic mineral matrix

    Energy Technology Data Exchange (ETDEWEB)

    Facelli, Julio [Univ. of Utah, Salt Lake City, UT (United States); Pugmire, Ronald [Univ. of Utah, Salt Lake City, UT (United States); Pimienta, Ian [Univ. of Utah, Salt Lake City, UT (United States)

    2011-03-31

    The goal of this project is to obtain and validate three dimensional atomistic models for the organic matter in both oil shales and oil sands. In the case of oil shales the modeling was completed for kerogen, the insoluble portion of the organic matter; for oil sands it was for asphaltenes, a class of molecules found in crude oil. The three dimensional models discussed in this report were developed starting from existing literature two dimensional models. The models developed included one kerogen, based on experimental data on a kerogen isolated from a Green River oil shale, and a set of six representative asphaltenes. Subsequently, the interactions between these organic models and an inorganic matrix was explored in order to gain insight into the chemical nature of this interaction, which could provide vital information in developing efficient methods to remove the organic material from inorganic mineral substrate. The inorganic substrate used to model the interaction was illite, an aluminum silicate oxide clay. In order to obtain the feedback necessary to validate the models, it is necessary to be able to calculate different observable quantities and to show that these observables both reproduce the results of experimental measurements on actual samples as well as that the observables are sensitive to structural differences between models. The observables that were calculated using the models include 13C NMR spectra, the IR vibrational spectra, and the atomic pair wise distribution function; these were chosen as they are among the methods for which both experimental and calculated values can be readily obtained. Where available, comparison was made to experiment results. Finally, molecular dynamic simulations of pyrolysis were completed on the models to gain an understanding into the nature of the decomposition of these materials when heated.

  19. A stochastic approximation approach to improve the convergence behavior of hierarchical atomistic-to-continuum multiscale models

    Science.gov (United States)

    Wurm, Patrick; Ulz, Manfred H.

    2016-10-01

    The aim of this work is to provide an improved information exchange in hierarchical atomistic-to-continuum settings by applying stochastic approximation methods. For this purpose a typical model belonging to this class is chosen and enhanced. On the macroscale of this particular two-scale model, the balance equations of continuum mechanics are solved using a nonlinear finite element formulation. The microscale, on which a canonical ensemble of statistical mechanics is simulated using molecular dynamics, replaces a classic material formulation. The constitutive behavior is computed on the microscale by computing time averages. However, these time averages are thermal noise-corrupted as the microscale may practically not be tracked for a sufficiently long period of time due to limited computational resources. This noise prevents the model from a classical convergence behavior and creates a setting that shows remarkable resemblance to iteration schemes known from stochastic approximation. This resemblance justifies the use of two averaging strategies known to improve the convergence behavior in stochastic approximation schemes under certain, fairly general, conditions. To demonstrate the effectiveness of the proposed strategies, three numerical examples are studied.

  20. Atomistic modeling of a KRT35/KRT85 keratin dimer: folding in aqueous solution and unfolding under tensile load.

    Science.gov (United States)

    Duchstein, Patrick; Clark, Tim; Zahn, Dirk

    2015-09-14

    We present an atomistic model of a full KRT35/KRT85 dimer, a fundamental building block of human hair. For both monomers initial structures were generated using empirical tools based on homology considerations, followed by the formulation of a naiïve dimer model from docking the monomers in vacuum. Relaxation in aqueous solution was then explored from molecular dynamics simulation. Driven by hydrophobic segregation and protein-protein hydrogen bonding relaxation dynamics result in a folded dimer arrangement which shows a striking encounter of cystein groups. Our simulations hence suggests that (i) cystein groups in the coil regions of keratin are well suited to establish disulfide bonds between the two monomers that constitute the dimer, and (ii) the particularly large number of cystein groups in the head and tail regions promotes the connection of dimers to establish meso- to macroscale fibers. Moreover, we show the molecular mechanisms of elastic and plastic deformation under tensile load. Upon elongation beyond the elastic regime, unfolding was identified as the exposure of hydrophobic moieties and the breaking of protein-protein hydrogen bonds. Therein, the step-wise character of the series of unfolding events leads to a broad regime of constant force in response to further elongation.

  1. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Alan [The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Harlen, Oliver G. [University of Leeds, Leeds LS2 9JT (United Kingdom); Harris, Sarah A., E-mail: s.a.harris@leeds.ac.uk [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Leeds, Leeds LS2 9JT (United Kingdom); Khalid, Syma; Leung, Yuk Ming [University of Southampton, Southampton SO17 1BJ (United Kingdom); Lonsdale, Richard [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg (Germany); Mulholland, Adrian J. [University of Bristol, Bristol BS8 1TS (United Kingdom); Pearson, Arwen R. [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Hamburg, Hamburg (Germany); Read, Daniel J.; Richardson, Robin A. [University of Leeds, Leeds LS2 9JT (United Kingdom); The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom)

    2015-01-01

    The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  2. Insight into the influence of liquid paraffin for methanol synthesis on Cu(110) surface using continuum and atomistic models

    Science.gov (United States)

    Jiao, Wei-Hong; Liu, Shi-Zhong; Zuo, Zhi-Jun; Ren, Rui-Peng; Gao, Zhi-Hua; Huang, Wei

    2016-11-01

    Methanol synthesis from CO/CO2 hydrogenation and water-gas shift (WGS) reaction on Cu(110) in liquid paraffin and vacuum have been systematically researched with density functional theory calculation (DFT). For methanol synthesis from CO hydrogenation, the reaction pathways in liquid paraffin and vacuum are CO + H → HCO → H2CO → H3CO → H3COH; in the case of WGS, the reaction pathways in liquid paraffin and vacuum are CO + 2H2O → CO + 2OH + 2H → CO + H2O + O + H2 → CO2 + H2O + H2; the reaction pathways of methanol synthesis from CO2 hydrogenation in liquid paraffin and vacuum are CO2 + H → HCOO → H2COO → H2CO → H3CO → H3COH and CO2 + H → HCOO → HCOOH → H2COOH → H3CO → H3COH, respectively. The result shows that liquid paraffin does not affect the reaction mechanisms of methanol synthesis from CO and WGS, but it changes the reaction mechanisms of methanol synthesis from CO2 hydrogenation. Hirshfeld charge and the d-band centers indicate that the catalytic activity of Cu(110) in liquid paraffin is smaller than that in vacuum. Our results also show that it is necessary to consider both continuum and atomistic models in the slurry bed.

  3. Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

    Science.gov (United States)

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

    2016-10-15

    Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  4. The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II

    Science.gov (United States)

    Limmer, David T.; Chandler, David

    2013-06-01

    This paper extends our earlier studies of free energy functions of density and crystalline order parameters for models of supercooled water, which allows us to examine the possibility of two distinct metastable liquid phases [D. T. Limmer and D. Chandler, J. Chem. Phys. 135, 134503 (2011), 10.1063/1.3643333 and preprint arXiv:1107.0337 (2011)]. Low-temperature reversible free energy surfaces of several different atomistic models are computed: mW water, TIP4P/2005 water, Stillinger-Weber silicon, and ST2 water, the last of these comparing three different treatments of long-ranged forces. In each case, we show that there is one stable or metastable liquid phase, and there is an ice-like crystal phase. The time scales for crystallization in these systems far exceed those of structural relaxation in the supercooled metastable liquid. We show how this wide separation in time scales produces an illusion of a low-temperature liquid-liquid transition. The phenomenon suggesting metastability of two distinct liquid phases is actually coarsening of the ordered ice-like phase, which we elucidate using both analytical theory and computer simulation. For the latter, we describe robust methods for computing reversible free energy surfaces, and we consider effects of electrostatic boundary conditions. We show that sensible alterations of models and boundary conditions produce no qualitative changes in low-temperature phase behaviors of these systems, only marginal changes in equations of state. On the other hand, we show that altering sampling time scales can produce large and qualitative non-equilibrium effects. Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light.

  5. Bridging Atomistic/Continuum Scales in Solids with Moving Dislocations

    Institute of Scientific and Technical Information of China (English)

    TANG Shao-Qiang; LIU Wing K.; KARPOV Eduard G.; HOU Thomas Y.

    2007-01-01

    @@ We propose a multiscale method for simulating solids with moving dislocations. Away from atomistic subdomains where the atomistic dynamics are fully resolved, a dislocation is represented by a localized jump profile, superposed on a defect-free field. We assign a thin relay zone around an atomistic subdomain to detect the dislocation profile and its propagation speed at a selected relay time. The detection technique utilizes a lattice time history integral treatment. After the relay, an atomistic computation is performed only for the defect-free field. The method allows one to effectively absorb the fine scale fluctuations and the dynamic dislocations at the interface between the atomistic and continuum domains. In the surrounding region, a coarse grid computation is adequate.

  6. Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

    Science.gov (United States)

    Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

    2010-12-01

    Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs

  7. Modeling and characterization of the elastic behavior of interfaces in nanostructured materials: From an atomistic description to a continuum approach

    Science.gov (United States)

    Dingreville, Remi

    Steady technological progresses in all fields of nanoscale technology and probe technology have enabled the synthesis, the assembly, the development, the characterization and the improvement of nanostructured materials. The lack of understanding of their macroscopic behavior is a major roadblock for inserting these materials into engineering applications. Partially due to these rapid advances in nano-scale and nano-structured materials, there has been a resurgence of interest in surface elastic properties such as surface energy, surface stresses, and surface elastic stiffness. Because of the large surface-to-volume ratio in nano-materials, surface elastic properties become more prominent. They have strong influence on the overall thermo-mechanical behavior of the nano-materials. In this dissertation, an innovative approach combining continuum mechanics and atomistic simulations is exposed to develop a nanomechanics theory for modeling and predicting the macroscopic behavior of nanomaterials. This nanomechanics theory exhibits the simplicity of the continuum formulation while taking into account the discrete atomic structure and interaction near surfaces/interfaces. There are four primary objectives to this dissertation. First, theory of interfaces is revisited to better understand its behavior and effects on the overall behavior of nanostructures. Second, atomistic tools are provided in order to efficiently determine the properties of free surfaces and interfaces. Interface properties are reported in this work, with comparison to both theoretical and experimental characterizations of interfaces. Specifically, we report surface elastic properties of groups 10--11 transition metals as well as properties for low-CSL grain boundaries in copper. Third, we propose a continuum framework that casts the atomic level information into continuum quantities that can be used to analyze, model and simulate macroscopic behavior of nanostructured materials. In particular, we study

  8. Domain-wall induced XY disorder in the fully frustrated XY model

    Science.gov (United States)

    Granato, Enzo

    1987-02-01

    The defect-mediated phase transition in the fully frustrated XY model is discussed. A Migdal-Kadanoff position-space renormalization group analysis is employed to investigate the critical behavior of a similar model in the same universality class as the fully frustrated XY model. The resulting phase diagram shows that XY order cannot co-exist with Ising disorder. This is in agreement with recently suggested phase-transition scenario in the fully frustrated XY model.

  9. Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

    Energy Technology Data Exchange (ETDEWEB)

    Zapol, Peter (Argonne National Laboratory, Argonne, IL); Bourg, Ian (Lawrence Berkeley National Laboratories, Berkeley, CA); Criscenti, Louise Jacqueline; Steefel, Carl I. (Lawrence Berkeley National Laboratories, Berkeley, CA); Schultz, Peter Andrew

    2011-10-01

    This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers, classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.

  10. Fully nonlinear and exact perturbations of the Friedmann world model

    CERN Document Server

    Hwang, Jai-chan

    2012-01-01

    In 1988 Bardeen has suggested a pragmatic formulation of cosmological perturbation theory which is powerful in practice to employ various fundamental gauge conditions easily depending on the character of the problem. The perturbation equations are presented without fixing the temporal gauge condition and are arranged so that one can easily impose fundamental gauge conditions by simply setting one of the perturbation variables in the equations equal to zero. In this way one can use the gauge degrees of freedom as an advantage in handling problems. Except for the synchronous gauge condition, all the other fundamental gauge conditions completely fix the gauge mode, and consequently, each variable in such a gauge has a unique gauge invariant counterpart, so that we can identify the variable as the gauge-invariant one. Here, we extend Bardeen's linear formulation to fully nonlinear order in perturbations, with the gauge advantage kept intact. Derived equations are exact, and from these we can easily expand to high...

  11. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

    Directory of Open Access Journals (Sweden)

    Nikolay Korolev

    2014-05-01

    Full Text Available Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1–100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

  12. On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation

    Science.gov (United States)

    Garrido, J. M.; Algaba, J.; Míguez, J. M.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.; Piñeiro, M. M.; Blas, F. J.

    2016-04-01

    We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

  13. The structure and physical properties of paracrystalline atomistic models of amorphous silicon.

    Energy Technology Data Exchange (ETDEWEB)

    Voyles, P. M.; Zotov, N.; Nakhmanson, S. M.; Drabold, D. A.; Gibson, J. M.; Treacy, M. M. J.; Keblinski, P.; Materials Science Division; Univ. of Illinois; Univ. Bayreuth; Ohio Univ.; NEC Research Inst.; Rensselaer Polytechnic Inst.

    2001-11-01

    We have examined the structure and physical properties of paracrystalline molecular dynamics models of amorphous silicon. Simulations from these models show qualitative agreement with the results of recent mesoscale fluctuation electron microscopy experiments on amorphous silicon and germanium. Such agreement is not found in simulations from continuous random network models. The paracrystalline models consist of topologically crystalline grains which are strongly strained and a disordered matrix between them. We present extensive structural and topological characterization of the medium range order present in the paracrystalline models and examine their physical properties, such as the vibrational density of states, Raman spectra, and electron density of states. We show by direct simulation that the ratio of the transverse acoustic mode to transverse optical mode intensities I{sub TA}/I{sub TO} in the vibrational density of states and the Raman spectrum can provide a measure of medium range order. In general, we conclude that the current paracrystalline models are a good qualitative representation of the paracrystalline structures observed in the experiment and thus provide guidelines toward understanding structure and properties of medium-range-ordered structures of amorphous semiconductors as well as other amorphous materials.

  14. Atomistic Model of Physical Ageing in Se-rich As-Se Glasses

    Energy Technology Data Exchange (ETDEWEB)

    Golovchak,R.; Shpotyuk, O.; Kozdras, A.; Bureau, B.; Vlcek, M.; Ganjoo, A.; Jain, H.

    2007-01-01

    Thermal, optical, X-ray excited and magnetic methods were used to develop a microstructural model of physical ageing in Se-rich glasses. The glass composition As10Se90, possessing a typical cross-linked chain structure, was chosen as a model object for the investigations. The effect of physical ageing in this glass was revealed by differential scanning calorimetry, whereas the corresponding changes in its atomic arrangement were studied by extended X-ray absorption fine structure, Raman and solid-state 77Se nuclear magnetic resonance spectroscopy. Straightening-shrinkage processes are shown to be responsible for the physical ageing in this Se-rich As-Se glass.

  15. Warps and waves in fully cosmological models of galactic discs

    CERN Document Server

    Gómez, Facundo A; Grand, Robert J J; Marinacci, Federico; Springel, Volker; Pakmor, Rüdiger

    2016-01-01

    Recent studies have revealed an oscillating asymmetry in the vertical structure of the Milky Way's disc. Here we analyze 16 high-resolution, fully cosmological simulations of the evolution of individual Milky Way-sized galaxies, carried out with the MHD code AREPO. At redshift zero, about $70\\%$ of our galactic discs show strong vertical patterns, with amplitudes that can exceed 2 kpc. Half of these are typical `integral sign' warps. The rest are oscillations similar to those observed in the Milky Way. Such structures are thus expected to be common. The associated mean vertical motions can be as large as 30 km/s. Cold disc gas typically follows the vertical patterns seen in the stars. These perturbations have a variety of causes: close encounters with satellites, distant flybys of massive objects, accretion of misaligned cold gas from halo infall or from mergers. Tidally induced vertical patterns can be identified in both young and old stellar populations, whereas those originating from cold gas accretion are...

  16. A fully cosmological model of a Monoceros-like ring

    CERN Document Server

    Gómez, Facundo A; Marinacci, Federico; Slater, Colin T; Grand, Robert J J; Springel, Volker; Pakmor, Rüdiger

    2015-01-01

    We study the vertical structure of a stellar disk obtained from a fully cosmological high-resolution hydrodynamical simulation of the formation of a Milky Way-like galaxy. At the present day, the disk's mean vertical height shows a well-defined and strong pattern, with amplitudes as large as 3 kpc in its outer regions. This pattern is the result of a satellite - host halo - disk interaction and reproduces, qualitatively, many of the observable properties of the Monoceros Ring. In particular we find disk material at the distance of Monoceros extending far above the mid plane (30$^{\\circ}$) in both hemispheres, as well as well-defined arcs of disk material at heliocentric distances $\\gtrsim 5$ kpc. The pattern was first excited $\\approx 3$ Gyr ago as an $m=1$ mode that later winds up into a leading spiral pattern. Interestingly, the main driver behind this perturbation is a low-mass low-velocity fly-by encounter. The satellite has total mass, pericentre distance and pericentric velocity of $\\sim 5\\%$ of the hos...

  17. Finite Deformation by Elasticity, Slip, and Twinning: Atomistic Considerations, Continuum Modeling, and Application to Ceramic Crystals

    Science.gov (United States)

    2009-03-01

    finite shear strains associated with slip and deformation twinning and improper lattice rotations across twin boundaries . Nonlinear anisotropic...of (2) results from gradients in twin fractions, e.g. interface dislocations at tapered twin boundaries . Disclination models of twins (Clayton et

  18. Fluid Simulations with Atomistic Resolution: Multiscale Model with Account of Nonlocal Momentum Transfer

    NARCIS (Netherlands)

    Svitenkov, A.I.; Chivilikhin, S.A.; Hoekstra, A.G.; Boukhanovsky, A.V.

    2015-01-01

    Nano- and microscale flow phenomena turn out to be highly non-trivial for simulation and require the use of heterogeneous modeling approaches. While the continuum Navier-Stokes equations and related boundary conditions quickly break down at those scales, various direct simulation methods and hybrid

  19. Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations

    CERN Document Server

    Yu, Jin

    2015-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We keep away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while address only statistical physics modeling approach and all-atom molecular dynamics simulation approach. We organize this review around our own modeling and simulation practices on a single-subunit T7 RNA poly...

  20. Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

    Science.gov (United States)

    van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; Dohn, Asmus O.; Harlang, Tobias; Chollet, Matthieu; Christensen, Morten; Gawelda, Wojciech; Henriksen, Niels E.; Kim, Jong Goo; Haldrup, Kristoffer; Kim, Kyung Hwan; Ihee, Hyotcherl; Kim, Jeongho; Lemke, Henrik; Sun, Zheng; Sundström, Villy; Zhang, Wenkai; Zhu, Diling; Møller, Klaus B.; Nielsen, Martin M.; Gaffney, Kelly J.

    2016-11-01

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute-solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.

  1. Atomistic modeling of different loading paths in single crystal copper and aluminum

    Directory of Open Access Journals (Sweden)

    R. Pezer

    2016-10-01

    Full Text Available Utilizing molecular dynamics (MD integration model we have investigated some of the relevant physical processes caused by different loading paths at the atomic level in Cu and Al monocrystal specimen. Interactions among the atoms in the bulk are modeled with the standard realistic Embedded Atom Method (EAM potentials. MD simulation gives us the detailed information about non-equilibrium dynamics including crystal structure defects, vacancies and dislocations. In particular, we have obtained result that indicate increase in the total energy of the crystal during loading (especially cyclic that provides us direct quantitative evidence of the metal weakening. For the basic response, we have deformed copper and aluminum single crystal according to the simple loading path and a series of multiaxial loading-paths including cyclic repetition. We compute equivalent stress-strain diagrams as well as dislocation total length vs time graphs to describe signatures of the anisotropic response of the crystal

  2. Atomistic simulations of electrolyte solutions and hydrogels with explicit solvent models

    CERN Document Server

    Walter, Jonathan; Reiser, Steffen; Horsch, Martin; Vrabec, Jadran; Hasse, Hans

    2011-01-01

    Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the development and optimization of molecular force fields and models, a large number of simulation runs have to be evaluated to obtain the sensitivity of the target properties with respect to the model parameters. The present work discusses force field development for electrolytes regarding thermodynamic properties of their aqueous solutions. Furthermore, simulations are conducted for the volume transition of hydrogels in the presence of electrolytes. It is shown that the properties of these complex systems can be captured by molecular simulation.

  3. Hybrid Methods and Atomistic Models to Explore Free Energies, Rates and Pathways of Protein Shape Changes

    DEFF Research Database (Denmark)

    Wang, Yong

    biologist, I was proud and excited for the breaking news as this prize is not only to them, but also to the whole community of computational biology. There has been progress in the modeling of protein dynamics in recent years and it has also started to be clear that computer simulations play...... folding, conformational exchange and binding with ligands at long time scales. In Chapter 2, we benchmarked how well the current force elds and molecular dynamics (MD) simulations could model changes in structure, dynamics, free energy and kinetics for an extensively studied protein called T4 lysozyme (T4...... allows us to utilize the limited computational resources in a more reasonable way. In Chapter 5, we further illustrated the possibility to combine the free energy ooding potential obtained from the variational method with infrequent metadynamics to calculate the long timescale rate. This hybrid method...

  4. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations

    Science.gov (United States)

    Jin, Yu

    2016-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We stay away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while addressing statistical physics modeling approaches along with all-atom molecular dynamics simulation studies. We organize this review around our own modeling and simulation practices on a single subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases as well. For multi-subunit RNA polymerases that have been actively studied in recent years, we leave systematical reviews of the simulation achievements to latest computational chemistry surveys, while covering only representative studies published very recently, including our own work modeling structure-based elongation kinetic of yeast RNA polymerase II. In the end, we briefly go through physical modeling on elongation pauses and backtracking activities of the multi-subunit RNAPs. We emphasize on the fluctuation and control mechanisms of the polymerase actions, highlight the non-equilibrium nature of the operation system, and try to build some perspectives toward understanding the polymerase impacts from the single molecule level to a genome-wide scale. Project supported by the National Natural Science Foundation (Grant No. 11275022).

  5. Simulating surface-enhanced Raman optical activity using atomistic electrodynamics-quantum mechanical models.

    Science.gov (United States)

    Chulhai, Dhabih V; Jensen, Lasse

    2014-10-01

    Raman optical activity has proven to be a powerful tool for probing the geometry of small organic and biomolecules. It has therefore been expected that the same mechanisms responsible for surface-enhanced Raman scattering may allow for similar enhancements in surface-enhanced Raman optical activity (SEROA). However, SEROA has proved to be an experimental challenge and mirror-image SEROA spectra of enantiomers have so far not been measured. There exists a handful of theories to simulate SEROA, all of which treat the perturbed molecule as a point-dipole object. To go beyond these approximations, we present two new methods to simulate SEROA: the first is a dressed-tensors model that treats the molecule as a point-dipole and point-quadrupole object; the second method is the discrete interaction model/quantum mechanical (DIM/QM) model, which considers the entire charge density of the molecule. We show that although the first method is acceptable for small molecules, it fails for a medium-sized one such as 2-bromohexahelicene. We also show that the SEROA mode intensities and signs are highly sensitive to the nature of the local electric field and gradient, the orientation of the molecule, and the surface plasmon frequency width. Our findings give some insight into why experimental SEROA, and in particular observing mirror-image SEROA for enantiomers, has been difficult.

  6. A Fully Coupled Computational Model of the Silylation Process

    Energy Technology Data Exchange (ETDEWEB)

    G. H. Evans; R. S. Larson; V. C. Prantil; W. S. Winters

    1999-02-01

    This report documents the development of a new finite element model of the positive tone silylation process. Model development makes use of pre-existing Sandia technology used to describe coupled thermal-mechanical behavior in deforming metals. Material properties and constitutive models were obtained from the literature. The model is two-dimensional and transient and focuses on the part of the lithography process in which crosslinked and uncrosslinked resist is exposed to a gaseous silylation agent. The model accounts for the combined effects of mass transport (diffusion of silylation agent and reaction product), chemical reaction resulting in the uptake of silicon and material swelling, the generation of stresses, and the resulting material motion. The influence of stress on diffusion and reaction rates is also included.

  7. Deciphering the details of RNA aminoglycoside interactions: from atomistic models to biotechnological applications

    Energy Technology Data Exchange (ETDEWEB)

    Ilgu, Muslum [Iowa State Univ., Ames, IA (United States)

    2012-01-01

    A detailed study was done of the neomycin-B RNA aptamer for determining its selectivity and binding ability to both neomycin– and kanamycin-class aminoglycosides. A novel method to increase drug concentrations in cells for more efficiently killing is described. To test the method, a bacterial model system was adopted and several small RNA molecules interacting with aminoglycosides were cloned downstream of T7 RNA polymerase promoter in an expression vector. Then, the growth analysis of E. coli expressing aptamers was observed for 12-hour period. Our analysis indicated that aptamers helped to increase the intracellular concentration of aminoglycosides thereby increasing their efficacy.

  8. Atomistic Simulations of Dislocations in a Model BCC Multicomponent Concentrated Solid Solution Alloy (Postprint)

    Science.gov (United States)

    2016-12-19

    temperature. The initial condition for the MD simulations was a molecular statics relaxed core under the applied stress of interest. The system was...kink-pair model, the kink-pair activation energy DН(t) at an applied stress t is written as DHðtÞ ¼ DH0 1 ðt=t0Þp q (1) where t0 is the T¼ 0 K...effective activation energy for glide as evidenced by the direct MD simulation data in Fig. 6. 3.3. Critical resolved shear stress for the edge

  9. Visualizing KcsA conformational changes upon ion binding by infrared spectroscopy and atomistic modeling.

    Science.gov (United States)

    Stevenson, Paul; Götz, Christoph; Baiz, Carlos R; Akerboom, Jasper; Tokmakoff, Andrei; Vaziri, Alipasha

    2015-05-07

    The effect of ion binding in the selectivity filter of the potassium channel KcsA is investigated by combining amide I Fourier-transform infrared spectroscopy with structure-based spectral modeling. Experimental difference IR spectra between K(+)-bound KcsA and Na(+)-bound KcsA are in good qualitative agreement with spectra modeled from structural ensembles generated from molecular dynamics simulations. The molecular origins of the vibrational modes contributing to differences in these spectra are determined not only from structural differences in the selectivity filter but also from the pore helices surrounding this region. Furthermore, the coordination of K(+) or Na(+) to carbonyls in the selectivity filter effectively decouples the vibrations of those carbonyls from the rest of the protein, creating local probes of the electrostatic environment. The results suggest that it is necessary to include the influence of the surrounding helices in discussing selectivity and transport in KcsA and, on a more general level, that IR spectroscopy offers a nonperturbative route to studying the structure and dynamics of ion channels.

  10. Performance of SuSi: a method for generating atomistic models of amorphous polymers based on a random search of energy minima.

    Science.gov (United States)

    Curcó, David; Alemán, Carlos

    2004-04-30

    The performance of a recently developed method to generate representative atomistic models of amorphous polymers has been investigated. This method, which is denoted SuSi, can be defined as a random generator of energy minima. The effects produced by different parameters used to define the size of the system and the characteristics of the generation algorithm have been examined. Calculations have been performed on poly(L,D-lactic) acid (rho = 1.25 g/cm3) and nylon 6 (rho = 1.084 g/cm(3)), which are important commercial polymers.

  11. Structure Based Modeling of Small Molecules Binding to the TLR7 by Atomistic Level Simulations

    Directory of Open Access Journals (Sweden)

    Francesco Gentile

    2015-05-01

    Full Text Available Toll-Like Receptors (TLR are a large family of proteins involved in the immune system response. Both the activation and the inhibition of these receptors can have positive effects on several diseases, including viral pathologies and cancer, therefore prompting the development of new compounds. In order to provide new indications for the design of Toll-Like Receptor 7 (TLR7-targeting drugs, the mechanism of interaction between the TLR7 and two important classes of agonists (imidazoquinoline and adenine derivatives was investigated through docking and Molecular Dynamics simulations. To perform the computational analysis, a new model for the dimeric form of the receptors was necessary and therefore created. Qualitative and quantitative differences between agonists and inactive compounds were determined. The in silico results were compared with previous experimental observations and employed to define the ligand binding mechanism of TLR7.

  12. Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations

    Science.gov (United States)

    Kreis, K.; Fogarty, A. C.; Kremer, K.; Potestio, R.

    2015-09-01

    In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One of the main advantages of such approaches is the computational efficiency gained in the coarse-grained region. In this respect the best coarse-grained system to employ in the low resolution region would be the ideal gas, making intermolecular force calculations in the coarse-grained subdomain redundant. In this case, however, a smooth coupling is challenging due to the high energetic imbalance between typical liquids and a system of non-interacting particles. In the present work, we investigate this approach, using as a test case the most biologically relevant fluid, water. We demonstrate that a successful coupling of water to the ideal gas can be achieved with current adaptive resolution methods, and discuss the issues that remain to be addressed.

  13. Atomistic modeling of electron relaxation effect on femtosecond laser-induced thermoelastic response of gold films

    Science.gov (United States)

    Xiong, Q. L.; Tian, X. G.; Lu, T. J.

    2012-07-01

    The thermoelastic response of thin gold films induced by femtosecond laser irradiation is numerically simulated using a modified combined two-temperature model (TTM) and molecular dynamics (MD) method, with focus placed upon the influence of the electron relaxation effect. The validity of the numerical approach is checked against existing experimental results. While the electron relaxation effect is found negligible when the laser duration is much longer than the electron thermal relaxation time, it becomes significant if the laser duration matches the electron relaxation time, especially when the former is much shorter than the latter. The characteristics of thermo-mechanical interaction in the thin film are analyzed, and the influence of temperature-dependent material properties upon the thermoelastic response of the film quantified.

  14. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference.

    Science.gov (United States)

    MacCallum, Justin L; Perez, Alberto; Dill, Ken A

    2015-06-02

    More than 100,000 protein structures are now known at atomic detail. However, far more are not yet known, particularly among large or complex proteins. Often, experimental information is only semireliable because it is uncertain, limited, or confusing in important ways. Some experiments give sparse information, some give ambiguous or nonspecific information, and others give uncertain information-where some is right, some is wrong, but we don't know which. We describe a method called Modeling Employing Limited Data (MELD) that can harness such problematic information in a physics-based, Bayesian framework for improved structure determination. We apply MELD to eight proteins of known structure for which such problematic structural data are available, including a sparse NMR dataset, two ambiguous EPR datasets, and four uncertain datasets taken from sequence evolution data. MELD gives excellent structures, indicating its promise for experimental biomolecule structure determination where only semireliable data are available.

  15. Partial Orders and Fully Abstract Models for Concurrency

    DEFF Research Database (Denmark)

    Engberg, Uffe Henrik

    1990-01-01

    In this thesis sets of labelled partial orders are employed as fundamental mathematical entities for modelling nondeterministic and concurrent processes thereby obtaining so-called noninterleaving semantics. Based on different closures of sets of labelled partial orders, simple algebraic languages...

  16. A fully coupled thermo-mechanical model for unsaturated soil

    OpenAIRE

    2007-01-01

    This paper addresses a new, unified thermomechanical constitutive model for unsaturated soils through a coupled study. In the context of elastoplasticity and the critical state theory, the model uses the concepts of multi-mechanism and bounding surface theory. This advanced constitutive approach involves thermo-plasticity of saturated and unsaturated soils. Bishop’s effective stress framework is adopted to represent the stress state in the soil. This stress is linked to the water retention...

  17. Atomistic simulations, mesoscopic modeling, and theoretical analysis of thermal conductivity of bundles composed of carbon nanotubes

    Science.gov (United States)

    Volkov, Alexey N.; Salaway, Richard N.; Zhigilei, Leonid V.

    2013-09-01

    The propensity of carbon nanotubes (CNTs) to self-organize into continuous networks of bundles has direct implications for thermal transport properties of CNT network materials and defines the importance of clear understanding of the mechanisms and scaling laws governing the heat transfer within the primary building blocks of the network structures—close-packed bundles of CNTs. A comprehensive study of the thermal conductivity of CNT bundles is performed with a combination of non-equilibrium molecular dynamics (MD) simulations of heat transfer between adjacent CNTs and the intrinsic conductivity of CNTs in a bundle with a theoretical analysis that reveals the connections between the structure and thermal transport properties of CNT bundles. The results of MD simulations of heat transfer in CNT bundles consisting of up to 7 CNTs suggest that, contrary to the widespread notion of strongly reduced conductivity of CNTs in bundles, van der Waals interactions between defect-free well-aligned CNTs in a bundle have negligible effect on the intrinsic conductivity of the CNTs. The simulations of inter-tube heat conduction performed for partially overlapping parallel CNTs indicate that the conductance through the overlap region is proportional to the length of the overlap for CNTs and CNT-CNT overlaps longer than several tens of nm. Based on the predictions of the MD simulations, a mesoscopic-level model is developed and applied for theoretical analysis and numerical modeling of heat transfer in bundles consisting of CNTs with infinitely large and finite intrinsic thermal conductivities. The general scaling laws predicting the quadratic dependence of the bundle conductivity on the length of individual CNTs in the case when the thermal transport is controlled by the inter-tube conductance and the independence of the CNT length in another limiting case when the intrinsic conductivity of CNTs plays the dominant role are derived. An application of the scaling laws to bundles of

  18. Flash flood warning based on fully dynamic hydrology modelling

    Science.gov (United States)

    Pejanovic, Goran; Petkovic, Slavko; Cvetkovic, Bojan; Nickovic, Slobodan

    2016-04-01

    Numerical hydrologic modeling has achieved limited success in the past due to, inter alia, lack of adequate input data. Over the last decade, data availability has improved substantially. For modelling purposes, high-resolution data on topography, river routing, and land cover and soil features have meanwhile become available, as well as the observations such as radar precipitation information. In our study, we have implemented the HYPROM model (Hydrology Prognostic Model) to predict a flash flood event at a smaller-scale basin in Southern Serbia. HYPROM is based on the full set of governing equations for surface hydrological dynamics, in which momentum components, along with the equation of mass continuity, are used as full prognostic equations. HYPROM also includes a river routing module serving as a collector for the extra surface water. Such approach permits appropriate representation of different hydrology scales ranging from flash floods to flows of large and slow river basins. The use of full governing equations, if not appropriately parameterized, may lead to numerical instability systems when the surface water in a model is vanishing. To resolve these modelling problems, an unconditionally stable numerical scheme and a method for height redistribution avoiding shortwave height noise have been developed in HYPROM, which achieve numerical convergence of u, v and h when surface water disappears. We have applied HYPROM, driven by radar-estimated precipitation, to predict flash flooding occurred over smaller and medium-size river basins. Two torrential rainfall cases have been simulated to check the accuracy of the model: the exceptional flooding of May 2014 in Western Serbia, and the convective flash flood of January 2015 in Southern Serbia. The second episode has been successfully predicted by HYPROM in terms of timing and intensity six hours before the event occurred. Such flash flood warning system is in preparation to be operationally implemented in the

  19. Atomistic modeling of the low-temperature atom-beam deposition of magnesium fluoride.

    Science.gov (United States)

    Neelamraju, Sridhar; Schön, Johann Christian; Jansen, Martin

    2015-02-02

    We model the deposition and growth of MgF(2) on a sapphire substrate as it occurs in a low-temperature atom-beam-deposition experiment. In the experiment, an (X-ray) amorphous film of MgF(2) is obtained at low temperatures of 170-180 K, and upon heating, this transforms to the expected rutile phase via the CaCl(2)-type structure. We confirm this from our simulations and propose a mechanism for this transformation. The growth process is analyzed as a function of the synthesis parameters, which include the substrate temperature, deposition rate of clusters, and types of clusters deposited. Upon annealing an initially amorphous deposit, we observe the formation of two competing nanocrystalline modifications during this process, which exhibit the CaCl(2) and CdI(2) structure types, respectively. We argue that this joint growth of the two nanocrystalline polymorphs stabilizes the kinetically unstable CaCl(2)-type structure on the macroscopic level long enough to be observed in the experiment.

  20. A mathematical model for preflush treatment in an oil reservoir using a fully miscible fluid

    NARCIS (Netherlands)

    F.J. Vermolen; G.-J. Pieters; P.L.J. Zitha; J. Bruining

    1999-01-01

    textabstractIn this paper we propose and analyse a mathematical model for preflush treatment in an oil reservoir. The model is based on two phase flow in which both phases are fully miscible. For the case of constant injection rate condition, fully implicit solutions can be constructed. Saturation p

  1. Atomistic Modeling of Dislocations in MgSiO3 Post-Perovskite

    Science.gov (United States)

    Goryaeva, A.; Carrez, P.; Cordier, P.

    2014-12-01

    The recently discovered MgSiO3 post-perovskite phase (Cmcm) is only stable at high pressure and temperature conditions corresponding to the lowermost ~150 km of the mantle (the D'' layer) [1, 2]. The unusual, for a high-pressure phase, layer-like structure of the post-perovskite may be responsible for the observed seismic anisotropy of the D'' layer. However, information about mechanical properties, easier slip systems, dislocations and their behaviour under stress are not well known still. This work represents a theoretical study of the post-perovskite within the semi-empirical approach using the Buckingham interatomic potential parameters previously derived by [3]. To describe the energy cost incurred as a result of a shear and to deduce the most favorable slip systems, the GSF excess energies are calculated at 120 GPa. The lowest energy barrier as well as the smallest values of the ideal shear stress (ISS), are related to the slip systems with the smallest [100] Burgers vector (b=2.521 Å) and to the slip system [001](010) with the glide plane cutting only Mg-O bonds. Good agreement with the ab-initio results [4] verifies the accuracy of the chosen inteatomic potential model [3]. The C-lattice of the post-perovskite results in four potential Burgers vectors: [100], [010], [001] and ½[011]. Taking into account the estimated GSF energies for different slip systems, we focus on mobility of screw and edge dislocations with Burgers vectors [100], [010] and ½[011]. The evaluated values of lattice friction suggest (010) slip plane parallel to the Si- and Mg-layers in the post-perovskite strucure to be the most probable .References[1] Murakami, M. et al., Geophys. Res. Lett. (2005), 32, L03304. [2] Oganov, A. & Ono S., Nature (2004), 430, 44- 448. [3] Oganov A. et al., Phys. Earth Planet. Int. (2000), 122, 277-288. [4] Carrez Ph. et al., Philosoph. Mag. (2007), 87, 3229-3247.

  2. Fully variational average atom model with ion-ion correlations.

    Science.gov (United States)

    Starrett, C E; Saumon, D

    2012-02-01

    An average atom model for dense ionized fluids that includes ion correlations is presented. The model assumes spherical symmetry and is based on density functional theory, the integral equations for uniform fluids, and a variational principle applied to the grand potential. Starting from density functional theory for a mixture of classical ions and quantum mechanical electrons, an approximate grand potential is developed, with an external field being created by a central nucleus fixed at the origin. Minimization of this grand potential with respect to electron and ion densities is carried out, resulting in equations for effective interaction potentials. A third condition resulting from minimizing the grand potential with respect to the average ion charge determines the noninteracting electron chemical potential. This system is coupled to a system of point ions and electrons with an ion fixed at the origin, and a closed set of equations is obtained. Solution of these equations results in a self-consistent electronic and ionic structure for the plasma as well as the average ionization, which is continuous as a function of temperature and density. Other average atom models are recovered by application of simplifying assumptions.

  3. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

    Science.gov (United States)

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

    2012-07-01

    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

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

    Science.gov (United States)

    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.

  5. The Concept of Data Model Pattern Based on Fully Communication Oriented Information Modeling (FCO-IM

    Directory of Open Access Journals (Sweden)

    Fazat Nur Azizah

    2010-04-01

    Full Text Available Just as in many areas of software engineering, patterns have been used in data modeling to create high quality data models. We provide a concept of data model pattern based on Fully Communication Oriented Information Modeling (FCO-IM, a fact oriented data modeling method. A data model pattern is defined as the relation between context, problem, and solution. This definition is adopted from the concept of pattern by Christopher Alexander. We define the concept of Information Grammar for Pattern (IGP in the solution part of a pattern, which works as a template to create a data model. The IGP also shows how a pattern can relate to other patterns. The data model pattern concept is then used to describe 15 data model patterns, organized into 4 categories. A case study on geographical location is provided to show the use of the concept in a real case.

  6. Comparison between fully distributed model and semi-distributed model in urban hydrology modeling

    Science.gov (United States)

    Ichiba, Abdellah; Gires, Auguste; Giangola-Murzyn, Agathe; Tchiguirinskaia, Ioulia; Schertzer, Daniel; Bompard, Philippe

    2013-04-01

    Water management in urban areas is becoming more and more complex, especially because of a rapid increase of impervious areas. There will also possibly be an increase of extreme precipitation due to climate change. The aims of the devices implemented to handle the large amount of water generate by urban areas such as storm water retention basins are usually twofold: ensure pluvial flood protection and water depollution. These two aims imply opposite management strategies. To optimize the use of these devices there is a need to implement urban hydrological models and improve fine-scale rainfall estimation, which is the most significant input. In this paper we suggest to compare two models and their sensitivity to small-scale rainfall variability on a 2.15 km2 urban area located in the County of Val-de-Marne (South-East of Paris, France). The average impervious coefficient is approximately 34%. In this work two types of models are used. The first one is CANOE which is semi-distributed. Such models are widely used by practitioners for urban hydrology modeling and urban water management. Indeed, they are easily configurable and the computation time is reduced, but these models do not take fully into account either the variability of the physical properties or the variability of the precipitations. An alternative is to use distributed models that are harder to configure and require a greater computation time, but they enable a deeper analysis (especially at small scales and upstream) of the processes at stake. We used the Multi-Hydro fully distributed model developed at the Ecole des Ponts ParisTech. It is an interacting core between open source software packages, each of them representing a portion of the water cycle in urban environment. Four heavy rainfall events that occurred between 2009 and 2011 are analyzed. The data comes from the Météo-France radar mosaic and the resolution is 1 km in space and 5 min in time. The closest radar of the Météo-France network is

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

    Science.gov (United States)

    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.

  8. Atomistic computer simulations a practical guide

    CERN Document Server

    Brazdova, Veronika

    2013-01-01

    Many books explain the theory of atomistic computer simulations; this book teaches you how to run them This introductory ""how to"" title enables readers to understand, plan, run, and analyze their own independent atomistic simulations, and decide which method to use and which questions to ask in their research project. It is written in a clear and precise language, focusing on a thorough understanding of the concepts behind the equations and how these are used in the simulations. As a result, readers will learn how to design the computational model and which parameters o

  9. Modeling of magnetoelastic nanostructures with a fully coupled mechanical-micromagnetic model

    Science.gov (United States)

    Liang, Cheng-Yen; Keller, Scott M.; Sepulveda, Abdon E.; Bur, Alexandre; Sun, Wei-Yang; Wetzlar, Kyle; Carman, Gregory P.

    2014-10-01

    Micromagnetic simulations of magnetoelastic nanostructures traditionally rely on either the Stoner-Wohlfarth model or the Landau-Lifshitz-Gilbert (LLG) model, assuming uniform strain (and/or assuming uniform magnetization). While the uniform strain assumption is reasonable when modeling magnetoelastic thin films, this constant strain approach becomes increasingly inaccurate for smaller in-plane nanoscale structures. This paper presents analytical work intended to significantly improve the simulation of finite structures by fully coupling the LLG model with elastodynamics, i.e., the partial differential equations are intrinsically coupled. The coupled equations developed in this manuscript, along with the Stoner-Wohlfarth model and the LLG (constant strain) model are compared to experimental data on nickel nanostructures. The nickel nanostructures are 100 × 300 × 35 nm single domain elements that are fabricated on a Si/SiO2 substrate; these nanostructures are mechanically strained when they experience an applied magnetic field, which is used to generate M vs H curves. Results reveal that this paper’s fully-coupled approach corresponds the best with the experimental data on coercive field changes. This more sophisticated modeling technique is critical for guiding the design process of future nanoscale strain-mediated multiferroic elements, such as those needed in memory systems.

  10. Atomistic modeling of two-dimensional electronic spectra and excited-state dynamics for a Light Harvesting 2 complex.

    Science.gov (United States)

    van der Vegte, C P; Prajapati, J D; Kleinekathöfer, U; Knoester, J; Jansen, T L C

    2015-01-29

    The Light Harvesting 2 (LH2) complex is a vital part of the photosystem of purple bacteria. It is responsible for the absorption of light and transport of the resulting excitations to the reaction center in a highly efficient manner. A general description of the chromophores and the interaction with their local environment is crucial to understand this highly efficient energy transport. Here we include this interaction in an atomistic way using mixed quantum-classical (molecular dynamics) simulations of spectra. In particular, we present the first atomistic simulation of nonlinear optical spectra for LH2 and use it to study the energy transport within the complex. We show that the frequency distributions of the pigments strongly depend on their positions with respect to the protein scaffold and dynamics of their local environment. Furthermore, we show that although the pigments are closely packed the transition frequencies of neighboring pigments are essentially uncorrelated. We present the simulated linear absorption spectra for the LH2 complex and provide a detailed explanation of the states responsible for the observed two-band structure. Finally, we discuss the energy transfer within the complex by analyzing population transfer calculations and 2D spectra for different waiting times. We conclude that the energy transfer from the B800 ring to the B850 ring is mediated by intermediate states that are delocalized over both rings, allowing for a stepwise downhill energy transport.

  11. Embedding complex hydrology in the climate system - towards fully coupled climate-hydrology models

    DEFF Research Database (Denmark)

    Butts, M.; Rasmussen, S.H.; Ridler, M.

    2013-01-01

    Motivated by the need to develop better tools to understand the impact of future management and climate change on water resources, we present a set of studies with the overall aim of developing a fully dynamic coupling between a comprehensive hydrological model, MIKE SHE, and a regional climate...... distributed parameters using satellite remote sensing. Secondly, field data are used to investigate the effects of model resolution and parameter scales for use in a coupled model. Finally, the development of the fully coupled climate-hydrology model is described and some of the challenges associated...... with coupling models for hydrological processes on sub-grid scales of the regional climate model are presented....

  12. Cut-HDMR-based fully equivalent operational model for analysis of unreinforced masonry structures

    Indian Academy of Sciences (India)

    D Mukherjee; B N Rao; A M Prasad

    2012-10-01

    Mesoscale models are highly competent for understanding behaviour of unreinforced masonry structures. Their only limitation is large computational expense. Fully Equivalent Operational Model forms an equivalent mathematical model to represent a particular phenomenon where explicit relationship between inputs and outputs are unknown. This paper explores the ability of a major variant of High Dimensional Model Representation (HDMR) technique, namely Cut-HDMR, to construct the most efficient Fully Equivalent Operational Model for nonlinear finite element analysis of mesoscale model of an unreinforced masonry structure. Conclusions are reached on various aspects such as, suitability of interpolation schemes and order of Cut-HDMR approximation.

  13. NiTi superelasticity via atomistic simulations

    Science.gov (United States)

    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.

  14. Parallel Atomistic Simulations

    Energy Technology Data Exchange (ETDEWEB)

    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. Atomistic simulations of fracture

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Dept. of Materials Science and Engineering

    1997-12-31

    Embedded atom interaction potentials are used to simulate the atomistic aspects of the fracture process. Simulations are presented for the behavior of cracks in pure metals and intermetallics, near the Griffith condition. The materials considered include Fe, Cu, Ni as well as Fe, Ni, Co, and Ti aluminides. The work focuses on the comparative study of fracture behavior in the different materials. The role of the atomic relaxation at the crack tip and of lattice trapping phenomena is analyzed.

  16. Initial stages of ITO/Si interface formation: In situ x-ray photoelectron spectroscopy measurements upon magnetron sputtering and atomistic modelling using density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Løvvik, O. M.; Diplas, S.; Ulyashin, A. [SINTEF Materials and Chemistry, Forskningsveien 1, NO-0314 Oslo (Norway); Romanyuk, A. [University of Basel, Kingelbergstr. 82, CH-4056 Basel (Switzerland)

    2014-02-28

    Initial stages of indium tin oxide (ITO) growth on a polished Si substrate upon magnetron sputtering were studied experimentally using in-situ x-ray photoelectron spectroscopy measurements. The presence of pure indium and tin, as well as Si bonded to oxygen at the ITO/Si interface were observed. The experimental observations were compared with several atomistic models of ITO/Si interfaces. A periodic model of the ITO/Si interface was constructed, giving detailed information about the local environment at the interface. Molecular dynamics based on density functional theory was performed, showing how metal-oxygen bonds are broken on behalf of silicon-oxygen bonds. These theoretical results support and provide an explanation for the present as well as previous ex-situ and in-situ experimental observations pointing to the creation of metallic In and Sn along with the growth of SiO{sub x} at the ITO/Si interface.

  17. Study of gap conductance model for thermo mechanical fully coupled finite element model

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyo Cha; Yang, Yong Sik; Kim, Dae Ho; Bang, Je Geon; Kim, Sun Ki; Koo, Yang Hyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-10-15

    accurately, gap conductance model for thermomechanical fully coupled FE should be developed. However, gap conductance in FE can be difficult issue in terms of convergence because all elements which are positioned in gap have different gap conductance at each iteration step. It is clear that our code should have gap conductance model for thermo-mechanical fully coupled FE in three-dimension. In this paper, gap conductance model for thermomechanical coupled FE has been built using commercial FE code to understand gap conductance model in FE. We coded commercial FE code using APDL because it does not have iterative gap conductance model. Through model, convergence parameter and characteristics were studied.

  18. Modeling of WalkMECH: a fully-passive energy-efficient transfemoral prosthesis prototype

    NARCIS (Netherlands)

    Ünal, Ramazan; Klijnstra, F.; Burkink, B.; Behrens, Sebastiaan Maria; Hekman, Edsko E.G.; Stramigioli, Stefano; Koopman, Hubertus F.J.M.; Carloni, Raffaella

    In this paper we present the port-based model of WalkMECH, a fully-passive transfemoral prosthesis prototype that has been designed and realized for normal walking. The model has been implemented in a simulation environment so to analyze the performance of the prosthetic leg in walking experiments

  19. A fully coupled air foil bearing model considering friction – Theory & experiment

    DEFF Research Database (Denmark)

    von Osmanski, Alexander Sebastian; Larsen, Jon Steffen; Santos, Ilmar

    2017-01-01

    The dynamics of air foil bearings (AFBs) are not yet fully captured by any model. The recent years have, however, seen promising results from nonlinear time domain models, and simultaneously coupled formulations are now available, avoiding the previous requirements for undesirably small time step...

  20. Large-time behaviour of some fully discrete kinetic models in bounded domains

    Directory of Open Access Journals (Sweden)

    Ester Gabetta

    1991-05-01

    Full Text Available We investigate the large-time behaviour of the fully discretized version both of the three velocity Broadwell model and of the four velocity model in a strip. We analyze the different behaviours on the light of some recent results by M. Slemrod [7] and C. Cercignani [3].

  1. Atomistic stimulation of defective oxides

    CERN Document Server

    Minervini, L

    2000-01-01

    defect processes. The predominant intrinsic disorder reaction and the mechanism by which excess oxygen is accommodated are established. Furthermore, the most favourable migration mechanism and pathway for oxygen ions is predicted. Chapters 7 and 8 investigate pyrochlore oxides. These materials are candidates for solid oxide fuel cell components and as actinide host phases. Such applications require a detailed understanding of the defect processes. The defect energies, displayed as contour maps, are able to account for structure stability and, given an appropriate partial charge potential model, to accurately determine the oxygen positional parameter. In particular, the dependence of the positional parameter on intrinsic disorder is predicted. It is demonstrated, by radiation damage experiments, that these results are able to predict the radiation performance of pyrochlore oxides. Atomistic simulation calculations based on energy minimization techniques and classical pair potentials are used to study several i...

  2. Atomistic modeling of femtosecond laser-induced melting and atomic mixing in Au film - Cu substrate system

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, Derek A.; Lin Zhibin [Department of Materials Science and Engineering, University of Virginia, 395 McCormick Road, Charlottesville, VA 22904-4745 (United States); Zhigilei, Leonid V., E-mail: lz2n@virginia.edu [Department of Materials Science and Engineering, University of Virginia, 395 McCormick Road, Charlottesville, VA 22904-4745 (United States); Gurevich, Evgeny L.; Kittel, Silke; Hergenroeder, Roland [ISAS - Institute for Analytical Sciences, Department of Material Analysis Bunsen-Kirchhoff-Str. 11, 44139 Dortmund (Germany)

    2009-09-30

    The mechanisms of femtosecond laser-induced transient melting and atomic mixing in a target composed of a 30 nm Au film deposited on a bulk Cu substrate are investigated in a series of atomistic simulations. The relative strength and the electron temperature dependence of the electron-phonon coupling of the metals composing the layered target are identified as major factors affecting the initial energy redistribution and the location of the region(s) undergoing transient melting and resolidification. The higher strength of the electron-phonon coupling in Cu, as compared to Au, results in a preferential sub-surface heating and melting of the Cu substrate, while the overlaying Au film largely retains its original crystalline structure. The large difference in the atomic mobility in the transiently melted and crystalline regions of the target makes it possible to connect the final distributions of the components in the resolidified targets to the history of the laser-induced melting process, thus allowing for experimental verification of the computational predictions.

  3. Atomistic modeling of femtosecond laser-induced melting and atomic mixing in Au film - Cu substrate system

    Science.gov (United States)

    Thomas, Derek A.; Lin, Zhibin; Zhigilei, Leonid V.; Gurevich, Evgeny L.; Kittel, Silke; Hergenröder, Roland

    2009-09-01

    The mechanisms of femtosecond laser-induced transient melting and atomic mixing in a target composed of a 30 nm Au film deposited on a bulk Cu substrate are investigated in a series of atomistic simulations. The relative strength and the electron temperature dependence of the electron-phonon coupling of the metals composing the layered target are identified as major factors affecting the initial energy redistribution and the location of the region(s) undergoing transient melting and resolidification. The higher strength of the electron-phonon coupling in Cu, as compared to Au, results in a preferential sub-surface heating and melting of the Cu substrate, while the overlaying Au film largely retains its original crystalline structure. The large difference in the atomic mobility in the transiently melted and crystalline regions of the target makes it possible to connect the final distributions of the components in the resolidified targets to the history of the laser-induced melting process, thus allowing for experimental verification of the computational predictions.

  4. A fully coupled method for numerical modeling and dynamic analysis of floating vertical axis wind turbines

    DEFF Research Database (Denmark)

    Cheng, Zhengshun; Aagaard Madsen, Helge; Gao, Zhen

    2017-01-01

    •Aerodynamic modeling of floating VAWTs is established using the Actuator Cylinder (AC) flow method.•A fully coupled aero-hydro-servo-elastic simulation tool, i.e. SIMO-RIFLEX-AC, is developed for floating VAWTs.•The developedsimulation tool is verified to be accurate by a series of code-to-code ......•Aerodynamic modeling of floating VAWTs is established using the Actuator Cylinder (AC) flow method.•A fully coupled aero-hydro-servo-elastic simulation tool, i.e. SIMO-RIFLEX-AC, is developed for floating VAWTs.•The developedsimulation tool is verified to be accurate by a series of code...

  5. Saturable Lorentz model for fully explicit three-dimensional modeling of nonlinear optics

    CERN Document Server

    Varin, Charles; Emms, Rhys; Brabec, Thomas

    2014-01-01

    Inclusion of the instantaneous Kerr nonlinearity in the FDTD framework leads to implicit equations that have to be solved iteratively. In principle, explicit integration can be achieved with the use of anharmonic oscillator equations, but it tends to be unstable and inappropriate for studying strong-field phenomena like laser filamentation. In this paper, we show that nonlinear susceptibility can be provided instead by an harmonic oscillator driven by a nonlinear force. When the nonlinear force is tailored to mimic atomic transition saturation, the model agree quantitatively with the quantum mechanical solutions of a two-level system, up to the 9th harmonic. Moreover, we demonstrate that fully explicit leapfrog integration of the saturable harmonic oscillator is stable, even for the intense laser fields that characterize laser filamentation and high harmonic generation.

  6. Modeling of Magnetoelastic Nanostructures with a Fully-coupled Mechanical-Micromagnetic Model and Its Applications

    Science.gov (United States)

    Liang, Cheng-Yen

    Micromagnetic simulations of magnetoelastic nanostructures traditionally rely on either the Stoner-Wohlfarth model or the Landau-Lifshitz-Gilbert (LLG) model assuming uniform strain (and/or assuming uniform magnetization). While the uniform strain assumption is reasonable when modeling magnetoelastic thin films, this constant strain approach becomes increasingly inaccurate for smaller in-plane nanoscale structures. In this dissertation, a fully-coupled finite element micromagnetic method is developed. The method deals with the micromagnetics, elastodynamics, and piezoelectric effects. The dynamics of magnetization, non-uniform strain distribution, and electric fields are iteratively solved. This more sophisticated modeling technique is critical for guiding the design process of the nanoscale strain-mediated multiferroic elements such as those needed in multiferroic systems. In this dissertation, we will study magnetic property changes (e.g., hysteresis, coercive field, and spin states) due to strain effects in nanostructures. in addition, a multiferroic memory device is studied. The electric-field-driven magnetization switching by applying voltage on patterned electrodes simulation in a nickel memory device is shown in this work. The deterministic control law for the magnetization switching in a nanoring with electric field applied to the patterned electrodes is investigated. Using the patterned electrodes, we show that strain-induced anisotropy is able to be controlled, which changes the magnetization deterministically in a nano-ring.

  7. Fully Bayesian mixture model for differential gene expression: simulations and model checks.

    Science.gov (United States)

    Lewin, Alex; Bochkina, Natalia; Richardson, Sylvia

    2007-01-01

    We present a Bayesian hierarchical model for detecting differentially expressed genes using a mixture prior on the parameters representing differential effects. We formulate an easily interpretable 3-component mixture to classify genes as over-expressed, under-expressed and non-differentially expressed, and model gene variances as exchangeable to allow for variability between genes. We show how the proportion of differentially expressed genes, and the mixture parameters, can be estimated in a fully Bayesian way, extending previous approaches where this proportion was fixed and empirically estimated. Good estimates of the false discovery rates are also obtained. Different parametric families for the mixture components can lead to quite different classifications of genes for a given data set. Using Affymetrix data from a knock out and wildtype mice experiment, we show how predictive model checks can be used to guide the choice between possible mixture priors. These checks show that extending the mixture model to allow extra variability around zero instead of the usual point mass null fits the data better. A software package for R is available.

  8. Embedding complex hydrology in the climate system - towards fully coupled climate-hydrology models

    DEFF Research Database (Denmark)

    Butts, M.; Rasmussen, S.H.; Ridler, M.

    2013-01-01

    model, HIRHAM. The physics of the coupling is formulated using an energy-based SVAT (land surface) model while the numerical coupling exploits the OpenMI modelling interface. First, some investigations of the applicability of the SVAT model are presented, including our ability to characterise...... distributed parameters using satellite remote sensing. Secondly, field data are used to investigate the effects of model resolution and parameter scales for use in a coupled model. Finally, the development of the fully coupled climate-hydrology model is described and some of the challenges associated...

  9. Comparison of fully coupled hydroelastic computation and segmented model test results for slamming and whipping loads

    Directory of Open Access Journals (Sweden)

    Jung-Hyun Kim

    2014-12-01

    Full Text Available This paper presents a numerical analysis of slamming and whipping using a fully coupled hydroelastic model. The coupled model uses a 3-D Rankine panel method, a 1-D or 3-D finite element method, and a 2-D Generalized Wagner Model (GWM, which are strongly coupled in time domain. First, the GWM is validated against results of a free drop test of wedges. Second, the fully coupled method is validated against model test results for a 10,000 twenty-foot equivalent unit (TEU containership. Slamming pressures and whipping responses to regular waves are compared. A spatial distribution of local slamming forces is measured using 14 force sensors in the model test, and it is compared with the integration of the pressure distribution by the computation. Furthermore, the pressure is decomposed into the added mass, impact, and hydrostatic components, in the computational results. The validity and characteristics of the numerical model are discussed.

  10. A novel fully-humanised 3D skin equivalent to model early melanoma invasion

    Science.gov (United States)

    Hill, David S; Robinson, Neil D P; Caley, Matthew P; Chen, Mei; O’Toole, Edel A; Armstrong, Jane L; Przyborski, Stefan; Lovat, Penny E

    2015-01-01

    Metastatic melanoma remains incurable, emphasising the acute need for improved research models to investigate the underlying biological mechanisms mediating tumour invasion and metastasis, and to develop more effective targeted therapies to improve clinical outcome. Available animal models of melanoma do not accurately reflect human disease and current in vitro human skin equivalent models incorporating melanoma cells are not fully representative of the human skin microenvironment. We have developed a robust and reproducible, fully-humanised 3D skin equivalent comprising a stratified, terminally differentiated epidermis and a dermal compartment consisting of fibroblast-generated extracellular matrix. Melanoma cells incorporated into the epidermis were able to invade through the basement membrane and into the dermis, mirroring early tumour invasion in vivo. Comparison of our novel 3D melanoma skin equivalent with melanoma in situ and metastatic melanoma indicates this model accurately recreates features of disease pathology, making it a physiologically representative model of early radial and vertical growth phase melanoma invasion. PMID:26330548

  11. A dynamic atomistic-continuum method for the simulation of crystalline materials

    CERN Document Server

    Huang Zhon Gy

    2002-01-01

    We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics in crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away from defects and interfaces. We propose a new class of matching conditions between the atomistic and the continuum regions. These conditions ensure the accurate passage of large-scale information between the atomistic and the continuum regions and at the same time minimize the reflection of phonons at the atomistic-continuum interface. They can be made adaptive by choosing appropriate weight functions. We present applications to dislocation dynamics, friction between two-dimensional crystal surfaces, and fracture dynamics. We compare results of the coupled method and of the detailed atomistic model.

  12. A Comparison of Joint Model and Fully Conditional Specification Imputation for Multilevel Missing Data

    Science.gov (United States)

    Mistler, Stephen A.; Enders, Craig K.

    2017-01-01

    Multiple imputation methods can generally be divided into two broad frameworks: joint model (JM) imputation and fully conditional specification (FCS) imputation. JM draws missing values simultaneously for all incomplete variables using a multivariate distribution, whereas FCS imputes variables one at a time from a series of univariate conditional…

  13. Neural Network Identification Model for Technology Selection of Fully-Mechanized Top-Coal Caving Mining

    Institute of Scientific and Technical Information of China (English)

    孟宪锐; 徐永勇; 汪进

    2001-01-01

    This paper mainly discusses the selection of the technical parameters of fully-mechanized top-coal caving mining using the neural network technique. The comparison between computing results and experiment data shows that the set-up neural network model has high accuracy and decision-making benefit.

  14. Improved atomistic Monte Carlo models based on ab-initio-trained neural networks: Application to FeCu and FeCr alloys

    Science.gov (United States)

    Castin, N.; Messina, L.; Domain, C.; Pasianot, R. C.; Olsson, P.

    2017-06-01

    We significantly improve the physical models underlying atomistic Monte Carlo (MC) simulations, through the use of ab initio fitted high-dimensional neural network potentials (NNPs). In this way, we can incorporate energetics derived from density functional theory (DFT) in MC, and avoid using empirical potentials that are very challenging to design for complex alloys. We take significant steps forward from a recent work where artificial neural networks (ANNs), exclusively trained on DFT vacancy migration energies, were used to perform kinetic MC simulations of Cu precipitation in Fe. Here, a more extensive transfer of knowledge from DFT to our cohesive model is achieved via the fitting of NNPs, aimed at accurately mimicking the most important aspects of the ab initio predictions. Rigid-lattice potentials are designed to monitor the evolution during the simulation of the system energy, thus taking care of the thermodynamic aspects of the model. In addition, other ANNs are designed to evaluate the activation energies associated with the MC events (migration towards first-nearest-neighbor positions of single point defects), thereby providing an accurate kinetic modeling. Because our methodology inherently requires the calculation of a substantial amount of reference data, we design as well lattice-free potentials, aimed at replacing the very costly DFT method with an approximate, yet accurate and considerably more computationally efficient, potential. The binary FeCu and FeCr alloys are taken as sample applications considering the extensive literature covering these systems.

  15. Atomistic Properties of Solids

    CERN Document Server

    Sirdeshmukh, Dinker B; Subhadra, K G

    2011-01-01

    The book deals with atomistic properties of solids which are determined by the crystal structure, interatomic forces and atomic displacements influenced by the effects of temperature, stress and electric fields. The book gives equal importance to experimental details and theory. There are full chapters dedicated to the tensor nature of physical properties, mechanical properties, lattice vibrations, crystal structure determination and ferroelectricity. The other crystalline states like nano-, poly-, liquid- and quasi crystals are discussed. Several new topics like nonlinear optics and the Rietveld method are presented in the book. The book lays emphasis on the role of symmetry in crystal properties. Comprehensiveness is the strength of the book; this allows users at different levels a choice of chapters according to their requirements.

  16. Polarizabilities and van der Waals C6 coefficients of fullerenes from an atomistic electrodynamics model: Anomalous scaling with number of carbon atoms

    Science.gov (United States)

    Saidi, Wissam A.; Norman, Patrick

    2016-07-01

    The van der Waals C6 coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C6 ∝ N2.2 as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N2.75 as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes by fitting against accurate ab initio calculations. This model shows that C6 ∝ N2.8, which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole-dipole term scales almost linearly with the number of carbon atoms.

  17. Combined atomistic-continuum model for simulation of laser interaction with metals: application in the calculation of melting thresholds in Ni targets of varying thickness

    Science.gov (United States)

    Ivanov, D. S.; Zhigilei, L. V.

    The threshold laser fluence for the onset of surface melting is calculated for Ni films of different thicknesses and for a bulk Ni target using a combined atomistic-continuum computational model. The model combines the classical molecular dynamics (MD) method for simulation of non-equilibrium processes of lattice superheating and fast phase transformations with a continuum description of the laser excitation and subsequent relaxation of the conduction band electrons based on the two-temperature model (TTM). In the hybrid TTM-MD method, MD substitutes the TTM equation for the lattice temperature, and the diffusion equation for the electron temperature is solved simultaneously with MD integration of the equations of motion of atoms. The dependence of the threshold fluence on the film thickness predicted in TTM-MD simulations qualitatively agrees with TTM calculations, while the values of the thresholds for thick films and bulk targets are 10% higher in TTM-MD. The quantitative differences between the predictions of TTM and TTM-MD demonstrate that the kinetics of laser melting as well as the energy partitioning between the thermal energy of atomic vibrations and energy of the collective atomic motion driven by the relaxation of the laser-induced pressure should be taken into account in interpretation of experimental results on surface melting.

  18. Polarizabilities and van der Waals C6 coefficients of fullerenes from an atomistic electrodynamics model: Anomalous scaling with number of carbon atoms.

    Science.gov (United States)

    Saidi, Wissam A; Norman, Patrick

    2016-07-14

    The van der Waals C6 coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C6 ∝ N(2.2) as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N(2.75) as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes by fitting against accurate ab initio calculations. This model shows that C6 ∝ N(2.8), which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole-dipole term scales almost linearly with the number of carbon atoms.

  19. Two-dimensional analytical models for asymmetric fully depleted double-gate strained silicon MOSFETs

    Institute of Scientific and Technical Information of China (English)

    Liu Hong-Xia; Li Jin; Li Bin; Cao Lei; Yuan Bo

    2011-01-01

    This paper develops the simple and accurate two-dimensional analytical models for new asymmetric double-gate fully depleted strained-Si MOSFET. The models mainly include the analytical equations of the surface potential, surface electric field and threshold voltage, which are derived by solving two dimensional Poisson equation in strained-Si layer.The models are verified by numerical simulation. Besides offering the physical insight into device physics in the model,the new structure also provides the basic designing guidance for further immunity of short channel effect and drain-induced barrier-lowering of CMOS-based devices in nanometre scale.

  20. Fully non-linear hyper-viscoelastic modeling of skeletal muscle in compression.

    Science.gov (United States)

    Wheatley, Benjamin B; Pietsch, Renée B; Haut Donahue, Tammy L; Williams, Lakiesha N

    2016-01-01

    Understanding the behavior of skeletal muscle is critical to implementing computational methods to study how the body responds to compressive loading. This work presents a novel approach to studying the fully nonlinear response of skeletal muscle in compression. Porcine muscle was compressed in both the longitudinal and transverse directions under five stress relaxation steps. Each step consisted of 5% engineering strain over 1 s followed by a relaxation period until equilibrium was reached at an observed change of 1 g/min. The resulting data were analyzed to identify the peak and equilibrium stresses as well as relaxation time for all samples. Additionally, a fully nonlinear strain energy density-based Prony series constitutive model was implemented and validated with independent constant rate compressive data. A nonlinear least squares optimization approach utilizing the Levenberg-Marquardt algorithm was implemented to fit model behavior to experimental data. The results suggested the time-dependent material response plays a key role in the anisotropy of skeletal muscle as increasing strain showed differences in peak stress and relaxation time (p 0.05). The optimizing procedure produced a single set of hyper-viscoelastic parameters which characterized compressive muscle behavior under stress relaxation conditions. The utilized constitutive model was the first orthotropic, fully nonlinear hyper-viscoelastic model of skeletal muscle in compression while maintaining agreement with constitutive physical boundaries. The model provided an excellent fit to experimental data and agreed well with the independent validation in the transverse direction.

  1. Fully undrained cyclic loading simulation on unsaturated soils using an elastoplastic model for unsaturated soils

    Directory of Open Access Journals (Sweden)

    Komolvilas Veerayut

    2016-01-01

    Full Text Available Several researchers have reported that Bishop’s mean effective stress decreases in unsaturated soils under fully undrained cyclic loading conditions, and unsaturated soils are finally liquefied in a similar manner as saturated soils. This paper presents a series of simulations of such fully undrained cyclic loading on unsaturated soils using an elastoplastic model of the unsaturated soil. This model is formulated using the Bishop’s effective stress tensor incorporating the following concepts: the volumetric movement of the state boundary surface containing the normal consolidation line and the critical state line due to the variation in the degree of saturation, a soil water characteristic curve model considering the effect of specific volume and hysteresis, the subloading surface model, and Boyle’s law. Comparisons between the simulation results and the experimental ones show that the model agreed well with the unsaturated soil behavior under cyclic loading. Finally, the typical cyclic behavior of unsaturated soils under fully undrained conditions, such as the mechanism of liquefaction of unsaturated soils, the compression behavior, and an increase in the degree of saturation, are described through the proposed simulation results.

  2. Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed.

    Science.gov (United States)

    Qin, Sanbo; Zhou, Huan-Xiang

    2014-07-08

    Recently, we (Qin, S.; Zhou, H. X. J. Chem. Theory Comput.2013, 9, 4633-4643) developed the FFT-based method for Modeling Atomistic Proteins-crowder interactions, henceforth FMAP. Given its potential wide use for calculating effects of crowding on protein folding and binding free energies, here we aimed to optimize the accuracy and speed of FMAP. FMAP is based on expressing protein-crowder interactions as correlation functions and evaluating the latter via fast Fourier transform (FFT). The numerical accuracy of FFT improves as the grid spacing for discretizing space is reduced, but at increasing computational cost. We sought to speed up FMAP calculations by using a relatively coarse grid spacing of 0.6 Å and then correcting for discretization errors. This strategy was tested for different types of interactions (hard-core repulsion, nonpolar attraction, and electrostatic interaction) and over a wide range of protein-crowder systems. We were able to correct for the numerical errors on hard-core repulsion and nonpolar attraction by an 8% inflation of atomic hard-core radii and on electrostatic interaction by a 5% inflation of the magnitudes of protein atomic charges. The corrected results have higher accuracy and enjoy a speedup of more than 100-fold over those obtained using a fine grid spacing of 0.15 Å. With this optimization of accuracy and speed, FMAP may become a practical tool for realistic modeling of protein folding and binding in cell-like environments.

  3. A Fully Bayesian Approach to Improved Calibration and Prediction of Groundwater Models With Structure Error

    Science.gov (United States)

    Xu, T.; Valocchi, A. J.

    2014-12-01

    Effective water resource management typically relies on numerical models to analyse groundwater flow and solute transport processes. These models are usually subject to model structure error due to simplification and/or misrepresentation of the real system. As a result, the model outputs may systematically deviate from measurements, thus violating a key assumption for traditional regression-based calibration and uncertainty analysis. On the other hand, model structure error induced bias can be described statistically in an inductive, data-driven way based on historical model-to-measurement misfit. We adopt a fully Bayesian approach that integrates a Gaussian process error model to account for model structure error to the calibration, prediction and uncertainty analysis of groundwater models. The posterior distributions of parameters of the groundwater model and the Gaussian process error model are jointly inferred using DREAM, an efficient Markov chain Monte Carlo sampler. We test the usefulness of the fully Bayesian approach towards a synthetic case study of surface-ground water interaction under changing pumping conditions. We first illustrate through this example that traditional least squares regression without accounting for model structure error yields biased parameter estimates due to parameter compensation as well as biased predictions. In contrast, the Bayesian approach gives less biased parameter estimates. Moreover, the integration of a Gaussian process error model significantly reduces predictive bias and leads to prediction intervals that are more consistent with observations. The results highlight the importance of explicit treatment of model structure error especially in circumstances where subsequent decision-making and risk analysis require accurate prediction and uncertainty quantification. In addition, the data-driven error modelling approach is capable of extracting more information from observation data than using a groundwater model alone.

  4. Effect of excitation methods on electrical characteristics of fully superconducting generator model

    Science.gov (United States)

    Muta, Itsuya; Tsukiji, H.; Handa, N.; Hoshino, Tsutomu; Mukai, E.

    1994-07-01

    We have fabricated a fully superconducting generator of 20 kW class, in which both of armature and field coils are made of superconductors. Two different types of excitation system were selected and tested: a brushless excitation method consisted of 'magnetic flux pump' and a conventional excitation method equipped with collector ring and brushes. The paper describes the experimental machine model and the comparison of test results between the two different types of excitation methods.

  5. Verification of a fully coupled FE model for tunneling under compressed air

    Energy Technology Data Exchange (ETDEWEB)

    Oettl, G.; Stark, R.F.; Hofstetter, G. [Innsbruck Univ. (Austria). Inst. for Structural Analysis and Strength of Materials

    2001-07-01

    This paper deals with the verification of a fully coupled finite element model for tunneling under compressed air. The formulation is based on mixture theory treating the soil as a three-phase medium with the constituents: deformable porous soil skeleton, water and air. Starting with a brief outline of the governing equations results of numerical simulations of different laboratory tests and of a large-scale in-situ test are presented and compared with experimental data. (orig.)

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

    Science.gov (United States)

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

    2012-03-01

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

  7. A fully coupled depth-integrated model for surface water and groundwater flows

    Science.gov (United States)

    Li, Yuanyi; Yuan, Dekui; Lin, Binliang; Teo, Fang-Yenn

    2016-11-01

    This paper presents the development of a fully coupled surface water and groundwater flow model. The governing equations of the model are derived based on a control volume approach, with the velocity profiles of the two types of flows being both taken into consideration. The surface water and groundwater flows are both modelled based on the unified equations and the water exchange and interaction between the two types of flows can be taken into account. The model can be used to simulate the surface water and groundwater flows simultaneously with the same numerical scheme without other effort being needed to link them. The model is not only suitable for the porous medium consisting of fine sediments, but also for coarse sediments and crushed rocks by adding a quadratic friction term. Benchmark tests are conducted to validate the model. The model predictions agree well with the data.

  8. A Simulation Model for the Toroidal Ion Temperature Gradient Instability with Fully Kinetic Ions

    Science.gov (United States)

    Sturdevant, Benjamin; Parker, Scott; Chen, Yang

    2016-10-01

    A simulation model for the toroidal ITG mode in which the ions follow the primitive Lorentz force equations of motion is presented. Such a model can provide an important validation tool or replacement for gyrokinetic ion models in applications where higher order terms may be important. A number of multiple-scale simulation techniques are employed in this work, based on the previous success in slab geometry with an implicit orbit averaged and sub-cycled δf model. For the toroidal geometry model, we have derived a particle integration scheme based on variational principles, which is demonstrated to produce stable and accurate ion trajectories on long time scales. Orbit averaging and sub-cycling will be implemented with the variational integration scheme. The inclusion of equilibrium gradients in the fully kinetic δf formulation is achieved through the use of a guiding center coordinate transformation of the weight equation. Simulation results for the fully kinetic ion model will be presented for the cyclone base case and comparisons will be made with gyrokinetic ion models.

  9. IMPLEMENTATION AND VALIDATION OF A FULLY IMPLICIT ACCUMULATOR MODEL IN RELAP-7

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Haihua [Idaho National Laboratory; Zou, Ling [Idaho National Laboratory; Zhang, Hongbin [Idaho National Laboratory; Martineau, Richard Charles [Idaho National Laboratory

    2016-01-01

    This paper presents the implementation and validation of an accumulator model in RELAP-7 under the framework of preconditioned Jacobian free Newton Krylov (JFNK) method, based on the similar model used in RELAP5. RELAP-7 is a new nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). RELAP-7 is a fully implicit system code. The JFNK and preconditioning methods used in RELAP-7 is briefly discussed. The slightly modified accumulator model is summarized for completeness. The implemented model was validated with LOFT L3-1 test and benchmarked with RELAP5 results. RELAP-7 and RELAP5 had almost identical results for the accumulator gas pressure and water level, although there were some minor difference in other parameters such as accumulator gas temperature and tank wall temperature. One advantage of the JFNK method is its easiness to maintain and modify models due to fully separation of numerical methods from physical models. It would be straightforward to extend the current RELAP-7 accumulator model to simulate the advanced accumulator design.

  10. A fully-explicit discontinuous Galerkin hydrodynamic model for variably-satu- rated porous media

    Institute of Scientific and Technical Information of China (English)

    De MAET T.; HANERT E.; VANCLOOSTER M

    2014-01-01

    Groundwater flows play a key role in the recharge of aquifers, the transport of solutes through subsurface systems or the control of surface runoff. Predicting these processes requires the use of groundwater models with their applicability directly linked to their accuracy and computational efficiency. In this paper, we present a new method to model water dynamics in variably- saturated porous media. Our model is based on a fully-explicit discontinuous-Galerkin formulation of the 3D Richards equation, which shows a perfect scaling on parallel architectures. We make use of an adapted jump penalty term for the discontinuous-Galerkin scheme and of a slope limiter algorithm to produce oscillation-free exactly conservative solutions. We show that such an approach is particularly well suited to infiltration fronts. The model results are in good agreement with the reference model Hydrus-1D and seem promising for large scale applications involving a coarse representation of saturated soil.

  11. A fully associative, nonisothermal, nonlinear kinematic, unified viscoplastic model for titanium alloys

    Science.gov (United States)

    Arnold, S. M.; Saleeb, A. F.; Castelli, M. G.

    1995-01-01

    Specific forms for both the Gibb's and complementary dissipation potentials are chosen such that a complete (i.e., fully associative) potential base multiaxial, nonisothermal unified viscoplastic model is obtained. This model possesses one tensorial internal state variable (that is, associated with dislocation substructure) and an evolutionary law that has nonlinear kinematic hardening and both thermal and strain induced recovery mechanisms. A unique aspect of the present model is the inclusion of nonlinear hardening through the use of a compliance operator, derived from the Gibb's potential, in the evolution law for the back stress. This nonlinear tensorial operator is significant in that it allows both the flow and evolutionary laws to be fully associative (and therefore easily integrated), greatly influences the multiaxial response under non-proportional loading paths, and in the case of nonisothermal histories, introduces an instantaneous thermal softening mechanism proportional to the rate of change in temperature. In addition to this nonlinear compliance operator, a new consistent, potential preserving, internal strain unloading criterion has been introduced to prevent abnormalities in the predicted stress-strain curves, which are present with nonlinear hardening formulations, during unloading and reversed loading of the external variables. The specific model proposed is characterized for a representative titanium alloy commonly used as the matrix material in SiC fiber reinforced composites, i.e., TIMETAL 21S. Verification of the proposed model is shown using 'specialized' non-standard isothermal and thermomechanical deformation tests.

  12. A Fully Associative, Non-Linear Kinematic, Unified Viscoplastic Model for Titanium Based Matrices

    Science.gov (United States)

    Arnold, S. M.; Saleeb, A. F.; Castelli, M. G.

    1994-01-01

    Specific forms for both the Gibb's and complementary dissipation potentials are chosen such that a complete (i.e., fully associative) potential based multiaxial unified viscoplastic model is obtained. This model possesses one tensorial internal state variable that is associated with dislocation substructure, with an evolutionary law that has nonlinear kinematic hardening and both thermal and strain induced recovery mechanisms. A unique aspect of the present model is the inclusion of non-linear hardening through the use of a compliance operator, derived from the Gibb's potential, in the evolution law for the back stress. This non-linear tensorial operator is significant in that it allows both the flow and evolutionary laws to be fully associative (and therefore easily integrated) and greatly influences the multiaxial response under non-proportional loading paths. In addition to this nonlinear compliance operator, a new consistent, potential preserving, internal strain unloading criterion has been introduced to prevent abnormalities in the predicted stress-strain curves, which are present with nonlinear hardening formulations, during unloading and reversed loading of the external variables. Specification of an experimental program for the complete determination of the material functions and parameters for characterizing a metallic matrix, e.g., TIMETAL 21S, is given. The experiments utilized are tensile, creep, and step creep tests. Finally, a comparison of this model and a commonly used Bodner-Partom model is made on the basis of predictive accuracy and numerical efficiency.

  13. Atomistic modeling and experimental studies of radiation damage in monazite-type LaPO4 ceramics

    Science.gov (United States)

    Ji, Yaqi; Kowalski, Piotr M.; Neumeier, Stefan; Deissmann, Guido; Kulriya, Pawan K.; Gale, Julian D.

    2017-02-01

    We simulated the threshold displacement energies (Ed), the related displacement and defect formation probabilities, and the energy barriers in LaPO4 monazite-type ceramics. The obtained Ed values for La, P, O primary knock-on atoms (PKA) are 56 eV, 75 eV and 8 eV, respectively. We found that these energies can be correlated with the energy barriers that separate the defect from the initial states. The Ed values are about twice the values of energy barriers, which is explained through an efficient dissipation of the PKA kinetic energy in the considered system. The computed Ed were used in simulations of the extent of radiation damage in La0.2Gd0.8PO4 solid solution, investigated experimentally. We found that this lanthanide phosphate fully amorphises in the ion beam experiments for fluences higher than ∼1013 ions/cm2.

  14. Atomistic simulation of Voronoi-based coated nanoporous metals

    Science.gov (United States)

    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.

  15. Global fully kinetic models of planetary magnetospheres with iPic3D

    Science.gov (United States)

    Gonzalez, D.; Sanna, L.; Amaya, J.; Zitz, A.; Lembege, B.; Markidis, S.; Schriver, D.; Walker, R. J.; Berchem, J.; Peng, I. B.; Travnicek, P. M.; Lapenta, G.

    2016-12-01

    We report on the latest developments of our approach to model planetary magnetospheres, mini magnetospheres and the Earth's magnetosphere with the fully kinetic, electromagnetic particle in cell code iPic3D. The code treats electrons and multiple species of ions as full kinetic particles. We review: 1) Why a fully kinetic model and in particular why kinetic electrons are needed for capturing some of the most important aspects of the physics processes of planetary magnetospheres. 2) Why the energy conserving implicit method (ECIM) in its newest implementation [1] is the right approach to reach this goal. We consider the different electron scales and study how the new IECIM can be tuned to resolve only the electron scales of interest while averaging over the unresolved scales preserving their contribution to the evolution. 3) How with modern computing planetary magnetospheres, mini magnetosphere and eventually Earth's magnetosphere can be modeled with fully kinetic electrons. The path from petascale to exascale for iPiC3D is outlined based on the DEEP-ER project [2], using dynamic allocation of different processor architectures (Xeon and Xeon Phi) and innovative I/O technologies.Specifically results from models of Mercury are presented and compared with MESSENGER observations and with previous hybrid (fluid electrons and kinetic ions) simulations. The plasma convection around the planets includes the development of hydrodynamic instabilities at the flanks, the presence of the collisionless shocks, the magnetosheath, the magnetopause, reconnection zones, the formation of the plasma sheet and the magnetotail, and the variation of ion/electron plasma flows when crossing these frontiers. Given the full kinetic nature of our approach we focus on detailed particle dynamics and distribution at locations that can be used for comparison with satellite data. [1] Lapenta, G. (2016). Exactly Energy Conserving Implicit Moment Particle in Cell Formulation. arXiv preprint ar

  16. Addressing uncertainty in atomistic machine learning

    DEFF Research Database (Denmark)

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

    2017-01-01

    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 predi......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...

  17. Addressing uncertainty in atomistic machine learning.

    Science.gov (United States)

    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.

  18. Atomistic simulations of bicelle mixtures.

    Science.gov (United States)

    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.

  19. Local control on precipitation in a fully coupled climate-hydrology model

    DEFF Research Database (Denmark)

    Larsen, Morten A. D.; Christensen, Jens H.; Drews, Martin

    2016-01-01

    simulations of precipitation often exhibit substantial biases that affect the reliability of future projections. Here we demonstrate how a regional climate model (RCM) coupled to a distributed hydrological catchment model that fully integrates water and energy fluxes between the subsurface, land surface......-surface processes including groundwater and moisture feedback. A high degree of local influence on the atmosphere suggests that coupled climate-hydrology models have a potential for improving climate projections and the results further indicate a diminished need for bias correction in climate-hydrology impact......The ability to simulate regional precipitation realistically by climate models is essential to understand and adapt to climate change. Due to the complexity of associated processes, particularly at unresolved temporal and spatial scales this continues to be a major challenge. As a result, climate...

  20. Development of Fully Coupled Aeroelastic and Hydrodynamic Models for Offshore Wind Turbines: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Jonkman, J. M.; Sclavounos, P. D.

    2006-01-01

    Aeroelastic simulation tools are routinely used to design and analyze onshore wind turbines, in order to obtain cost effective machines that achieve favorable performance while maintaining structural integrity. These tools employ sophisticated models of wind-inflow; aerodynamic, gravitational, and inertial loading of the rotor, nacelle, and tower; elastic effects within and between components; and mechanical actuation and electrical responses of the generator and of control and protection systems. For offshore wind turbines, additional models of the hydrodynamic loading in regular and irregular seas, the dynamic coupling between the support platform motions and wind turbine motions, and the dynamic characterization of mooring systems for compliant floating platforms are also important. Hydrodynamic loading includes contributions from hydrostatics, wave radiation, and wave scattering, including free surface memory effects. The integration of all of these models into comprehensive simulation tools, capable of modeling the fully coupled aeroelastic and hydrodynamic responses of floating offshore wind turbines, is presented.

  1. Fully packed loops on random surfaces and the 1/N expansion of tensor models

    CERN Document Server

    Bonzom, Valentin

    2013-01-01

    Starting with the observation that some fully packed loop models on random surfaces can be mapped to random edge-colored graphs, we show that the expansion in the number of loops is organized like the 1/N expansion of rank-three tensor models. In particular, configurations which maximize the number of loops are precisely the melonic graphs of tensor models and a scaling limit which projects onto the melonic sector is found. This also shows that some three-dimensional topologies can be obtained from discrete surfaces decorated with loops. We generalize this approach to higher-rank tensor models, for random tensors of size $N^{d-1} \\times \\tau N^{\\beta}$ with beta between 0 and 1. They generate loops with fugacity $\\tau N^\\beta$ on triangulations in dimension d-1 and we show that the 1/N expansion is beta-dependent.

  2. Fractal Potential Flows as an Exact Model for Fully Developed Turbulence

    CERN Document Server

    Vass, József

    2013-01-01

    Fully Developed Turbulence (FDT) occurs at the infinite extreme of the Reynolds spectrum. It is a theoretical phenomenon which can only be approximated experimentally or computationally, and thus its precise properties are only hypothetical, though widely accepted. It is considered to be a chaotic yet steady flow field, with self-similar fractalline features. A number of approximate models exist, often exploiting this self-similarity. We hereby present the exact mathematical model of Fractal Potential Flows, and link it philosophically to the phenomenon of FDT, building on its experimental characteristics. The model hinges on the recursive iteration of a fluid dynamical transfer operator. We show the existence of its unique attractor in an appropriate function space - called the invariant flow - which will serve as our model for the FDT flow field. Its sink singularities are shown to form an IFS fractal, resolving Mandelbrot's Conjecture. Meanwhile we present an isometric isomorphism between flows and probabi...

  3. Fully Automated Non-Native Speech Recognition Using Confusion-Based Acoustic Model Integration

    OpenAIRE

    Bouselmi, Ghazi; Fohr, Dominique; Illina, Irina; Haton, Jean-Paul

    2005-01-01

    This paper presents a fully automated approach for the recognition of non-native speech based on acoustic model modification. For a native language (L1) and a spoken language (L2), pronunciation variants of the phones of L2 are automatically extracted from an existing non-native database as a confusion matrix with sequences of phones of L1. This is done using L1's and L2's ASR systems. This confusion concept deals with the problem of non existence of match between some L2 and L1 phones. The c...

  4. A Well-Balanced and Fully Coupled Noncapacity Model for Dam-Break Flooding

    Directory of Open Access Journals (Sweden)

    Zhiyuan Yue

    2015-01-01

    Full Text Available The last two decades have seen great progress in mathematical modeling of fluvial processes and flooding in terms of either approximation of the physical processes or dealing with the numerical difficulties. Yet attention to simultaneously taking advancements of both aspects is rarely paid. Here a well-balanced and fully coupled noncapacity model is presented of dam-break flooding over erodible beds. The governing equations are based on the complete mass and momentum conservation laws, implying fully coupled interactions between the dam-break flow and sediment transport. A well-balanced Godunov-type finite volume method is used to solve the governing equations, facilitating satisfactory representation of the complex flow phenomena. The well-balanced property is attained by using the divergence form of matrix related to the static force for the bottom slope source term. Existing classical tests, including idealized dam-break flooding over irregular topography and experimental dam-break flooding with/without sediment transport, are numerically simulated, showing a satisfactory quantitative performance of this model.

  5. A perturbative formalism for electronic transitions through conical intersections in a fully quadratic vibronic model

    CERN Document Server

    Endicott, Julia S; Izmaylov, Artur F

    2014-01-01

    We consider a fully quadratic vibronic model Hamiltonian for studying photoinduced electronic transitions through conical intersections. Using a second order perturbative approximation for diabatic couplings we derive an analytical expression for the time evolution of electronic populations at a given temperature. This formalism extends upon a previously developed perturbative technique for a linear vibronic coupling Hamiltonian. The advantage of the quadratic model Hamiltonian is that it allows one to use separate quadratic representations for potential energy surfaces of different electronic states and a more flexible representation of interstate couplings. We explore features introduced by the quadratic Hamiltonian in a series of 2D models, and then apply our formalism to the 2,6-bis(methylene) adamantyl cation, and its dimethyl derivative. The Hamiltonian parameters for the molecular systems have been obtained from electronic structure calculations followed by a diabatization procedure. The evolution of e...

  6. DrugOn: a fully integrated pharmacophore modeling and structure optimization toolkit

    Directory of Open Access Journals (Sweden)

    Dimitrios Vlachakis

    2015-01-01

    Full Text Available During the past few years, pharmacophore modeling has become one of the key components in computer-aided drug design and in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design to perform pharmacophore modeling through an efficient combination of the PharmACOphore, Gromacs, Ligbuilder and PDB2PQR suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process. For the pharmacophore modeling we are focusing on either the characteristics of the receptor or the full molecular system, including a set of selected ligands. DrugOn can be freely downloaded from our dedicated server system at www.bioacademy.gr/bioinformatics/drugon/.

  7. A fully unsteady prescribed wake model for HAWT performance prediction in yawed flow

    Energy Technology Data Exchange (ETDEWEB)

    Coton, F.N.; Tongguang, Wang; Galbraith, R.A.M.; Lee, D. [Univ. of Glasgow (United Kingdom)

    1997-12-31

    This paper describes the development of a fast, accurate, aerodynamic prediction scheme for yawed flow on horizontal axis wind turbines (HAWTs). The method is a fully unsteady three-dimensional model which has been developed over several years and is still being enhanced in a number of key areas. The paper illustrates the current ability of the method by comparison with field data from the NREL combined experiment and also describes the developmental work in progress. In particular, an experimental test programme designed to yield quantitative wake convection information is summarised together with modifications to the numerical model which are necessary for meaningful comparison with the experiments. Finally, current and future work on aspects such as tower-shadow and improved unsteady aerodynamic modelling are discussed.

  8. A fully-coupled geomechanics and flow model for hydraulic fracturing and reservoir engineering applications

    Energy Technology Data Exchange (ETDEWEB)

    Charoenwongsa, S.; Kazemi, H.; Miskimins, J.; Fakcharoenphol [Colorado School of Mines, Golden, CO (United States)

    2010-07-01

    A fully coupled geomechanics flow model was used to assess how the changes in pore pressure and temperature influence rock stresses in tight gas reservoirs. The finite difference method was used to develop simulations for phases, components, and thermal stresses. A wave component was used to model the propagation of the strain displacement front as well as changes in stress with time. Fluid and heat flow volumes were modelled separately from rock formation properties. The influence of hydraulic fracturing on stress distributions surrounding the fracture was investigated as well as the effect of filter cake and filtrate. Results of the study showed that significant changes in shear stresses near hydraulic fractures occur as a result of hydraulic fracture face displacement perpendicular to the fracture face. While temperature effects also caused changes in stress distributions, changes in pore pressure did not significantly impact shear stresses as the filtrate did not travel very far into the reservoir. 17 refs., 17 figs.

  9. A Fully Nonlinear, Dynamically Consistent Numerical Model for Ship Maneuvering in a Seaway

    Directory of Open Access Journals (Sweden)

    Ray-Qing Lin

    2011-01-01

    Full Text Available This is the continuation of our research on development of a fully nonlinear, dynamically consistent, numerical ship motion model (DiSSEL. In this paper we report our results on modeling ship maneuvering in arbitrary seaway that is one of the most challenging and important problems in seakeeping. In our modeling, we developed an adaptive algorithm to maintain dynamical balances numerically as the encounter frequencies (the wave frequencies as measured on the ship varying with the ship maneuvering state. The key of this new algorithm is to evaluate the encounter frequency variation differently in the physical domain and in the frequency domain, thus effectively eliminating possible numerical dynamical imbalances. We have tested this algorithm with several well-documented maneuvering experiments, and our results agree very well with experimental data. In particular, the numerical time series of roll and pitch motions and the numerical ship tracks (i.e., surge, sway, and yaw are nearly identical to those of experiments.

  10. Pion generalized parton distributions within a fully covariant constituent quark model

    Energy Technology Data Exchange (ETDEWEB)

    Fanelli, Cristiano [Massachusetts Institute of Technology, Cambridge, MA (United States). Lab. for Nuclear Science; Pace, Emanuele [' ' Tor Vergata' ' Univ., Rome (Italy). Physics Dept.; INFN Sezione di TorVergata, Rome (Italy); Romanelli, Giovanni [Rutherford-Appleton Laboratory, Didcot (United Kingdom). STFC; Salme, Giovanni [Istituto Nazionale di Fisica Nucleare, Rome (Italy); Salmistraro, Marco [Rome La Sapienza Univ. (Italy). Physics Dept.; I.I.S. G. De Sanctis, Rome (Italy)

    2016-05-15

    We extend the investigation of the generalized parton distribution for a charged pion within a fully covariant constituent quark model, in two respects: (1) calculating the tensor distribution and (2) adding the treatment of the evolution, needed for achieving a meaningful comparison with both the experimental parton distribution and the lattice evaluation of the so-called generalized form factors. Distinct features of our phenomenological covariant quark model are: (1) a 4D Ansatz for the pion Bethe-Salpeter amplitude, to be used in the Mandelstam formula for matrix elements of the relevant current operators, and (2) only two parameters, namely a quark mass assumed to be m{sub q} = 220 MeV and a free parameter fixed through the value of the pion decay constant. The possibility of increasing the dynamical content of our covariant constituent quark model is briefly discussed in the context of the Nakanishi integral representation of the Bethe-Salpeter amplitude. (orig.)

  11. Terahertz Nanoscience of Multifunctional Materials: Atomistic Exploration

    Science.gov (United States)

    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

  12. Modeling of Calcite Precipitation Driven by Bacteria-facilitated Urea Hydrolysis in A Flow Column Using A Fully Coupled, Fully Implicit Parallel Reactive Transport Simulator

    Science.gov (United States)

    Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.

    2009-12-01

    One approach for immobilizing subsurface metal contaminants involves stimulating the in situ production of mineral phases that sequester or isolate contaminants. One example is using calcium carbonate to immobilize strontium. The success of such approaches depends on understanding how various processes of flow, transport, reaction and resulting porosity-permeability change couple in subsurface systems. Reactive transport models are often used for such purpose. Current subsurface reactive transport simulators typically involve a de-coupled solution approach, such as operator-splitting, that solves the transport equations for components and batch chemistry sequentially, which has limited applicability for many biogeochemical processes with fast kinetics and strong medium property-reaction interactions. A massively parallel, fully coupled, fully implicit reactive transport simulator has been developed based on a parallel multi-physics object oriented software environment computing framework (MOOSE) developed at the Idaho National Laboratory. Within this simulator, the system of transport and reaction equations is solved simultaneously in a fully coupled manner using the Jacobian Free Newton-Krylov (JFNK) method with preconditioning. The simulator was applied to model reactive transport in a one-dimensional column where conditions that favor calcium carbonate precipitation are generated by urea hydrolysis that is catalyzed by urease enzyme. Simulation results are compared to both laboratory column experiments and those obtained using the reactive transport simulator STOMP in terms of: the spatial and temporal distributions of precipitates and reaction rates and other major species in the reaction system; the changes in porosity and permeability; and the computing efficiency based on wall clock simulation time.

  13. Equipment for fully homologous bulb turbine model testing in Laval University

    Science.gov (United States)

    R, Fraser; D, Vallée; Y, Jean; C, Deschênes

    2014-03-01

    Within the context of liberalisation of the energy market, hydroelectricity remains a first class source of clean and renewable energy. Combining the growing demand of energy, its increasing value and the appreciation associated to the sustainable development, low head sites formerly considered as non-profitable are now exploitable. Bulb turbines likely to equip such sites are traditionally developed on model using right angle transmission leading to piers enlargement for power take off shaft passage, thus restricting possibilities to have fully homologous hydraulic passages. Aiming to sustain good quality development on fully homologous scale model of bulb turbines, the Hydraulic Machines Laboratory (LAMH) of Laval University has developed a brake with an enhanced power to weight ratio. This powerful brake is small enough to be located in the bulb shell while dissipating power without mandatory test head reduction. This paper first presents the basic technology of this brake and its application. Then both its main performance capabilities and dimensional characteristics will be detailed. The instrumentation used to perform accurate measurements will be finally presented.

  14. Prediction of Ship Unsteady Maneuvering in Calm Water by a Fully Nonlinear Ship Motion Model

    Directory of Open Access Journals (Sweden)

    Ray-Qing Lin

    2012-01-01

    Full Text Available This is the continuation of our research on development of a fully nonlinear, dynamically consistent, numerical ship motion model (DiSSEL. In this study we will report our results in predicting ship motions in unsteady maneuvering in calm water. During the unsteady maneuvering, both the rudder angle, and ship forward speed vary with time. Therefore, not only surge, sway, and yaw motions occur, but roll, pitch and heave motions will also occur even in calm water as heel, trim, and sinkage, respectively. When the rudder angles and ship forward speed vary rapidly with time, the six degrees-of-freedom ship motions and their interactions become strong. To accurately predict the six degrees-of-freedom ship motions in unsteady maneuvering, a universal method for arbitrary ship hull requires physics-based fully-nonlinear models for ship motion and for rudder forces and moments. The numerical simulations will be benchmarked by experimental data of the Pre-Contract DDG51 design and an Experimental Hull Form. The benchmarking shows a good agreement between numerical simulations by the enhancement DiSSEL and experimental data. No empirical parameterization is used, except for the influence of the propeller slipstream on the rudder, which is included using a flow acceleration factor.

  15. Atomistic modeling of crystal structure of Ca{sub 1.67}SiH{sub x}

    Energy Technology Data Exchange (ETDEWEB)

    Kovačević, Goran; Persson, Björn [Theoretical Chemistry, P.O.B. 124, Lund University, Lund 22100 (Sweden); Nicoleau, Luc [BASF Construction Solutions GmbH, Advanced Materials and Systems Research, Albert Frank Straße 32, 83304 Trostberg (Germany); Nonat, André [Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne, BP 47870, F-21078 Dijon Cedex (France); Veryazov, Valera, E-mail: valera.veryazov@teokem.lu.se [Theoretical Chemistry, P.O.B. 124, Lund University, Lund 22100 (Sweden)

    2015-01-15

    The atomic structure of calcium-silicate-hydrate (C{sub 1.67}-S-H{sub x}) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three models. The C-S-H model related to the lowest energy is considered as the most probable. It turns out to be characterized by the distribution of dimeric and pentameric silicates and the absence of monomers. This model has mass density which is closest to the experimental one.

  16. Fully Electrical Modeling of Thermoelectric Generators with Contact Thermal Resistance Under Different Operating Conditions

    Science.gov (United States)

    Siouane, Saima; Jovanović, Slaviša; Poure, Philippe

    2017-01-01

    The Seebeck effect is used in thermoelectric generators (TEGs) to supply electronic circuits by converting the waste thermal into electrical energy. This generated electrical power is directly proportional to the temperature difference between the TEG module's hot and cold sides. Depending on the applications, TEGs can be used either under constant temperature gradient between heat reservoirs or constant heat flow conditions. Moreover, the generated electrical power of a TEG depends not only on these operating conditions, but also on the contact thermal resistance. The influence of the contact thermal resistance on the generated electrical power have already been extensively reported in the literature. However, as reported in Park et al. (Energy Convers Manag 86:233, 2014) and Montecucco and Knox (IEEE Trans Power Electron 30:828, 2015), while designing TEG-powered circuit and systems, a TEG module is mostly modeled with a Thévenin equivalent circuit whose resistance is constant and voltage proportional to the temperature gradient applied to the TEG's terminals. This widely used simplified electrical TEG model is inaccurate and not suitable under constant heat flow conditions or when the contact thermal resistance is considered. Moreover, it does not provide realistic behaviour corresponding to the physical phenomena taking place in a TEG. Therefore, from the circuit designer's point of view, faithful and fully electrical TEG models under different operating conditions are needed. Such models are mainly necessary to design and evaluate the power conditioning electronic stages and the maximum power point tracking algorithms of a TEG power supply. In this study, these fully electrical models with the contact thermal resistance taken into account are presented and the analytical expressions of the Thévenin equivalent circuit parameters are provided.

  17. Fully Electrical Modeling of Thermoelectric Generators with Contact Thermal Resistance Under Different Operating Conditions

    Science.gov (United States)

    Siouane, Saima; Jovanović, Slaviša; Poure, Philippe

    2016-09-01

    The Seebeck effect is used in thermoelectric generators (TEGs) to supply electronic circuits by converting the waste thermal into electrical energy. This generated electrical power is directly proportional to the temperature difference between the TEG module's hot and cold sides. Depending on the applications, TEGs can be used either under constant temperature gradient between heat reservoirs or constant heat flow conditions. Moreover, the generated electrical power of a TEG depends not only on these operating conditions, but also on the contact thermal resistance. The influence of the contact thermal resistance on the generated electrical power have already been extensively reported in the literature. However, as reported in Park et al. (Energy Convers Manag 86:233, 2014) and Montecucco and Knox (IEEE Trans Power Electron 30:828, 2015), while designing TEG-powered circuit and systems, a TEG module is mostly modeled with a Thévenin equivalent circuit whose resistance is constant and voltage proportional to the temperature gradient applied to the TEG's terminals. This widely used simplified electrical TEG model is inaccurate and not suitable under constant heat flow conditions or when the contact thermal resistance is considered. Moreover, it does not provide realistic behaviour corresponding to the physical phenomena taking place in a TEG. Therefore, from the circuit designer's point of view, faithful and fully electrical TEG models under different operating conditions are needed. Such models are mainly necessary to design and evaluate the power conditioning electronic stages and the maximum power point tracking algorithms of a TEG power supply. In this study, these fully electrical models with the contact thermal resistance taken into account are presented and the analytical expressions of the Thévenin equivalent circuit parameters are provided.

  18. Analytical modeling of drain current and RF performance for double-gate fully depleted nanoscale SOI MOSFETs

    Institute of Scientific and Technical Information of China (English)

    Rajiv Sharma; Sujata Pandey; Shail Bala Jain

    2012-01-01

    A new 2D analytical drain current model is presented for symmetric double-gate fully depleted nanoscale SOI MOSFETs.Investigation of device parameters like transconductance for double-gate fully depleted nanoscale SOI MOSFETs is also carried out.Finally this work is concluded by modeling the cut-off frequency,which is one of the main figures of merit for analog/RF performance for double-gate fully depleted nanoscale SOI MOSFETs.The results of the modeling are compared with those obtained by a 2D ATLAS device simulator to verify the accuracy of the proposed model.

  19. An Improved Nearshore Wave Breaking Model Based on the Fully Nonlinear Boussinesq Equations

    Institute of Scientific and Technical Information of China (English)

    LI Shao-wu; LI Chun-ying; SHI Zhong; GU Han-bin

    2005-01-01

    This paper aims to propose an improved numerical model for wave breaking in the nearshore region based on the fully nonlinear form of Boussinesq equations. The model uses the κ equation turbulence scheme to determine the eddy viscosity in the Boussinesq equations. To calculate the turbulence production term in the equation, a new formula is derived based on the concept of surface roller. By use of this formula, the turbulence production in the one-equation turbulence scheme is directly related to the difference between the water particle velocity and the wave celerity. The model is verified by Hansen and Svendsen's experimental data (1979) in terms of wave height and setup and setdown. The comparison between the model and experimental results of wave height and setup and setdown shows satisfactory agreement. The modeled turbulence energy decreases as waves attenuate in the surf zone. The modeled production term peaks at the breaking point and decreases as waves propagate shoreward. It is also suggested that both convection and diffusion play their important roles in the transport of turbulence energy immediately after wave breaking. When waves approach to the shoreline, the production and dissipation of turbulence energy are almost balanced. By use of the slot technique for the simulation of the movable shoreline boundary, wave runup in the swash zone is well simulated by the present model.

  20. Analysis of a Fully Packed Loop Model Arising in a Magnetic Coulomb Phase

    Science.gov (United States)

    Jaubert, L. D. C.; Haque, M.; Moessner, R.

    2011-10-01

    The Coulomb phase of spin ice, and indeed the Ic phase of water ice, naturally realize a fully packed two-color loop model in 3D. We present a detailed analysis of the statistics of these loops: we find loops spanning the system multiple times hosting a finite fraction of all sites while the average loop length remains finite. We contrast the behavior with an analogous 2D model. We connect this body of results to properties of polymers, percolation and insights from Schramm-Loewner evolution processes. We also study another extended degree of freedom, called worms, which appear as “Dirac strings” in spin ice. We discuss implications of these results for the efficiency of numerical cluster algorithms, and address implications for the ordering properties of a broader class of magnetic systems, e.g., with Heisenberg spins, such as CsNiCrF6 or ZnCr2O4.

  1. Assessing the Vulnerability of Large Critical Infrastructure Using Fully-Coupled Blast Effects Modeling

    Energy Technology Data Exchange (ETDEWEB)

    McMichael, L D; Noble, C R; Margraf, J D; Glascoe, L G

    2009-03-26

    Structural failures, such as the MacArthur Maze I-880 overpass in Oakland, California and the I-35 bridge in Minneapolis, Minnesota, are recent examples of our national infrastructure's fragility and serve as an important reminder of such infrastructure in our everyday lives. These two failures, as well as the World Trade Center's collapse and the levee failures in New Orleans, highlight the national importance of protecting our infrastructure as much as possible against acts of terrorism and natural hazards. This paper describes a process for evaluating the vulnerability of critical infrastructure to large blast loads using a fully-coupled finite element approach. A description of the finite element software and modeling technique is discussed along with the experimental validation of the numerical tools. We discuss how such an approach can be used for specific problems such as modeling the progressive collapse of a building.

  2. In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding.

    Science.gov (United States)

    Henzler, Angela M; Rarey, Matthias

    2010-03-15

    Modern structure-based drug design aims at accounting for the intrinsic flexibility of therapeutic relevant targets. Over the last few years a considerable amount of docking approaches that encounter this challenging problem has emerged. Here we provide the readership with an overview of established methods for fully flexible protein-ligand docking and current developments in the field. All methods are based on one of two fundamental models which describe the dynamic behavior of proteins upon ligand binding. Methods for ensemble docking (ED) model the protein conformational change before the ligand is placed, whereas induced-fit docking (IFD) optimizes the protein structure afterwards. A third category of docking approaches is formed by recent approaches that follow both concepts. This categorization allows to comprehensively discover strengths and weaknesses of the individual processes and to extract information for their applicability in real world docking scenarios.

  3. A splitting approach for the fully nonlinear and weakly dispersive Green-Naghdi model

    CERN Document Server

    Bonneton, Philippe; Lannes, David; Marche, Fabien; Tissier, Marion

    2010-01-01

    The fully nonlinear and weakly dispersive Green-Naghdi model for shallow water waves of large amplitude is studied. The original model is first recast under a new formulation more suitable for numerical resolution. An hybrid finite volume and finite difference splitting approach is then proposed. The hyperbolic part of the equations is handled with a high-order finite volume scheme allowing for breaking waves and dry areas. The dispersive part is treated with a classical finite difference approach. Extensive numerical validations are then performed in one horizontal dimension, relying both on analytical solutions and experimental data. The results show that our approach gives a good account of all the processes of wave transformation in coastal areas: shoaling, wave breaking and run-up.

  4. Methodology to develop crash modification functions for road safety treatments with fully specified and hierarchical models.

    Science.gov (United States)

    Chen, Yongsheng; Persaud, Bhagwant

    2014-09-01

    Crash modification factors (CMFs) for road safety treatments are developed as multiplicative factors that are used to reflect the expected changes in safety performance associated with changes in highway design and/or the traffic control features. However, current CMFs have methodological drawbacks. For example, variability with application circumstance is not well understood, and, as important, correlation is not addressed when several CMFs are applied multiplicatively. These issues can be addressed by developing safety performance functions (SPFs) with components of crash modification functions (CM-Functions), an approach that includes all CMF related variables, along with others, while capturing quantitative and other effects of factors and accounting for cross-factor correlations. CM-Functions can capture the safety impact of factors through a continuous and quantitative approach, avoiding the problematic categorical analysis that is often used to capture CMF variability. There are two formulations to develop such SPFs with CM-Function components - fully specified models and hierarchical models. Based on sample datasets from two Canadian cities, both approaches are investigated in this paper. While both model formulations yielded promising results and reasonable CM-Functions, the hierarchical model was found to be more suitable in retaining homogeneity of first-level SPFs, while addressing CM-Functions in sub-level modeling. In addition, hierarchical models better capture the correlations between different impact factors.

  5. Effect of cation dopants in zirconia on interfacial properties in nickel/zirconia systems: an atomistic modeling study

    Science.gov (United States)

    Iskandarov, Albert M.; Ding, Yingna; Umeno, Yoshitaka

    2017-02-01

    Cation doping is often used to stabilize the cubic or tetragonal phase of zirconia for enhanced thermomechanical and electrochemical properties. In the present paper we report a combined density functional theory (DFT) and molecular dynamics study of the effect of Sc, Y, and Ce dopants on properties of Ni/\\text{Zr}{{\\text{O}}2} interfaces and nickel sintering. First, we develop an MD model that is based on DFT data for various nickel/zirconia interfaces. Then, we employ the model to simulate Ni nanoparticles coalescing on a zirconia surface. The results show the possibility of particle migration by means of fast sliding over the surface when the work of separation is small (nanoparticle migration. DFT calculations for the interface revealed that dopants with a smaller covalent radius result in a larger energy barriers for Ni diffusion. We analyze this effect and discuss how it can be used to suppress nickel sintering by using the dopant selection.

  6. A Fully Bayesian Method for Jointly Fitting Instrumental Calibration and X-Ray Spectral Models

    Science.gov (United States)

    Xu, Jin; van Dyk, David A.; Kashyap, Vinay L.; Siemiginowska, Aneta; Connors, Alanna; Drake, Jeremy; Meng, Xiao-Li; Ratzlaff, Pete; Yu, Yaming

    2014-10-01

    Owing to a lack of robust principled methods, systematic instrumental uncertainties have generally been ignored in astrophysical data analysis despite wide recognition of the importance of including them. Ignoring calibration uncertainty can cause bias in the estimation of source model parameters and can lead to underestimation of the variance of these estimates. We previously introduced a pragmatic Bayesian method to address this problem. The method is "pragmatic" in that it introduced an ad hoc technique that simplified computation by neglecting the potential information in the data for narrowing the uncertainty for the calibration product. Following that work, we use a principal component analysis to efficiently represent the uncertainty of the effective area of an X-ray (or γ-ray) telescope. Here, however, we leverage this representation to enable a principled, fully Bayesian method that coherently accounts for the calibration uncertainty in high-energy spectral analysis. In this setting, the method is compared with standard analysis techniques and the pragmatic Bayesian method. The advantage of the fully Bayesian method is that it allows the data to provide information not only for estimation of the source parameters but also for the calibration product—here the effective area, conditional on the adopted spectral model. In this way, it can yield more accurate and efficient estimates of the source parameters along with valid estimates of their uncertainty. Provided that the source spectrum can be accurately described by a parameterized model, this method allows rigorous inference about the effective area by quantifying which possible curves are most consistent with the data.

  7. A fully Bayesian method for jointly fitting instrumental calibration and X-ray spectral models

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Jin; Yu, Yaming [Department of Statistics, University of California, Irvine, Irvine, CA 92697-1250 (United States); Van Dyk, David A. [Statistics Section, Imperial College London, Huxley Building, South Kensington Campus, London SW7 2AZ (United Kingdom); Kashyap, Vinay L.; Siemiginowska, Aneta; Drake, Jeremy; Ratzlaff, Pete [Smithsonian Astrophysical Observatory, 60 Garden Street, Cambridge, MA 02138 (United States); Connors, Alanna; Meng, Xiao-Li, E-mail: jinx@uci.edu, E-mail: yamingy@ics.uci.edu, E-mail: dvandyk@imperial.ac.uk, E-mail: vkashyap@cfa.harvard.edu, E-mail: asiemiginowska@cfa.harvard.edu, E-mail: jdrake@cfa.harvard.edu, E-mail: pratzlaff@cfa.harvard.edu, E-mail: meng@stat.harvard.edu [Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138 (United States)

    2014-10-20

    Owing to a lack of robust principled methods, systematic instrumental uncertainties have generally been ignored in astrophysical data analysis despite wide recognition of the importance of including them. Ignoring calibration uncertainty can cause bias in the estimation of source model parameters and can lead to underestimation of the variance of these estimates. We previously introduced a pragmatic Bayesian method to address this problem. The method is 'pragmatic' in that it introduced an ad hoc technique that simplified computation by neglecting the potential information in the data for narrowing the uncertainty for the calibration product. Following that work, we use a principal component analysis to efficiently represent the uncertainty of the effective area of an X-ray (or γ-ray) telescope. Here, however, we leverage this representation to enable a principled, fully Bayesian method that coherently accounts for the calibration uncertainty in high-energy spectral analysis. In this setting, the method is compared with standard analysis techniques and the pragmatic Bayesian method. The advantage of the fully Bayesian method is that it allows the data to provide information not only for estimation of the source parameters but also for the calibration product—here the effective area, conditional on the adopted spectral model. In this way, it can yield more accurate and efficient estimates of the source parameters along with valid estimates of their uncertainty. Provided that the source spectrum can be accurately described by a parameterized model, this method allows rigorous inference about the effective area by quantifying which possible curves are most consistent with the data.

  8. Study of the machining process of nano-electrical discharge machining based on combined atomistic-continuum modeling method

    Science.gov (United States)

    Zhang, Guojun; Guo, Jianwen; Ming, Wuyi; Huang, Yu; Shao, Xinyu; Zhang, Zhen

    2014-01-01

    Nano-electrical discharge machining (nano-EDM) is an attractive measure to manufacture parts with nanoscale precision, however, due to the incompleteness of its theories, the development of more advanced nano-EDM technology is impeded. In this paper, a computational simulation model combining the molecular dynamics simulation model and the two-temperature model for single discharge process in nano-EDM is constructed to study the machining mechanism of nano-EDM from the thermal point of view. The melting process is analyzed. Before the heated material gets melted, thermal compressive stress higher than 3 GPa is induced. After the material gets melted, the compressive stress gets relieved. The cooling and solidifying processes are also analyzed. It is found that during the cooling process of the melted material, tensile stress higher than 3 GPa arises, which leads to the disintegration of material. The formation of the white layer is attributed to the homogeneous solidification, and additionally, the resultant residual stress is analyzed.

  9. A fully-coupled atmosphere-ocean-wave model of the Caspian Sea

    Science.gov (United States)

    Bruneau, Nicolas; Toumi, Ralf

    2016-11-01

    Located in the mid-latitudes, the Caspian Sea is the largest enclosed basin in the world. A fully-coupled atmosphere-ocean-wave model of the Caspian Sea at high resolution (8 km) for a period of three years is presented. After validating each component of the modelling platform, the wave state of the Caspian Sea is studied. Results show very different wave regimes between the three different basins, a strong seasonality and an almost swell-free state. It is shown here that waves modify the horizontal eddy viscosity and vertical heat diffusion. However, due to a reasonably weak annual wave state, these effects are restricted to the upper-ocean layer (cooling of the SST accompanied with a deepening of the MLD is modelled during autumn and winter. The results also show a significant improvement of the model skill in the representation of the dynamics when ROMS is coupled to WRF. Finally, as ocean surface waves imply feedback at the interface atmosphere-ocean through the transfer of momentum, mass and heat, we investigate their potential effects on the Caspian Sea dynamics. Results are mixed and show a reasonably weak impact of wave-induced processes. While waves have a negligible effect during the winter as wave-induced mixing is confined to the MLD, the summer global SST are less accurately modelled due to the enhancement of mixing in shallow MLDs. However the SST bias, temperature at a subsurface location are improved.

  10. Atomistic insights into milling mechanisms in an Fe-Y{sub 2}O{sub 3} model alloy

    Energy Technology Data Exchange (ETDEWEB)

    Ressel, G.; Holec, D.; Mendez-Martin, F.; Leitner, H. [Montanuniversitaet Leoben, Department of Physical Metallurgy and Materials Testing, Leoben (Austria); Fian, A. [Joanneum Research Forschungsgesellschaft GmbH, Institute for Surface Technologies and Photonics, Weiz (Austria)

    2014-06-15

    This experimental study combined with first principles modeling focuses on the distribution and behavior of yttria in pure iron powder particles prepared by mechanical alloying. A profound verification of the mechanism during milling is still missing in literature. Atom probe tomography and X-ray photoelectron spectroscopy measurements directly after mechanical alloying revealed yttria dissolved in the iron matrix, which later rearranged in clusters. These findings are corroborated by ab initio calculations demonstrating that the formation energy for Y substitutional defect in bcc-Fe is significantly lower in the close neighborhood of vacancies. X-ray diffraction measurements revealed that mechanical alloying for at least 12 hours caused a dramatic decrease in domain size and an extraordinary increase of defect density. (orig.)

  11. Atomistic modeling of the reordering process of γ‧ disordered particles in Ni-Al alloys

    Science.gov (United States)

    Martínez, Enrique; Soisson, Frédéric; Caro, Alfredo; Uberuaga, Blas P.

    2016-09-01

    Ni-based alloys are used in nuclear applications, including as a window material at isotope production facilities, withstanding high fluxes of different energetic particles like protons. Irradiation disorders the γ‧ precipitates that in large extent confer the mechanical properties characterizing these materials. Upon disordering, the γ‧ phase transforms into oversaturated γ, degrading the materials properties. Experimentally it is observed that disordering might take place at fairly low irradiation doses. Once the particles are disordered, a competition between dissolution, due to strong concentration gradients in an oversaturated solid solution, and reordering appears. Here, we examine this competition in a model Ni-Al alloy under thermal conditions for different precipitates sizes and temperatures. We observe Al interdiffusion from the supersaturated particle to the matrix. Also, stochasticity appears as an important factor in to where precipitates locate. Stress relaxation seems to modify the precipitation process, with a stronger interface effect compared to rigid lattice simulations. bib-reference>

  12. Evaluation of satellite rainfall products through hydrologic simulation in a fully distributed hydrologic model

    Science.gov (United States)

    Bitew, Menberu M.; Gebremichael, Mekonnen

    2011-06-01

    The goal of this study is to evaluate the accuracy of four global high-resolution satellite rainfall products (CMORPH, TMPA 3B42RT, TMPA 3B42, and PERSIANN) through the hydrologic simulation of a 1656 km2 mountainous watershed in the fully distributed MIKE SHE hydrologic model. This study shows that there are significant biases in the satellite rainfall estimates and large variations in rainfall amounts, leading to large variations in hydrologic simulations. The rainfall algorithms that use primarily microwave data (CMORPH and TMPA 3B42RT) show consistent and better performance in streamflow simulation (bias in the order of -53% to -3%, Nash-Sutcliffe efficiency (NSE) from 0.34 to 0.65); the rainfall algorithm that uses primarily infrared data (PERSIANN) shows lower performance (bias from -82% to -3%, Nash-Sutcliffe efficiency from -0.39 to 0.43); and the rainfall algorithm that merges the satellite data with rain gage data (TMPA 3B42) shows inconsistencies and the lowest performance (bias from -86% to 0.43%, Nash-Sutcliffe efficiency from -0.50 to 0.27). A dilemma between calibrating the hydrologic model with rain gage data and calibrating it with the corresponding satellite rainfall data is presented. Calibrating the model with corresponding satellite rainfall data increases the performance of satellite streamflow simulation compared to the model calibrated with rain gage data, but decreases the performance of satellite evapotranspiration simulation.

  13. Local control on precipitation in a fully coupled climate-hydrology model.

    Science.gov (United States)

    Larsen, Morten A D; Christensen, Jens H; Drews, Martin; Butts, Michael B; Refsgaard, Jens C

    2016-03-10

    The ability to simulate regional precipitation realistically by climate models is essential to understand and adapt to climate change. Due to the complexity of associated processes, particularly at unresolved temporal and spatial scales this continues to be a major challenge. As a result, climate simulations of precipitation often exhibit substantial biases that affect the reliability of future projections. Here we demonstrate how a regional climate model (RCM) coupled to a distributed hydrological catchment model that fully integrates water and energy fluxes between the subsurface, land surface, plant cover and the atmosphere, enables a realistic representation of local precipitation. Substantial improvements in simulated precipitation dynamics on seasonal and longer time scales is seen for a simulation period of six years and can be attributed to a more complete treatment of hydrological sub-surface processes including groundwater and moisture feedback. A high degree of local influence on the atmosphere suggests that coupled climate-hydrology models have a potential for improving climate projections and the results further indicate a diminished need for bias correction in climate-hydrology impact studies.

  14. Electrostatic Properties of Polymers Subjected to Atmospheric Pressure Plasma Treatment; Correlation of Experimental Results with Atomistic Modeling

    Science.gov (United States)

    Trigwell, S.; Boucher, D.; Calle, C. I.

    2007-01-01

    this study, PE, PTFE, PS and PMMA were exposed to a He+O2, APGD and pre and post treatment surface chemistries were analyzed by X-ray photoelectron spectroscopy and contact angle measurements. Semi-empirical and ab-initio calculations were performed to correlate the experimental results with sonic plausible molecular and electronic structure features of the oxidation process. For the PE and PS, significant surface oxidation showing C-O, C=O, and O-C=O bonding, and a decrease in the surface contact angles was observed. For the PTFE and PM MA, little change in the surface composition was observed. The molecular modeling calculations were performed on single and multiple oligomers and showed regardless of oxidation mechanism, e.g. -OH, =O or a combination thereof, experimentally observed levels of surface oxidation were unlikely to lead to a significant change in the electronic structure of PE and PS, and that the increased hydrophilic properties are the primary reason for the observed changes in its electrostatic behavior. Calculations for PTFE and PMMA argue strongly against significant oxidation of those materials, as confirmed by the XPS results.

  15. Fully-developed Turbulent Pipe Flow Using a Zero-Equation Model

    Directory of Open Access Journals (Sweden)

    Khalid Alammar

    2013-06-01

    Full Text Available Aim of this study is to evaluate a zero-equation turbulence model. A fully-developed turbulent pipe flow was simulated. Uncertainty was approximated through grid-independence and model validation. Results for mean axial velocity, u+ and Reynolds stress had maximum error of 5%, while results for the friction factor had negligible error. The mean axial velocity was shown to increase and extend farther in the outer layer with increasing Reynolds number, up to 106. There was no effect of Reynolds number on u+ below wall distance, Y+, of 100. Similar to the friction velocity, peak of the Reynolds stress was shown to increase and extend farther in the outer layer with increasing Reynolds number. There was no effect of Reynolds number on Reynolds stress below wall distance of 20. The new turbulence model is equally applicable to developing and external flows using the same constant. For wall-bounded flows, the constant is a function of wall roughness.

  16. Fully Coupled Fluid-Structure Interaction Model Based on Distributed Lagrange Multiplier/Fictitious Domain Method

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper, with a finite element method, studies the interaction of a coupled incompressible fluid-rigid structure system with a free surface subjected to external wave excitations. With this fully coupled model, the rigid structure is taken as "fictitious" fluid with zero strain rate. Both fluid and structure are described by velocity and pressure. The whole domain, including fluid region and structure region, is modeled by the incompressible Navier-Stokes equations which are discretized with fixed Eulerian mesh. However, to keep the structure's rigid body shape and behavior, a rigid body constraint is enforced on the "fictitious" fluid domain by use of the Distributed Lagrange Multiplier/Fictitious Domain (DLM/FD) method which is originally introduced to solve particulate flow problems by Glowinski et al. For the verification of the model presented herein, a 2D numerical wave tank is established to simulate small amplitude wave propagations, and then numerical results are compared with analytical solutions. Finally, a 2D example of fluid-structure interaction under wave dynamic forces provides convincing evidences for the method excellent solution quality and fidelity.

  17. Fully kinetic model of breakdown during sheath expansion after interruption of vacuum arcs

    Science.gov (United States)

    Wang, Zhenxing; Wang, Haoran; Zhou, Zhipeng; Tian, Yunbo; Geng, Yingsan; Wang, Jianhua; Liu, Zhiyuan

    2016-08-01

    Research on sheath expansion is critical to the understanding of the dielectric recovery process in a vacuum interrupter after interruption of vacuum arcs. In this paper, we investigated how residual plasma affects breakdown in the sheath expansion period after the current zero. To simulate sheath expansion and breakdown, we developed a fully kinetic particle-in-cell Monte Carlo collision model with one spatial dimension and three velocity dimensions. The model accounted for various collisions, including ionization, excitation, elastic collisions, charge exchange, and momentum exchange, and we added an external circuit to the model to make the calculations self-consistent. The existence of metal vapor slowed the sheath expansion in the gap and caused high electric field formation in front of the cathode surface. The initial residual plasma, which was at sufficiently low density, seemed to have a limited impact on breakdown, and the metal vapor dominated the breakdown in this case. Additionally, the breakdown probability was sensitive to the initial plasma density if the value exceeded a specific threshold, and plasma at sufficiently high density could mean that breakdown would occur more easily. We found that if the simulation does not take the residual plasma into account, it could overestimate the critical value of the metal vapor density, which is always used to describe the boundary of breakdown after interruption of vacuum arcs. We discussed the breakdown mechanism in sheath expansion, and the breakdown is determined by a combination of metal vapor, residual plasma, and the electric field in front of the cathode surface.

  18. A perturbative formalism for electronic transitions through conical intersections in a fully quadratic vibronic model.

    Science.gov (United States)

    Endicott, Julia S; Joubert-Doriol, Loïc; Izmaylov, Artur F

    2014-07-21

    We consider a fully quadratic vibronic model Hamiltonian for studying photoinduced electronic transitions through conical intersections. Using a second order perturbative approximation for diabatic couplings, we derive an analytical expression for the time evolution of electronic populations at a given temperature. This formalism extends upon a previously developed perturbative technique for a linear vibronic coupling Hamiltonian. The advantage of the quadratic model Hamiltonian is that it allows one to use separate quadratic representations for potential energy surfaces of different electronic states and a more flexible representation of interstate couplings. We explore features introduced by the quadratic Hamiltonian in a series of 2D models, and then apply our formalism to the 2,6-bis(methylene) adamantyl cation and its dimethyl derivative. The Hamiltonian parameters for the molecular systems have been obtained from electronic structure calculations followed by a diabatization procedure. The evolution of electronic populations in the molecular systems using the perturbative formalism shows a good agreement with that from variational quantum dynamics.

  19. A fully-online Neuro-Fuzzy model for flow forecasting in basins with limited data

    Science.gov (United States)

    Ashrafi, Mohammad; Chua, Lloyd Hock Chye; Quek, Chai; Qin, Xiaosheng

    2017-02-01

    Current state-of-the-art online neuro fuzzy models (NFMs) such as DENFIS (Dynamic Evolving Neural-Fuzzy Inference System) have been used for runoff forecasting. Online NFMs adopt a local learning approach and are able to adapt to changes continuously. The DENFIS model however requires upper/lower bound for normalization and also the number of rules increases monotonically. This requirement makes the model unsuitable for use in basins with limited data, since a priori data is required. In order to address this and other drawbacks of current online models, the Generic Self-Evolving Takagi-Sugeno-Kang (GSETSK) is adopted in this study for forecast applications in basins with limited data. GSETSK is a fully-online NFM which updates its structure and parameters based on the most recent data. The model does not require the need for historical data and adopts clustering and rule pruning techniques to generate a compact and up-to-date rule-base. GSETSK was used in two forecast applications, rainfall-runoff (a catchment in Sweden) and river routing (Lower Mekong River) forecasts. Each of these two applications was studied under two scenarios: (i) there is no prior data, and (ii) only limited data is available (1 year for the Swedish catchment and 1 season for the Mekong River). For the Swedish Basin, GSETSK model results were compared to available results from a calibrated HBV (Hydrologiska Byråns Vattenbalansavdelning) model. For the Mekong River, GSETSK results were compared against the URBS (Unified River Basin Simulator) model. Both comparisons showed that results from GSETSK are comparable with the physically based models, which were calibrated with historical data. Thus, even though GSETSK was trained with a very limited dataset in comparison with HBV or URBS, similar results were achieved. Similarly, further comparisons between GSETSK with DENFIS and the RBF (Radial Basis Function) models highlighted further advantages of GSETSK as having a rule-base (compared to

  20. A fully resolved active musculo-mechanical model for esophageal transport

    Science.gov (United States)

    Kou, Wenjun; Bhalla, Amneet Pal Singh; Griffith, Boyce E.; Pandolfino, John E.; Kahrilas, Peter J.; Patankar, Neelesh A.

    2015-10-01

    Esophageal transport is a physiological process that mechanically transports an ingested food bolus from the pharynx to the stomach via the esophagus, a multi-layered muscular tube. This process involves interactions between the bolus, the esophagus, and the neurally coordinated activation of the esophageal muscles. In this work, we use an immersed boundary (IB) approach to simulate peristaltic transport in the esophagus. The bolus is treated as a viscous fluid that is actively transported by the muscular esophagus, and the esophagus is modeled as an actively contracting, fiber-reinforced tube. Before considering the full model of the esophagus, however, we first consider a standard benchmark problem of flow past a cylinder. Next a simplified version of our model is verified by comparison to an analytic solution to the tube dilation problem. Finally, three different complex models of the multi-layered esophagus, which differ in their activation patterns and the layouts of the mucosal layers, are extensively tested. To our knowledge, these simulations are the first of their kind to incorporate the bolus, the multi-layered esophagus tube, and muscle activation into an integrated model. Consistent with experimental observations, our simulations capture the pressure peak generated by the muscle activation pulse that travels along the bolus tail. These fully resolved simulations provide new insights into roles of the mucosal layers during bolus transport. In addition, the information on pressure and the kinematics of the esophageal wall resulting from the coordination of muscle activation is provided, which may help relate clinical data from manometry and ultrasound images to the underlying esophageal motor function.

  1. A Fully-Coupled, Fully-Implicit, Finite Element Model for Solving Multiphase Fluid Flow, Heat Transport and Rock Deformation in Enhanced Geothermal Systems

    Science.gov (United States)

    Lu, C.; Deng, S.; Podgorney, R. K.; Huang, H.

    2011-12-01

    Reliable reservoir performance predictions of enhanced geothermal reservoir systems require accurate and robust modeling for the coupled thermal-hydrological-mechanical processes. Conventionally, in order to reduce computational cost, these types of problems are solved using operator splitting method, usually by sequentially coupling a subsurface flow and heat transport simulator with a solid mechanics simulator via input files. However, such operator splitting approaches are applicable only to loosely coupled problems and usually converge slowly. As in most enhanced geothermal systems (EGS), fluid flow, heat transport, and rock deformation are typically strongly nonlinearly coupled, an alternative is to solve the system of nonlinear partial differential equations that govern the system simultaneously using a fully coupled solution procedure for fluid flow, heat transport, and solid mechanics. This procedure solves for all solution variables (fluid pressure, temperature and rock displacement fields) simultaneously, which leads to one large nonlinear algebraic system that needs to be solved by a strongly convergent nonlinear solver. Development over the past 10 years in the area of physics-based conditioning, strongly convergent nonlinear solvers (such as Jacobian Free Newton methods) and efficient linear solvers (such as GMRES, AMG), makes such an approach competitive. In this presentation, we will introduce a continuum-scaled parallel physics-based, fully coupled, modeling tool for predicting the dynamics of fracture initiation and propagation, fluid flow, rock deformation, and heat transport in a single integrated code named FALCON (Fracturing And Liquid-steam CONvection). FALCON is built upon a parallel computing framework developed at Idaho National Laboratory (INL) for solving coupled systems of nonlinear equations with finite element method with unstructured and adaptively refined/coarsened grids. Currently, FALCON contains poro- and thermal- elastic models

  2. Atomistic Models of Amorphous Semiconductors

    NARCIS (Netherlands)

    Jarolimek, K.

    2011-01-01

    Crystalline silicon is probably the best studied material, widely used by the semiconductor industry. The subject of this thesis is an intriguing form of this element namely amorphous silicon. It can contain a varying amount of hydrogen and is denoted as a-Si:H. It completely lacks the neat long

  3. Individualizing Opioid Use Disorder (OUD Treatment: Time to Fully Embrace a Chronic Disease Model

    Directory of Open Access Journals (Sweden)

    Richard Gustin

    2015-02-01

    Full Text Available The current opioid epidemic in the United States is changing our perceptions of the face of addiction. Opioid Use Disorder (OUD has become pervasive and is affecting all ethnicities, races, socioeconomic classes, the young and the old. In 2015, 46 people will lose their life each day to a chronic brain disease that is going unnoticed and undertreated. Over the last five decades, numerous scientific and clinical breakthroughs have allowed for a better understanding of the mechanisms underlying addiction, and the development of medications that can help support a patient’s long-term recovery. All of those that have contributed to these advancements have aided in redefining addiction as a primary, chronic disease of the brain reward, motivation, memory and related circuitry; however, our treatment strategies have not necessarily advanced to the same extent as our current understanding of the disease. This commentary will explore how personal philosophies can bias treatments strategies and definitions of treatment success, and prevent adoption of chronic disease treatment models that would significantly improve the quality of life of those suffering with OUD. This is a challenge to consider how our views and stigma can impact a patient’s recovery. We are currently losing a battle with a disease that is taking the lives of 46 individuals daily; it is time to fully embrace a chronic disease model which comprises an integrated pharmacopsychosocial approach for treating the biopsychosocial disorder that is addiction to reverse these trends.

  4. Asteroseismology of the \\emph{Kepler} V777 Her variable white dwarf with fully evolutionary models

    CERN Document Server

    Córsico, Alejandro H; Bertolami, Marcelo M Miller; Bischoff-Kim, Agnès

    2011-01-01

    DBV stars are pulsating white dwarfs with atmospheres rich in He. Asteroseismology of DBV stars can provide valuable clues about the origin, structure and evolution of hydrogen-deficient white dwarfs, and may allow to study neutrino and axion physics. Recently, a new DBV star, KIC 8626021, has been discovered in the field of the \\emph{Kepler} spacecraft. It is expected that further monitoring of this star in the next years will enable astronomers to determine its detailed asteroseismic profile. We perform an asteroseismological analysis of KIC 8626021 on the basis of fully evolutionary DB white-dwarf models. We employ a complete set of evolutionary DB white-dwarf structures covering a wide range of effective temperatures and stellar masses. They have been obtained on the basis of a complete treatment of the evolutionary history of progenitors stars. We compute g-mode adiabatic pulsation periods for this set of models and compare them with the pulsation properties exhibited by KIC 8626021. On the basis of the ...

  5. A fully resolved fluid-structure-muscle-activation model for esophageal transport

    Science.gov (United States)

    Kou, Wenjun; Bhalla, Amneet P. S.; Griffith, Boyce E.; Johnson, Mark; Patankar, Neelesh A.

    2013-11-01

    Esophageal transport is a mechanical and physiological process that transfers the ingested food bolus from the pharynx to the stomach through a multi-layered esophageal tube. The process involves interactions between the bolus, esophageal wall composed of mucosal, circular muscle (CM) and longitudinal muscle (LM) layers, and neurally coordinated muscle activation including CM contraction and LM shortening. In this work, we present a 3D fully-resolved model of esophageal transport based on the immersed boundary method. The model describes the bolus as a Newtonian fluid, the esophageal wall as a multi-layered elastic tube represented by springs and beams, and the muscle activation as a traveling wave of sequential actuation/relaxation of muscle fibers, represented by springs with dynamic rest lengths. Results on intraluminal pressure profile and bolus shape will be shown, which are qualitatively consistent with experimental observations. Effects of activating CM contraction only, LM shortening only or both, for the bolus transport, are studied. A comparison among them can help to identify the role of each type of muscle activation. The support of grant R01 DK56033 and R01 DK079902 from NIH is gratefully acknowledged.

  6. Atomistic and Coarse-grained Simulations of Hexabenzocoronene Crystals

    Science.gov (United States)

    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.

  7. On the modeling of planetary plasma environments by a fully kinetic electromagnetic global model HYB-em

    Directory of Open Access Journals (Sweden)

    V. Pohjola

    2010-03-01

    Full Text Available We have developed a fully kinetic electromagnetic model to study instabilities and waves in planetary plasma environments. In the particle-in-a-cell (PIC model both ions and electrons are modeled as particles. An important feature of the developed global kinetic model, called HYB-em, compared to other electromagnetic codes is that it is built up on an earlier quasi-neutral hybrid simulation platform called HYB and that it can be used in conjunction with earlier hybrid models. The HYB models have been used during the past ten years to study globally the flowing plasma interaction with various Solar System objects: Mercury, Venus, the Moon, Mars, Saturnian moon Titan and asteroids. The new stand-alone fully kinetic model enables us to (1 study the stability of various planetary plasma regions in three-dimensional space, (2 analyze the propagation of waves in a plasma environment derived from the other global HYB models. All particle processes in a multi-ion plasma which are implemented on the HYB platform (e.g. ion-neutral-collisions, chemical processes, particle loss and production processes are also automatically included in HYB-em model.

    In this brief report we study the developed approach by analyzing the propagation of high frequency electromagnetic waves in non-magnetized plasma in two cases: We study (1 expansion of a spherical wave generated from a point source and (2 propagation of a plane wave in plasma. The analysis shows that the HYB-em model is capable of describing these space plasma situations successfully. The analysis also suggests the potential of the developed model to study both high density-high magnetic field plasma environments, such as Mercury, and low density-low magnetic field plasma environments, such as Venus and Mars.

  8. Atomistic Simulations of Bicelle Mixtures

    OpenAIRE

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

    2010-01-01

    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 microenvironmen...

  9. Atomistic Simulations of Bicelle Mixtures

    OpenAIRE

    Jiang, Yong; WANG, HAO; Kindt, James T.

    2010-01-01

    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 microenvironmen...

  10. Snowpack Microstructure Characterization and Partial Coherent and Fully Coherent Forward Scattering Models in Microwave Remote Sensing

    Science.gov (United States)

    Tan, S.; Tsang, L.; Xu, X.; Ding, K. H.

    2015-12-01

    In this paper we describe partial coherent model and fully coherent snowpack scattering model based on numerical simulation of Maxwell's equation. In medium characterization, we derive the correlation functions from the pair distribution functions of sticky spheres and multiple-size spheres used in QCA. We show that both the Percus-Yevick pair functions and the bicontinuous model have tails in the correlation functions that are distinctly different from the traditional exponential correlation functions. The methodologies of using ground measurements of grain size distributions and correlation functions to obtain model parameters are addressed. The DMRT theory has been extended to model the backscattering enhancement. We developed the methodology of cyclical corrections beyond first order to all orders of multiple scattering. This enables the physical modeling of combined active and passive microwave remote sensing of snow over the same scene. The bicontinuous /DMRT is applied to compare with data acquired in the NoSREx campaign, and the model results are validated against coincidental active and passive measurements using the same set of physical parameters of snow in all frequency and polarization channels. The DMRT is a partially coherent approach that one accounts for the coherent wave interaction only within few wavelengths as represented by phase matrix. However, the phase information of field is lost in propagating the specific intensity via RT and this hinders the use of DMRT in coherent synthetic aperture radar (SAR) analysis, including InSAR, PolInSAR and Tomo-SAR. One can alternatively calculate the scattering matrix of the terrestrial snowpack above ground by solving the volume integral equations directly with half space Green's function. The scattering matrix of the snowpack is computed for each realization giving rise to the speckle statistics. The resulting bistatic scattering automatically includes the backscattering enhancement effects. Tomograms of

  11. Atomistic Investigation of Cu-Induced Misfolding in the Onset of Parkinson's Disease

    Science.gov (United States)

    Rose, Francis; Hodak, Miroslav; Bernholc, Jerry

    2009-03-01

    A nucleation mechanism for the misfolding of α-synuclein, the protein implicated in Parkinson's Disease (PD), is investigated using computer simulations. Through a combination of ab initio and classical simulation techniques, the conformational evolution of copper-ion-initiated misfolding of α-synuclein is determined. Based on these investigations and available experimental evidence, an atomistic model detailing the nucleation-initiated pathogenesis of PD is proposed. Once misfolded, the proteins can assemble into fibrils, the primary structural components of the deleterious PD plaques. Our model identifies a process of structural modifications to an initially unfolded α-synuclein that results in a partially folded intermediate with a well defined nucleation site as a precursor to the fully misfolded protein. The identified pathway can enable studies of reversal mechanisms and inhibitory agents, potentially leading to the development of effective therapies.

  12. Analysis of Seismicity Risk Increase Triggered by Longtan Reservoir, China, Using a Fully Coupled Poroelastic Model

    Science.gov (United States)

    Deng, K.; Zhang, S.; Guo, Y.; Zhou, S.; Liu, Y.

    2015-12-01

    Impoundment of reservoirs can lead to increase in crustal pore pressure and Coulomb stress, and promotes nearby faults to fail. Abnormal seismicity increase around reservoir is often thought to be triggered by the water impounded behind the dam. In this study, we analyze the impact of Longtan reservoir in Guangxi province, southwest China, on local seismicity, which has increased significantly since the initial impoundment in October, 2006. Most of the earthquakes cluster around the reservoir according to local seismic network and CEA reports, and the greatest earthquake is of magnitude 4.2. We introduce an improved Bayesian method to show that the temporal variation of b-value is inversely correlated with the seasonal fluctuation of reservoir water level. Upon extracting background seismicity using the Epidemic Type Aftershock Sequence (ETAS) model, we show that background seismicity variation is highly related to the filling rate and volume We further investigate the mechanism of seismicity increase and reservoir impoundment by performing a fully coupled 3-D poroelastic model with the reservoir loading history as a dynamic boundary condition. An optimally oriented fault plane is chosen according to the regional stress field and GPS deformation data when calculating the induced Coulomb stress. Our results demonstrate that most earthquakes occurred within positive Coulomb stress regime, and the seismicity rate is highly related to the rate of pore pressure increase. In the next step we plan to apply the coupled poroelastic model to understand hydraulic fracturing induced earthquakes in shale gas exploration, such as the recent Fox Creek event cluster, in the western Canada sedimentary basin.

  13. The One-Water Hydrologic Flow Model - The next generation in fully integrated hydrologic simulation software

    Science.gov (United States)

    Boyce, S. E.; Hanson, R. T.

    2015-12-01

    The One-Water Hydrologic Flow Model (MF-OWHM) is a MODFLOW-based integrated hydrologic flow model that is the most complete version, to date, of the MODFLOW family of hydrologic simulators needed for the analysis of a broad range of conjunctive-use issues. MF-OWHM fully links the movement and use of groundwater, surface water, and imported water for consumption by agriculture and natural vegetation on the landscape, and for potable and other uses within a supply-and-demand framework. MF-OWHM is based on the Farm Process for MODFLOW-2005 combined with Local Grid Refinement, Streamflow Routing, Surface-water Routing Process, Seawater Intrusion, Riparian Evapotranspiration, and the Newton-Raphson solver. MF-OWHM also includes linkages for deformation-, flow-, and head-dependent flows; additional observation and parameter options for higher-order calibrations; and redesigned code for facilitation of self-updating models and faster simulation run times. The next version of MF-OWHM, currently under development, will include a new surface-water operations module that simulates dynamic reservoir operations, the conduit flow process for karst aquifers and leaky pipe networks, a new subsidence and aquifer compaction package, and additional features and enhancements to enable more integration and cross communication between traditional MODFLOW packages. By retaining and tracking the water within the hydrosphere, MF-OWHM accounts for "all of the water everywhere and all of the time." This philosophy provides more confidence in the water accounting by the scientific community and provides the public a foundation needed to address wider classes of problems such as evaluation of conjunctive-use alternatives and sustainability analysis, including potential adaptation and mitigation strategies, and best management practices. By Scott E. Boyce and Randall T. Hanson

  14. Application of a fully-integrated groundwater-surface water flow model in municipal asset management

    Science.gov (United States)

    Bowman, L. K.; Unger, A.; Jones, J. P.

    2014-12-01

    Access to affordable potable water is critical in the development and maintenance of urban centres. Given that water is a public good in Canada, all funds related to operation and maintenance of the drinking water and wastewater networks must come from consumers. An asset management system can be put in place by municipalities to more efficiently manage their water and wastewater distribution system to ensure proper use of these funds. The system works at the operational, tactical, and strategic levels, thus ensuring optimal scheduling of operation and maintenance activities, as well as prediction of future water demand scenarios. At the operational level, a fully integrated model is used to simulate the groundwater-surface water interaction of the Laurel Creek Watershed, of which 80% is urbanized by the City of Waterloo. Canadian municipalities typically lose 13% of their potable water through leaks in watermains and sanitary sewers, and sanitary sewers often generate substantial inflows from fractures in pipe walls. The City of Waterloo sanitary sewers carry an additional 10,000 cubic meters of water to wastewater treatment plants. Therefore, watermain and sanitary sewers present a significant impact on the groundwater-surface water interaction, as well as the affordability of the drinking water and wastewater networks as a whole. To determine areas of concern within the network, the integrated groundwater-surface water model also simulates flow through the City of Waterloo's watermain and sanitary sewer networks. The final model will be used to assess the interaction between measured losses of water from the City of Waterloo's watermain system, infiltration into the sanitary sewer system adjacent to the watermains, and the response of the groundwater system to deteriorated sanitary sewers or to pipes that have been recently renovated. This will ultimately contribute to the City of Waterloo's municipal asset management plan.

  15. Accelerating molecular Monte Carlo simulations using distance and orientation dependent energy tables: tuning from atomistic accuracy to smoothed “coarse-grained” models

    Science.gov (United States)

    Lettieri, S.; Zuckerman, D.M.

    2011-01-01

    Typically, the most time consuming part of any atomistic molecular simulation is due to the repeated calculation of distances, energies and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (pre-calculation) of distance and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic – but rigid – benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary (“exact”) Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules. PMID:22120971

  16. Asteroseismological Study of Massive ZZ Ceti Stars with Fully Evolutionary Models

    Science.gov (United States)

    Romero, A. D.; Kepler, S. O.; Córsico, A. H.; Althaus, L. G.; Fraga, L.

    2013-12-01

    We present the first asteroseismological study for 42 massive ZZ Ceti stars based on a large set of fully evolutionary carbon-oxygen core DA white dwarf models characterized by a detailed and consistent chemical inner profile for the core and the envelope. Our sample comprises all of the ZZ Ceti stars with spectroscopic stellar masses between 0.72 and 1.05 M ⊙ known to date. The asteroseismological analysis of a set of 42 stars enables study of the ensemble properties of the massive, pulsating white dwarf stars with carbon-oxygen cores, in particular the thickness of the hydrogen envelope and the stellar mass. A significant fraction of stars in our sample have stellar mass that is high enough to crystallize at the effective temperatures of the ZZ Ceti instability strip, which enables us to study the effects of crystallization on the pulsation properties of these stars. Our results show that the phase diagram presented in Horowitz et al. seems to be a good representation of the crystallization process inside white dwarf stars, in agreement with the results from white dwarf luminosity function in globular clusters.

  17. Asteroseismological study of massive ZZ Ceti stars with fully evolutionary models

    CERN Document Server

    Romero, A D; Córsico, A H; Althaus, L G; Fraga, L

    2013-01-01

    We present the first asteroseismological study for 42 massive ZZ Ceti stars based on a large set of fully evolutionary carbon$-$oxygen core DA white dwarf models characterized by a detailed and consistent chemical inner profile for the core and the envelope. Our sample comprise all the ZZ Ceti stars with spectroscopic stellar masses between 0.72 and $1.05M_{\\odot}$ known to date. The asteroseismological analysis of a set of 42 stars gives the possibility to study the ensemble properties of the massive pulsating white dwarf stars with carbon$-$oxygen cores, in particular the thickness of the hydrogen envelope and the stellar mass. A significant fraction of stars in our sample have stellar mass high enough as to crystallize at the effective temperatures of the ZZ Ceti instability strip, which enables us to study the effects of crystallization on the pulsation properties of these stars. Our results show that the phase diagram presented in Horowitz et al. (2010) seems to be a good representation of the crystalliz...

  18. Asteroseismological study of massive ZZ Ceti stars with fully evolutionary models

    Energy Technology Data Exchange (ETDEWEB)

    Romero, A. D.; Kepler, S. O. [Departamento de Astronomia, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves 9500, Porto Alegre 91501-970, RS (Brazil); Córsico, A. H.; Althaus, L. G. [Facultad de Ciencias Astronómicas y Geofísicas, Universidad Nacional de La Plata, Paseo del Bosque s/n, (1900) La Plata (Argentina); Fraga, L., E-mail: alejandra.romero@ufrgs.br [Southern Observatory for Astrophysical Research, Casilla 603, La Serena (Chile)

    2013-12-10

    We present the first asteroseismological study for 42 massive ZZ Ceti stars based on a large set of fully evolutionary carbon-oxygen core DA white dwarf models characterized by a detailed and consistent chemical inner profile for the core and the envelope. Our sample comprises all of the ZZ Ceti stars with spectroscopic stellar masses between 0.72 and 1.05 M {sub ☉} known to date. The asteroseismological analysis of a set of 42 stars enables study of the ensemble properties of the massive, pulsating white dwarf stars with carbon-oxygen cores, in particular the thickness of the hydrogen envelope and the stellar mass. A significant fraction of stars in our sample have stellar mass that is high enough to crystallize at the effective temperatures of the ZZ Ceti instability strip, which enables us to study the effects of crystallization on the pulsation properties of these stars. Our results show that the phase diagram presented in Horowitz et al. seems to be a good representation of the crystallization process inside white dwarf stars, in agreement with the results from white dwarf luminosity function in globular clusters.

  19. Fully 3D modeling of tokamak vertical displacement events with realistic parameters

    Science.gov (United States)

    Pfefferle, David; Ferraro, Nathaniel; Jardin, Stephen; Bhattacharjee, Amitava

    2016-10-01

    In this work, we model the complex multi-domain and highly non-linear physics of Vertical Displacement Events (VDEs), one of the most damaging off-normal events in tokamaks, with the implicit 3D extended MHD code M3D-C1. The code has recently acquired the capability to include finite thickness conducting structures within the computational domain. By exploiting the possibility of running a linear 3D calculation on top of a non-linear 2D simulation, we monitor the non-axisymmetric stability and assess the eigen-structure of kink modes as the simulation proceeds. Once a stability boundary is crossed, a fully 3D non-linear calculation is launched for the remainder of the simulation, starting from an earlier time of the 2D run. This procedure, along with adaptive zoning, greatly increases the efficiency of the calculation, and allows to perform VDE simulations with realistic parameters and high resolution. Simulations are being validated with NSTX data where both axisymmetric (toroidally averaged) and non-axisymmetric induced and conductive (halo) currents have been measured. This work is supported by US DOE Grant DE-AC02-09CH11466.

  20. A fully model-based MPC solution including VSB shot dose assignment and shape correction

    Science.gov (United States)

    Bork, Ingo; Buck, Peter; Reddy, Murali; Durvasula, Bhardwaj

    2015-10-01

    The value of using multiple dose levels for individual shots on VSB (Variable Shaped Beam) mask writers has been demonstrated earlier [1][2]. The main advantage of modulating dose on a per shot basis is the fact that higher dose levels can be used selectively for critical features while other areas of the mask with non-critical feature types can be exposed at lower dose levels. This reduces the amount of backscattering and mask write time penalty compared to a global overdose-undersize approach. While dose assignment to certain polygons or parts of polygons (VSB shots) can easily be accomplished via DRC rules on layers with limited shape variations like contact or VIA layers, it can be challenging to come up with consistent rules for layers consisting of a very broad range of shapes, generally found on metal layers. This work introduces a method for fully model-based modulation of shot dose for VSB machines supporting between two and eight dose levels and demonstrates results achieved with this method.

  1. Fully Three-dimensional Simulation and Modeling of a Dense Plasma Focus

    CERN Document Server

    Meehan, B T

    2014-01-01

    A Dense Plasma Focus (DPF) is a pulsed-power machine that electromagnetically accelerates and cylindrically compresses a shocked plasma in a Z-pinch. The pinch results in a brief (about 100 nanosecond) pulse of X-rays, and, for some working gases, also a pulse of neutrons. A great deal of experimental research has been done into the physics of DPF reactions, and there exist mathematical models describing its behavior during the different time phases of the reaction. Two of the phases, known as the inverse pinch and the rundown, are approximately governed by magnetohydrodynamics, and there are a number of well-established codes for simulating these phases in two dimensions or in three dimensions under the assumption of axial symmetry. There has been little success, however, in developing fully three-dimensional simulations. In this work we present three-dimensional simulations of DPF reactions and demonstrate that 3D simulations predict qualitatively and quantitatively different behavior than their 2D counterp...

  2. Fully three-dimensional simulation and modeling of a dense plasma focus

    Energy Technology Data Exchange (ETDEWEB)

    Meehan, B. T.; Niederhaus, J. H. J.

    2014-10-01

    A dense plasma focus (DPF) is a pulsed-power machine that electromagnetically accelerates and cylindrically compresses a shocked plasma in a Z-pinch. The pinch results in a brief (~ 100 ns) pulse of X-rays, and, for some working gases, also a pulse of neutrons. A great deal of experimental research has been done into the physics of DPF reactions, and there exist mathematical models describing its behavior during the different time phases of the reaction. Two of the phases, known as the inverse pinch and the rundown, are approximately governed by magnetohydrodynamics, and there are a number of well-established codes for simulating these phases in two dimensions or in three dimensions under the assumption of axial symmetry. There has been little success, however, in developing fully three-dimensional simulations. In this work we present three-dimensional simulations of DPF reactions and demonstrate that three-dimensional simulations predict qualitatively and quantitatively different behavior than their two-dimensional counterparts. One of the most important quantities to predict is the time duration between the formation of the gas shock and Z-pinch, and the three-dimensional simulations more faithfully represent experimental results for this time duration and are essential for accurate prediction of future experiments.

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

    Science.gov (United States)

    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.

  4. Semi- vs. Fully-Distributed Urban Stormwater Models: Model Set Up and Comparison with Two Real Case Studies

    Directory of Open Access Journals (Sweden)

    Rui Daniel Pina

    2016-02-01

    Full Text Available Urban stormwater models can be semi-distributed (SD or fully distributed (FD. SD models are based on subcatchment units with various land use types, where rainfall is applied and runoff volumes are estimated and routed. FD models are based on the two dimensional (2D discretization of the overland surface, which has a finer resolution with each grid-cell representing one land use type, where runoff volumes are estimated and directly routed by the 2D overland flow module. While SD models have been commonly applied in urban stormwater modeling, FD models are generally more detailed and theoretically more realistic. This paper presents a comparison between SD and FD models using two case studies in Coimbra (Portugal and London (UK. To enable direct comparison between SD and FD setups, a model-building process is proposed and a novel sewer inlet representation is applied. SD and FD modeling results are compared against observed records in sewers and photographic records of flood events. The results suggest that FD models are more sensitive to surface storage parameters and require higher detail of the sewer network representation.

  5. Modeling greenhouse gas emissions and nutrient transport in managed arable soils with a fully coupled hydrology-biogeochemical modeling system

    Science.gov (United States)

    Haas, Edwin; Klatt, Steffen; Kiese, Ralf; Butterbach-Bahl, Klaus; Kraft, Philipp; Breuer, Lutz

    2015-04-01

    The use of mineral nitrogen fertilizer sustains the global food production and therefore the livelihood of human kind. The rise in world population will put pressure on the global agricultural system to increase its productivity leading most likely to an intensification of mineral nitrogen fertilizer use. The fate of excess nitrogen and its distribution within landscapes is manifold. Process knowledge on the site scale has rapidly grown in recent years and models have been developed to simulate carbon and nitrogen cycling in managed ecosystems on the site scale. Despite first regional studies, the carbon and nitrogen cycling on the landscape or catchment scale is not fully understood. In this study we present a newly developed modelling approach by coupling the fully distributed hydrology model CMF (catchment modelling framework) to the process based regional ecosystem model LandscapeDNDC for the investigation of hydrological processes and carbon and nitrogen transport and cycling, with a focus on nutrient displacement and resulting greenhouse gas emissions in various virtual landscapes / catchment to demonstrate the capabilities of the modelling system. The modelling system was applied to simulate water and nutrient transport at the at the Yanting Agro-ecological Experimental Station of Purple Soil, Sichuan province, China. The catchment hosts cypress forests on the outer regions, arable fields on the sloping croplands cultivated with wheat-maize rotations and paddy rice fields in the lowland. The catchment consists of 300 polygons vertically stratified into 10 soil layers. Ecosystem states (soil water content and nutrients) and fluxes (evapotranspiration) are exchanged between the models at high temporal scales (hourly to daily) forming a 3-dimensional model application. The water flux and nutrients transport in the soil is modelled using a 3D Richards/Darcy approach for subsurface fluxes with a kinematic wave approach for surface water runoff and the

  6. Reconstruction of the Eemian climate using a fully coupled Earth system model

    Science.gov (United States)

    Rybak, Oleg; Volodin, Evgeny; Morozova, Polina; Huybrechts, Philippe

    2017-04-01

    Climate of the Last Interglacial (LIG) between ca. 130 and 115 kyr BP is thought to be a good analogue for future climate warming. Though the driving mechanisms of the past and current climate evolution differ, analysis of the LIG climate may provide important insights for projections of future environmental changes. We do not know properly what was spatial distribution and magnitude of surface air temperature and precipitation anomalies with respect to present. Sparse proxy data are attributed mostly to the continental margins, internal areas of ice sheets and particular regions of the World Ocean. Combining mathematical modeling and indirect evidence can help to identify driving mechanisms and feed-backs which formed climatic conditions of the LIG. In order to reproduce the LIG climate, we carried out transient numerical experiments using a fully coupled Earth System Model (ESM) consisting of an AO GCM, which includes decription of the biosphere, atmospheric and oceanic chemistry ets. (INMCM), developed in the Institute of Numerical Mathematics (Moscow, Russia) and the models of Greenland and Antarctic ice sheets (GrISM and AISM, Vrije Uninersiteit Brussel, Belgium). Though the newest version of the INMCM has rather high spatial resolution, it canot be used in long transient numerical experimemts because of high computational demand. Coupling of the GrISM and AISM to the low resolution version of the INMCM is complicated by essential differences in spatial and temporal scales of cryospheric, atmosphere and the ocean components of the ESM (spatial resolution 5˚×4˚, 21 vertical layers in the atmospheric block, 2.5°×2°, 6 min. temporal resolution; 33 vertical layers in the oceanic block; 20×20 km, 51 vertical layers and 1 yr temporal resolution in the GrISM and AISM). We apply two different coupling strategies. AISM is incorporated into the ESM via using procedures of resampling and interpolation of the input fields of annually averaged air surface

  7. Using R for Global Optimization of a Fully-distributed Hydrologic Model at Continental Scale

    Science.gov (United States)

    Zambrano-Bigiarini, M.; Zajac, Z.; Salamon, P.

    2013-12-01

    Nowadays hydrologic model simulations are widely used to better understand hydrologic processes and to predict extreme events such as floods and droughts. In particular, the spatially distributed LISFLOOD model is currently used for flood forecasting at Pan-European scale, within the European Flood Awareness System (EFAS). Several model parameters can not be directly measured, and they need to be estimated through calibration, in order to constrain simulated discharges to their observed counterparts. In this work we describe how the free software 'R' has been used as a single environment to pre-process hydro-meteorological data, to carry out global optimization, and to post-process calibration results in Europe. Historical daily discharge records were pre-processed for 4062 stream gauges, with different amount and distribution of data in each one of them. The hydroTSM, raster and sp R packages were used to select ca. 700 stations with an adequate spatio-temporal coverage. Selected stations span a wide range of hydro-climatic characteristics, from arid and ET-dominated watersheds in the Iberian Peninsula to snow-dominated watersheds in Scandinavia. Nine parameters were selected to be calibrated based on previous expert knowledge. Customized R scripts were used to extract observed time series for each catchment and to prepare the input files required to fully set up the calibration thereof. The hydroPSO package was then used to carry out a single-objective global optimization on each selected catchment, by using the Standard Particle Swarm 2011 (SPSO-2011) algorithm. Among the many goodness-of-fit measures available in the hydroGOF package, the Nash-Sutcliffe efficiency was used to drive the optimization. User-defined functions were developed for reading model outputs and passing them to the calibration engine. The long computational time required to finish the calibration at continental scale was partially alleviated by using 4 multi-core machines (with both GNU

  8. A fully traits-based approach to modeling global vegetation distribution.

    Science.gov (United States)

    van Bodegom, Peter M; Douma, Jacob C; Verheijen, Lieneke M

    2014-09-23

    Dynamic Global Vegetation Models (DGVMs) are indispensable for our understanding of climate change impacts. The application of traits in DGVMs is increasingly refined. However, a comprehensive analysis of the direct impacts of trait variation on global vegetation distribution does not yet exist. Here, we present such analysis as proof of principle. We run regressions of trait observations for leaf mass per area, stem-specific density, and seed mass from a global database against multiple environmental drivers, making use of findings of global trait convergence. This analysis explained up to 52% of the global variation of traits. Global trait maps, generated by coupling the regression equations to gridded soil and climate maps, showed up to orders of magnitude variation in trait values. Subsequently, nine vegetation types were characterized by the trait combinations that they possess using Gaussian mixture density functions. The trait maps were input to these functions to determine global occurrence probabilities for each vegetation type. We prepared vegetation maps, assuming that the most probable (and thus, most suited) vegetation type at each location will be realized. This fully traits-based vegetation map predicted 42% of the observed vegetation distribution correctly. Our results indicate that a major proportion of the predictive ability of DGVMs with respect to vegetation distribution can be attained by three traits alone if traits like stem-specific density and seed mass are included. We envision that our traits-based approach, our observation-driven trait maps, and our vegetation maps may inspire a new generation of powerful traits-based DGVMs.

  9. Atomistic-Continuum Hybrid Simulation of Heat Transfer between Argon Flow and Copper Plates

    CERN Document Server

    Mao, Yijin; Chen, C L

    2016-01-01

    A simulation work aiming to study heat transfer coefficient between argon fluid flow and copper plate is carried out based on atomistic-continuum hybrid method. Navier-Stokes equations for continuum domain are solved through the Pressure Implicit with Splitting of Operators (PISO) algorithm, and the atom evolution in molecular domain is solved through the Verlet algorithm. The solver is validated by solving Couette flow and heat conduction problems. With both momentum and energy coupling method applied, simulations on convection of argon flows between two parallel plates are performed. The top plate is kept as a constant velocity and has higher temperature, while the lower one, which is modeled with FCC copper lattices, is also fixed but has lower temperature. It is found that, heat transfer between argon fluid flow and copper plate in this situation is much higher than that at macroscopic when the flow is fully developed.

  10. Atomistic Simulations of Nanotube Fracture

    CERN Document Server

    Belytschko, T; Schatz, G; Ruoff, R S

    2002-01-01

    The fracture of carbon nanotubes is studied by atomistic simulations. The fracture behavior is found to be almost independent of the separation energy and to depend primarily on the inflection point in the interatomic potential. The rangle of fracture strians compares well with experimental results, but predicted range of fracture stresses is marketly higher than observed. Various plausible small-scale defects do not suffice to bring the failure stresses into agreement with available experimental results. As in the experiments, the fracture of carbon nanotubes is predicted to be brittle. The results show moderate dependence of fracture strength on chirality.

  11. Fully nonlinear and exact perturbations of the Friedmann world model: non-flat background

    Energy Technology Data Exchange (ETDEWEB)

    Noh, Hyerim, E-mail: hr@kasi.ac.kr [Korea Astronomy and Space Science Institute, Daejeon, 305-348 (Korea, Republic of)

    2014-07-01

    We extend the fully non-linear and exact cosmological perturbation equations in a Friedmann background universe to include the background curvature. The perturbation equations are presented in a gauge ready form, so any temporal gauge condition can be adopted freely depending on the problem to be solved. We consider the scalar, and vector perturbations without anisotropic stress. As an application, we analyze the equations in the special case of irrotational zero-pressure fluid in the comoving gauge condition. We also present the fully nonlinear formulation for a minimally coupled scalar field.

  12. Body factor conscious modeling of single gate fully depleted SOI MOSFETs for low power applications

    Science.gov (United States)

    Kumar, Anil; Nagumo, Toshiharu; Tsutsui, Gen; Ohtou, Tetsu; Hiramoto, Toshiro

    2005-06-01

    Degradation of body factor (γ) and subthreshold factor (S) of single gate fully depleted SOI MOSFETs due to short channel effects has been studied analytically. The effect of source/drain fringing fields in buried oxide is found to play a more significant role in the reduction of body factor at smaller gate lengths. Present work provides the analytical expressions of effective back gate voltage, body factor and subthreshold factor of short channel fully depleted SOI MOSFETs. The results obtained are found in good approximation with 2D simulation.

  13. Fully nonlinear and exact perturbations of the Friedmann world model: Non-flat background

    CERN Document Server

    Noh, Hyerim

    2014-01-01

    We extend the fully non-linear and exact cosmological perturbation equations in a Friedmann background universe to include the background curvature. The perturbation equations are presented in a gauge ready form, so any temporal gauge condition can be adopted freely depending on the problem to be solved. %The background curvature term explicitly appears only in the energy and momentum constraint equations. We consider the scalar, and vector perturbations without anisotropic stress. As an application, we analyze the equations in the special case of irrotational zero-pressure fluid in the comoving gauge condition. We also present the fully nonlinear formulation for a minimally coupled scalar field.

  14. Efficient Hybrid-Spectral Model for Fully Nonlinear Numerical Wave Tank

    DEFF Research Database (Denmark)

    Christiansen, Torben; Bingham, Harry B.; Engsig-Karup, Allan Peter;

    2013-01-01

    A new hybrid-spectral solution strategy is proposed for the simulation of the fully nonlinear free surface equations based on potential flow theory. A Fourier collocation method is adopted horisontally for the discretization of the free surface equations. This is combined with a modal Chebyshev T...

  15. Atomistic properties of γ uranium.

    Science.gov (United States)

    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.

  16. Strain Functionals for Characterizing Atomistic Geometries

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. A multiscale finite element method for modeling fully coupled thermomechanical problems in solids

    KAUST Repository

    Sengupta, Arkaprabha

    2012-05-18

    This article proposes a two-scale formulation of fully coupled continuum thermomechanics using the finite element method at both scales. A monolithic approach is adopted in the solution of the momentum and energy equations. An efficient implementation of the resulting algorithm is derived that is suitable for multicore processing. The proposed method is applied with success to a strongly coupled problem involving shape-memory alloys. © 2012 John Wiley & Sons, Ltd.

  20. Flood forecasting using a fully distributed model: application of the TOPKAPI model to the Upper Xixian Catchment

    Directory of Open Access Journals (Sweden)

    Z. Liu

    2005-01-01

    Full Text Available TOPKAPI is a physically-based, fully distributed hydrological model with a simple and parsimonious parameterisation. The original TOPKAPI is structured around five modules that represent evapotranspiration, snowmelt, soil water, surface water and channel water, respectively. Percolation to deep soil layers was ignored in the old version of the TOPKAPI model since it was not important in the basins to which the model was originally applied. Based on published literature, this study developed a new version of the TOPKAPI model, in which the new modules of interception, infiltration, percolation, groundwater flow and lake/reservoir routing are included. This paper presents an application study that makes a first attempt to derive information from public domains through the internet on the topography, soil and land use types for a case study Chinese catchment - the Upper Xixian catchment in Huaihe River with an area of about 10000 km2, and apply a new version of TOPKAPI to the catchment for flood simulation. A model parameter value adjustment was performed using six months of the 1998 dataset. Calibration did not use a curve fitting process, but was chiefly based upon moderate variations of parameter values from those estimated on physical grounds, as is common in traditional calibration. The hydrometeorological dataset of 2002 was then used to validate the model, both against the outlet discharge as well as at an internal gauging station. Finally, to complete the model performance analysis, parameter uncertainty and its effects on predictive uncertainty were also assessed by estimating a posterior parameter probability density via Bayesian inference.

  1. Modeling the Rise of Fibril Magnetic Fields in Fully Convective Stars

    Science.gov (United States)

    Weber, Maria A.; Browning, Matthew K.

    2016-08-01

    Many fully convective stars exhibit a wide variety of surface magnetism, including starspots and chromospheric activity. The manner by which bundles of magnetic field traverse portions of the convection zone to emerge at the stellar surface is not especially well understood. In the solar context, some insight into this process has been gleaned by regarding the magnetism as consisting partly of idealized thin flux tubes (TFTs). Here we present the results of a large set of TFT simulations in a rotating spherical domain of convective flows representative of a 0.3 M ⊙ main-sequence star. This is the first study to investigate how individual flux tubes in such a star might rise under the combined influence of buoyancy, convection, and differential rotation. A time-dependent hydrodynamic convective flow field, taken from separate 3D simulations calculated with the anelastic equations, impacts the flux tube as it rises. Convective motions modulate the shape of the initially buoyant flux ring, promoting localized rising loops. Flux tubes in fully convective stars have a tendency to rise nearly parallel to the rotation axis. However, the presence of strong differential rotation allows some initially low-latitude flux tubes of moderate strength to develop rising loops that emerge in the near-equatorial region. Magnetic pumping suppresses the global rise of the flux tube most efficiently in the deeper interior and at lower latitudes. The results of these simulations aim to provide a link between dynamo-generated magnetic fields, fluid motions, and observations of starspots for fully convective stars.

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

    Science.gov (United States)

    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.

  3. Redox reactions with empirical potentials: Atomistic battery discharge simulations

    OpenAIRE

    Dapp, Wolf B.; Müser, Martin H.

    2013-01-01

    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 ...

  4. Atomistic simulations of high strain rate loading of nanocrystals

    Science.gov (United States)

    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.

  5. Modeling of Solidification Microstructures Based on Fully Coupling of Macro-transport Phenomena with Cellular Automata

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    This paper has attempted to simulate the microstructure formation based on fully coupling of temperature field, concentration field and velocity field with micro-kinetics. The authors presented a new way, wlich is the combination of FDM and cellular automata (CAFD) to visualize the microstructure formation of the thin complex superalloy turbine blades cast by the vacuum investment process. The distribution, orientation and mechanism of the heterogeneous nucleation, the growth kinetics of dendrites and the columnar to equiaxed transition (CET) are considered. Capitalizing on these simulating schemes, the comprehensive influence of key process variables on the scale and uniformity of grains has been investigated quantitatively. The simulated grain size and morphology agree well with the experimental results.

  6. Recovering Photospheric Velocities from Vector Magnetograms by using a Three-Dimensional, Fully Magnetohydrodynamic (MHD) Model

    Science.gov (United States)

    Wang, A. H.; Wu, S. T.; Liu, Yang; Hathaway, D.

    2008-01-01

    We introduce a numerical simulation method for recovering the photospheric velocity field from the vector magnetograms. The traditional method is local correlation tracking (LCT) which is based on measuring the relative displacements of features in blocks of pixels between successive white-light images or magnetograms. Within this method, there are a variety of implementations. One of recently developed implementations is induction local correlation tracking (ILCT) as described by Welsch et al. (2004). They employ the normal component of magnetic induction equation as a constraint to assure consistent solutions. Our numerical method uses the fully three-dimensional MHD equations to recover the photospheric velocity field with individual vector magnetograms. We compare our method to the ILCT method using NOAA AR8210 as an example. The differences and similarities are discussed in detail.

  7. Numerical modeling of damping capacity of Zn-Al alloys with fully lamellar microstructures

    Institute of Scientific and Technical Information of China (English)

    WANG Jin-cheng; ZHANG Zhong-ming; YANG Gen-cang

    2005-01-01

    The damping behaviors of Zn-Al alloys with fully lamellar microstructures were simulated with the cell method. The influences of the grain boundary condition, the strain amplitude, the number of the lamellae in the grain (N) and the content ratio of Zn and Al in Zn-Al alloys on the damping capacity were investigated. The results indicate that the grain boundary condition has great influence on the damping capacity of Zn-Al alloys, and also affects the relationship between the damping capacity and the number of lamellae (N). The variation of damping capacity with the strain amplitude is increasing exponentially with the strain amplitude and the damping capacity increases with the increasing of content of Zn.

  8. Concurrent multiscale modeling of amorphous materials

    Science.gov (United States)

    Tan, Vincent

    2013-03-01

    An approach to multiscale modeling of amorphous materials is presented whereby atomistic scale domains coexist with continuum-like domains. The atomistic domains faithfully predict severe deformation while the continuum domains allow the computation to scale up the size of the model without incurring excessive computational costs associated with fully atomistic models and without the introduction of spurious forces across the boundary of atomistic and continuum-like domains. The material domain is firstly constructed as a tessellation of Amorphous Cells (AC). For regions of small deformation, the number of degrees of freedom is then reduced by computing the displacements of only the vertices of the ACs instead of the atoms within. This is achieved by determining, a priori, the atomistic displacements within such Pseudo Amorphous Cells associated with orthogonal deformation modes of the cell. Simulations of nanoscale polymer tribology using full molecular mechanics computation and our multiscale approach give almost identical prediction of indentation force and the strain contours of the polymer. We further demonstrate the capability of performing adaptive simulations during which domains that were discretized into cells revert to full atomistic domains when their strain attain a predetermined threshold. The authors would like to acknowledge the financial support given to this study by the Agency of Science, Technology and Research (ASTAR), Singapore (SERC Grant No. 092 137 0013).

  9. A Fully Developed Flow Thermofluid Model for Topology Optimization of 3D-Printed Air-Cooled Heat Exchangers

    DEFF Research Database (Denmark)

    Haertel, Jan Hendrik Klaas; Nellis, Gregory F.

    2017-01-01

    . The conductance of the heat exchanger is maximized for a prescribed pressure drop and prescribed air-side temperature change across the heat exchanger. Polymer with infilled thermally conducting metal filaments is considered as the heat exchanger material which allows cost effective additive manufacturing...... optimized slot channel model in order to demonstrate the superior performance of the topology optimized designs. Thus, this work demonstrates the usefulness of topology optimization to fully exploit the design freedom afforded by additive manufacturing technologies....

  10. Atomistic simulations of dislocation processes in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Jacobsen, K.W.

    2002-01-01

    We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example, the sta......We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example...

  11. Modeling the Rise of Fibril Magnetic Fields in Fully Convective Stars

    CERN Document Server

    Weber, Maria A

    2016-01-01

    Many fully convective stars exhibit a wide variety of surface magnetism, including starspots and chromospheric activity. The manner by which bundles of magnetic field traverse portions of the convection zone to emerge at the stellar surface is not especially well understood. In the Solar context, some insight into this process has been gleaned by regarding the magnetism as consisting partly of idealized thin flux tubes (TFT). Here, we present the results of a large set of TFT simulations in a rotating spherical domain of convective flows representative of a 0.3 solar-mass, main-sequence star. This is the first study to investigate how individual flux tubes in such a star might rise under the combined influence of buoyancy, convection, and differential rotation. A time-dependent hydrodynamic convective flow field, taken from separate 3D simulations calculated with the anelastic equations, impacts the flux tube as it rises. Convective motions modulate the shape of the initially buoyant flux ring, promoting loca...

  12. Towards Fully Coupled Atmosphere-Hydrology Model Systems: Recent Developments and Performance Evaluation For Different Climate Regions

    Science.gov (United States)

    Kunstmann, Harald; Fersch, Benjamin; Rummler, Thomas; Wagner, Sven; Arnault, Joel; Senatore, Alfonso; Gochis, David

    2015-04-01

    Limitations in the adequate representation of terrestrial hydrologic processes controlling the land-atmosphere coupling are assumed to be a significant factor currently limiting prediction skills of regional atmospheric models. The necessity for more comprehensive process descriptions accounting for the interdependencies between water- and energy fluxes at the compartmental interfaces are driving recent developments in hydrometeorological modeling towards more sophisticated treatment of terrestrial hydrologic processes. It is particularly the lateral surface and subsurface water fluxes that are neglected in standard regional atmospheric models. Current developments in enhanced lateral hydrological process descriptions in the WRF model system will be presented. Based on WRF and WRF-Hydro, new modules and concepts for integrating the saturated zone by a 2-dim groundwater scheme and coupling approaches to the unsaturated zone will be presented. The fully coupled model system allows to model the complete regional water cycle, from the top of the atmosphere, via the boundary layer, the land surface, the unsaturated zone and the saturated zone till the flow in the river beds. With this increasing complexity, that also allows to describe the complex interaction of the regional water cycle on different spatial and temporal scales, the reliability and predictability of model simulations can only be shown, if performance is tested for a variety of hydrological variables for different climatological environments. We will show results of fully coupled simulations for the regions of sempiternal humid Southern Bavaria/Germany (rivers Isar and Ammer) and semiarid to subhumid Westafrica (river Sissilli). In both regions, in addition to streamflow measurements, also the validation of heat fluxes is possible via Eddy-Covariance stations within hydrometeorological testbeds. In the German Isar/Ammer region, e.g., we apply the extended WRF-Hydro modeling system in 3km atmospheric- grid

  13. Incorporating Floating Surface Objects into a Fully Dispersive Surface Wave Model

    Science.gov (United States)

    2016-04-19

    solutions and a VOF model for a 2D floating box and with laboratory measurements of wave generation by a ver- tically oscillating sphere. A steep...breaking waves or sud - en surface impacts. These simplifications also considerably reduce he computational requirements of the model. The Pressure...recently, erakhti et al. (2015) carried out extensive model validations of HWAVE against laboratory data. The focus of their study was to xamine the

  14. DYNAMIC MODEL AND SIMULATION OF A NOVEL ELECTRO-HYDRAULIC FULLY VARIABLE VALVE SYSTEM FOR FOUR-STROKE AUTOMOTIVE ENGINES

    Institute of Scientific and Technical Information of China (English)

    WONG Pak-kin; TAM Lap-mou; LI Ke

    2007-01-01

    In modern four-stroke engine technology, variable valve timing and lift control offers potential benefits for making a high-performance engine. A novel electro-hydraulic fully variable valve train for four-stroke automotive engines is introduced. The construction of the nonlinear mathematic model of the valve train system and its dynamic analysis are also presented. Experimental and simulation results show that the novel electro-hydraulic valve train can achieve fully variable valve timing and lift control. Consequently the engine performance on different loads and speeds will be significantly increased. The technology also permits the elimination of the traditional throttle valve in the gasoline engines and increases engine design flexibility.

  15. Frontal Crash Analysis of a Fully Detailed Car Model Based on Finite Element Method

    Institute of Scientific and Technical Information of China (English)

    Han Shan-Ling; Zhu Ping; Lin Zhong-Qin; Shi Yu-Liang

    2004-01-01

    This paper sets up a highly detailed finite element model of a car for frontal crashworthiness applications, and then explains the characteristics of it. The geometry model is preprocessed by Hypermesh software. The finite element method solver program selected for the simulation is LS-DYNA. After the crash simulation is carefully analyzed, the frontal crash experiment is aimed to validate the finite element model. The simulation results are basically in agreement with the experimental results. The validation of the finite element model is crucial for the further research in optimization of the automotive structure or lightweighting of the vehicle.

  16. Double-π fully scalable model for on-chip spiral inductors

    Institute of Scientific and Technical Information of China (English)

    Liu Jun; Zhong Lin; Wang Huang; Wen Jincai; Sun Lingling; Yu Zhiping; Marissa Condon

    2012-01-01

    A novel double-π equivalent circuit model for on-chip spiral inductors is presented.A hierarchical structure,similar to that of MOS models is introduced.This enables a strict partition of the geometry scaling in the global model and the model equations in the local model.The major parasitic effects,including the skin effect,the proximity effect,the inductive and capacitive loss in the substrate,and the distributed effect,are analytically calculated with geometric and process parameters in the local-level.As accurate values of the layout and process parameters are difficult to obtain,a set of model parameters is introduced to correct the errors caused by using these given inaccurate layout and process parameters at the local level.Scaling rules are defined to enable the formation of models that describe the behavior of the inductors of a variety of geometric dimensions.A series of asymmetric inductors with different geometries are fabricated on a standard 0.18-μm SiGe BiCMOS process with 100Ω/cm substrate resistivity to verify the proposed model.Excellent agreement has been obtained between the measured results and the proposed model over a wide frequency range.

  17. Development and Sensitivity Analysis of a Fully Kinetic Model of Sequential Reductive Dechlorination in Groundwater

    DEFF Research Database (Denmark)

    Malaguerra, Flavio; Chambon, Julie Claire Claudia; Bjerg, Poul Løgstrup

    2011-01-01

    been modeled using modified Michaelis–Menten kinetics and has been implemented in the geochemical code PHREEQC. The model have been calibrated using a Shuffled Complex Evolution Metropolis algorithm to observations of chlorinated solvents, organic acids, and H2 concentrations in laboratory batch...

  18. A fully adaptive forecasting model for short-term drinking water demand

    NARCIS (Netherlands)

    Bakker, M.; Vreeburg, J.H.G.; Schagen, van K.M.; Rietveld, L.C.

    2013-01-01

    For the optimal control of a water supply system, a short-term water demand forecast is necessary. We developed a model that forecasts the water demand for the next 48 h with 15-min time steps. The model uses measured water demands and static calendar data as single input. Based on this input, the m

  19. A fully coupled elasto-plastic damage model applied to anisotropic materials

    OpenAIRE

    Wauters, M; Habraken, Anne; Duchene, Laurent

    2000-01-01

    In this paper, an elastoplastic energy-based anisotropic damage model for ductile fracture is described. A calibration method is also presented. The potential applicability of this model is illustrated by numerical examples of tensile test and Forming Limit Diagram establishment on a steel. Peer reviewed

  20. Hierarchical Linear Modeling with Maximum Likelihood, Restricted Maximum Likelihood, and Fully Bayesian Estimation

    Science.gov (United States)

    Boedeker, Peter

    2017-01-01

    Hierarchical linear modeling (HLM) is a useful tool when analyzing data collected from groups. There are many decisions to be made when constructing and estimating a model in HLM including which estimation technique to use. Three of the estimation techniques available when analyzing data with HLM are maximum likelihood, restricted maximum…

  1. Fully-coupled magnetoelastic model for Galfenol alloys incorporating eddy current losses and thermal relaxation

    Science.gov (United States)

    Evans, Phillip G.; Dapino, Marcelo J.

    2008-03-01

    A general framework is developed to model the nonlinear magnetization and strain response of cubic magnetostrictive materials to 3-D dynamic magnetic fields and 3-D stresses. Dynamic eddy current losses and inertial stresses are modeled by coupling Maxwell's equations to Newton's second law through a nonlinear constitutive model. The constitutive model is derived from continuum thermodynamics and incorporates rate-dependent thermal effects. The framework is implemented in 1-D to describe a Tonpilz transducer in both dynamic actuation and sensing modes. The model is shown to qualitatively describe the effect of increase in magnetic hysteresis with increasing frequency, the shearing of the magnetization loops with increasing stress, and the decrease in the magnetostriction with increasing load stiffness.

  2. Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model.

    Science.gov (United States)

    Bertaccini, Edward J; Trudell, James R; Lindahl, Erik

    2010-08-18

    We have previously used molecular modeling and normal-mode analyses combined with experimental data to visualize a plausible model of a transmembrane ligand-gated ion channel. We also postulated how the gating motion of the channel may be affected by the presence of various ligands, especially anesthetics. As is typical for normal-mode analyses, those studies were performed in vacuo to reduce the computational complexity of the problem. While such calculations constitute an efficient way to model the large scale structural flexibility of transmembrane proteins, they can be criticized for neglecting the effects of an explicit phospholipid bilayer or hydrated environment. Here, we show the successful calculation of normal-mode motions for our model of a glycine α-1 receptor, now suspended in a fully hydrated lipid bilayer. Despite the almost uniform atomic density, the introduction of water and lipid does not grossly distort the overall gating motion. Normal-mode analysis revealed that even a fully immersed glycine α-1 receptor continues to demonstrate an iris-like channel gating motion as a low-frequency, high-amplitude natural harmonic vibration consistent with channel gating. Furthermore, the introduction of periodic boundary conditions allows the examination of simultaneous harmonic vibrations of lipid in synchrony with the protein gating motions that are compatible with reasonable lipid bilayer perturbations. While these perturbations tend to influence the overall protein motion, this work provides continued support for the iris-like motion model that characterizes gating within the family of ligand-gated ion channels.

  3. Integrated hydrometeorological predictions with the fully-coupled WRF-Hydro modeling system in western North America

    Science.gov (United States)

    Gochis, D. J.; Yu, W.

    2013-12-01

    Prediction of heavy rainfall and associated streamflow responses remain as critical hydrometeorological challenges and require improved understanding of the linkages between atmospheric and land surface processes. Streamflow prediction skill is intrinsically liked to quantitative precipitation forecast skill, which emphasizes the need to produce mesoscale predictions of rainfall of high fidelity. However, in many cases land surface parameters can also exert significant control on the runoff response to heavy rainfall and on the formation or localization of heavy rainfall as well. A new generation of integrated atmospheric-hydrologic modeling systems is emerging from different groups around the world to meet the challenge of integrated water cycle predictions. In this talk the community WRF-Hydro modeling system will be presented. After a brief reviewing the architectural features of the WRF-Hydro system short-term forecasting and regional hydroclimate prediction applications of the model from western North America will be presented. In these applications, analyses will present results from observation-validated prediction experiments where atmospheric and terrestrial hydrologic model components are run in both a fully coupled mode and separately without two-way interactions. Emphasis is placed on illustrating an assessment framework using an initial state perturbation methodology to quantify the role of land-atmosphere energy and moisture flux partitioning in controlling precipitation and runoff forecast skill. Issues related to experimental design of fully-coupled model prediction experiments will also be discussed as will issues related to computational performance.

  4. Fractal derivative multi-scale model of fluid particle transverse accelerations in fully developed turbulence

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The Tsallis distribution and the stretched exponential distribution were successfully used to fit the experimental data of turbulence particle acceleration published in Nature (2001), which manifested a clear departure from the normal distribution. These studies, however, fall short of a clear physical mechanism behind the statistical phenomenological description. In this study, we propose a multi- scale diffusion model which considers both normal diffusion in molecular-scale and anomalous diffu- sion in vortex-scale, and the latter is described by a novel fractal derivative modeling approach. This multi-scale model gives rise to a new probability density function which fits experimental data very well.

  5. Fractal derivative multi-scale model of fluid particle transverse accelerations in fully developed turbulence

    Institute of Scientific and Technical Information of China (English)

    SUN HongGuang; CHEN Wen

    2009-01-01

    The Tsallis distribution and the stretched exponential distribution were successfully used to fit the experimental data of turbulence particle acceleration published in Nature (2001), which manifested a clear departure from the normal distribution. These studies, however, fall short of a clear physical mechanism behind the statistical phenomenological description. In this study, we propose a multi-scale diffusion model which considers both normal diffusion in molecular-scale and anomalous diffu-sion in vortex-scale, and the latter is described by a novel fractal derivative modeling approach. This multi-scale model gives rise to a new probability density function which fits experimental data very well.

  6. An improved and fully implicit multi-group non-local electron transport model and its validations

    Science.gov (United States)

    Sijoy, C. D.; Mishra, V.; Chaurasia, S.

    2017-09-01

    The combined effect of thermal flux inhibition and non-local electron heat flux in the radiation hydrodynamics (RHD) simulation of laser-driven systems can be accurately predicted by using non-local electron transport (NLET) models. These models can avoid commonly used space and time-independent ad-hoc flux-limiting procedures. However, the use of classical electron collision frequency in these models is rigorously valid for high temperature non-degenerate plasmas. In laser-driven systems, the electron thermal energy transport is important in regions between the critical density and ablation surface where the plasma is partially degenerate. Therefore, an improved model for electron collision frequency in this regime is required to accurately predict the thermal energy transport. Previously, we have reported an improved single group non-local electron transport model by using a wide-range electron collision frequency model valid from warm-dense matter (WDM) to fully ionized plasmas. In this work, we have extended this idea into a two-dimensional multi-group non-local electron transport (MG-NLET) model. Moreover, we have used a fully implicit numerical integration scheme in which the models for multi-group thermal radiation transport, laser absorption, electron-ion thermal energy relaxation and ion heat conduction are included in a single step. The performance of this improved MG-NLET model has been assessed by comparing the simulated foil trajectories with the reported experimental data for laser-driven plastic foils. The results indicate that the improved model yields results that are in better agreement with the experimental data.

  7. I-RaCM: A Fully Integrated Risk and Lifecycle Cost Model Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SpaceWorks Engineering, Inc. (SEI) proposes development of the Integrated Risk and Cost Model I-RaCM, as the innovation to meet the need for integrated cost and risk...

  8. Subthreshold current model of fully depleted dual material gate SOI MOSFET

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Dual material gate SOI MOSFET with asymmetrical halo can suppress short channel effect and increase carriers transport efficiency. The analytical model of its subthreshold drain current is derived based on the explicit solution of two-dimensional Poisson's equation in the depletion region. The model takes into consideration the channel length modulation effect and the contribution of the back channel current component. Its validation is verified by comparision with two dimensional device simulator MEDICI.

  9. Atomistic modeling of intrinsic and radiation-enhanced fission gas (Xe) diffusion in UO2 +/- x: Implications for nuclear fuel performance modeling

    Energy Technology Data Exchange (ETDEWEB)

    Giovanni Pastore; Michael R. Tonks; Derek R. Gaston; Richard L. Williamson; David Andrs; Richard Martineau

    2014-03-01

    Based on density functional theory (DFT) and empirical potential calculations, the diffusivity of fission gas atoms (Xe) in UO2 nuclear fuel has been calculated for a range of non-stoichiometry (i.e. UO2x), under both out-of-pile (no irradiation) and in-pile (irradiation) conditions. This was achieved by first deriving expressions for the activation energy that account for the type of trap site that the fission gas atoms occupy, which includes the corresponding type of mobile cluster, the charge state of these defects and the chemistry acting as boundary condition. In the next step DFT calculations were used to estimate migration barriers and internal energy contributions to the thermodynamic properties and calculations based on empirical potentials were used to estimate defect formation and migration entropies (i.e. pre-exponentials). The diffusivities calculated for out-of-pile conditions as function of the UO2x nonstoichiometrywere used to validate the accuracy of the diffusion models and the DFT calculations against available experimental data. The Xe diffusivity is predicted to depend strongly on the UO2x non-stoichiometry due to a combination of changes in the preferred Xe trap site and in the concentration of uranium vacancies enabling Xe diffusion, which is consistent with experiments. After establishing the validity of the modeling approach, it was used for studying Xe diffusion under in-pile conditions, for which experimental data is very scarce. The radiation-enhanced Xe diffusivity is compared to existing empirical models. Finally, the predicted fission gas diffusion rates were implemented in the BISON fuel performance code and fission gas release from a Risø fuel rod irradiation experiment was simulated. 2014 Elsevier B.V. All rights

  10. Improved Analysis of GW150914 Using a Fully Spin-Precessing Waveform Model

    Science.gov (United States)

    Abbott, B. P.; Abbott, R.; Abbott, T. D.; Abernathy, M. R.; Acernese, F.; Ackley, K.; Adams, C.; Adams, T.; Addesso, P.; Adhikari, R. X.; Adya, V. B.; Affeldt, C.; Agathos, M.; Agatsuma, K.; Aggarwal, N.; Aguiar, O. D.; Aiello, L.; Ain, A.; Ajith, P.; Allen, B.; Allocca, A.; Altin, P. A.; Anderson, S. B.; Anderson, W. G.; Arai, K.; Araya, M. C.; Arceneaux, C. C.; Areeda, J. S.; Arnaud, N.; Arun, K. G.; Ascenzi, S.; Ashton, G.; Ast, M.; Aston, S. M.; Astone, P.; Aufmuth, P.; Aulbert, C.; Babak, S.; Bacon, P.; Bader, M. K. M.; Baker, P. T.; Baldaccini, F.; Ballardin, G.; Ballmer, S. W.; Barayoga, J. C.; Barclay, S. E.; Barish, B. C.; Barker, D.; Barone, F.; Barr, B.; Barsotti, L.; Barsuglia, M.; Barta, D.; Bartlett, J.; Bartos, I.; Bassiri, R.; Basti, A.; Batch, J. C.; Baune, C.; Bavigadda, V.; Bazzan, M.; Bejger, M.; Bell, A. S.; Berger, B. K.; Bergmann, G.; Berry, C. P. L.; Bersanetti, D.; Bertolini, A.; Betzwieser, J.; Bhagwat, S.; Bhandare, R.; Bilenko, I. A.; Billingsley, G.; Birch, J.; Birney, R.; Birnholtz, O.; Biscans, S.; Bisht, A.; Bitossi, M.; Biwer, C.; Bizouard, M. A.; Blackburn, J. K.; Blair, C. D.; Blair, D. G.; Blair, R. M.; Bloemen, S.; Bock, O.; Boer, M.; Bogaert, G.; Bogan, C.; Bohe, A.; Bond, C.; Bondu, F.; Bonnand, R.; Boom, B. A.; Bork, R.; Boschi, V.; Bose, S.; Bouffanais, Y.; Bozzi, A.; Bradaschia, C.; Brady, P. R.; Braginsky, V. B.; Branchesi, M.; Brau, J. E.; Briant, T.; Brillet, A.; Brinkmann, M.; Brisson, V.; Brockill, P.; Broida, J. E.; Brooks, A. F.; Brown, D. A.; Brown, D. D.; Brown, N. M.; Brunett, S.; Buchanan, C. C.; Buikema, A.; Bulik, T.; Bulten, H. J.; Buonanno, A.; Buskulic, D.; Buy, C.; Byer, R. L.; Cabero, M.; Cadonati, L.; Cagnoli, G.; Cahillane, C.; Calderón Bustillo, J.; Callister, T.; Calloni, E.; Camp, J. B.; Cannon, K. C.; Cao, J.; Capano, C. D.; Capocasa, E.; Carbognani, F.; Caride, S.; Casanueva Diaz, C.; Casentini, J.; Caudill, S.; Cavaglià, M.; Cavalier, F.; Cavalieri, R.; Cella, G.; Cepeda, C. B.; Cerboni Baiardi, L.; Cerretani, G.; Cesarini, E.; Chamberlin, S. J.; Chan, M.; Chao, S.; Charlton, P.; Chassande-Mottin, E.; Cheeseboro, B. D.; Chen, H. Y.; Chen, Y.; Cheng, C.; Chincarini, A.; Chiummo, A.; Cho, H. S.; Cho, M.; Chow, J. H.; Christensen, N.; Chu, Q.; Chua, S.; Chung, S.; Ciani, G.; Clara, F.; Clark, J. A.; Cleva, F.; Coccia, E.; Cohadon, P.-F.; Colla, A.; Collette, C. G.; Cominsky, L.; Constancio, M.; Conte, A.; Conti, L.; Cook, D.; Corbitt, T. R.; Cornish, N.; Corsi, A.; Cortese, S.; Costa, C. A.; Coughlin, M. W.; Coughlin, S. B.; Coulon, J.-P.; Countryman, S. T.; Couvares, P.; Cowan, E. E.; Coward, D. M.; Cowart, M. J.; Coyne, D. C.; Coyne, R.; Craig, K.; Creighton, J. D. E.; Cripe, J.; Crowder, S. G.; Cumming, A.; Cunningham, L.; Cuoco, E.; Dal Canton, T.; Danilishin, S. L.; D'Antonio, S.; Danzmann, K.; Darman, N. S.; Dasgupta, A.; Da Silva Costa, C. F.; Dattilo, V.; Dave, I.; Davier, M.; Davies, G. S.; Daw, E. J.; Day, R.; De, S.; DeBra, D.; Debreczeni, G.; Degallaix, J.; De Laurentis, M.; Deléglise, S.; Del Pozzo, W.; Denker, T.; Dent, T.; Dergachev, V.; De Rosa, R.; DeRosa, R. T.; DeSalvo, R.; Devine, R. C.; Dhurandhar, S.; Díaz, M. C.; Di Fiore, L.; Di Giovanni, M.; Di Girolamo, T.; Di Lieto, A.; Di Pace, S.; Di Palma, I.; Di Virgilio, A.; Dolique, V.; Donovan, F.; Dooley, K. L.; Doravari, S.; Douglas, R.; Downes, T. P.; Drago, M.; Drever, R. W. P.; Driggers, J. C.; Ducrot, M.; Dwyer, S. E.; Edo, T. B.; Edwards, M. C.; Effler, A.; Eggenstein, H.-B.; Ehrens, P.; Eichholz, J.; Eikenberry, S. S.; Engels, W.; Essick, R. C.; Etienne, Z.; Etzel, T.; Evans, M.; Evans, T. M.; Everett, R.; Factourovich, M.; Fafone, V.; Fair, H.; Fairhurst, S.; Fan, X.; Fang, Q.; Farinon, S.; Farr, B.; Farr, W. M.; Fauchon-Jones, E.; Favata, M.; Fays, M.; Fehrmann, H.; Fejer, M. M.; Fenyvesi, E.; Ferrante, I.; Ferreira, E. C.; Ferrini, F.; Fidecaro, F.; Fiori, I.; Fiorucci, D.; Fisher, R. P.; Flaminio, R.; Fletcher, M.; Fournier, J.-D.; Frasca, S.; Frasconi, F.; Frei, Z.; Freise, A.; Frey, R.; Frey, V.; Fritschel, P.; Frolov, V. V.; Fulda, P.; Fyffe, M.; Gabbard, H. A. G.; Gaebel, S.; Gair, J. R.; Gammaitoni, L.; Gaonkar, S. G.; Garufi, F.; Gaur, G.; Gehrels, N.; Gemme, G.; Geng, P.; Genin, E.; Gennai, A.; George, J.; Gergely, L.; Germain, V.; Ghosh, Abhirup; Ghosh, Archisman; Ghosh, S.; Giaime, J. A.; Giardina, K. D.; Giazotto, A.; Gill, K.; Glaefke, A.; Goetz, E.; Goetz, R.; Gondan, L.; González, G.; Gonzalez Castro, J. M.; Gopakumar, A.; Gordon, N. A.; Gorodetsky, M. L.; Gossan, S. E.; Gosselin, M.; Gouaty, R.; Grado, A.; Graef, C.; Graff, P. B.; Granata, M.; Grant, A.; Gras, S.; Gray, C.; Greco, G.; Green, A. C.; Groot, P.; Grote, H.; Grunewald, S.; Guidi, G. M.; Guo, X.; Gupta, A.; Gupta, M. K.; Gushwa, K. E.; Gustafson, E. K.; Gustafson, R.; Hacker, J. J.

    2016-10-01

    This paper presents updated estimates of source parameters for GW150914, a binary black-hole coalescence event detected by the Laser Interferometer Gravitational-wave Observatory (LIGO) in 2015 [Abbott et al. Phys. Rev. Lett. 116, 061102 (2016).]. Abbott et al. [Phys. Rev. Lett. 116, 241102 (2016).] presented parameter estimation of the source using a 13-dimensional, phenomenological precessing-spin model (precessing IMRPhenom) and an 11-dimensional nonprecessing effective-one-body (EOB) model calibrated to numerical-relativity simulations, which forces spin alignment (nonprecessing EOBNR). Here, we present new results that include a 15-dimensional precessing-spin waveform model (precessing EOBNR) developed within the EOB formalism. We find good agreement with the parameters estimated previously [Abbott et al. Phys. Rev. Lett. 116, 241102 (2016).], and we quote updated component masses of 35-3+5 M⊙ and 3 0-4+3 M⊙ (where errors correspond to 90% symmetric credible intervals). We also present slightly tighter constraints on the dimensionless spin magnitudes of the two black holes, with a primary spin estimate <0.65 and a secondary spin estimate <0.75 at 90% probability. Abbott et al. [Phys. Rev. Lett. 116, 241102 (2016).] estimated the systematic parameter-extraction errors due to waveform-model uncertainty by combining the posterior probability densities of precessing IMRPhenom and nonprecessing EOBNR. Here, we find that the two precessing-spin models are in closer agreement, suggesting that these systematic errors are smaller than previously quoted.

  11. A fully resolved active musculo-mechanical model for esophageal transport

    CERN Document Server

    Kou, Wenjun; Griffith, Boyce E; Pandolfino, John E; Kahrilas, Peter J; Patankar, Neelesh A

    2015-01-01

    Esophageal transport is a physiological process that mechanically transports an ingested food bolus from the pharynx to the stomach via the esophagus, a multi-layered muscular tube. This process involves interactions between the bolus, the esophagus, and the neurally coordinated activation of the esophageal muscles. In this work, we use an immersed boundary (IB) approach to simulate peristaltic transport in the esophagus. The bolus is treated as a viscous fluid that is actively transported by the muscular esophagus, which is modeled as an actively contracting, fiber-reinforced tube. A simplified version of our model is verified by comparison to an analytic solution to the tube dilation problem. Three different complex models of the multi-layered esophagus, which differ in their activation patterns and the layouts of the mucosal layers, are then extensively tested. To our knowledge, these simulations are the first of their kind to incorporate the bolus, the multi-layered esophagus tube, and muscle activation i...

  12. An improved analysis of GW150914 using a fully spin-precessing waveform model

    CERN Document Server

    Abbott, B P; Abbott, T D; Abernathy, M R; Acernese, F; Ackley, K; Adams, C; Adams, T; Addesso, P; Adhikari, R X; Adya, V B; Affeldt, C; Agathos, M; Agatsuma, K; Aggarwal, N; Aguiar, O D; Aiello, L; Ain, A; Ajith, P; Allen, B; Allocca, A; Altin, P A; Anderson, S B; Anderson, W G; Arai, K; Araya, M C; Arceneaux, C C; Areeda, J S; Arnaud, N; Arun, K G; Ascenzi, S; Ashton, G; Ast, M; Aston, S M; Astone, P; Aufmuth, P; Aulbert, C; Babak, S; Bacon, P; Bader, M K M; Baker, P T; Baldaccini, F; Ballardin, G; Ballmer, S W; Barayoga, J C; Barclay, S E; Barish, B C; Barker, D; Barone, F; Barr, B; Barsotti, L; Barsuglia, M; Barta, D; Bartlett, J; Bartos, I; Bassiri, R; Basti, A; Batch, J C; Baune, C; Bavigadda, V; Bazzan, M; Bejger, M; Bell, A S; Berger, B K; Bergmann, G; Berry, C P L; Bersanetti, D; Bertolini, A; Betzwieser, J; Bhagwat, S; Bhandare, R; Bilenko, I A; Billingsley, G; Birch, J; Birney, R; Birnholtz, O; Biscans, S; Bisht, A; Bitossi, M; Biwer, C; Bizouard, M A; Blackburn, J K; Blair, C D; Blair, D G; Blair, R M; Bloemen, S; Bock, O; Boer, M; Bogaert, G; Bogan, C; Bohe, A; Bond, C; Bondu, F; Bonnand, R; Boom, B A; Bork, R; Boschi, V; Bose, S; Bouffanais, Y; Bozzi, A; Bradaschia, C; Brady, P R; Braginsky, V B; Branchesi, M; Brau, J E; Briant, T; Brillet, A; Brinkmann, M; Brisson, V; Brockill, P; Broida, J E; Brooks, A F; Brown, D A; Brown, D D; Brown, N M; Brunett, S; Buchanan, C C; Buikema, A; Bulik, T; Bulten, H J; Buonanno, A; Buskulic, D; Buy, C; Byer, R L; Cabero, M; Cadonati, L; Cagnoli, G; Cahillane, C; Bustillo, J Calder'on; Callister, T; Calloni, E; Camp, J B; Cannon, K C; Cao, J; Capano, C D; Capocasa, E; Carbognani, F; Caride, S; Diaz, J Casanueva; Casentini, C; Caudill, S; Cavagli`a, M; Cavalier, F; Cavalieri, R; Cella, G; Cepeda, C B; Baiardi, L Cerboni; Cerretani, G; Cesarini, E; Chan, M; Chao, S; Charlton, P; Chassande-Mottin, E; Cheeseboro, B D; Chen, H Y; Chen, Y; Cheng, C; Chincarini, A; Chiummo, A; Cho, H S; Cho, M; Chow, J H; Christensen, N; Chu, Q; Chua, S; Chung, S; Ciani, G; Clara, F; Clark, J A; Cleva, F; Coccia, E; Cohadon, P -F; Colla, A; Collette, C G; Cominsky, L; Constancio, M; Conte, A; Conti, L; Cook, D; Corbitt, T R; Cornish, N; Corsi, A; Cortese, S; Costa, C A; Coughlin, M W; Coughlin, S B; Coulon, J -P; Countryman, S T; Couvares, P; Cowan, E E; Coward, D M; Cowart, M J; Coyne, D C; Coyne, R; Craig, K; Creighton, J D E; Cripe, J; Crowder, S G; Cumming, A; Cunningham, L; Cuoco, E; Canton, T Dal; Danilishin, S L; D'Antonio, S; Danzmann, K; Darman, N S; Dasgupta, A; Costa, C F Da Silva; Dattilo, V; Dave, I; Davier, M; Davies, G S; Daw, E J; Day, R; De, S; DeBra, D; Debreczeni, G; Degallaix, J; De Laurentis, M; Del'eglise, S; Del Pozzo, W; Denker, T; Dent, T; Dergachev, V; De Rosa, R; DeRosa, R T; DeSalvo, R; Devine, R C; Dhurandhar, S; D'iaz, M C; Di Fiore, L; Di Giovanni, M; Di Girolamo, T; Di Lieto, A; Di Pace, S; Di Palma, I; Di Virgilio, A; Dolique, V; Donovan, F; Dooley, K L; Doravari, S; Douglas, R; Downes, T P; Drago, M; Drever, R W P; Driggers, J C; Ducrot, M; Dwyer, S E; Edo, T B; Edwards, M C; Effler, A; Eggenstein, H -B; Ehrens, P; Eichholz, J; Eikenberry, S S; Engels, W; Essick, R C; Etienne, Z; Etzel, T; Evans, M; Evans, T M; Everett, R; Factourovich, M; Fafone, V; Fair, H; Fairhurst, S; Fan, X; Fang, Q; Farinon, S; Farr, B; Farr, W M; Fauchon-Jones, E; Favata, M; Fays, M; Fehrmann, H; Fejer, M M; Fenyvesi, E; Ferrante, I; Ferreira, E C; Ferrini, F; Fidecaro, F; Fiori, I; Fiorucci, D; Fisher, R P; Flaminio, R; Fletcher, M; Fournier, J -D; Frasca, S; Frasconi, F; Frei, Z; Freise, A; Frey, R; Frey, V; Fritschel, P; Frolov, V V; Fulda, P; Fyffe, M; Gabbard, H A G; Gaebel, S; Gair, J R; Gammaitoni, L; Gaonkar, S G; Garufi, F; Gaur, G; Gehrels, N; Gemme, G; Geng, P; Genin, E; Gennai, A; George, J; Gergely, L; Germain, V; Ghosh, Abhirup; Ghosh, Archisman; Ghosh, S; Giaime, J A; Giardina, K D; Giazotto, A; Gill, K; Glaefke, A; Goetz, E; Goetz, R; Gondan, L; Gonz'alez, G; Castro, J M Gonzalez; Gopakumar, A; Gordon, N A; Gorodetsky, M L; Gossan, S E; Gosselin, M; Gouaty, R; Grado, A; Graef, C; Graff, P B; Granata, M; Grant, A; Gras, S; Gray, C; Greco, G; Green, A C; Groot, P; Grote, H; Grunewald, S; Guidi, G M; Guo, X; Gupta, A; Gupta, M K; Gushwa, K E; Gustafson, E K; Gustafson, R; Haas, R; Hacker, J J; Hall, B R; Hall, E D; Hammond, G; Haney, M; Hanke, M M; Hanks, J; Hanna, C; Hannam, M D; Hanson, J; Hardwick, T; Harms, J; Harry, G M; Harry, I W; Hart, M J; Hartman, M T; Haster, C -J; Haughian, K; Healy, J; Heidmann, A; Heintze, M C; Heitmann, H; Hello, P; Hemming, G; Hendry, M; Heng, I S; Hennig, J; Henry, J; Heptonstall, A W; Heurs, M; Hild, S; Hinder, I; Hoak, D; Hofman, D; Holt, K; Holz, D E; Hopkins, P; Hough, J; Houston, E A; Howell, E J; Hu, Y M; Huang, S; Huerta, E A; Huet, D; Hughey, B; Husa, S; Huttner, S H; Huynh-Dinh, T; Indik, N; Ingram, D R; Inta, R; Isa, H N; Isac, J -M; Isi, M; Isogai, T; Iyer, B R; Izumi, K; Jacqmin, T; Jang, H; Jani, K; Jaranowski, P; Jawahar, S; Jian, L; Jim'enez-Forteza, F; 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Rolland, L; Rollins, J G; Roma, V J; Romano, J D; Romano, R; Romanov, G; Romie, J H; Rosi'nska, D; Rowan, S; R"udiger, A; Ruggi, P; Ryan, K; Sachdev, S; Sadecki, T; Sadeghian, L; Sakellariadou, M; Salconi, L; Saleem, M; Salemi, F; Samajdar, A; Sammut, L; Sanchez, E J; Sandberg, V; Sandeen, B; Sanders, J R; Sassolas, B; Sathyaprakash, B S; Saulson, P R; Sauter, O E S; Savage, R L; Sawadsky, A; Schale, P; Schilling, R; Schmidt, J; Schmidt, P; Schnabel, R; Schofield, R M S; Sch"onbeck, A; Schreiber, E; Schuette, D; Schutz, B F; Scott, J; Scott, S M; Sellers, D; Sengupta, A S; Sentenac, D; Sequino, V; Sergeev, A; Setyawati, Y; Shaddock, D A; Shaffer, T; Shahriar, M S; Shaltev, M; Shapiro, B; Shawhan, P; Sheperd, A; Shoemaker, D H; Shoemaker, D M; Siellez, K; Siemens, X; Sieniawska, M; Sigg, D; Silva, A D; Singer, A; Singer, L P; Singh, A; Singh, R; Singhal, A; Sintes, A M; Slagmolen, B J J; Smith, J R; Smith, N D; Smith, R J E; Son, E J; Sorazu, B; Sorrentino, F; Souradeep, T; Srivastava, A K; Staley, A; Steinke, M; Steinlechner, J; Steinlechner, S; Steinmeyer, D; Stephens, B C; Stevenson, S P; Stone, R; Strain, K A; Straniero, N; Stratta, G; Strauss, N A; Strigin, S; Sturani, R; Stuver, A L; Summerscales, T Z; Sun, L; Sunil, S; Sutton, P J; Swinkels, B L; Szczepa'nczyk, M J; Tacca, M; Talukder, D; Tanner, D B; T'apai, M; Tarabrin, S P; Taracchini, A; Taylor, R; Theeg, T; Thirugnanasambandam, M P; Thomas, E G; Thomas, M; Thomas, P; Thorne, K A; Thorne, K S; Thrane, E; Tiwari, S; Tiwari, V; Tokmakov, K V; Toland, K; Tomlinson, C; Tonelli, M; Tornasi, Z; Torres, C V; Torrie, C I; T"oyr"a, D; Travasso, F; Traylor, G; Trifir`o, D; Tringali, M C; Trozzo, L; Tse, M; Turconi, M; Tuyenbayev, D; Ugolini, D; Unnikrishnan, C S; Urban, A L; Usman, S A; Vahlbruch, H; Vajente, G; Valdes, G; Vallisneri, M; van Bakel, N; van Beuzekom, M; Brand, J F J van den; Broeck, C Van Den; Vander-Hyde, D C; van der Schaaf, L; van der Sluys, M V; van Heijningen, J V; Vano-Vinuales, A; van Veggel, A A; Vardaro, M; Vass, S; Vas'uth, M; Vaulin, R; Vecchio, A; Vedovato, G; Veitch, J; Veitch, P J; Venkateswara, K; Verkindt, D; Vetrano, F; Vicer'e, A; Vinciguerra, S; Vine, D J; Vinet, J -Y; Vitale, S; Vo, T; Vocca, H; Vorvick, C; Voss, D V; Vousden, W D; Vyatchanin, S P; Wade, A R; Wade, L E; Wade, M; Walker, M; Wallace, L; Walsh, S; Wang, G; Wang, H; Wang, M; Wang, X; Wang, Y; Ward, R L; Warner, J; Was, M; Weaver, B; Wei, L -W; Weinert, M; Weinstein, A J; Weiss, R; Wen, L; Wessels, P; Westphal, T; Wette, K; Whelan, J T; Whiting, B F; Williams, R D; Williamson, A R; Willis, J L; Willke, B; Wimmer, M H; Winkler, W; Wipf, C C; Wittel, H; Woan, G; Woehler, J; Worden, J; Wright, J L; Wu, D S; Wu, G; Yablon, J; Yam, W; Yamamoto, H; Yancey, C C; Yu, H; Yvert, M; zny, A Zadro; Zangrando, L; Zanolin, M; Zendri, J -P; Zevin, M; Zhang, L; Zhang, M; Zhang, Y; Zhao, C; Zhou, M; Zhou, Z; Zhu, X J; Zucker, M E; Zuraw, S E; Zweizig, J

    2016-01-01

    This paper presents updated estimates of source parameters for GW150914, a binary black-hole coalescence event detected by the Laser Interferometer Gravitational-wave Observatory (LIGO) on September 14, 2015 [1]. Reference presented parameter estimation [2] of the source using a 13-dimensional, phenomenological precessing-spin model (precessing IMRPhenom) and a 11-dimensional nonprecessing effective-one-body (EOB) model calibrated to numerical-relativity simulations, which forces spin alignment (nonprecessing EOBNR). Here we present new results that include a 15-dimensional precessing-spin waveform model (precessing EOBNR) developed within the EOB formalism. We find good agreement with the parameters estimated previously [2], and we quote updated component masses of $35^{+5}_{-3}\\mathrm{M}_\\odot$ and $30^{+3}_{-4}\\mathrm{M}_\\odot$ (where errors correspond to 90% symmetric credible intervals). We also present slightly tighter constraints on the dimensionless spin magnitudes of the two black holes, with a prima...

  13. Efficient uncertainty quantification of a fully nonlinear and dispersive water wave model with random inputs

    DEFF Research Database (Denmark)

    Bigoni, Daniele; Engsig-Karup, Allan Peter; Eskilsson, Claes

    2016-01-01

    of the evolution of waves. The model is analyzed using random sampling techniques and nonintrusive methods based on generalized polynomial chaos (PC). These methods allow us to accurately and efficiently estimate the probability distribution of the solution and require only the computation of the solution...... at different points in the parameter space, allowing for the reuse of existing simulation software. The choice of the applied methods is driven by the number of uncertain input parameters and by the fact that finding the solution of the considered model is computationally intensive. We revisit experimental...

  14. A massively parallel GPU-accelerated model for analysis of fully nonlinear free surface waves

    DEFF Research Database (Denmark)

    Engsig-Karup, Allan Peter; Madsen, Morten G.; Glimberg, Stefan Lemvig

    2011-01-01

    -throughput co-processors to the CPU. We describe and demonstrate how this approach makes it possible to do fast desktop computations for large nonlinear wave problems in numerical wave tanks (NWTs) with close to 50/100 million total grid points in double/ single precision with 4 GB global device memory...... space dimensions and is useful for fast analysis and prediction purposes in coastal and offshore engineering. A dedicated numerical model based on the proposed algorithm is executed in parallel by utilizing affordable modern special purpose graphics processing unit (GPU). The model is based on a low...

  15. A collision model for fully-resolved simulations of flows laden with finite-size particles

    CERN Document Server

    Costa, Pedro; Westerweel, Jerry; Breugem, Wim-Paul

    2015-01-01

    We present a collision model for particle-particle and particle-wall interactions in interface-resolved simulations of particle-laden flows. Three types of inter-particle interactions are taken into account: (1) long- and (2) short-range hydrodynamic interactions, and (3) solid-solid contact. Long-range interactions are incorporated through an efficient and second-order accurate immersed boundary method (IBM). Short-range interactions are also partly reproduced by the IBM. However, since the IBM uses a fixed-grid, a lubrication model is needed for an inter-particle gap width smaller than the grid spacing. The lubrication model is based on asymptotic expansions of analytical solutions for canonical lubrication interactions between spheres in the Stokes regime. Roughness effects are incorporated by making the lubrication correction independent of the gap width for gap widths smaller than $\\sim 1\\%$ of the particle radius. This correction is applied until the particles reach solid-solid contact. To model solid-s...

  16. Bifurcation analysis of 3D ocean flows using a parallel fully-implicit ocean model

    NARCIS (Netherlands)

    Thies, J.; Wubs, F.W.; Dijkstra, H.A.

    2009-01-01

    To understand the physics and dynamics of the ocean circulation, techniques of numerical bifurcation theory such as continuation methods have proved to be useful. Up to now these techniques have been applied to models with relatively few degrees of freedom such as multi-layer quasi-geostrophic and s

  17. A variational model for fully non-linear water waves of Boussinesq type

    NARCIS (Netherlands)

    Klopman, Gert; Dingemans, Maarten W.; Groesen, van Brenny; Grue, J.

    2005-01-01

    Using a variational principle and a parabolic approximation to the vertical structure of the velocity potential, the equations of motion for surface gravity waves over mildly sloping bathymetry are derived. No approximations are made concerning the non-linearity of the waves. The resulting model equ

  18. A fully traits-based approach to modeling global vegetation distribution

    NARCIS (Netherlands)

    Bodegom, van P.M.; Douma, J.C.; Verheijen, L.M.

    2014-01-01

    Dynamic Global Vegetation Models (DGVMs) are indispensable for our understanding of climate change impacts. The application of traits in DGVMs is increasingly refined. However, a comprehensive analysis of the direct impacts of trait variation on global vegetation distribution does not yet exist. Her

  19. Bifurcation analysis of 3D ocean flows using a parallel fully-implicit ocean model

    NARCIS (Netherlands)

    Thies, J.; Wubs, F.W.; Dijkstra, H.A.

    2009-01-01

    To understand the physics and dynamics of the ocean circulation, techniques of numerical bifurcation theory such as continuation methods have proved to be useful. Up to now these techniques have been applied to models with relatively few degrees of freedom such as multi-layer quasi-geostrophic and s

  20. Bifurcation analysis of 3D ocean flows using a parallel fully-implicit ocean model

    NARCIS (Netherlands)

    Thies, Jonas; Wubs, Fred; Dijkstra, Henk A.

    2009-01-01

    To understand the physics and dynamics of the ocean circulation, techniques of numerical bifurcation theory such as continuation methods have proved to be useful. Up to now these techniques have been applied to models with relatively few (O(10(5))) degrees of freedom such as multi-layer

  1. Development of an Efficient GPU-Accelerated Model for Fully Nonlinear Water Waves

    DEFF Research Database (Denmark)

    of an optimized sequential single-CPU algorithm based on a flexible-order Finite Difference Method. High performance is pursued by utilizing many-core processing in the model focusing on GPUs for acceleration of code execution. This involves combining analytical methods with an algorithm redesign of the current...

  2. A Fully-Coupled Approach for Modelling Plastic Deformation and Liquid Lubrication in Metal Forming

    DEFF Research Database (Denmark)

    Üstünyagiz, Esmeray; Christiansen, Peter; Nielsen, Chris V.;

    2016-01-01

    This paper presents a new approach for combined modelling of plastic deformation andliquid lubrication in the contact interfaces between material and tooling in metal forming includingsituations where the lubricant is functioning as a pressure carrier. The approach is an alternative toconventiona...... and numerical fundamentals of the proposedapproach and includes selected examples in order to illustrate its advantages and limitations....

  3. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Science.gov (United States)

    Mellem, Daniel; Fischer, Frank; Jaspers, Sören; Wenck, Horst; Rübhausen, Michael

    2016-01-01

    Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes.

  4. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model

    Science.gov (United States)

    Mellem, Daniel; Fischer, Frank; Jaspers, Sören; Wenck, Horst; Rübhausen, Michael

    2016-01-01

    Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes. PMID:26771181

  5. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Directory of Open Access Journals (Sweden)

    Daniel Mellem

    Full Text Available Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes.

  6. Improved Analysis of GW150914 Using a Fully Spin-Precessing Waveform Model

    Directory of Open Access Journals (Sweden)

    2016-10-01

    Full Text Available This paper presents updated estimates of source parameters for GW150914, a binary black-hole coalescence event detected by the Laser Interferometer Gravitational-wave Observatory (LIGO in 2015 [Abbott et al. Phys. Rev. Lett. 116, 061102 (2016.]. Abbott et al. [Phys. Rev. Lett. 116, 241102 (2016.] presented parameter estimation of the source using a 13-dimensional, phenomenological precessing-spin model (precessing IMRPhenom and an 11-dimensional nonprecessing effective-one-body (EOB model calibrated to numerical-relativity simulations, which forces spin alignment (nonprecessing EOBNR. Here, we present new results that include a 15-dimensional precessing-spin waveform model (precessing EOBNR developed within the EOB formalism. We find good agreement with the parameters estimated previously [Abbott et al. Phys. Rev. Lett. 116, 241102 (2016.], and we quote updated component masses of 35_{-3}^{+5} M_{⊙} and 30_{-4}^{+3} M_{⊙} (where errors correspond to 90% symmetric credible intervals. We also present slightly tighter constraints on the dimensionless spin magnitudes of the two black holes, with a primary spin estimate <0.65 and a secondary spin estimate <0.75 at 90% probability. Abbott et al. [Phys. Rev. Lett. 116, 241102 (2016.] estimated the systematic parameter-extraction errors due to waveform-model uncertainty by combining the posterior probability densities of precessing IMRPhenom and nonprecessing EOBNR. Here, we find that the two precessing-spin models are in closer agreement, suggesting that these systematic errors are smaller than previously quoted.

  7. The impact of iceberg calving on climate: a model study with a fully coupled ice-sheet - climate model

    Science.gov (United States)

    Bugelmayer, Marianne; Roche, Didier; Renssen, Hans

    2013-04-01

    In the current period of climate change the understanding of the interactions between different parts of the climate system gets more and more important. The ice-sheets and ice-shelves, an important part of this system, experienced strong changes in the geological past, ranging from fully ice free to ice covered - thereby altering the whole climate. In the present climate, thousands of icebergs are released every year from Greenland and Antarctica, acting as a moving source of freshwater and a sink of latent heat. As a consequence, these icebergs alter the oceans' stratification and facilitate the formation of sea ice, thus influencing the state of the ocean and of the atmosphere. Up to now, the impact of icebergs on climate has been addressed in different studies which utilize climate models using freshwater and latent heat fluxes to parameterize icebergs. Mostly these fluxes were equally distributed around the coast. However, more recently iceberg modules were integrated into climate models to take into account the temporal and spatial distribution of the iceberg melting. In the presented study, an earth system model of intermediate complexity - iLOVECLIM - that includes a 3D dynamic - thermodynamic iceberg module (Jongma et al., 2008) is coupled to the Grenoble ice shelves and land ice model - GRISLI (Ritz et al., 1997, 2001). In GRISLI, ice sheets evolve according to the precipitation and temperature received from iLOVECLIM. In turn, GRISLI provides its topography and the ice mask to the atmospheric component of iLOVECLIM and all freshwater fluxes (ablation and calving) to its oceanic component. The ablation is directly put into the uppermost layer of the ocean, whereas the calving is used to generate icebergs at the calving sites following the size distribution of Bigg et al. (1997). Using this model set-up we analyse the evolution and the equilibrium state of the Greenland ice-sheet under pre-industrial conditions within three different coupling methods. All

  8. Integrated view and path planning for a fully autonomous mobile-manipulator system for 3D object modeling

    OpenAIRE

    Torabi, Liila

    2011-01-01

    We have designed and implemented a fully autonomous system for building a 3D model of an object in situ. Our system assumes no knowledge of object other than that it is within a bounding box whose location and size are known a priori, and furthermore, the environment is unknown. The system consists of a mobile manipulator, a powerbot mobile base with a six degrees of freedom (DOF) powercube arm mounted on it. The arm and the powerbot are equipped with line-scan range sensors, which provide ra...

  9. Stand Alone, Fully Equipped, Wind Mill Matlab/Simulink Model, Case Study

    Directory of Open Access Journals (Sweden)

    VIOREL Alina Cristina

    2011-05-01

    Full Text Available The wind energy for power generation purposes is becoming increasingly attractive and is gaining a great share in electrical power production market worldwide. The major problem appears instandalone systems where a network grid system doesn’t have economical sustainability. This paper proposes a model of a simple full equipped small power wind mill of 10 kW with transverse flux generator (TFG, diode rectifier-bridge, inverter, chargecontroller and energy storage devices. Two of the main parts of the wind system are the wind turbine and the TFG of 10 kW, 20 rpm. Are presented modeling and simulations waveforms for the main parts of the system, as practical results.

  10. A Fully-Coupled Approach for Modelling Plastic Deformation and Liquid Lubrication in Metal Forming

    DEFF Research Database (Denmark)

    Üstünyagiz, Esmeray; Christiansen, Peter; Nielsen, Chris Valentin

    2016-01-01

    This paper presents a new approach for combined modelling of plastic deformation andliquid lubrication in the contact interfaces between material and tooling in metal forming includingsituations where the lubricant is functioning as a pressure carrier. The approach is an alternative toconventional...... elements with fictitious small stiffness to physical modelling based on a fullycoupled procedure in which the lubricant flow and the plastic deformation of the metallic materialare solved simultaneously. The approach takes advantage of the intrinsic velocity-pressurecharacteristics of the finite element...... flow formulation which stands on the border line between fluidand solid mechanics and allows treating the lubricants as viscous incompressible (or nearlyincompressible) fluid and the metallic materials as non-Newtonian, high viscous, incompressiblefluids. The presentation is focused on the theoretical...

  11. ASAMgpu V1.0 - a moist fully compressible atmospheric model using graphics processing units (GPUs)

    Science.gov (United States)

    Horn, S.

    2012-03-01

    In this work the three dimensional compressible moist atmospheric model ASAMgpu is presented. The calculations are done using graphics processing units (GPUs). To ensure platform independence OpenGL and GLSL are used, with that the model runs on any hardware supporting fragment shaders. The MPICH2 library enables interprocess communication allowing the usage of more than one GPU through domain decomposition. Time integration is done with an explicit three step Runge-Kutta scheme with a time-splitting algorithm for the acoustic waves. The results for four test cases are shown in this paper. A rising dry heat bubble, a cold bubble induced density flow, a rising moist heat bubble in a saturated environment, and a DYCOMS-II case.

  12. A Cascade Model for Particle Concentration and Enstrophy in Fully Developed Turbulence with Mass Loading Feedback

    CERN Document Server

    Hogan, Robert C

    2007-01-01

    A cascade model is described based on multiplier distributions determined from 3D direct numerical simulations (DNS) of turbulent particle laden flows, which include two-way coupling between the phases at global mass loadings equal to unity. The governing Eulerian equations are solved using pseudo-spectral methods on up to 512**3 computional grid points. DNS results for particle concentration and enstrophy at Taylor microscale Reynolds numbers in the range 34 - 170 were used to directly determine multiplier distributions (PDFs) on spatial scales 3 times the Kolmogorov length scale. The width of the PDFs, which is a measure of intermittency, decreases with increasing mass loading within the local region where the multipliers are measured. The functional form of this dependence is not sensitive to Reynolds numbers in the range considered. A partition correlation probability is included in the cascade model to account for the observed spatial anticorrelation between particle concentration and enstrophy. Joint pr...

  13. Improved analysis of GW150914 using a fully spin-precessing waveform model

    OpenAIRE

    2016-01-01

    This paper presents updated estimates of source parameters for GW150914, a binary black-hole coalescence event detected by the Laser Interferometer Gravitational-wave Observatory (LIGO) in 2015 [Abbott et al. Phys. Rev. Lett. 116, 061102 (2016).]. Abbott et al. [Phys. Rev. Lett. 116, 241102 (2016).] presented parameter estimation of the source using a 13-dimensional, phenomenological precessing-spin model (precessing IMRPhenom) and an 11-dimensional nonprecessing effective-one-body (EOB) mode...

  14. A Boolean Approach to Unbounded, Fully Symbolic Model Checking of Timed Automata

    Science.gov (United States)

    2003-03-01

    reachability properties (these can express safety and bounded-liveness properties [1]). Uppaal2k and Kronos are unbounded, symbolic model checkers that...explicitly enumerate the discrete component of the state space. Kronos uses Difference Bound Matrices (DBMs) as the symbolic representation [19] of the...difference. Note that while Kronos can check arbitrary TCTL formulas, Uppaal2k is limited to checking reachability properties and very restricted liveness

  15. Cascade model for particle concentration and enstrophy in fully developed turbulence with mass-loading feedback.

    Science.gov (United States)

    Hogan, R C; Cuzzi, J N

    2007-05-01

    A cascade model is described based on multiplier distributions determined from three-dimensional (3D) direct numerical simulations (DNS) of turbulent particle laden flows, which include two-way coupling between the phases at global mass loadings equal to unity. The governing Eulerian equations are solved using psuedospectral methods on up to 512(3) computional grid points. DNS results for particle concentration and enstrophy at Taylor microscale Reynolds numbers in the range 34-170 were used to directly determine multiplier distributions on spatial scales three times the Kolmogorov length scale. The multiplier probability distribution functions (PDFs) are well characterized by the beta distribution function. The width of the PDFs, which is a measure of intermittency, decreases with increasing mass loading within the local region where the multipliers are measured. The functional form of this dependence is not sensitive to Reynolds numbers in the range considered. A partition correlation probability is included in the cascade model to account for the observed spatial anticorrelation between particle concentration and enstrophy. Joint probability distribution functions of concentration and enstrophy generated using the cascade model are shown to be in excellent agreement with those derived directly from our 3D simulations. Probabilities predicted by the cascade model are presented at Reynolds numbers well beyond what is achievable by direct simulation. These results clearly indicate that particle mass loading significantly reduces the probabilities of high particle concentration and enstrophy relative to those resulting from unloaded runs. Particle mass density appears to reach a limit at around 100 times the gas density. This approach has promise for significant computational savings in certain applications.

  16. First synchronous realistic simulations of Antarctic and Greenland SMB in a fully coupled climate model

    Science.gov (United States)

    Lenaerts, J.; van Kampenhout, L.; Lipscomb, W. H.; Gettelman, A.; van den Broeke, M.; Sacks, W.; Fyke, J. G.; Vizcaino, M.; Löfverström, M.

    2015-12-01

    Here we use the global, coupled ocean-atmosphere-land Community Earth System Model (CESM) at a 1o degree horizontal resolution to simulate recent past (1850-now) and future (21st century) Greenland and Antarctic ice sheet SMB in tandem. To that end, we have recently improved the representation of firn in CESM. We increased the vertical thickness of snow, which enhances the buffering of meltwater through refreezing, and firn density, to allow for wind-induced snow compaction. Other model improvements focused on atmospheric clouds; the most recent CESM atmosphere model allows for more liquid water in clouds, which increases positive longwave cloud forcing, and has profound and beneficial impact on the ice sheet surface radiation balance. In this contribution, we will show that the above improvements enable a realistic CESM simulation of both Greenland and Antarctic SMB. This allows for analysis of future evolution of ice sheet SMB and the interactions between ice sheets and other components of the climate system.

  17. Elastoplastic model for unsaturated, quasi-saturated and fully saturated fine soils

    Directory of Open Access Journals (Sweden)

    Lai Ba Tien

    2016-01-01

    Full Text Available In unsaturated soils, the gaseous phase is commonly assumed to be continuous. This assumption is no more valid at high saturation ratio. In that case, air bubbles and pockets can be trapped in the porous network by the liquid phase and the gas phase becomes discontinuous. This trapped air reduces the apparent compressibility of the pore fluid and affect the mechanical behavior of the soil. Although it is trapped in the pores, its dissolution can take place. Dissolved air can migrate through the pore space, either by following the flow of the fluid or by diffusion. In this context, this paper present a hydro mechanical model that separately considers the kinematics and the mechanical behavior of each fluid species (eg liquid water, dissolved air, gaseous air and the solid matrix. This new model was implemented in a C++ code. Some numerical simulations are performed to demonstrate the ability of this model to reproduce a continuous transition of unsaturated to saturated states.

  18. Improved cyberinfrastructure for integrated hydrometeorological predictions within the fully-coupled WRF-Hydro modeling system

    Science.gov (United States)

    gochis, David; hooper, Rick; parodi, Antonio; Jha, Shantenu; Yu, Wei; Zaslavsky, Ilya; Ganapati, Dinesh

    2014-05-01

    The community WRF-Hydro system is currently being used in a variety of flood prediction and regional hydroclimate impacts assessment applications around the world. Despite its increasingly wide use certain cyberinfrastructure bottlenecks exist in the setup, execution and post-processing of WRF-Hydro model runs. These bottlenecks result in wasted time, labor, data transfer bandwidth and computational resource use. Appropriate development and use of cyberinfrastructure to setup and manage WRF-Hydro modeling applications will streamline the entire workflow of hydrologic model predictions. This talk will present recent advances in the development and use of new open-source cyberinfrastructure tools for the WRF-Hydro architecture. These tools include new web-accessible pre-processing applications, supercomputer job management applications and automated verification and visualization applications. The tools will be described successively and then demonstrated in a set of flash flood use cases for recent destructive flood events in the U.S. and in Europe. Throughout, an emphasis on the implementation and use of community data standards for data exchange is made.

  19. Low-order dynamical system model of a fully developed turbulent channel flow

    Science.gov (United States)

    Hamilton, Nicholas; Tutkun, Murat; Cal, Raúl Bayoán

    2017-06-01

    A reduced order model of a turbulent channel flow is composed from a direct numerical simulation database hosted at the Johns Hopkins University. Snapshot proper orthogonal decomposition (POD) is used to identify the Hilbert space from which the reduced order model is obtained, as the POD basis is defined to capture the optimal energy content by mode. The reduced order model is defined by coupling the evolution of the dynamic POD mode coefficients through their respective time derivative with a least-squares polynomial fit of terms up to third order. Parameters coupling the dynamics of the POD basis are defined in analog to those produced in the classical Galerkin projection. The resulting low-order dynamical system is tested for a range of basis modes demonstrating that the non-linear mode interactions do not lead to a monotonic decrease in error propagation. A basis of five POD modes accounts for 50% of the integrated turbulence kinetic energy but captures only the largest features of the turbulence in the channel flow and is not able to reflect the anticipated flow dynamics. Using five modes, the low-order model is unable to accurately reproduce Reynolds stresses, and the root-mean-square error of the predicted stresses is as great as 30%. Increasing the basis to 28 modes accounts for 90% of the kinetic energy and adds intermediate scales to the dynamical system. The difference between the time derivatives of the random coefficients associated with individual modes and their least-squares fit is amplified in the numerical integration leading to unstable long-time solutions. Periodic recalibration of the dynamical system is undertaken by limiting the integration time to the range of the sampled data and offering the dynamical system new initial conditions. Renewed initial conditions are found by pushing the mode coefficients in the end of the integration time toward a known point along the original trajectories identified through a least-squares projection. Under

  20. Regression Models Using Fully Discharged Voltage and Internal Resistance for State of Health Estimation of Lithium-Ion Batteries

    Directory of Open Access Journals (Sweden)

    Kuo-Hsin Tseng

    2015-04-01

    Full Text Available Accurate estimation of lithium-ion battery life is essential to assure the reliable operation of the energy supply system. This study develops regression models for battery prognostics using statistical methods. The resultant regression models can not only monitor a battery’s degradation trend but also accurately predict its remaining useful life (RUL at an early stage. Three sets of test data are employed in the training stage for regression models. Another set of data is then applied to the regression models for validation. The fully discharged voltage (Vdis and internal resistance (R are adopted as aging parameters in two different mathematical models, with polynomial and exponential functions. A particle swarm optimization (PSO process is applied to search for optimal coefficients of the regression models. Simulations indicate that the regression models using Vdis and R as aging parameters can build a real state of health profile more accurately than those using cycle number, N. The Monte Carlo method is further employed to make the models adaptive. The subsequent results, however, show that this results in an insignificant improvement of the battery life prediction. A reasonable speculation is that the PSO process already yields the major model coefficients.

  1. detecting multiple sclerosis lesions with a fully bioinspired visual attention model

    Science.gov (United States)

    Villalon-Reina, Julio; Gutierrez-Carvajal, Ricardo; Thompson, Paul M.; Romero-Castro, Eduardo

    2013-11-01

    The detection, segmentation and quantification of multiple sclerosis (MS) lesions on magnetic resonance images (MRI) has been a very active field for the last two decades because of the urge to correlate these measures with the effectiveness of pharmacological treatment. A myriad of methods has been developed and most of these are non specific for the type of lesions and segment the lesions in their acute and chronic phases together. On the other hand, radiologists are able to distinguish between several stages of the disease on different types of MRI images. The main motivation of the work presented here is to computationally emulate the visual perception of the radiologist by using modeling principles of the neuronal centers along the visual system. By using this approach we are able to detect the lesions in the majority of the images in our population sample. This type of approach also allows us to study and improve the analysis of brain networks by introducing a priori information.

  2. FC-TLBO: fully constrained meta-heuristic algorithm for abundance estimation using linear mixing model

    Indian Academy of Sciences (India)

    OMPRAKASH TEMBHURNE; DEEPTI SHRIMANKAR

    2017-07-01

    A study of abundance estimation has vital importance in spectral unmixing of hyperspectral image. Recently, various methods have been proposed for spectral unmixing to achieve higher performance using an evolutionary approach. However, these methods are based on unconstrained optimisation problems. Theirperformance was also based on proper tuning parameters. We have proposed a new non-parametric algorithm using teaching-learning-based optimisation technique with an inbuilt constraints maintenance mechanism using the linear mixing model. In this approach, the unmixing problem is transformed into a combinatorial optimisation problem by introducing abundance sum to one constraint and abundance non-negative constraint. A comparative analysis of the proposed algorithm is conducted with other two state-of-the-art algorithms.Experimental results in known and unknown environments with varying signal-to-noise ratio on simulated and real hyper spectral data demonstrate that the proposed method outperforms the other methods.

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

    Science.gov (United States)

    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.).

  4. Technical note: Simultaneous fully dynamic characterization of multiple input–output relationships in climate models

    Energy Technology Data Exchange (ETDEWEB)

    Kravitz, Ben; MacMartin, Douglas G.; Rasch, Philip J.; Wang, Hailong

    2017-01-01

    We introduce system identification techniques to climate science wherein multiple dynamic input–output relationships can be simultaneously characterized in a single simulation. This method, involving multiple small perturbations (in space and time) of an input field while monitoring output fields to quantify responses, allows for identification of different timescales of climate response to forcing without substantially pushing the climate far away from a steady state. We use this technique to determine the steady-state responses of low cloud fraction and latent heat flux to heating perturbations over 22 regions spanning Earth's oceans. We show that the response characteristics are similar to those of step-change simulations, but in this new method the responses for 22 regions can be characterized simultaneously. Furthermore, we can estimate the timescale over which the steady-state response emerges. The proposed methodology could be useful for a wide variety of purposes in climate science, including characterization of teleconnections and uncertainty quantification to identify the effects of climate model tuning parameters.

  5. Vertical structure and turbulent saturation level in fully radiative protoplanetary disc models

    Science.gov (United States)

    Flaig, M.; Kley, W.; Kissmann, R.

    2010-12-01

    We investigate a massive (Sigma ~ 10 000 g cm-2 at 1 au) protoplanetary disc model by means of 3D radiation magnetohydrodynamic simulations. The vertical structure of the disc is determined self-consistently by a balance between turbulent heating caused by the magnetorotational turbulence and radiative cooling. Concerning the vertical structure, two different regions can be distinguished: a gas-pressure-dominated, optically thick mid-plane region where most of the dissipation takes place, and a magnetically dominated, optically thin corona which is dominated by strong shocks. At the location of the photosphere, the turbulence is supersonic (M ~ 2), which is consistent with previous results obtained from the fitting of spectra of young stellar objects. It is known that the turbulent saturation level in simulations of MRI-induced turbulence does depend on numerical factors such as the numerical resolution and the box size. However, by performing a suite of runs at different resolutions (using up to 64 x 128 x 512 grid cells) and with varying box sizes (with up to 16 pressure scaleheights in the vertical direction), we find that both the saturation levels and the heating rates show a clear trend to converge once a sufficient resolution in the vertical direction has been achieved.

  6. Thin-Film Photoluminescent Properties and the Atomistic Model of Mg2TiO4 as a Non-rare Earth Matrix Material for Red-Emitting Phosphor

    Science.gov (United States)

    Huang, Chieh-Szu; Chang, Ming-Chuan; Huang, Cheng-Liang; Lin, Shih-kang

    2016-12-01

    Thin-film electroluminescent devices are promising solid-state lighting devices. Red light-emitting phosphor is the key component to be integrated with the well-established blue light-emitting diode chips for stimulating natural sunlight. However, environmentally hazardous rare-earth (RE) dopants, e.g. Eu2+ and Ce2+, are commonly used for red-emitting phosphors. Mg2TiO4 inverse spinel has been reported as a promising matrix material for "RE-free" red light luminescent material. In this paper, Mg2TiO4 inverse spinel is investigated using both experimental and theoretical approaches. The Mg2TiO4 thin films were deposited on Si (100) substrates using either spin-coating with the sol-gel process, or radio frequency sputtering, and annealed at various temperatures ranging from 600°C to 900°C. The crystallinity, microstructures, and photoluminescent properties of the Mg2TiO4 thin films were characterized. In addition, the atomistic model of the Mg2TiO4 inverse spinel was constructed, and the electronic band structure of Mg2TiO4 was calculated based on density functional theory. Essential physical and optoelectronic properties of the Mg2TiO4 luminance material as well as its optimal thin-film processing conditions were comprehensively reported.

  7. Thin-Film Photoluminescent Properties and the Atomistic Model of Mg2TiO4 as a Non-rare Earth Matrix Material for Red-Emitting Phosphor

    Science.gov (United States)

    Huang, Chieh-Szu; Chang, Ming-Chuan; Huang, Cheng-Liang; Lin, Shih-kang

    2016-08-01

    Thin-film electroluminescent devices are promising solid-state lighting devices. Red light-emitting phosphor is the key component to be integrated with the well-established blue light-emitting diode chips for stimulating natural sunlight. However, environmentally hazardous rare-earth (RE) dopants, e.g. Eu2+ and Ce2+, are commonly used for red-emitting phosphors. Mg2TiO4 inverse spinel has been reported as a promising matrix material for "RE-free" red light luminescent material. In this paper, Mg2TiO4 inverse spinel is investigated using both experimental and theoretical approaches. The Mg2TiO4 thin films were deposited on Si (100) substrates using either spin-coating with the sol-gel process, or radio frequency sputtering, and annealed at various temperatures ranging from 600°C to 900°C. The crystallinity, microstructures, and photoluminescent properties of the Mg2TiO4 thin films were characterized. In addition, the atomistic model of the Mg2TiO4 inverse spinel was constructed, and the electronic band structure of Mg2TiO4 was calculated based on density functional theory. Essential physical and optoelectronic properties of the Mg2TiO4 luminance material as well as its optimal thin-film processing conditions were comprehensively reported.

  8. A Note on Automatic Kernel Carpentry for Atomistic Support of Continuum Stress

    CERN Document Server

    Ulz, Manfred H

    2015-01-01

    Research within the field of multiscale modelling seeks, amongst other questions, to reconcile atomistic scale interactions with thermodynamical quantities (such as stress) on the continuum scale. The estimation of stress at a continuum point on the atomistic scale requires a pre-defined kernel function. This kernel function derives the stress at a continuum point by averaging the contribution from atoms within a region surrounding the continuum point. Commonly the kernel weight assignment is isotropic: an identical weight is assigned to atoms at the same spatial distance, which is tantamount to a local constant regression model. In this paper we employ a local linear regression model and leverage the mechanism of automatic kernel carpentry to allow for spatial averaging adaptive to the local distribution of atoms. As a result, different weights may be assigned to atoms at the same spatial distance. This is of interest for determining atomistic stress at stacking faults, interfaces or surfaces. It is shown in...

  9. An inventory model of purchase quantity for fully-loaded vehicles with maximum trips in consecutive transport time

    Directory of Open Access Journals (Sweden)

    Chen Pоуu

    2013-01-01

    Full Text Available Products made overseas but sold in Taiwan are very common. Regarding the cross-border or interregional production and marketing of goods, inventory decision-makers often have to think about how to determine the amount of purchases per cycle, the number of transport vehicles, the working hours of each transport vehicle, and the delivery by ground or air transport to sales offices in order to minimize the total cost of the inventory in unit time. This model assumes that the amount of purchases for each order cycle should allow all rented vehicles to be fully loaded and the transport times to reach the upper limit within the time period. The main research findings of this study included the search for the optimal solution of the integer planning of the model and the results of sensitivity analysis.

  10. Ductile Tearing of Thin Aluminum Plates Under Blast Loading. Predictions with Fully Coupled Models and Biaxial Material Response Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Corona, Edmundo [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gullerud, Arne S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Haulenbeek, Kimberly K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Reu, Phillip L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-06-01

    The work presented in this report concerns the response and failure of thin 2024- T3 aluminum alloy circular plates to a blast load produced by the detonation of a nearby spherical charge. The plates were fully clamped around the circumference and the explosive charge was located centrally with respect to the plate. The principal objective was to conduct a numerical model validation study by comparing the results of predictions to experimental measurements of plate deformation and failure for charges with masses in the vicinity of the threshold between no tearing and tearing of the plates. Stereo digital image correlation data was acquired for all tests to measure the deflection and strains in the plates. The size of the virtual strain gage in the measurements, however, was relatively large, so the strain measurements have to be interpreted accordingly as lower bounds of the actual strains in the plate and of the severity of the strain gradients. A fully coupled interaction model between the blast and the deflection of the structure was considered. The results of the validation exercise indicated that the model predicted the deflection of the plates reasonably accurately as well as the distribution of strain on the plate. The estimation of the threshold charge based on a critical value of equivalent plastic strain measured in a bulge test, however, was not accurate. This in spite of efforts to determine the failure strain of the aluminum sheet under biaxial stress conditions. Further work is needed to be able to predict plate tearing with some degree of confidence. Given the current technology, at least one test under the actual blast conditions where the plate tears is needed to calibrate the value of equivalent plastic strain when failure occurs in the numerical model. Once that has been determined, the question of the explosive mass value at the threshold could be addressed with more confidence.

  11. Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

    NARCIS (Netherlands)

    Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.

    2016-01-01

    We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrou

  12. Atomistic Processes of Catalyst Degradation

    Energy Technology Data Exchange (ETDEWEB)

    None

    2004-11-27

    The purpose of this cooperative research and development agreement (CRADA) between Sasol North America, Inc., and the oak Ridge National Laboratory (ORNL) was to improve the stability of alumina-based industrial catalysts through the combination of aberration-corrected scanning transmission electron microscopy (STEM) at ORNL and innovative sample preparation techniques at Sasol. Outstanding progress has been made in task 1, 'Atomistic processes of La stabilization'. STEM investigations provided structural information with single-atom precision, showing the lattice location of La dopant atoms, thus enabling first-principles calculations of binding energies, which were performed in collaboration with Vanderbilt University. The stabilization mechanism turns out to be entirely due to a particularly strong binding energy of the La tom to the {gamma}-alumina surface. The large size of the La atom precludes incorporation of La into the bulk alumina and also strains the surface, thus preventing any clustering of La atoms. Thus highly disperse distribution is achieved and confirmed by STEM images. la also affects relative stability of the exposed surfaces of {gamma}-alumina, making the 100 surface more stable for the doped case, unlike the 110 surface for pure {gamma}-alumina. From the first-principles calculations, they can estimate the increase in transition temperature for the 3% loading of La used commercially, and it is in excellent agreement with experiment. This task was further pursued aiming to generate useable recommendations for the optimization of the preparation techniques for La-doped aluminas. The effort was primarily concentrated on the connection between the boehmitre-{gamma}-Al{sub 2}O{sub 3} phase transition (i.e. catalyst preparation) and the resulting dispersion of La on the {gamma}-Al{sub 2}O{sub 3} surface. It was determined that the La distribution on boehmite was non-uniform and different from that on the {gamma}-Al{sub 2}O{sub 3} and thus

  13. 2D Flood Modelling Using Advanced Terrain Analysis Techniques And A Fully Continuous DEM-Based Rainfall-Runoff Algorithm

    Science.gov (United States)

    Nardi, F.; Grimaldi, S.; Petroselli, A.

    2012-12-01

    Remotely sensed Digital Elevation Models (DEMs), largely available at high resolution, and advanced terrain analysis techniques built in Geographic Information Systems (GIS), provide unique opportunities for DEM-based hydrologic and hydraulic modelling in data-scarce river basins paving the way for flood mapping at the global scale. This research is based on the implementation of a fully continuous hydrologic-hydraulic modelling optimized for ungauged basins with limited river flow measurements. The proposed procedure is characterized by a rainfall generator that feeds a continuous rainfall-runoff model producing flow time series that are routed along the channel using a bidimensional hydraulic model for the detailed representation of the inundation process. The main advantage of the proposed approach is the characterization of the entire physical process during hydrologic extreme events of channel runoff generation, propagation, and overland flow within the floodplain domain. This physically-based model neglects the need for synthetic design hyetograph and hydrograph estimation that constitute the main source of subjective analysis and uncertainty of standard methods for flood mapping. Selected case studies show results and performances of the proposed procedure as respect to standard event-based approaches.

  14. A physically-based and fully coupled model of elasto-plasticity and damage for dynamic failure in ductile metals

    Science.gov (United States)

    Oussouaddi, O.; Campagne, L.; Daridon, L.; Ahzi, S.

    2006-08-01

    It is well established that spall fracture and other rapid failures in ductile materials are often dominated by nucleation and growth of micro-voids. In the present work, a mechanistic model for failure by cumulative nucleation and growth of voids is fully coupled with the thermo-elastoplastic constitutive equations of the Mechanical Threshold Stress (MTS) which is used to model the evolution of the flow stress. The damage modeling includes both ductile and brittle mechanisms. It accounts for the effects of inertia, rate sensitivity, fracture surface energy, and nucleation frequency. The MTS model used for plasticity includes the superposition of different thermal activation barriers for dislocation motion. Results obtained in the case of uncoupled and coupled model of plasticity and damage from the simulations of the planar impact with cylindrical target, are presented and compared with the experimental results for OFHC copper. This comparison shows the model capabilities in predicting the experimentally measured free surface velocity profile as well as the observed spall and other damage patterns in the material under impact loading. These results are obtained using the finite element code Abaqus/Explicit.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  16. A battery model that fully couples mechanics and electrochemistry at both particle and electrode levels by incorporation of particle interaction

    Science.gov (United States)

    Wu, Bin; Lu, Wei

    2017-08-01

    This paper develops a multi-scale mechanical-electrochemical model which enables fully coupled mechanics and electrochemistry at both particle and electrode levels. At the particle level, solid diffusion is modeled using a generalized chemical potential to capture the effects of mechanical stress and phase transformation. At the electrode level, the stress arising from particle interaction is incorporated in a continuum model. This particle interaction stress is in addition to the traditional concept of intercalation stress inside isolated particles. The particle and continuum electrode levels are linked by the particle interaction stress as loads on the particle surface, and by consideration of stress on the electrochemical reaction rate on the particle surface. The effect of mechanical stress on electrochemical reaction results in a stress-dependent over-potential between particle and electrolyte. Stress gradient in an electrode leads to inhomogeneous intercalation/deintercalation currents for particles depending on their interaction stress with neighbors, resulting in stress gradient induced inhomogeneous state of charge. Conversely, non-uniform intercalation/deintercalation currents in an electrode lead to stress between particles. With this model we have an important finding: an electrochemically inactive region in an electrode causes stress built-up. This model provides a powerful tool to address various problems such as fracture in-between particles.

  17. Towards a Fully Distributed Characterization of Water Residence and Transit Time by Coupled Hydrology-Transport Modeling

    Science.gov (United States)

    Remondi, F.; Fatichi, S.; Burlando, P.

    2015-12-01

    Water residence and transit time are crucial elements in flow pathways and catchment response characterization. The temporal distribution of catchment transit times has been generally studied and modelled with lumped parameter approaches. However, understanding the dominant controls in a more holistic manner requires attention to the spatially distributed catchment properties also in relation to their control on the basin response to different type of precipitation events. A tool that looks both at the time and space distribution of water residence and transport can be useful for predicting water and solute fluxes and ultimately for better understanding the dependence of catchment transit and residence times on geomorphological and climatic factors. To this purpose we couple a fully distributed, yet essential, process-based watershed model with a component to simulate solute transport. Key features of the developed tool include: (a) reduced complexity spatially-distributed hydrological model; (b) spatially-distributed water age and conservative tracer concentration; (c) possibility to explicitly compute transit time distributions for different precipitation events and locations. The presented framework is tested on the Plynlimon watershed (UK), where long-term records of hydrological variables are available. Among them, discharge and chloride concentration are used to investigate the model behavior. We present the integrated model concept, the underlying methodologies, the results from the case study application, as well as preliminary virtual experiments that allow exploring the full statistical space of travel and residence times.

  18. A numerical manifold method model for analyzing fully coupled hydro-mechanical processes in porous rock masses with discrete fractures

    Science.gov (United States)

    Hu, Mengsu; Rutqvist, Jonny; Wang, Yuan

    2017-04-01

    In this study, a numerical manifold method (NMM) model was developed for fully coupled analysis of hydro-mechanical (HM) processes in porous rock masses with discrete fractures. Using an NMM two-cover-mesh system of mathematical and physical covers, fractures are conveniently discretized by dividing the mathematical cover along fracture traces to physical cover, resulting in a discontinuous model on a non-conforming mesh. In this model, discrete fracture deformation (e.g. open and slip) and fracture fluid flow within a permeable and deformable porous rock matrix are rigorously considered. For porous rock, direct pore-volume coupling was modeled based on an energy-work scheme. For mechanical analysis of fractures, a fracture constitutive model for mechanically open states was introduced. For fluid flow in fractures, both along-fracture and normal-to-fracture fluid flow are modeled without introducing additional degrees of freedom. When the mechanical aperture of a fracture is changing, its hydraulic aperture and hydraulic conductivity is updated. At the same time, under the effect of coupled deformation and fluid flow, the contact state may dynamically change, and the corresponding contact constraint is updated each time step. Therefore, indirect coupling is realized under stringent considerations of coupled HM effects and fracture constitutive behavior transfer dynamically. To verify the new model, examples involving deformable porous media containing a single and two sets of fractures were designed, showing good accuracy. Last, the model was applied to analyze coupled HM behavior of fractured porous rock domains with complex fracture networks under effects of loading and injection.

  19. Capturing intracellular pH dynamics by coupling its molecular mechanisms within a fully tractable mathematical model.

    Directory of Open Access Journals (Sweden)

    Yann Bouret

    Full Text Available We describe the construction of a fully tractable mathematical model for intracellular pH. This work is based on coupling the kinetic equations depicting the molecular mechanisms for pumps, transporters and chemical reactions, which determine this parameter in eukaryotic cells. Thus, our system also calculates the membrane potential and the cytosolic ionic composition. Such a model required the development of a novel algebraic method that couples differential equations for slow relaxation processes to steady-state equations for fast chemical reactions. Compared to classical heuristic approaches based on fitted curves and ad hoc constants, this yields significant improvements. This model is mathematically self-consistent and allows for the first time to establish analytical solutions for steady-state pH and a reduced differential equation for pH regulation. Because of its modular structure, it can integrate any additional mechanism that will directly or indirectly affect pH. In addition, it provides mathematical clarifications for widely observed biological phenomena such as overshooting in regulatory loops. Finally, instead of including a limited set of experimental results to fit our model, we show examples of numerical calculations that are extremely consistent with the wide body of intracellular pH experimental measurements gathered by different groups in many different cellular systems.

  20. Modeling and simulation of deformation and fracture behavior of components made of fully lamellar {gamma}TiAl alloy

    Energy Technology Data Exchange (ETDEWEB)

    Kabir, Mohammad Rizviul [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Materialforschung

    2008-07-01

    The present work deals with the modeling and simulation of deformation and fracture behavior of fully lamellar {gamma}TiAl alloy; focusing on understanding the variability of local material properties and their influences on translamellar fracture. Afracture model has been presented that takes the inhomogeneity of the local deformation behavior of the lamellar colonies as well as the variability in fracture strength and toughness into consideration. To obtain the necessary model parameters, a hybrid methodology of experiments and simulations has been adopted. The experiments were performed at room temperature that demonstrates quasi-brittle response of the TiAl polycrystal. Aremarkable variation in stress-strain curves has been found in the tensile tests. Additional fracture tests showed significant variations in crack initiation and propagation during translamellar fracture. Analyzing the fracture surfaces, the micromechanical causes of these macroscopic scatter have been explained. The investigation shows that the global scatter in deformation and fracture response is highly influenced by the colony orientation and tilting angle with respect to the loading axis. The deformation and fracture behavior have been simulated by a finite element model including the material decohesion process described by a cohesive model. In order to capture the scatter of the macroscopic behavior, a stochastic approach is chosen. The local variability of stressstrain in the polycrystal and the variability of fracture parameters of the colonies are implemented in the stochastic approach of the cohesive model. It has been shown that the proposed approach is able to predict the stochastic nature of crack initiation and propagation as observed from the experiments. The global specimen failure with stable or unstable crack propagation can be explained in terms of the local variation of material properties. (orig.)

  1. Development of a fully 3D system model in iterative expectation-maximization reconstruction for cone-beam SPECT

    Science.gov (United States)

    Ye, Hongwei; Vogelsang, Levon; Feiglin, David H.; Lipson, Edward D.; Krol, Andrzej

    2008-03-01

    In order to improve reconstructed image quality for cone-beam collimator SPECT, we have developed and implemented a fully 3D reconstruction, using an ordered subsets expectation maximization (OSEM) algorithm, along with a volumetric system model - cone-volume system model (CVSM), a modified attenuation compensation, and a 3D depth- and angle-dependent resolution and sensitivity correction. SPECT data were acquired in a 128×128 matrix, in 120 views with a single circular orbit. Two sets of numerical Defrise phantoms were used to simulate CBC SPECT scans, and low noise and scatter-free projection datasets were obtained using the SimSET Monte Carlo package. The reconstructed images, obtained using OSEM with a line-length system model (LLSM) and a 3D Gaussian post-filter, and OSEM with FVSM and a 3D Gaussian post-filter were quantitatively studied. Overall improvement in the image quality has been observed, including better transaxial resolution, higher contrast-to-noise ratio between hot and cold disks, and better accuracy and lower bias in OSEM-CVSM, compared with OSEM-LLSM.

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

    Science.gov (United States)

    Chen, Youping

    2006-02-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R. [A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova Str. 28, 119991 Moscow (Russian Federation)

    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.

  4. Development of a compositional model fully coupled with geomechanics and its application to tight oil reservoir simulation

    Science.gov (United States)

    Xiong, Yi

    Tight oil reservoirs have received great attention in recent years as unconventional and promising petroleum resources; they are reshaping the U.S. crude oil market due to their substantial production. However, fluid flow behaviors in tight oil reservoirs are not well studied or understood due to the complexities in the physics involved. Specific characteristics of tight oil reservoirs, such as nano-pore scale and strong stress-dependency result in complex porous medium fluid flow behaviors. Recent field observations and laboratory experiments indicate that large effects of pore confinement and rock compaction have non-negligible impacts on the production performance of tight oil reservoirs. On the other hand, there are approximations or limitations for modeling tight oil reservoirs under the effects of pore confinement and rock compaction with current reservoir simulation techniques. Thus this dissertation aims to develop a compositional model coupled with geomechanics with capabilities to model and understand the complex fluid flow behaviors of multiphase, multi-component fluids in tight oil reservoirs. MSFLOW_COM (Multiphase Subsurface FLOW COMpositional model) has been developed with the capability to model the effects of pore confinement and rock compaction for multiphase fluid flow in tight oil reservoirs. The pore confinement effect is represented by the effect of capillary pressure on vapor-liquid equilibrium (VLE), and modeled with the VLE calculation method in MSFLOW_COM. The fully coupled geomechanical model is developed from the linear elastic theory for a poro-elastic system and formulated in terms of the mean stress. Rock compaction is then described using stress-dependent rock properties, especially stress-dependent permeability. Thus MSFLOW_COM has the capabilities to model the complex fluid flow behaviors of tight oil reservoirs, fully coupled with geomechanics. In addition, MSFLOW_COM is validated against laboratory experimental data, analytical

  5. Development, testing and application of DrainFlow: A fully distributed integrated surface-subsurface flow model for drainage study

    Science.gov (United States)

    Shokri, Ali; Bardsley, William Earl

    2016-06-01

    Hydrological and hydrogeological investigation of drained land is a complex and integrated procedure. The scale of drainage studies may vary from a high-resolution small scale project through to comprehensive catchment or regional scale investigations. This wide range of scales and integrated system behaviour poses a significant challenge for the development of suitable drainage models. Toward meeting these requirements, a fully distributed coupled surface-subsurface flow model titled DrainFlow has been developed and is described. DrainFlow includes both the diffusive wave equation for surface flow components (overland flow, open drain, tile drain) and Richard's equation for saturated/unsaturated zones. To overcome the non-linearity problem created from switching between wet and dry boundaries, a smooth transitioning technique is introduced to buffer the model at tile drains and at interfaces between surface and subsurface flow boundaries. This gives a continuous transition between Dirichlet and Neumann boundary conditions. DrainFlow is tested against five well-known integrated surface-subsurface flow benchmarks. DrainFlow as applied to some synthetic drainage study examples is quite flexible for changing all or part of the model dimensions as required by problem complexity, problem scale, and data availability. This flexibility enables DrainFlow to be modified to allow for changes in both scale and boundary conditions, as often encountered in real-world drainage studies. Compared to existing drainage models, DrainFlow has the advantage of estimating actual infiltration directly from the partial differential form of Richard's equation rather than through analytical or empirical infiltration approaches like the Green and Ampt equation.

  6. A Combined Random Forests and Active Contour Model Approach for Fully Automatic Segmentation of the Left Atrium in Volumetric MRI

    Directory of Open Access Journals (Sweden)

    Chao Ma

    2017-01-01

    Full Text Available Segmentation of the left atrium (LA from cardiac magnetic resonance imaging (MRI datasets is of great importance for image guided atrial fibrillation ablation, LA fibrosis quantification, and cardiac biophysical modelling. However, automated LA segmentation from cardiac MRI is challenging due to limited image resolution, considerable variability in anatomical structures across subjects, and dynamic motion of the heart. In this work, we propose a combined random forests (RFs and active contour model (ACM approach for fully automatic segmentation of the LA from cardiac volumetric MRI. Specifically, we employ the RFs within an autocontext scheme to effectively integrate contextual and appearance information from multisource images together for LA shape inferring. The inferred shape is then incorporated into a volume-scalable ACM for further improving the segmentation accuracy. We validated the proposed method on the cardiac volumetric MRI datasets from the STACOM 2013 and HVSMR 2016 databases and showed that it outperforms other latest automated LA segmentation methods. Validation metrics, average Dice coefficient (DC and average surface-to-surface distance (S2S, were computed as 0.9227±0.0598 and 1.14±1.205 mm, versus those of 0.6222–0.878 and 1.34–8.72 mm, obtained by other methods, respectively.

  7. A Combined Random Forests and Active Contour Model Approach for Fully Automatic Segmentation of the Left Atrium in Volumetric MRI

    Science.gov (United States)

    Luo, Gongning

    2017-01-01

    Segmentation of the left atrium (LA) from cardiac magnetic resonance imaging (MRI) datasets is of great importance for image guided atrial fibrillation ablation, LA fibrosis quantification, and cardiac biophysical modelling. However, automated LA segmentation from cardiac MRI is challenging due to limited image resolution, considerable variability in anatomical structures across subjects, and dynamic motion of the heart. In this work, we propose a combined random forests (RFs) and active contour model (ACM) approach for fully automatic segmentation of the LA from cardiac volumetric MRI. Specifically, we employ the RFs within an autocontext scheme to effectively integrate contextual and appearance information from multisource images together for LA shape inferring. The inferred shape is then incorporated into a volume-scalable ACM for further improving the segmentation accuracy. We validated the proposed method on the cardiac volumetric MRI datasets from the STACOM 2013 and HVSMR 2016 databases and showed that it outperforms other latest automated LA segmentation methods. Validation metrics, average Dice coefficient (DC) and average surface-to-surface distance (S2S), were computed as 0.9227 ± 0.0598 and 1.14 ± 1.205 mm, versus those of 0.6222–0.878 and 1.34–8.72 mm, obtained by other methods, respectively. PMID:28316992

  8. A fully coupled bolus-esophageal-gastric model for esophageal emptying based on the immersed boundary method

    Science.gov (United States)

    Kou, Wenjun; Pandolfino, John E.; Kahrilas, Peter J.; Patankar, Neelesh A.

    2016-11-01

    In this work, we develop a fully coupled bolus-esophageal-gastric model to study esophageal emptying based on the immersed boundary method. The model includes an esophageal segment, an ellipsoid-shaped stomach, and a bolus. It can easily handle the passive and active function of the lower esophageal sphincter (LES). Two groups of case studies are presented. The first group is about the influence from tissue anisotropy. Simulation shows that the weaker (or more compliant) part suffers from a higher wall shear stress and higher pressure load when the bolus is filled in and emptied from the LES segment. This implies a degradation cycle in which a weaker tissue becomes much weaker due to an increased load, a possible pathway to the esophageal lower diverticulum. The second group is about bulge formation resulting from asymmetric anatomy and a compliant LES. In particular, we find a right bulge tends to develop for a compliant LES. The bulge is most pronounced with a highest stiffness of the gastric wall. This implies that the competition between the LES stiffness and gastric wall stiffness might be another factor related to the esophageal lower diverticulum. The support of Grant R01 DK56033 and R01 DK079902 from NIH is gratefully acknowledged.

  9. The effect of choosing three different C factor formulae derived from NDVI on a fully raster-based erosion modelling

    Science.gov (United States)

    Sulistyo, Bambang

    2016-11-01

    The research was aimed at studying the efect of choosing three different C factor formulae derived from NDVI on a fully raster-based erosion modelling of The USLE using remote sensing data and GIS technique. Methods applied was by analysing all factors affecting erosion such that all data were in the form of raster. Those data were R, K, LS, C and P factors. Monthly R factor was evaluated based on formula developed by Abdurachman. K factor was determined using modified formula used by Ministry of Forestry based on soil samples taken in the field. LS factor was derived from Digital Elevation Model. Three C factors used were all derived from NDVI and developed by Suriyaprasit (non-linear) and by Sulistyo (linear and non-linear). P factor was derived from the combination between slope data and landcover classification interpreted from Landsat 7 ETM+. Another analysis was the creation of map of Bulk Density used to convert erosion unit. To know the model accuracy, model validation was done by applying statistical analysis and by comparing Emodel with Eactual. A threshold value of ≥ 0.80 or ≥ 80% was chosen to justify. The research result showed that all Emodel using three formulae of C factors have coeeficient of correlation value of > 0.8. The results of analysis of variance showed that there was significantly difference between Emodel and Eactual when using C factor formula developed by Suriyaprasit and Sulistyo (non-linear). Among the three formulae, only Emodel using C factor formula developed by Sulistyo (linear) reached the accuracy of 81.13% while the other only 56.02% as developed by Sulistyo (nonlinear) and 4.70% as developed by Suriyaprasit, respectively.

  10. Void Coalescence Processes Quantified Through Atomistic and Multiscale Simulation

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Heterogeneous Atomistic-Continuum Methods for Dense Fluid Systems

    Science.gov (United States)

    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.

  12. Evaluation of plan quality assurance models for prostate cancer patients based on fully automatically generated Pareto-optimal treatment plans

    Science.gov (United States)

    Wang, Yibing; Breedveld, Sebastiaan; Heijmen, Ben; Petit, Steven F.

    2016-06-01

    IMRT planning with commercial Treatment Planning Systems (TPSs) is a trial-and-error process. Consequently, the quality of treatment plans may not be consistent among patients, planners and institutions. Recently, different plan quality assurance (QA) models have been proposed, that could flag and guide improvement of suboptimal treatment plans. However, the performance of these models was validated using plans that were created using the conventional trail-and-error treatment planning process. Consequently, it is challenging to assess and compare quantitatively the accuracy of different treatment planning QA models. Therefore, we created a golden standard dataset of consistently planned Pareto-optimal IMRT plans for 115 prostate patients. Next, the dataset was used to assess the performance of a treatment planning QA model that uses the overlap volume histogram (OVH). 115 prostate IMRT plans were fully automatically planned using our in-house developed TPS Erasmus-iCycle. An existing OVH model was trained on the plans of 58 of the patients. Next it was applied to predict DVHs of the rectum, bladder and anus of the remaining 57 patients. The predictions were compared with the achieved values of the golden standard plans for the rectum D mean, V 65, and V 75, and D mean of the anus and the bladder. For the rectum, the prediction errors (predicted-achieved) were only  -0.2  ±  0.9 Gy (mean  ±  1 SD) for D mean,-1.0  ±  1.6% for V 65, and  -0.4  ±  1.1% for V 75. For D mean of the anus and the bladder, the prediction error was 0.1  ±  1.6 Gy and 4.8  ±  4.1 Gy, respectively. Increasing the training cohort to 114 patients only led to minor improvements. A dataset of consistently planned Pareto-optimal prostate IMRT plans was generated. This dataset can be used to train new, and validate and compare existing treatment planning QA models, and has been made publicly available. The OVH model was highly accurate

  13. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

    , 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......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...

  14. Surface Potential and Threshold Voltage Model of Fully Depleted Narrow Channel SOI MOSFET Using Analytical Solution of 3D Poisson’s Equation

    Directory of Open Access Journals (Sweden)

    Prashant Mani

    2015-06-01

    Full Text Available The present paper is about the modeling of surface potential and threshold voltage of Fully Depleted Silicon on Insulator MOSFET. The surface potential is calculated by solving the 3D Poisson’s equation analytically. The appropriate boundary conditions are used in calculations. The effect of narrow channel width and short channel length for suppression of SCE is analyzed. The narrow channel width effect in the threshold voltage is analyzed for thin film Fully Depleted SOI MOSFET.

  15. Atomistic simulation of laser ablation of gold : Effect of pressure relaxation

    NARCIS (Netherlands)

    Norman, G. E.; Starikov, S. V.; Stegailov, V. V.

    2012-01-01

    The process of ablation of a gold target by femto- and picosecond laser radiation pulses has been studied by numerical simulations using an atomistic model with allowance for the electron subsystem and the dependence of the ion-ion interaction potential on the electron temperature. Using this potent

  16. Electron and phonon transport in silicon nanowires: Atomistic approach to thermoelectric properties

    DEFF Research Database (Denmark)

    Markussen, Troels; Jauho, Antti-Pekka; Brandbyge, Mads

    2009-01-01

    We compute both electron and phonon transmissions in thin disordered silicon nanowires (SiNWs). Our atomistic approach is based on tight-binding and empirical potential descriptions of the electronic and phononic systems, respectively. Surface disorder is modeled by introducing surface silicon va...

  17. Climate and Habitability of Kepler 452b Simulated with a Fully Coupled Atmosphere–Ocean General Circulation Model

    Science.gov (United States)

    Hu, Yongyun; Wang, Yuwei; Liu, Yonggang; Yang, Jun

    2017-01-01

    The discovery of Kepler 452b is a milestone in searching for habitable exoplanets. While it has been suggested that Kepler 452b is the first Earth-like exoplanet discovered in the habitable zone of a Sun-like star, its climate states and habitability require quantitative studies. Here, we first use a three-dimensional fully coupled atmosphere–ocean climate model to study the climate and habitability of an exoplanet around a Sun-like star. Our simulations show that Kepler 452b is habitable if CO2 concentrations in its atmosphere are comparable or lower than that in the present-day Earth atmosphere. However, our simulations also suggest that Kepler 452b can become too hot to be habitable if there is the lack of silicate weathering to limit CO2 concentrations in the atmosphere. We also address whether Kepler 452b could retain its water inventory after 6.0 billion years of lifetime. These results in the present Letter will provide insights about climate and habitability for other undiscovered exoplanets similar to Kepler 452b, which may be observable by future observational missions.

  18. Influence of muscle activation and mucosal material property on esophageal transport: study based on a fully-resolved computational model

    Science.gov (United States)

    Kou, Wenjun; Pandolfino, John; Kahrilas, Peter; Patankar, Neelesh

    2014-11-01

    Esophageal transport involves interactions between food (bolus), the esophageal walls (composed of mucosal, circular muscle (CM) and longitudinal muscle (LM) layers), and neurally coordinated muscle activation including CM contraction and LM shortening. Due to the complexity of these interactions, few studies have been conducted on the mechanical role of the mucosal layer in esophageal transport. Also poorly understood are the collaborative roles of CM contraction and LM shortening and the influence of their synchronization. Here, based on a fully-resolved computational model that we developed, we investigated the individual roles of CM contraction and LM shortening, compared bolus transport with various levels of discoordination between CM and LM activation, and studied the role of the mucosa and how its stiffening influenced transport. These preliminary findings should help understand the synergy between LM, CM, and the mucosal layer in facilitating bolus transport, thereby providing insight into related physiology and pathophysiology. The support of Grant R01 DK56033 and R01 DK079902 from NIH is gratefully acknowledged.

  19. Fully aligned academic health centers: a model for 21st-century job creation and sustainable economic growth.

    Science.gov (United States)

    Reece, E Albert; Chrencik, Robert A; Miller, Edward D

    2012-07-01

    Alignment is the degree to which component parts of academic health centers (AHCs) work cohesively. Full alignment allows AHCs to act quickly and cohesively toward common goals and to take advantage of opportunities that present themselves, particularly where collaboration is essential. Maryland's two major AHCs-University of Maryland Medicine (UMM) and Johns Hopkins Medicine (JHM)-have experienced periods of significant misalignment during each of their histories. Their most recent periods of misalignment caused significant negative economic and academic impacts. However, the process of realigning their clinical and research missions has not only given them a renewed economic vigor but has also paid significant dividends for the state of Maryland, helping it weather the current recession much better than other regions of the country. The two AHCs' continued economic success during the recession has led Maryland lawmakers to increasingly seek out their expertise in attempts to stimulate economic development. Indeed, UMM, JHM, and other fully aligned AHCs have shown that they can be powerful economic engines and offer a model of job growth and economic development in the 21st century.

  20. An explicitly solvated full atomistic model of the cardiac thin filament and application on the calcium binding affinity effects from familial hypertrophic cardiomyopathy linked mutations

    Science.gov (United States)

    Williams, Michael; Schwartz, Steven

    2015-03-01

    The previous version of our cardiac thin filament (CTF) model consisted of the troponin complex (cTn), two coiled-coil dimers of tropomyosin (Tm), and 29 actin units. We now present the newest revision of the model to include explicit solvation. The model was developed to continue our study of genetic mutations in the CTF proteins which are linked to familial hypertrophic cardiomyopathies. Binding of calcium to the cTnC subunit causes subtle conformational changes to propagate through the cTnC to the cTnI subunit which then detaches from actin. Conformational changes propagate through to the cTnT subunit, which allows Tm to move into the open position along actin, leading to muscle contraction. Calcium disassociation allows for the reverse to occur, which results in muscle relaxation. The inclusion of explicit TIP3 water solvation allows for the model to get better individual local solvent to protein interactions; which are important when observing the N-lobe calcium binding pocket of the cTnC. We are able to compare in silica and in vitro experimental results to better understand the physiological effects from mutants, such as the R92L/W and F110V/I of the cTnT, on the calcium binding affinity compared to the wild type.

  1. Modeling, simulation, and fabrication of a fully integrated, acid-stable, scalable solar-driven water-splitting system.

    Science.gov (United States)

    Walczak, Karl; Chen, Yikai; Karp, Christoph; Beeman, Jeffrey W; Shaner, Matthew; Spurgeon, Joshua; Sharp, Ian D; Amashukeli, Xenia; West, William; Jin, Jian; Lewis, Nathan S; Xiang, Chengxiang

    2015-02-01

    A fully integrated solar-driven water-splitting system comprised of WO3 /FTO/p(+) n Si as the photoanode, Pt/TiO2 /Ti/n(+) p Si as the photocathode, and Nafion as the membrane separator, was simulated, assembled, operated in 1.0 M HClO4 , and evaluated for performance and safety characteristics under dual side illumination. A multi-physics model that accounted for the performance of the photoabsorbers and electrocatalysts, ion transport in the solution electrolyte, and gaseous product crossover was first used to define the optimal geometric design space for the system. The photoelectrodes and the membrane separators were then interconnected in a louvered design system configuration, for which the light-absorbing area and the solution-transport pathways were simultaneously optimized. The performance of the photocathode and the photoanode were separately evaluated in a traditional three-electrode photoelectrochemical cell configuration. The photocathode and photoanode were then assembled back-to-back in a tandem configuration to provide sufficient photovoltage to sustain solar-driven unassisted water-splitting. The current-voltage characteristics of the photoelectrodes showed that the low photocurrent density of the photoanode limited the overall solar-to-hydrogen (STH) conversion efficiency due to the large band gap of WO3 . A hydrogen-production rate of 0.17 mL hr(-1) and a STH conversion efficiency of 0.24 % was observed in a full cell configuration for >20 h with minimal product crossover in the fully operational, intrinsically safe, solar-driven water-splitting system. The solar-to-hydrogen conversion efficiency, ηSTH , calculated using the multiphysics numerical simulation was in excellent agreement with the experimental behavior of the system. The value of ηSTH was entirely limited by the performance of the photoelectrochemical assemblies employed in this study. The louvered design provides a robust platform for implementation of various types of

  2. A fully integrated Earth System Model: focus on dynamical coupling of climatic and cryospheric model sub-systems

    Science.gov (United States)

    Morozova, Polina; Volodin, Evgeny; Rybak, Oleg; Huybrechts, Philippe; Korneva, Irina; Kaminskaia, Mariia

    2017-04-01

    Earth system models (ESMs) have been widely used in the recent years for complex studies of the climate system of the planet in the context of interactions between the atmosphere, oceans, ice sheets and the biosphere. Incorporation of the Earth syb-systems with very different spatial and temporal scales and response times into one model is really a challenging task. In particular, coupling of an AO GCM and ice sheet models of Greenland and Antarctic ice sheets (GrIS and AIS) requires application of special downscaling procedures. Within the frameworks of our research study, we implemented several coupling strategies. The choice of a strategy is dictated mostly by two factors - by the purpose of the research and by spatial resolution of an AO GCM. Several versions of the latter (called INMCM) were developed in the Institute of Numerical Mathematics (Moscow, Russia). For instance, the version aimed primarily for the relatively long numerical experiments (for e.g. palaeostudies) has spatial resolution of 5°×4°, 21 vertical layers in the atmospheric block, 2.5°×2°, 33 vertical layers in the oceanic block. To provide proper data exchange between the INMCM and GrIS and AIS models (spatial resolution 20×20 km), we employ rather simple buffer (sub-) models, describing regional heat and moisture diffusion. Applying buffer models enables to avoid systematic shifts in INMCM-generated precipitation fields and to much more realistically describe influence orographically driven precipitation (in Greenland) and elevation-temperature dependence. Novel versions of the INMCM with the spatial resolution of 2,5°×2° and higher generate much more realistic climatic fields, therefore the coupling procedure can be simplified to just averaging, resampling and remapping data from the AO GCM global domain to regional domains enclosing ice sheets. Increase in spatial resolution inevitably causes additional computational cost and reduces the area of the ESM application to

  3. Atomistic modeling of peptide adsorption on rutile (100) in the presence of water and of contamination by low molecular weight alcohols.

    Science.gov (United States)

    Friedrichs, Wenke; Langel, Walter

    2014-09-01

    Previous models for the interface between titanium implants and biosystems take into account the oxide passivation layer and the hydroxylation, but omit the hydrocarbon contamination on air-exposed samples. The authors develop a consistent model for the contamination of the rutile (100) surface by small alcohols, which are known to be present in ambient atmosphere, and use this approach in molecular dynamics calculations. Contact angle evaluation reveals that hydrophobic surfaces can be generated. During molecular dynamics simulations with three peptides (RPRGFGMSRERQ, WFCLLGCDAGCW, and RKLPDA), polar side chains penetrate the hydrocarbons and become immobilized on the titanium dioxide. In the carbon layer, the peptide recognizes a hydrophobic environment, which was not present on the clean surface, and the authors attribute changes in the secondary structure in one case to this interaction. The authors further include the popular Matsui-Akaogi approach [M. Matsui and M. Akaogi, Mol. Simul. 6, 239 (1991)] into the frame of the AMBER force field and quote van der Waals parameters for fitting the original Buckingham part. With the new potential, the authors evaluated lattice parameters, thermal fluctuation, and bulk modulus. Translational diffusion coefficients and dipole autocorrelation functions of water on the surface are discussed in relation to surface properties, and it is shown that the water layers are more rigid than on earlier titanium dioxide models, and that contacts between peptide and surface are less direct.

  4. Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations.

    Science.gov (United States)

    Dobrev, Plamen; Donnini, Serena; Groenhof, Gerrit; Grubmüller, Helmut

    2017-01-10

    Correct protonation of titratable groups in biomolecules is crucial for their accurate description by molecular dynamics simulations. In the context of constant pH simulations, an additional protonation degree of freedom is introduced for each titratable site, allowing the protonation state to change dynamically with changing structure or electrostatics. Here, we extend previous approaches for an accurate description of chemically coupled titrating sites. A second reaction coordinate is used to switch between two tautomeric states of an amino acid with chemically coupled titratable sites, such as aspartate (Asp), glutamate (Glu), and histidine (His). To this aim, we test a scheme involving three protonation states. To facilitate charge neutrality as required for periodic boundary conditions and Particle Mesh Ewald (PME) electrostatics, titration of each respective amino acid is coupled to a "water" molecule that is charged in the opposite direction. Additionally, a force field modification for Amber99sb is introduced and tested for the description of carboxyl group protonation. Our three states model is tested by titration simulations of Asp, Glu, and His, yielding a good agreement, reproducing the correct geometry of the groups in their different protonation forms. We further show that the ion concentration change due to the neutralizing "water" molecules does not significantly affect the protonation free energies of the titratable groups, suggesting that the three states model provides a good description of biomolecular dynamics at constant pH.

  5. Atomistic modelling study of lanthanide incorporation in the crystal lattice of an apatite; Etude par modelisation atomistique de l'incorporation de lanthanides dans le reseau cristallin d'une apatite phosphocalcique

    Energy Technology Data Exchange (ETDEWEB)

    Louis-Achille, V

    1999-07-01

    Studies of natural and synthetic apatites allow to propose such crystals as matrix for nuclear waste storage. The neodymium substituted britholite, Ca{sub 9}Nd(PO{sub 4}){sub 5}(SiO{sub 4})F{sub 2}. is a model for the trivalent actinide storage Neodymium can be substituted in two types of sites. The aim of this thesis is to compare the chemical nature of this two sites in fluoro-apatite Ca{sub 9}(PO{sub 4}){sub 6}F{sub 2} and then in britholite, using ab initio atomistic modeling. Two approaches are used: one considers the infinite crystals and the second considers clusters. The calculations of the electronic structure for both were performed using Kohn and Sham density functional theory in the local approximation. For solids, pseudopotentials were used, and wave functions are expanded in plane waves. For clusters, a frozen core approximation was used, and the wave functions are expanded in a linear combination of Slater type atomic orbitals. The pseudopotential is semi-relativistic for neodymium, and the Hamiltonian is scalar relativistic for the clusters. The validation of the solid approach is performed using two test cases: YPO{sub 4} and ScPO{sub 4}. Two numerical tools were developed to compute electronic deformation density map, and calculate partial density of stases. A full optimisation of the lattice parameters with a relaxation of the atomic coordinates leads to correct structural and thermodynamic properties for the fluoro-apatite, compared to experience. The electronic deformation density maps do not show any significant differences. between the two calcium sites. but Mulliken analysis on the solid and on the clusters point out the more ionic behavior of the calcium in site 2. A neodymium substituted britholite is then studied. Neodymium location only induces local modifications in; the crystalline structure and few changes in the formation enthalpy. The electronic study points out an increase of the covalent character the bonding involving neodymium

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

    Science.gov (United States)

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

    2016-09-01

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

  7. Amplification of global warming through pH dependence of DMS production simulated with a fully coupled Earth system model

    Science.gov (United States)

    Schwinger, Jörg; Tjiputra, Jerry; Goris, Nadine; Six, Katharina D.; Kirkevåg, Alf; Seland, Øyvind; Heinze, Christoph; Ilyina, Tatiana

    2017-08-01

    We estimate the additional transient surface warming ΔTs caused by a potential reduction of marine dimethyl sulfide (DMS) production due to ocean acidification under the high-emission scenario RCP8.5 until the year 2200. Since we use a fully coupled Earth system model, our results include a range of feedbacks, such as the response of marine DMS production to the additional changes in temperature and sea ice cover. Our results are broadly consistent with the findings of a previous study that employed an offline model set-up. Assuming a medium (strong) sensitivity of DMS production to pH, we find an additional transient global warming of 0.30 K (0.47 K) towards the end of the 22nd century when DMS emissions are reduced by 7.3 Tg S yr-1 or 31 % (11.5 Tg S yr-1 or 48 %). The main mechanism behind the additional warming is a reduction of cloud albedo, but a change in shortwave radiative fluxes under clear-sky conditions due to reduced sulfate aerosol load also contributes significantly. We find an approximately linear relationship between reduction of DMS emissions and changes in top of the atmosphere radiative fluxes as well as changes in surface temperature for the range of DMS emissions considered here. For example, global average Ts changes by -0. 041 K per 1 Tg S yr-1 change in sea-air DMS fluxes. The additional warming in our model has a pronounced asymmetry between northern and southern high latitudes. It is largest over the Antarctic continent, where the additional temperature increase of 0.56 K (0.89 K) is almost twice the global average. We find that feedbacks are small on the global scale due to opposing regional contributions. The most pronounced feedback is found for the Southern Ocean, where we estimate that the additional climate change enhances sea-air DMS fluxes by about 9 % (15 %), which counteracts the reduction due to ocean acidification.

  8. Amplification of global warming through pH dependence of DMS production simulated with a fully coupled Earth system model

    Directory of Open Access Journals (Sweden)

    J. Schwinger

    2017-08-01

    Full Text Available We estimate the additional transient surface warming ΔTs caused by a potential reduction of marine dimethyl sulfide (DMS production due to ocean acidification under the high-emission scenario RCP8.5 until the year 2200. Since we use a fully coupled Earth system model, our results include a range of feedbacks, such as the response of marine DMS production to the additional changes in temperature and sea ice cover. Our results are broadly consistent with the findings of a previous study that employed an offline model set-up. Assuming a medium (strong sensitivity of DMS production to pH, we find an additional transient global warming of 0.30 K (0.47 K towards the end of the 22nd century when DMS emissions are reduced by 7.3 Tg S yr−1 or 31 % (11.5 Tg S yr−1 or 48 %. The main mechanism behind the additional warming is a reduction of cloud albedo, but a change in shortwave radiative fluxes under clear-sky conditions due to reduced sulfate aerosol load also contributes significantly. We find an approximately linear relationship between reduction of DMS emissions and changes in top of the atmosphere radiative fluxes as well as changes in surface temperature for the range of DMS emissions considered here. For example, global average Ts changes by −0. 041 K per 1 Tg S yr−1 change in sea–air DMS fluxes. The additional warming in our model has a pronounced asymmetry between northern and southern high latitudes. It is largest over the Antarctic continent, where the additional temperature increase of 0.56 K (0.89 K is almost twice the global average. We find that feedbacks are small on the global scale due to opposing regional contributions. The most pronounced feedback is found for the Southern Ocean, where we estimate that the additional climate change enhances sea–air DMS fluxes by about 9 % (15 %, which counteracts the reduction due to ocean acidification.

  9. Fully integrated surface-subsurface flow modelling of groundwater-lake interaction in an esker aquifer: Model verification with stable isotopes and airborne thermal imaging

    Science.gov (United States)

    Ala-aho, Pertti; Rossi, Pekka M.; Isokangas, Elina; Kløve, Bjørn

    2015-03-01

    Water resources management is moving towards integration, where groundwater (GW), surface water (SW) and related aquatic ecosystems are considered one management unit. Because of this paradigm shift, more information and new tools are needed to understand the ecologically relevant fluxes (water, heat, solutes) at the GW-SW interface. This study estimated the magnitude, temporal variability and spatial distribution of water fluxes at the GW-SW interface using a fully integrated hydrological modelling code (HydroGeoSphere). The model domain comprised a hydrologically complex esker aquifer in Northern Finland with interconnected lakes, streams and wetlands. The model was calibrated in steady state for soil hydraulic conductivity and anisotropy and it reproduced the hydraulic head and stream baseflow distribution throughout the aquifer in both transient and steady state modes. In a novel analysis, model outputs were compared with the locations and magnitude of GW discharge to lakes estimated using field techniques. Spatial occurrence of GW-lake interaction was interpreted from airborne thermal infrared imaging. The observed GW inflow locations coincided well with model nodes showing positive exchange flux between surface and subsurface domains. Order of magnitude of simulated GW inflow to lakes showed good agreement with flux values calculated with a stable water isotope technique. Finally, time series of GW inflow, extracted as model output, showed moderate annual variability and demonstrated different interannual inflow changes in seepage and drainage lakes of the aquifer. Overall, this study demonstrated the ability of a fully integrated numerical model to reproduce observed GW-SW exchange processes in a complex unconfined aquifer system. The model-based estimates obtained for GW influx magnitude and spatial distribution, along with information on GW quality can be used to estimate ecologically relevant fluxes in future water resources management.

  10. Analysis of Surface Leaching Processes in Vitrified High-Level Nuclear Wastes Using In-Situ Raman Imaging and Atomistic Modeling - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Joseph H.

    2001-04-24

    The in situ analysis of surface conditions of vitrified nuclear wastes can provide an important check of the burial status of radioactive objects without risk of radiation exposure. Raman spectroscopy was initially chosen as the most promising method for testing the surface conditions of glasses undergoing chemical corrosion, and was used extensively during the first year. However, it was determined that infrared reflection spectroscopy was better suited to this particular need and was used for the remaining two years to investigate the surface corrosion behavior of model silicate glasses for extension to nuclear waste glasses. The developed methodology is consistent with the known theory of optical propagation of dielectric media and uses the Kramers-Kronig formalism. The results show that it is possible to study the corrosion of glass by analyzing the glass surface using reflection fast Fourier infrared measurements and the newly developed ''dispersion analysis method.'' The data show how this analysis can be used to monitor the corrosion behavior of vitrified waste glasses over extended periods of storage.

  11. Rigidity and soft percolation in the glass transition of an atomistic model of ionic liquid, 1-ethyl-3-methyl imidazolium nitrate, from molecular dynamics simulations—Existence of infinite overlapping networks in a fragile ionic liquid

    Energy Technology Data Exchange (ETDEWEB)

    Habasaki, Junko, E-mail: habasaki.j.aa@m.titech.ac.jp [Department of Innovative and Engineered Materials, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8502 (Japan); Ngai, K. L. [CNR-IPCF Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa (Italy)

    2015-04-28

    The typical ionic liquid, 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO{sub 3}), was examined by molecular dynamics simulations of an all-atomistic model to show the characteristics of networks of cages and/or bonds in the course of vitrification of this fragile glass-former. The system shows changes of dynamics at two characteristic temperatures, T{sub B} (or T{sub c}) and the glass transition temperature T{sub g}, found in other fragile glass forming liquids [K. L. Ngai and J. Habasaki, J. Chem. Phys. 141, 114502 (2014)]. On decreasing temperature, the number of neighboring cation-anion pairs, N{sub B}, within the first minimum of the pair correlation function, g(r){sub min}, increases. On crossing T{sub B} (>T{sub g}), the system volume and diffusion coefficient both show changes in temperature dependence, and as usual at T{sub g}. The glass transition temperature, T{sub g}, is characterized by the saturation of the total number of “bonds,” N{sub B} and the corresponding decrease in degree of freedom, F = [(3N − 6) − N{sub B}], of the system consisting of N particles. Similar behavior holds for the other ion-ion pairs. Therefore, as an alternative, the dynamics of glass transition can be interpreted conceptually by rigidity percolation. Before saturation occurring at T{sub g}, the number of bonds shows a remarkable change at around T{sub B}. This temperature is associated with the disappearance of the loosely packed coordination polyhedra of anions around cation (or vice versa), related to the loss of geometrical freedom of the polyhedra, f{sub g}, of each coordination polyhedron, which can be defined by f{sub g} = [(3N{sub V} − 6) − N{sub b}]. Here, 3N{sub v} is the degree of freedom of N{sub V} vertices of the polyhedron, and N{sub b} is number of fictive bonds. The packing of polyhedra is characterized by the soft percolation of cages, which allows further changes with decreasing temperature. The power spectrum of displacement of the central ion

  12. On Atomistic Models for Molecular Oxygen

    DEFF Research Database (Denmark)

    Javanainen, Matti; Vattulainen, Ilpo; Monticelli, Luca

    2017-01-01

    Molecular oxygen (O2) is key to all life on earth, as it is constantly cycled via photosynthesis and cellular respiration. Substantial scientific effort has been devoted to understanding every part of this cycle. Classical molecular dynamics (MD) simulations have been used to study some of the key...... processes involved in cellular respiration: O2 permeation through alveolar monolayers and cellular membranes, its binding to hemoglobin during transport in the bloodstream, as well as its transport along optimal pathways toward its reduction sites in proteins. Moreover, MD simulations can help interpret...

  13. Fully automated calculation of image-derived input function in simultaneous PET/MRI in a sheep model

    Energy Technology Data Exchange (ETDEWEB)

    Jochimsen, Thies H.; Zeisig, Vilia [Department of Nuclear Medicine, Leipzig University Hospital, Liebigstr. 18, Leipzig (Germany); Schulz, Jessica [Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstr. 1a, Leipzig, D-04103 (Germany); Werner, Peter; Patt, Marianne; Patt, Jörg [Department of Nuclear Medicine, Leipzig University Hospital, Liebigstr. 18, Leipzig (Germany); Dreyer, Antje Y. [Fraunhofer Institute of Cell Therapy and Immunology, Perlickstr. 1, Leipzig, D-04103 (Germany); Translational Centre for Regenerative Medicine, University Leipzig, Philipp-Rosenthal-Str. 55, Leipzig, D-04103 (Germany); Boltze, Johannes [Fraunhofer Institute of Cell Therapy and Immunology, Perlickstr. 1, Leipzig, D-04103 (Germany); Translational Centre for Regenerative Medicine, University Leipzig, Philipp-Rosenthal-Str. 55, Leipzig, D-04103 (Germany); Fraunhofer Research Institution of Marine Biotechnology and Institute for Medical and Marine Biotechnology, University of Lübeck, Lübeck (Germany); Barthel, Henryk; Sabri, Osama; Sattler, Bernhard [Department of Nuclear Medicine, Leipzig University Hospital, Liebigstr. 18, Leipzig (Germany)

    2016-02-13

    Obtaining the arterial input function (AIF) from image data in dynamic positron emission tomography (PET) examinations is a non-invasive alternative to arterial blood sampling. In simultaneous PET/magnetic resonance imaging (PET/MRI), high-resolution MRI angiographies can be used to define major arteries for correction of partial-volume effects (PVE) and point spread function (PSF) response in the PET data. The present study describes a fully automated method to obtain the image-derived input function (IDIF) in PET/MRI. Results are compared to those obtained by arterial blood sampling. To segment the trunk of the major arteries in the neck, a high-resolution time-of-flight MRI angiography was postprocessed by a vessel-enhancement filter based on the inertia tensor. Together with the measured PSF of the PET subsystem, the arterial mask was used for geometrical deconvolution, yielding the time-resolved activity concentration averaged over a major artery. The method was compared to manual arterial blood sampling at the hind leg of 21 sheep (animal stroke model) during measurement of blood flow with O15-water. Absolute quantification of activity concentration was compared after bolus passage during steady state, i.e., between 2.5- and 5-min post injection. Cerebral blood flow (CBF) values from blood sampling and IDIF were also compared. The cross-calibration factor obtained by comparing activity concentrations in blood samples and IDIF during steady state is 0.98 ± 0.10. In all examinations, the IDIF provided a much earlier and sharper bolus peak than in the time course of activity concentration obtained by arterial blood sampling. CBF using the IDIF was 22 % higher than CBF obtained by using the AIF yielded by blood sampling. The small deviation between arterial blood sampling and IDIF during steady state indicates that correction of PVE and PSF is possible with the method presented. The differences in bolus dynamics and, hence, CBF values can be explained by the

  14. Atomistic deformation mechanisms in twinned copper nanospheres.

    Science.gov (United States)

    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.

  15. Atomistic Mechanisms of Fatigue in Nanocrystalline Metals

    Science.gov (United States)

    Farkas, D.; Willemann, M.; Hyde, B.

    2005-04-01

    We investigate the mechanisms of fatigue behavior in nanocrystalline metals at the atomic scale using empirical force laws and molecular level simulations. A combination of molecular statics and molecular dynamics was used to deal with the time scale limitations of molecular dynamics. We show that the main atomistic mechanism of fatigue crack propagation in these materials is the formation of nanovoids ahead of the main crack. The results obtained for crack advance as a function of stress intensity amplitude are consistent with experimental studies and a Paris law exponent of about 2.

  16. Study of dispersive and nonlinear effects of coastal wave dynamics with a fully nonlinear potential flow model

    Science.gov (United States)

    Benoit, Michel; Yates, Marissa L.; Raoult, Cécile

    2017-04-01

    Efficient and accurate numerical models simulating wave propagation are required for a variety of engineering projects including the evaluation of coastal risks, the design of protective coastal structures, and the estimation of the potential for marine renewable energy devices. Nonlinear and dispersive effects are particularly significant in the coastal zone where waves interact with the bottom, the shoreline, and coastal structures. The main challenge in developing a numerical models is finding a compromise between computational efficiency and the required accuracy of the simulated wave field. Here, a potential approach is selected and the (fully nonlinear) water wave problem is formulated using the Euler-Zakharov equations (Zakharov, 1968) describing the temporal evolution of the free surface elevation and velocity potential. The proposed model (Yates and Benoit, 2015) uses a spectral approach in the vertical (i.e. the vertical variation of the potential is approximated by a linear combination of the first NT+1 Chebyshev polynomials, following the work of Tian and Sato (2008)). The Zakharov equations are integrated in time using a fourth-order Runge-Kutta scheme with a constant time step. At each sub-timestep, the Laplace Boundary Value Problem (BVP) is solved to estimate the free surface vertical velocity using the spectral approach, with typical values of NT between 5 to 8 for practical applications. The 1DH version of the code is validated with comparisons to the experimental data set of Becq-Girard et al. (1999), which studied the propagation of irregular waves over a beach profile with a submerged bar. The nonlinear and dispersive capacities of the model are verified with the correct representation of wave-wave interactions, in particular the transfer of energy between different harmonic components during wave propagation (analysis of the transformation of the variance spectrum along the channel). Evolution of wave skewness, asymmetry and kurtosis along the

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

    Directory of Open Access Journals (Sweden)

    Aruna Prakash

    2017-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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

  19. Introduction: Atomistic Nature of Materials

    Science.gov (United States)

    Kaxiras, Efthimios; Yip, Sidney

    Materials are made of atoms. The atomic hypothesis was put forward by the Greek philosopher Demokritos about 25 centuries ago, but was only proven by quantitative arguments in the 19th and 20th centuries, beginning with the work of John Dalton (1766-1844) and through the development of quantum mechanics, the theory that provided a complete and accurate description of the properties of atoms. The very large number of atoms encountered in a typical material (of order ˜1024or more) precludes any meaningful description of its properties based on a complete account of the behavior of each and every atom that comprises it. Special cases, such as perfect crystals, are exceptions where symmetry reduces the number of independent atoms to very few; in such cases, the properties of the solid are indeed describable in terms of the behavior of the few independent atoms and this can be accomplished using quantum mechanical methods. However, this is only an idealized model of actual solids in which perfect order is broken either by thermal disorder or by the presence of defects that play a crucial role in determining the physical properties of the system.

  20. Comparison between a coupled 1D-2D model and a fully 2D model for supercritical flow simulation in crossroads

    KAUST Repository

    Ghostine, Rabih

    2014-12-01

    In open channel networks, flow is usually approximated by the one-dimensional (1D) Saint-Venant equations coupled with an empirical junction model. In this work, a comparison in terms of accuracy and computational cost between a coupled 1D-2D shallow water model and a fully two-dimensional (2D) model is presented. The paper explores the ability of a coupled model to simulate the flow processes during supercritical flows in crossroads. This combination leads to a significant reduction in the computational time, as a 1D approach is used in branches and a 2D approach is employed in selected areas only where detailed flow information is essential. Overall, the numerical results suggest that the coupled model is able to accurately simulate the main flow processes. In particular, hydraulic jumps, recirculation zones, and discharge distribution are reasonably well reproduced and clearly identified. Overall, the proposed model leads to a 30% reduction in run times. © 2014 International Association for Hydro-Environment Engineering and Research.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Strong, Steven E; Eaves, Joel D

    2016-05-19

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

  3. Quantum-based Atomistic Simulation of Transition Metals

    Energy Technology Data Exchange (ETDEWEB)

    Moriarty, J A; Benedict, L X; Glosli, J N; Hood, R Q; Orlikowski, D A; Patel, M V; Soderlind, P; Streitz, F H; Tang, M; Yang, L H

    2005-08-29

    First-principles generalized pseudopotential theory (GPT) provides a fundamental basis for transferable multi-ion interatomic potentials in d-electron transition metals within density-functional quantum mechanics. In mid-period bcc metals, where multi-ion angular forces are important to structural properties, simplified model GPT or MGPT potentials have been developed based on canonical d bands to allow analytic forms and large-scale atomistic simulations. Robust, advanced-generation MGPT potentials have now been obtained for Ta and Mo and successfully applied to a wide range of structural, thermodynamic, defect and mechanical properties at both ambient and extreme conditions of pressure and temperature. Recent algorithm improvements have also led to a more general matrix representation of MGPT beyond canonical bands allowing increased accuracy and extension to f-electron actinide metals, an order of magnitude increase in computational speed, and the current development of temperature-dependent potentials.

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

    Science.gov (United States)

    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

  5. Atomistic Monte Carlo simulation of lipid membranes.

    Science.gov (United States)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-24

    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.

  6. Atomistic simulations of nanoscale electrokinetic transport

    Science.gov (United States)

    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.

  7. Atomistic Monte Carlo Simulation of Lipid Membranes

    Directory of Open Access Journals (Sweden)

    Daniel Wüstner

    2014-01-01

    Full Text Available 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.

  8. How do icebergs affect the Greenland ice sheet under pre-industrial conditions? – A model study with a fully coupled ice sheet–climate model

    Directory of Open Access Journals (Sweden)

    M. Bügelmayer

    2014-01-01

    Full Text Available Icebergs have a potential impact on climate since they release freshwater over a wide spread area and cool the ocean due to the take up of latent heat. Yet, so far, icebergs have never been modelled using an ice sheet model coupled to a global climate model. Thus, in climate models their impact on climate was restricted to the ocean. In this study, we investigate the effect of icebergs on the Northern Hemisphere climate and the Greenland ice sheet itself within a fully coupled ice sheet (GRISLI–Earth system (iLOVECLIM model set-up under pre-industrial climate conditions. This set-up enables us to dynamically compute the calving sites as well as the ice discharge and to close the water cycle between the climate and the cryosphere model components. Further, we analyse the different impact of moving icebergs compared to releasing the ice discharge at the calving sites directly. We performed a suite of sensitivity experiments to investigate the individual role of the different factors presiding at the impact of ice release to the ocean: release of ice discharge as icebergs vs. as freshwater fluxes; freshening and latent heat effects. We find that icebergs enhance the sea ice thickness south and east of Greenland, thereby cooling the atmosphere and decreasing the Greenland ice sheet's height. In contrast, melting the ice discharge locally at the calving sites, causes an increased ice sheet thickness due to enhanced precipitation. Yet, releasing the ice discharge into the ocean at the calving sites while taking up the latent heat homogeneously, results in a similar ice sheet configuration and climate as the icebergs. Therefore, we conclude that in our fully coupled atmosphere–ocean–cryosphere model set-up, the spatial distribution of the take-up of latent heat related to icebergs melting has a bigger impact on the climate than the input of their melt water. Moreover, we find that icebergs affect the ice sheet's geometry even under pre

  9. Modeling of Hydraulic Fracture Propagation at the kISMET Site Using a Fully Coupled 3D Network-Flow and Quasi- Static Discrete Element Model

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jing [Idaho National Lab. (INL), Idaho Falls, ID (United States); Huang, Hai [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mattson, Earl [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wang, Herb F. [Univ. of Wisconsin, Madison, WI (United States); Haimson, Bezalel C. [Univ. of Wisconsin, Madison, WI (United States); Doe, Thomas W. [Golder Associates Inc., Redmond, VA (United States); Oldenburg, Curtis M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Dobson, Patrick F. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2017-02-01

    Aimed at supporting the design of hydraulic fracturing experiments at the kISMET site, ~1500 m below ground in a deep mine, we performed pre-experimental hydraulic fracturing simulations in order to estimate the breakdown pressure, propagation pressure, fracture geometry, and the magnitude of induced seismicity using a newly developed fully coupled three-dimensional (3D) network flow and quasi-static discrete element model (DEM). The quasi-static DEM model, which is constructed by Delaunay tessellation of the rock volume, considers rock fabric heterogeneities by using the “disordered” DEM mesh and adding random perturbations to the stiffness and tensile/shear strengths of individual DEM elements and the elastic beams between them. A conjugate 3D flow network based on the DEM lattice is constructed to calculate the fluid flow in both the fracture and porous matrix. One distinctive advantage of the model is that fracturing is naturally described by the breakage of elastic beams between DEM elements. It is also extremely convenient to introduce mechanical anisotropy into the model by simply assigning orientation-dependent tensile/shear strengths to the elastic beams. In this paper, the 3D hydraulic fracturing model was verified against the analytic solution for a penny-shaped crack model. We applied the model to simulate fracture propagation from a vertical open borehole based on initial estimates of rock mechanical properties and in-situ stress conditions. The breakdown pressure and propagation pressure are directly obtained from the simulation. In addition, the released elastic strain energies of individual fracturing events were calculated and used as a conservative estimate for the magnitudes of the potential induced seismic activities associated with fracturing. The comparisons between model predictions and experimental results are still ongoing.

  10. Role of Ionic Clusters in Dynamics of Ionomer Melts: From Atomistic to Coarse Grained Simulations

    Science.gov (United States)

    Agrawal, Anupriya

    Ionomers, polymers decorated with ionizable groups, have found application in numerous technologies where ionic transport is required. The ionic groups associate into random clusters resulting in substantial effect on structure, dynamics and transport of these materials. The effects of topology, size and dynamics of these aggregates however remain an open question. Here we probe cluster formation correlated with polymer dynamics through a model system of randomly sulfonated polystyrene (SPS) melts with molecular dynamics (MD) simulations over a broad time and length scales ranging from that within the ionic clusters through polymer segmental dynamics to the motion of the entire molecules. The cluster evolution was probed by fully atomistic studies. We find ladder-like aggregates that transform to globule-like with increasing the dielectric constant of media for sodium neutralized SPS. With increasing dielectric constant, the size of the aggregates decrease and their number increases. Concurrently, the mobility of the polymer increases. The counterion radius and valency affect both morphology and dynamics as is evident in the calculated static and dynamic structure factors. It is further manifested in the results of viscosity obtained through non-equilibrium molecular dynamics technique. Finally, to access larger length scales a three bead coarse-grained model to describe sulfonated styrene that we have developed will be discussed in view of the outstanding challenges in ionic polymers. Supported in part by DOE Grant No. DE-SC007908. This work was carried out in collaboration with Dvora Perahia and Gary Grest while I was a postdoc at Clemson University. I gratefully acknowledge both of them for their support and encouragement.

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

    Science.gov (United States)

    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.

  12. REACTIVE TRANSPORT MODELING USING A PARALLEL FULLY-COUPLED SIMULATOR BASED ON PRECONDITIONED JACOBIAN-FREE NEWTON-KRYLOV

    Energy Technology Data Exchange (ETDEWEB)

    Luanjing Guo; Chuan Lu; Hai Huang; Derek R. Gaston

    2012-06-01

    Systems of multicomponent reactive transport in porous media that are large, highly nonlinear, and tightly coupled due to complex nonlinear reactions and strong solution-media interactions are often described by a system of coupled nonlinear partial differential algebraic equations (PDAEs). A preconditioned Jacobian-Free Newton-Krylov (JFNK) solution approach is applied to solve the PDAEs in a fully coupled, fully implicit manner. The advantage of the JFNK method is that it avoids explicitly computing and storing the Jacobian matrix during Newton nonlinear iterations for computational efficiency considerations. This solution approach is also enhanced by physics-based blocking preconditioning and multigrid algorithm for efficient inversion of preconditioners. Based on the solution approach, we have developed a reactive transport simulator named RAT. Numerical results are presented to demonstrate the efficiency and massive scalability of the simulator for reactive transport problems involving strong solution-mineral interactions and fast kinetics. It has been applied to study the highly nonlinearly coupled reactive transport system of a promising in situ environmental remediation that involves urea hydrolysis and calcium carbonate precipitation.

  13. Modeling Bone Surface Morphology: A Fully Quantitative Method for Age-at-Death Estimation Using the Pubic Symphysis.

    Science.gov (United States)

    Slice, Dennis E; Algee-Hewitt, Bridget F B

    2015-07-01

    The pubic symphysis is widely used in age estimation for the adult skeleton. Standard practice requires the visual comparison of surface morphology against criteria representing predefined phases and the estimation of case-specific age from an age range associated with the chosen phase. Known problems of method and observer error necessitate alternative tools to quantify age-related change in pubic morphology. This paper presents an objective, fully quantitative method for estimating age-at-death from the skeleton, which exploits a variance-based score of surface complexity computed from vertices obtained from a scanner sampling the pubic symphysis. For laser scans from 41 modern American male skeletons, this method produces results that are significantly associated with known age-at-death (RMSE = 17.15 years). Chronological age is predicted, therefore, equally well, if not, better, with this robust, objective, and fully quantitative method than with prevailing phase-aging systems. This method contributes to forensic casework by responding to medico-legal expectations for evidence standards.

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

    Science.gov (United States)

    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.

  15. Scalable Atomistic Simulation Algorithms for Materials Research

    Directory of Open Access Journals (Sweden)

    Aiichiro Nakano

    2002-01-01

    Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

  16. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    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......, 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....

  17. Consistent Energy-Based Atomistic/Continuum Coupling for Two-Body Potential: 1D and 2D Case

    CERN Document Server

    Shapeev, Alexander V

    2010-01-01

    This paper concerns the problem of consistent energy-based coupling of atomistic and continuum models of materials, limited to zero-temperature statics of simple crystalline materials. It has been widely recognized that the most practical coupled methods exhibit finite errors on the atomistic/continuum interface (which are often attributed to spurious forces called "ghost forces"). There are only few existing works that propose a coupling which is sufficiently accurate near the interface under certain limitations. In this paper a novel coupling that is free from "ghost forces" is proposed for a two-body interaction potential under the assumptions of either (i) one spatial dimension, or (ii) two spatial dimensions and piecewise affine finite elements for describing the continuum deformation. The computational efficiency of the proposed coupling is demonstrated with numerical experiments. The coupling strategy is based on judiciously defining the contributions of the atomistic bonds to the discrete and the cont...

  18. Influence of the Boundary Condition on the Short-Time Dynamic Behaviour of the Ising-Like Phase Transition in Square-Lattice Fully Frustrated XY Models

    Institute of Scientific and Technical Information of China (English)

    罗孟波; 陈庆虎; 焦正宽

    2002-01-01

    We investigate the influence of the boundary condition on the short-time dynamic behaviour of the Ising-like phase transition in square-lattice fully frustrated (FF) XY models with periodic and fluctuating twist boundary conditions. The transition temperature Tc and the dynamic and static critical exponents z, 2β/v and v are estimated for both cases using short-time dynamic scaling analysis. The results show that both models have the same critical exponents, indicating that the boundary condition has nearly no effect on the short-time dynamic behaviour of the FFXY model.

  19. Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

    Science.gov (United States)

    2017-01-01

    Control over the morphology of the active layer of bulk heterojunction (BHJ) organic solar cells is paramount to achieve high-efficiency devices. However, no method currently available can predict morphologies for a novel donor–acceptor blend. An approach which allows reaching relevant length scales, retaining chemical specificity, and mimicking experimental fabrication conditions, and which is suited for high-throughput schemes has been proven challenging to find. Here, we propose a method to generate atom-resolved morphologies of BHJs which conforms to these requirements. Coarse-grain (CG) molecular dynamics simulations are employed to simulate the large-scale morphological organization during solution-processing. The use of CG models which retain chemical specificity translates into a direct path to the rational design of donor and acceptor compounds which differ only slightly in chemical nature. Finally, the direct retrieval of fully atomistic detail is possible through backmapping, opening the way for improved quantum mechanical calculations addressing the charge separation mechanism. The method is illustrated for the poly(3-hexyl-thiophene) (P3HT)–phenyl-C61-butyric acid methyl ester (PCBM) mixture, and found to predict morphologies in agreement with experimental data. The effect of drying rate, P3HT molecular weight, and thermal annealing are investigated extensively, resulting in trends mimicking experimental findings. The proposed methodology can help reduce the parameter space which has to be explored before obtaining optimal morphologies not only for BHJ solar cells but also for any other solution-processed soft matter device. PMID:28209056

  20. Modeling the atmospheric and terrestrial water and energy cycles in the ScaleX experiment through a fully-coupled atmosphere-hydrology model

    Science.gov (United States)

    Senatore, Alfonso; Benjamin, Fersch; Thomas, Rummler; Caroline, Brosy; Christian, Chwala; Junkermann, Wolfgang; Ingo, Völksch; Harald, Kunstmann

    2016-04-01

    The TERENO preAlpine Observatory, comprising a series of observatory sites along an altitudinal gradient within the Ammer catchment (southern Bavaria, Germany), has been designed as an international research platform, open for participation and integration, and has been provided with comprehensive technical infrastructure to allow joint analyses of water-, energy- and nutrient fluxes. In June and July 2015 the operational monitoring has been complemented by the ScaleX intensive measurement campaign, where additional precipitation and soil moisture measurements, remote sensing measurements of atmospheric wind, humidity and temperature profiles have been performed, complemented by micro-light aircraft- and UAV-based remote sensing for three-dimensional pattern information. The comprehensive observations serve as validation and evaluation basis for compartment-crossing modeling systems. Specifically, the fully two-way dynamically coupled atmosphere-hydrology modeling system WRF-Hydro has been used to investigate the interplay of energy and water cycles at the regional scale and across the compartments atmosphere, stream, vadose zone and groundwater during the ScaleX campaign and to assess the closure of the budgets involved. Here, several high-resolution modeled hydro-meteorological variables, such as precipitation, soil moisture, river discharge and air moisture and temperature along vertical profiles are compared with observations from multiple sources, such as rain gauges and soil moisture networks, rain radars, stream gauges, UAV and a micro-light aircraft. Results achieved contribute to the objective of addressing questions on energy- and water-cycling within the TERENO-Ammer region at a very high scale and degree of integration, and provides hints on how well can observations constrain uncertainties associated with the modeling of atmospheric and terrestrial water and energy balances.

  1. Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

    Science.gov (United States)

    Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

    2017-01-01

    This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

  2. Atomistic simulation of hydrogen dynamics near dislocations in vanadium hydrides

    Energy Technology Data Exchange (ETDEWEB)

    Ogawa, Hiroshi, E-mail: h.ogawa@aist.go.jp

    2015-10-05

    Highlights: • Hydrogen–dislocation interaction was simulated by molecular dynamics method. • Different distribution of H atoms were observed at edge and screw dislocation. • Planner distribution of hydrogen may be caused by partialized edge dislocation. • Hydrogen diffusivity was reduced in both edge and screw dislocation models. • Pipe diffusion was observed for edge dislocation but not for screw dislocation. - Abstract: Kinetics of interstitial hydrogen atoms near dislocation cores were analyzed by atomistic simulation. Classical molecular dynamics method was applied to model structures of edge and screw dislocations in α-phase vanadium hydride. Simulation showed that hydrogen atoms aggregate near dislocation cores. The spatial distribution of hydrogen has a planner shape at edge dislocation due to dislocation partialization, and a cylindrical shape at screw dislocation. Simulated self-diffusion coefficients of hydrogen atoms in dislocation models were a half- to one-order lower than that of dislocation-free model. Arrhenius plot of self-diffusivity showed slightly different activation energies for edge and screw dislocations. Directional dependency of hydrogen diffusion near dislocation showed high and low diffusivity along edge and screw dislocation lines, respectively, hence so called ‘pipe diffusion’ possibly occur at edge dislocation but does not at screw dislocation.

  3. Evaluation of a fully absorbable poly-4-hydroxybutyrate/absorbable barrier composite mesh in a porcine model of ventral hernia repair.

    Science.gov (United States)

    Scott, Jeffrey R; Deeken, Corey R; Martindale, Robert G; Rosen, Michael J

    2016-09-01

    The objective of this study was to evaluate the mechanical and histological properties of a fully absorbable poly-4-hydroxybutyrate/absorbable barrier composite mesh (Phasix™ ST) compared to partially absorbable (Ventralight™ ST), fully absorbable (Phasix™), and biologically derived (Strattice™) meshes in a porcine model of ventral hernia repair. Bilateral abdominal surgical defects were created in twenty-four Yucatan pigs, repaired with intraperitoneal (Phasix™ ST, Ventralight™ ST) or retromuscular (Phasix™, Strattice™) mesh, and evaluated at 12 and 24 weeks (n = 6 mesh/group/time point). Prior to implantation, Strattice™ demonstrated significantly higher (p weeks, mesh/repair strength was significantly greater than NAW (p weeks (p > 0.05). Phasix™ mesh/repair strength was significantly greater than Strattice™ (p weeks, and Ventralight™ ST mesh/repair strength was significantly greater than Phasix™ ST mesh (p weeks. At 12 and 24 weeks, Phasix™ ST and Ventralight™ ST were associated with mild inflammation and minimal-mild fibrosis/neovascularization, with no significant differences between groups. At both time points, Phasix™ was associated with minimal-mild inflammation/fibrosis and mild neovascularization. Strattice™ was associated with minimal inflammation/fibrosis, with minimal neovascularization at 12 weeks, which increased to mild by 24 weeks. Strattice™ exhibited significantly less neovascularization than Phasix™ at 12 weeks and significantly greater inflammation at 24 weeks due to remodeling. Phasix™ ST demonstrated mechanical and histological properties comparable to partially absorbable (Ventralight™ ST) and fully resorbable (Phasix™) meshes at 12 and 24 weeks in this model. Data also suggest that fully absorbable meshes with longer-term resorption profiles may provide improved mechanical and histological properties compared to biologically derived scaffolds.

  4. ECHMERIT V1.0 – a new global fully coupled mercury-chemistry and transport model

    Directory of Open Access Journals (Sweden)

    N. Pirrone

    2009-05-01

    Full Text Available Mercury is a global pollutant due to its long lifetime in the atmosphere. Its hemispheric transport patterns and eventual deposition are therefore of major concern. For the purpose of global atmospheric mercury chemistry and transport modelling the ECHMERIT model was developed. ECHMERIT, based on the global circulation model ECHAM5 differs from most global mercury models in that the emissions, chemistry (including general tropospheric chemistry and mercury chemistry, transport and deposition are coupled on-line to the GCM. The chemistry mechanism includes an online calculation of photolysis rate constants using the Fast-J photolysis mechanism, the CBM-Z tropospheric gas-phase mechanism and aqueous-phase chemistry based on the MECCA mechanism. Additionally, a mercury chemistry mechanism that incorporates gas and aqueous phase mercury chemistry is included. A detailed description of the model, including the wet and dry deposition modules, and the implemented emissions is given in this technical report. First model testing and evaluation show a satisfactory model performance for surface ozone and mercury concentrations (with a mean bias of 1.46 ppb for ozone and a mean bias of 13.55 ppq for TGM when compared with EMEP station data. Requirements regarding measurement data and emission inventories which could considerably improve model skill are discussed.

  5. ECHMERIT V1.0 – a new global fully coupled mercury-chemistry and transport model

    Directory of Open Access Journals (Sweden)

    G. Jung

    2009-11-01

    Full Text Available Mercury is a global pollutant due to its long lifetime in the atmosphere. Its hemispheric transport patterns and eventual deposition are therefore of major concern. For the purpose of global atmospheric mercury chemistry and transport modelling the ECHMERIT model was developed. ECHMERIT, based on the global circulation model ECHAM5 differs from most global mercury models in that the emissions, chemistry (including general tropospheric chemistry and mercury chemistry, transport and deposition are coupled on-line to the GCM. The chemistry mechanism includes an online calculation of photolysis rate constants using the Fast-J photolysis mechanism, the CBM-Z tropospheric gas-phase mechanism and aqueous-phase chemistry based on the MECCA mechanism. Additionally, a mercury chemistry mechanism that incorporates gas and aqueous phase mercury chemistry is included. A detailed description of the model, including the wet and dry deposition modules, and the implemented emissions is given in this technical report. First model testing and evaluation show a satisfactory model performance for surface ozone and mercury mixing ratios (with a mean bias of 1.46 nmol/mol for ozone and a mean bias of 13.55 fmol/mol for TGM when compared with EMEP station data. Requirements regarding measurement data and emission inventories which could considerably improve model skill are discussed.

  6. The injection of a screw dislocation into a crystal: Atomistics vs. continuum elastodynamics

    Science.gov (United States)

    Verschueren, J.; Gurrutxaga-Lerma, B.; Balint, D. S.; Dini, D.; Sutton, A. P.

    2017-01-01

    The injection (creation) process of a straight screw dislocation is compared atomistically with elastodynamic continuum theory. A method for injecting quiescent screw dislocations into a crystal of tungsten is simulated using non-equilibrium molecular dynamics. The resulting stress fields are compared to the those of elastodynamic solutions for the injection of a quiescent screw dislocation. A number of differences are found: a plane wave emission is observed to emanate from the whole surface of the cut used to create the dislocation, affecting the displacement field along the dislocation line (z), and introducing displacement field components perpendicular to the line (along x and y). It is argued that, in part, this emission is the result of the finite time required to inject the dislocation, whereby the atoms in the cut surface must temporarily be displaced to unstable positions in order to produce the required slip. By modelling this process in the continuum it is shown that the displacements components normal to the dislocation line arise from transient displacements of atoms in the cut surface parallel to x and y. It is shown that once these displacements are included in the elastodynamic continuum formulation the plane wave emission in uz is correctly captured. A detailed comparison between the atomistic and continuum models is then offered, showing that the main atomistic features can also be captured in the continuum.

  7. On the hydrological performance in preparation for fully coupled climate-hydrology modelling in a data-sparse region

    Science.gov (United States)

    Dahl Larsen, Morten Andreas; Senatore, Alfonso; Drews, Martin; Mendicino, Giuseppe

    2016-04-01

    Within the recently emerging field of research employing a dynamical coupling between existing advanced atmosphere-hydrology model codes lays a demand for a wide range of data. The data are needed to both drive and validate the models and need to be of a high quality in terms of spatial coverage, temporal resolution, representation of local attributes and data selection. As a consequence, most studies have been performed over regions of vast data coverage. Although good data coverage is mainly seen in regions of more economically developed countries, the advantages of the coupled models could be of at least equal relevance in lesser developed regions. We here evaluate the prediction capabilities of the joint MIKE SHE-SWET hydrology and land surface model which has recently been employed in a dynamical coupling with the HIRHAM regional climate model (RCM). As a test case, we use the Crati River catchment in Southern Italy. The catchment is used due to: 1) A reasonable availability of data in terms of discharge, a flux tower station, climate stations and gridded data products such as ERA-I, E-OBS, SWBM and RCM output (e.g. MED-CORDEX) albeit with problems resembling those of data sparse regions (lack of temporal overlap, gap filling, availability, hydrogeological interpretations and land use). 2) The location (the Mediterranean) has previously been shown to exhibit substantial biases which potentially could be reduced the future coupling. 3) The Mediterranean highlands with large variations in orography provide an interesting test case as this is poorly represented in models. And 4) Model runs using the WRF-Hydro model have been performed enabling the basis for valuable comparison studies. In the present study the model is parameterized through inverse calibration using variations of the available data to highlight the influence of data quality and availability on the model outcome and assets/disadvantages of individual products.

  8. Atomistic simulation of the premelting of iron and aluminum : Implications for high-pressure melting-curve measurements

    NARCIS (Netherlands)

    Starikov, Sergey V.; Stegailov, Vladimir V.

    2009-01-01

    Using atomistic simulations we show the importance of the surface premelting phenomenon for the melting-curve measurements at high pressures. The model under consideration mimics the experimental conditions deployed for melting studies with diamond-anvil cells. The iron is considered in this work be

  9. Generalization techniques to reduce the number of volume elements for terrain effect calculations in fully analytical gravitational modeling

    Science.gov (United States)

    Benedek, Judit; Papp, Gabor; Kalmár, János; Szűcs, Eszter

    2017-04-01

    The available volumetric models of the crust of the Alps - Pannonian basin - Carpathians region and the 30 m x 30 m resolution DTM of Hungary contain several million and hundred million volume elements, respectively. Either rectangular prisms or polyhedrons can be used to discretize the density distribution inside these 3D structures. The calculation of the closed formulae given for the gravitational potential and its higher order derivatives, however, needs twice more runtime than that of the rectangular prism computations. Although the more detailed the better principle is generally accepted (or assumed) it is basically true only for errorless data. As soon as errors are present any calculation from the model is only a possible realization of the true gravitational field at the significance level determined by the errors. So if one really considers the reliability of input data (e.g. Moho depths, topographic heights) used in the calculations then sometimes the "less" can be equivalent to the "more" in statistical sense. As a consequence, the computational time can be significantly reduced by the optimization of the number of volume elements based on the accuracy estimates of the input data. New algorithms are proposed to minimize the number of model elements defined both in local and global coordinate systems. Common gravity field modeling programs generate optimized models for every computation points (dynamic approach), whereas the static approach provides only one optimized model for all computational points. The number of volume elements depends on a threshold value pre-defined by the error statistics of the input data. It represents the maximum difference allowed along the vertical direction Z between the initial and optimized model. Based on the static approach two different algorithms were developed. The grid-based algorithm starts with the maximum resolution polyhedral model defined on a uniform grid and generates a new polyhedral surface. The other

  10. Fully coupled ice sheet-earth system model: How does the Greenlandic ice sheet interact in a changing climate

    Science.gov (United States)

    Rodehacke, C.; Mikolajewicz, U.; Vizcaino, M.

    2012-04-01

    As ice sheets belong to the slowest climate components, they are usually not interactively coupled in current climate models. Therefore, long-term climate projections are incomplete and only the consideration of ice sheet interactions allows tackling fundamental questions, such as how do ice sheets modify the reaction of the climate systems under a strong CO2 forcing? The earth system model MPI-ESM, with the atmosphere model ECHAM6 and ocean model MPIOM, is coupled to the modified ice sheet model PISM. This ice sheet model, which is developed at the University of Fairbanks, represents the ice sheet of Greenland at a horizontal resolution of 10 km. The coupling is performed by calculating the surface mass balance based on 6-hourly atmospheric data to determine the boundary condition for the ice sheet model. The response of the ice sheet to this forcing, which includes orographic changes and fresh water fluxes, are passed back to the ESM. In contrast to commonly used strategies, we use a mass conserving scheme and do therefore neither apply flux corrections nor utilize anomaly coupling. Under a strong CO2 forcing a disintegrating Greenlandic ice sheet contributes to a rising sea level and has the potential to alter the formation of deep water masses in the adjacent formation sites Labrador Sea and Nordic Seas. We will present results for an idealized forcing with a growing atmospheric CO2 concentration that rises by 1% per year until four-times the pre-industrial level has been reached. We will discuss the reaction of the ice sheet and immediate responses of the ocean to ice loss.

  11. Quantitative comparison of semi- and fully-distributed hydrologic models in simulating flood hydrographs on a mountain watershed in southwest China

    Institute of Scientific and Technical Information of China (English)

    张会兰; 王玉杰; 王云琦; 李丹勋; 王兴奎

    2013-01-01

    To investigate the performance of fully- and semi-distributed hydrologic models in simulating the process of transforma- tion from rainfall to runoff in mountain areas, the fully-distributed models Basin Pollution Calculation Center (BPCC) and HEC- HMS are calibrated for the Zhenjiangguan watershed located in the upper stream of Minjiang River Southwest China using stream- flow observations at the basin outlet. Semi-automatical optimization method is implemented to both models to improve simulated re- sults by removing artificial errors. Based on the consistency of the simulated hydrographs with the observed ones, the statistical coe- fficients such as the relative error, the probability distribution and the correlation coefficient, are further introduced to evaluate qua- ntitatively the performance of the two models. Analyses indicate that the hydrographs simulated by the BPCC are relatively closer to the observed ones than those simulated by the HEC-HMS in view of the spatial heterogeneity in terrain, soil texture, land cover and meteorological conditions in mountain areas.

  12. Multi-scale coupling strategy for fully two-dimensional and depth-averaged models for granular flows

    Science.gov (United States)

    Pudasaini, Shiva P.; Domnik, Birte; Miller, Stephen A.

    2013-04-01

    We developed a full two-dimensional Coulomb-viscoplastic model and applied it for inclined channel flows of granular materials from initiation to their deposition. The model includes the basic features and observed phenomena in dense granular flows like the exhibition of a yield strength and a non-zero slip velocity. A pressure-dependent yield strength is proposed to account for the frictional nature of granular materials. The yield strength can be related to the internal friction angle of the material and plays an important role, for example, in deposition processes. The interaction of the flow with the solid boundary is modelled by a pressure and rate-dependent Coulomb-viscoplastic sliding law. We developed an innovative multi-scale strategy to couple the full two-dimensional, non depth-averaged model (N-DAM) with a one-dimensional, depth-averaged model (DAM). The coupled model reduces computational complexity dramatically by using DAM only in regions with smooth changes of flow variables. The numerics uses N-DAM in regions where depth-averaging becomes inaccurate, for instance, in the initiation and deposition regions, and (particularly) when the flow hits an obstacle or a defense structure. In these regions, momentum transfer must be, and is, considered in all directions. We observe very high coupling performance, and show that the numerical results deviate only slightly from results of the much more cumbersome full two-dimensional model. This shows that the coupled model, which retains all the basic physics of the flow, is an attractive alternative to an expensive, full two-dimensional simulations. We compare simulation results with different experimental data for shock waves appearing in rapid granular flows down inclined channels and impacting a wall. The model predicts the evolution of the strong shock wave and the impact force on a rigid wall for different inclination angles and sliding surfaces. It is demonstrated that the internal friction angle plays an

  13. Developing Fully Coupled Dynamical Reactor Core Isolation System Models in RELAP-7 for Extended Station Black-Out Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Haihua Zhao; Ling Zou; Hongbin Zhang; David Andrs; Richard Martineau

    2014-04-01

    The reactor core isolation cooling (RCIC) system in a boiling water reactor (BWR) provides makeup water to the reactor vessel for core cooling when the main steam lines are isolated and the normal supply of water to the reactor vessel is lost. It was one of the very few safety systems still available during the Fukushima Daiichi accidents after the tsunamis hit the plants and the system successfully delayed the core meltdown for a few days for unit 2 & 3. Therefore, detailed models for RCIC system components are indispensable to understand extended station black-out accidents (SBO) for BWRs. As part of the effort to develop the new generation reactor system safety analysis code RELAP-7, major components to simulate the RCIC system have been developed. This paper describes the models for those components such as turbine, pump, and wet well. Selected individual component test simulations and a simplified SBO simulation up to but before core damage is presented. The successful implementation of the simplified RCIC and wet well models paves the way to further improve the models for safety analysis by including more detailed physical processes in the near future.

  14. A four-body fully distorted wave - eikonal initial state model for ionization of He targets by ion impact

    Energy Technology Data Exchange (ETDEWEB)

    Monti, J M; Fojon, O A; Rivarola, R D [Instituto de Fisica Rosario (CONICET-UNR) and Facultad de Ciencias Exactas, IngenierIa y Agrimensura, Universidad Nacional de Rosario, Pellegrini 250, 2000 Rosario (Argentina); Hanssen, J, E-mail: jmonti@ifir.edu.a [Institut de Physique, Laboratoire de Physique Moleculaire et des Collisions, Universite Paul Verlaine - Metz, 1 Bv. Arago, 57078 Metz Cedex 3 (France)

    2009-04-01

    A four body-distorted wave model is introduced to study collisions between swift bare ions and dielectronic atomic targets. Both electrons are considered as active, being one of them ionized while the other one remains bound to the residual target. The relevance of electron correlation on the resulting emission electron spectra is investigated for the case of protons impacting on He atoms.

  15. Stress in titania nanoparticles: An atomistic study

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model

    Science.gov (United States)

    Zhou, Jian; Qi, Jinyi

    2014-01-01

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D TOF PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's raytracer, we propose another more simplified geometrical projector based on the Bresenham's raytracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a nonfactored model such as the analytical model while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve optimal reconstruction performance based on a sparse factorization model with an only image domain resolution model. PMID:24434568

  17. ASAMgpu V1.0 – a moist fully compressible atmospheric model using graphics processing units (GPUs

    Directory of Open Access Journals (Sweden)

    S. Horn

    2012-03-01

    Full Text Available In this work the three dimensional compressible moist atmospheric model ASAMgpu is presented. The calculations are done using graphics processing units (GPUs. To ensure platform independence OpenGL and GLSL are used, with that the model runs on any hardware supporting fragment shaders. The MPICH2 library enables interprocess communication allowing the usage of more than one GPU through domain decomposition. Time integration is done with an explicit three step Runge-Kutta scheme with a time-splitting algorithm for the acoustic waves. The results for four test cases are shown in this paper. A rising dry heat bubble, a cold bubble induced density flow, a rising moist heat bubble in a saturated environment, and a DYCOMS-II case.

  18. ASAMgpu V1.0 – a moist fully compressible atmospheric model using graphics processing units (GPUs

    Directory of Open Access Journals (Sweden)

    S. Horn

    2011-10-01

    Full Text Available In this work the three dimensional compressible moist atmospheric model ASAMgpu is presented. The calculations are done using graphics processing units (GPUs. To ensure platform independence OpenGL and GLSL is used, with that the model runs on any hardware supporting fragment shaders. The MPICH2 library enables interprocess communication allowing the usage of more than one GPU through domain decomposition. Time integration is done with an explicit three step Runge-Kutta scheme with a timesplitting algorithm for the acoustic waves. The results for four test cases are shown in this paper. A rising dry heat bubble, a cold bubble induced density flow, a rising moist heat bubble in a saturated environment and a DYCOMS-II case.

  19. A new, high-resolution digital elevation model of Greenland fully validated with airborne laser altimeter data

    DEFF Research Database (Denmark)

    Bamber, J.L.; Ekholm, Simon; Krabill, W.B.

    2001-01-01

    A new digital elevation model of the Greenland ice sheet and surrounding rock outcrops has been produced at 1-km postings from a comprehensive suite of satellite remote sensing and cartographic data sets. Height data over the ice sheet were mainly from ERS-1 and Geosat radar altimetry. These data...... coverage existed. The data were interpolated onto a regular grid with a spacing of similar to1 km. The accuracy of the resultant digital elevation model over the ice sheet was assessed using independent and spatially extensive measurements from an airborne laser altimeter that had an accuracy of between 10...... and 12 cm. In a comparison with the laser altimetry the digital elevation model was found to have a slope-dependent accuracy ranging from -1.04 +/-1.98 m to -0.06 +/- 14.33 m over the ice sheet for a slope range of 0.0-1.0 degrees. The mean accuracy over the whole ice sheet was -0.33 +/-6.97 m. Over...

  20. A fully coupled Mediterranean regional climate system model: design and evaluation of the ocean component for the 1980–2012 period

    Directory of Open Access Journals (Sweden)

    Florence Sevault

    2014-11-01

    Full Text Available A fully coupled regional climate system model (CNRM-RCSM4 dedicated to the Mediterranean region is described and evaluated using a multidecadal hindcast simulation (1980–2012 driven by global atmosphere and ocean reanalysis. CNRM-RCSM4 includes the regional representation of the atmosphere (ALADIN-Climate model, land surface (ISBA model, rivers (TRIP model and the ocean (NEMOMED8 model, with a daily coupling by the OASIS coupler. This model aims to reproduce the regional climate system with as few constraints as possible: there is no surface salinity, temperature relaxation, or flux correction; the Black Sea budget is parameterised and river runoffs (except for the Nile are fully coupled. The atmospheric component of CNRM-RCSM4 is evaluated in a companion paper; here, we focus on the air–sea fluxes, river discharges, surface ocean characteristics, deep water formation phenomena and the Mediterranean thermohaline circulation. Long-term stability, mean seasonal cycle, interannual variability and decadal trends are evaluated using basin-scale climatologies and in-situ measurements when available. We demonstrate that the simulation shows overall good behaviour in agreement with state-of-the-art Mediterranean RCSMs. An overestimation of the shortwave radiation and latent heat loss as well as a cold Sea Surface Temperature (SST bias and a slight trend in the bottom layers are the primary current deficiencies. Further, CNRM-RCSM4 shows high skill in reproducing the interannual to decadal variability for air–sea fluxes, river runoffs, sea surface temperature and salinity as well as open-sea deep convection, including a realistic simulation of the Eastern Mediterranean Transient. We conclude that CNRM-RCSM4 is a mature modelling tool allowing the climate variability of the Mediterranean regional climate system to be studied and understood. It is used in hindcast and scenario modes in the HyMeX and Med-CORDEX programs.

  1. Modeling of high pressure arc-discharge with a fully-implicit Navier-Stokes stabilized finite element flow solver

    Science.gov (United States)

    Sahai, A.; Mansour, N. N.; Lopez, B.; Panesi, M.

    2017-05-01

    This work addresses the modeling of high pressure electric discharge in an arc-heated wind tunnel. The combined numerical solution of Poisson’s equation, radiative transfer equations, and the set of Favre-averaged thermochemical nonequilibrium Navier-Stokes equations allows for the determination of the electric, radiation, and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles with the Chapman-Enskog method. A multi-temperature formulation is used to account for thermal non-equilibrium. Finally, the turbulence closure of the flow equations is obtained by means of the Spalart-Allmaras model, which requires the solution of an additional scalar transport equation. A Streamline upwind Petrov-Galerkin stabilized finite element formulation is employed to solve the Navier-Stokes equation. The electric field equation is solved using the standard Galerkin formulation. A stable formulation for the radiative transfer equations is obtained using the least-squares finite element method. The developed simulation framework has been applied to investigate turbulent plasma flows in the 20 MW Aerodynamic Heating Facility at NASA Ames Research Center. The current model is able to predict the process of energy addition and re-distribution due to Joule heating and thermal radiation, resulting in a hot central core surrounded by colder flow. The use of an unsteady three-dimensional treatment also allows the asymmetry due to a dynamic electric arc attachment point in the cathode chamber to be captured accurately. The current work paves the way for detailed estimation of operating characteristics for arc-heated wind tunnels which are critical in testing thermal protection systems.

  2. Absence of first order transition in the random crystal field Blume-Capel model on a fully connected graph

    Science.gov (United States)

    Sumedha; Jana, Nabin Kumar

    2017-01-01

    In this paper we solve the Blume-Capel model on a complete graph in the presence of random crystal field with a distribution, P≤ft({{ Δ }i}\\right)=pδ ≤ft({{ Δ }i}- Δ \\right)+(1-p)δ ≤ft({{ Δ }i}+ Δ \\right) , using large deviation techniques. We find that the first order transition of the pure system is destroyed for 0.046    0.954) even at zero temperature.

  3. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model.

    Science.gov (United States)

    Zhou, Jian; Qi, Jinyi

    2014-02-07

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D time-of-flight PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon's ray-tracer, we propose another more simplified geometrical projector based on the Bresenham's ray-tracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a non-factored model, while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve the optimal reconstruction performance based on a sparse factorization model with an image domain resolution model.

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

    Energy Technology Data Exchange (ETDEWEB)

    Aubry, Sylvie; Webb, Edmund Blackburn, III (Sandia National Laboratories, Albuquerque, NM); Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John (Sandia National Laboratories, Albuquerque, NM); 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.

  5. UniPron is A Fully Effective Non-hormonal Reversible Contraceptive in Baboon Model(Papio Anubis)

    Institute of Scientific and Technical Information of China (English)

    Jael A.Obiero; Maureen N.Mburu; Benson M.Ndung'u; Kenneth K.Waititu; Isaac Mulei; Idle O.Farah; Peter G.Mwethera

    2008-01-01

    Objective To determine the safety and efficacy of UniPron as a reversible contraceptive.Methods Vaginal swabs were obtained before and after UniPron administration.cultured onto appropriate culture media and bacteria identification was done based on type of media used,Gram stain reactions,colony morphology and biochemical tests.Vaginal biopsy tissues were processed using paraffin wax method,stained with hematoxylin and eosin and examined under light microscopy to determine the effect of the product on vaginal tissues.The effect of UniPron on sperm was examined by mixing the product with electroejaculated spermatozoa in vitro at different concentrations.For efficacy studies,male baboons of proven fertility were mated with UniPron treated or untreated females of proven fertility during the fertile stages.Results All the five females(100%)that were treated with UniPron did not conceive and they regained total fertitity when the treatment was stopped while all the controls conceived.At a concentration of 40%,UniPron completely immobilized spermatozoa in an in-vitro system.UniPron mechanism of action was by lowering the vaginal pH and on application in baboon,the pH was lowered for at least 3 h after which it went back to normal.Conclusions As we plan for a study to test UniPron as a microbicide to prevent STIs including HIV,our current study has established that this novel product is effective in contraception and harmless to vaginal tissues and vaginal microbial flora in a baboon model(Papio anubis).

  6. wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    2013-01-01

    Full Text Available Molecular docking simulations of fully flexible protein receptor (FFR models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a docking simulation is executed and analyzed. An important challenge is to perform virtual screening of millions of ligands using an FFR model in a sequential mode since it can become computationally very demanding. In this paper, we propose a cloud-based web environment, called web Flexible Receptor Docking Workflow (wFReDoW, which reduces the CPU time in the molecular docking simulations of FFR models to small molecules. It is based on the new workflow data pattern called self-adaptive multiple instances (P-SaMIs and on a middleware built on Amazon EC2 instances. P-SaMI reduces the number of molecular docking simulations while the middleware speeds up the docking experiments using a High Performance Computing (HPC environment on the cloud. The experimental results show a reduction in the total elapsed time of docking experiments and the quality of the new reduced receptor models produced by discarding the nonpromising conformations from an FFR model ruled by the P-SaMI data pattern.

  7. Multiscale modeling of nanoindentation in copper thin films via the concurrent coupling of the meshless Hermite-Cloud method with molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Ng, T.Y., E-mail: MTYNG@ntu.edu.sg [School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore); Pandurangan, Venkataraman; Li Hua [School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798 (Singapore)

    2011-10-01

    This paper investigates the 2D nanoindentation of a copper thin film using a concurrent multiscale method. The method uses molecular dynamics (MD) simulation in the atomistic region, the strong-form meshless Hermite-Cloud method in the continuum region and a handshaking algorithm to concurrently couple them. A fully atomistic simulation is also carried out to validate the multiscale method. The results, namely the load versus indentation depth graph obtained from the multiscale method shows only slight quantitative variation from that of the full atomistic model. More importantly, the graphs from both simulations show a similar trend thus validating the 2D multiscale method. The displacement profile without discontinuities further supports the efficiency of the multiscale method in ensuring smooth exchange of information between the atomistic and continuum domains. The material properties extracted from the simulation include the force/unit length values obtained by dividing the maximum load on the indenter by its contact perimeter, instead of the hardness value obtained in 3D simulations. By restricting the atomic scale detail to the critical regions beneath the indenter, the multiscale method effectively saves computational resources to more than one order (close to 13 times less for this problem), thus making it feasible to simulate problems of larger dimensions that are not amenable to complete atomistic simulations.

  8. A threshold voltage model of short-channel fully-depleted recessed-source/drain (Re-S/D) SOI MOSFETs with high- dielectric

    Institute of Scientific and Technical Information of China (English)

    Gopi Krishna Saramekala; Sarvesh Dubey; Pramod Kumar Tiwari

    2015-01-01

    In this paper, a surface potential based threshold voltage model of fully-depleted (FD) recessed-source/drain (Re-S/D) silicon-on-insulator (SOI) metal-oxide semiconductor field-effect transistor (MOSFET) is presented while considering the effects of high-k gate-dielectric material induced fringing-field. The two-dimensional (2D) Poisson’s equation is solved in a channel region in order to obtain the surface potential under the assumption of the parabolic potential profile in the trans-verse direction of the channel with appropriate boundary conditions. The accuracy of the model is verified by comparing the model’s results with the 2D simulation results from ATLAS over a wide range of channel lengths and other parameters, including the dielectric constant of gate-dielectric material.

  9. Searching for the standard model Higgs boson produced by vector boson fusion in the fully hadronic four-jet topology with CMS

    CERN Document Server

    Chernyavskaya, Nadezda

    2017-01-01

    A search for the standard model Higgs boson produced by vector boson fusion in the fully hadronic four-jet topology is presented. The analysis is based on 2.3 fb$^{-1}$ of proton-proton collision data at $\\sqrt{s}$ = 13 TeV collected by CMS in 2015. Upper limits, at 95\\% confidence level, on the production cross section times branching fraction of the Higgs boson decaying to bottom quarks, are derived for a Higgs boson mass of 125 GeV. The fitted signal strength relative to the expectation for the standard model Higgs boson is obtained. Results are also combined with the ones obtained with Run1 data at $\\sqrt{s}$ = 8 TeV collected in 2012.

  10. Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization.

    Science.gov (United States)

    Lu, Jibao; Qiu, Yuqing; Baron, Riccardo; Molinero, Valeria

    2014-09-09

    Coarse-grained models are becoming a competitive alternative for modeling processes that occur over time and length scales beyond the reach of fully atomistic molecular simulations. Ideally, coarse-grained models should not only achieve high computational efficiency but also provide accurate predictions and fundamental insight into the role of molecular interactions, the characteristic behavior, and properties of the system they model. In this work we derive a series of monatomic coarse-grained water models mX(REM) from the most popular atomistic water models X = TIP3P, SPC/E, TIP4P-Ew, and TIP4P/2005, using the relative entropy minimization (REM) method. Each coarse-grained water molecule is represented by a single particle that interacts through short-ranged anisotropic interactions that encourage the formation of "hydrogen-bonded" structures. We systematically investigate the features of the coarse-grained models in reproducing over 20 structural, dynamic, and thermodynamic properties of the reference atomistic water models-including the existence and locus of the characteristic density anomaly. The mX(REM) coarse-grained models reproduce quite faithfully the radial and angular distribution function of water, produce a temperature of maximum density (TMD), and stabilize the ice I crystal. Moreover, the ratio between the TMD and the melting temperature of the crystal in the mX(REM) models and liquid-ice equilibrium properties show reasonable agreement with the results of the corresponding atomistic models. The mX(REM) models, however, severely underestimate the cohesive energy of the condensed water phases. We investigate which specific limitations of the coarse-grained models arise from the REM methodology, from the monatomic nature of the models, and from the Stillinger-Weber interaction potential form. Our analysis indicates that a small compromise in the accuracy of structural properties can result in a significant increase of the overall accuracy and

  11. Quantitative precipitation and streamflow forecast for two recent extreme hydro-meteorological events in Southern Italy with a fully-coupled model system

    Science.gov (United States)

    Mendicino, Giuseppe; Senatore, Alfonso

    2016-04-01

    Two severe hydro-meteorological events affected Calabria Region (Southern Italy) in the second half of the year 2015. The first event, on August 12th, focused on a relatively small area near the northern Ionian coast, resulted in a rainfall intensity of about 230 mm in 24 hours involving flash flooding with several million Euros of damages. The second event mainly affected the southern Ionian coast, was more persistent (it lasted from October 30th to November 2nd), interested a wider area and led to recorded rainfall values up to 400 mm in 24 hours and 700 mm in 48 hours, resulting in severe flooding, landslides and a human loss. The fully two-way dynamically coupled atmosphere-hydrology modeling system WRF-Hydro is used to reproduce both the events, in order to assess its skill in forecasting both quantitative precipitation and streamflow with initial and lateral atmospheric boundary conditions given by the recently available 0.25° output resolution GFS grid dataset. Precipitation estimates provided by 2 km-resolution atmospheric model are compared with both ground-based data and observations from a National Civil Protection Department single-polarization Doppler radar. Discharge data from the rivers and creeks affected by heavy precipitation are not available, then streamflow results are compared with either official discharge estimates provided by authorities (first event) or recorded river stages (second event). Results show good performances of the fully-coupled hydrometeorological prediction system which allows an improved representation of the coupled atmospheric and terrestrial processes and provides an integrated solution for the regional water cycle modeling, from atmospheric processes to river outlets.

  12. An object oriented Python interface for atomistic simulations

    Science.gov (United States)

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

    2016-01-01

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

  13. Spectroscopic diagnostics of low-pressure inductively coupled Kr plasma using a collisional-radiative model with fully relativistic cross sections

    Science.gov (United States)

    Gangwar, Reetesh K.; Dipti; Srivastava, Rajesh; Stafford, Luc

    2016-06-01

    A collisional-radiative (C-R) model for krypton plasma using fully relativistic distorted-wave cross sections for electron excitations was developed. The model was applied to the characterization of inductively coupled Kr plasma with cylindrical geometry over the pressure regime 1-50 mTorr. Radially averaged emission intensities from transitions of Kr (4p55p  →  4p55s) in the range 500-900 nm were recorded at 17 cm from the planar RF-driven coil, with the plasma operated in the inductive regime (H mode). The measured emission intensities were then fitted by varying the electron density, n e, and electron temperature, T e, in the C-R model. At both low and high pressures, variations of the electron density by over two orders of magnitude had only a minor role on the relative emission intensities. On the other hand, T e values deduced from the comparison between experiment and model decreased from 6.7 to 2.6 eV as pressure increased from 1 to 50 mTorr. These results are found to be in good agreement with the effective electron temperature determined from Langmuir probe measurements and the predictions of a model based on the particle balance equation of charged particles.

  14. Corner free energies and boundary effects for Ising, Potts and fully-packed loop models on the square and triangular lattices

    CERN Document Server

    Vernier, Eric

    2011-01-01

    We obtain long series expansions for the bulk, surface and corner free energies for several two-dimensional statistical models, by combining Enting's finite lattice method (FLM) with exact transfer matrix enumerations. The models encompass all integrable curves of the Q-state Potts model on the square and triangular lattices, including the antiferromagnetic transition curves and the Ising model (Q=2) at temperature T, as well as a fully-packed O(n) type loop model on the square lattice. The expansions are around the trivial fixed points at infinite Q, n or 1/T. By using a carefully chosen expansion parameter, q << 1, all expansions turn out to be of the form \\prod_{k=1}^\\infty (1-q^k)^{\\alpha_k + k \\beta_k}, where the coefficients \\alpha_k and \\beta_k are periodic functions of k. Thanks to this periodicity property we can conjecture the form of the expansions to all orders (except in a few cases where the periodicity is too large). These expressions are then valid for all 0 <= q < 1. We analyse in...

  15. Linking Atomistic and Mesoscale Simulations of Water Soluble Polymers

    Science.gov (United States)

    Jones, J. L.

    2003-03-01

    There exist a range of techniques for studying surfactants and polymers in the mesoscale regime. One of the challenges is to link mesoscale theories and simulations to other calculation methods which address different length scales of the system. We introduce some mesoscale methods of calculation for polymers and surfactants and then present a case study of where mesoscale modelling is used for mechanistic understanding, by linking the method to high throughput in-silico screening methods. We look at the adsorption onto silica of ethylene oxide (EO)/ propylene oxide (PO) block copolymers (lutrols) which have been modified by end-grafting of short, cationic dimethylamino ethyl methacrylate (DMAEMA)chains. Given that the silica surface is negatively charged, it is remarkable that in some circumstances, polymers with longercationic chains have a lower adsorption. The effect is attributed to a competition between strong adsorption of the cationic DMAEMA groups driven by electrostatics, and weaker adsorption of the more numerous EO groups. This then raises the question of how we produce the values for the mesoscale parameters in these models and in the second part of the talk we describe a calculation method for doing this for water soluble polymers. The most promising route, but notoriously costly, is based on free energy calculations at the atomistic level. Free energy calculations are computationally intensive in general, but in an aqueous system one is also faced with the additional problem of using complex continuum models and/or accurate interaction potentials for water. Here we show how potential of mean force (PMF)calculations offer a practical alternative which avoids these drawbacks, though one is still faced with extremely long simulations.

  16. FULLY AUTOMATED GIS-BASED INDIVIDUAL TREE CROWN DELINEATION BASED ON CURVATURE VALUES FROM A LIDAR DERIVED CANOPY HEIGHT MODEL IN A CONIFEROUS PLANTATION

    Directory of Open Access Journals (Sweden)

    R. J. L. Argamosa

    2016-06-01

    Full Text Available The generation of high resolution canopy height model (CHM from LiDAR makes it possible to delineate individual tree crown by means of a fully-automated method using the CHM’s curvature through its slope. The local maxima are obtained by taking the maximum raster value in a 3 m x 3 m cell. These values are assumed as tree tops and therefore considered as individual trees. Based on the assumptions, thiessen polygons were generated to serve as buffers for the canopy extent. The negative profile curvature is then measured from the slope of the CHM. The results show that the aggregated points from a negative profile curvature raster provide the most realistic crown shape. The absence of field data regarding tree crown dimensions require accurate visual assessment after the appended delineated tree crown polygon was superimposed to the hill shaded CHM.

  17. Steady- and transient-state analysis of fully ceramic microencapsulated fuel with randomly dispersed tristructural isotropic particles via two-temperature homogenized model-I: Theory and method

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Yoon Hee; Cho, Bum Hee; Cho, Nam Zin [Dept. of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2016-06-15

    As a type of accident-tolerant fuel, fully ceramic microencapsulated (FCM) fuel was proposed after the Fukushima accident in Japan. The FCM fuel consists of tristructural isotropic particles randomly dispersed in a silicon carbide (SiC) matrix. For a fuel element with such high heterogeneity, we have proposed a two-temperature homogenized model using the particle transport Monte Carlo method for the heat conduction problem. This model distinguishes between fuel-kernel and SiC matrix temperatures. Moreover, the obtained temperature profiles are more realistic than those of other models. In Part I of the paper, homogenized parameters for the FCM fuel in which tristructural isotropic particles are randomly dispersed in the fine lattice stochastic structure are obtained by (1) matching steady-state analytic solutions of the model with the results of particle transport Monte Carlo method for heat conduction problems, and (2) preserving total enthalpies in fuel kernels and SiC matrix. The homogenized parameters have two desirable properties: (1) they are insensitive to boundary conditions such as coolant bulk temperatures and thickness of cladding, and (2) they are independent of operating power density. By performing the Monte Carlo calculations with the temperature-dependent thermal properties of the constituent materials of the FCM fuel, temperature-dependent homogenized parameters are obtained.

  18. Evolution of ozone, particulates, and aerosol direct radiative forcing in the vicinity of Houston using a fully coupled meteorology-chemistry-aerosol model

    Science.gov (United States)

    Fast, Jerome D.; Gustafson, William I.; Easter, Richard C.; Zaveri, Rahul A.; Barnard, James C.; Chapman, Elaine G.; Grell, Georg A.; Peckham, Steven E.

    2006-11-01

    A new fully coupled meteorology-chemistry-aerosol model is used to simulate the urban- to regional-scale variations in trace gases, particulates, and aerosol direct radiative forcing in the vicinity of Houston over a 5 day summer period. Model performance is evaluated using a wide range of meteorological, chemistry, and particulate measurements obtained during the 2000 Texas Air Quality Study. The predicted trace gas and particulate distributions were qualitatively similar to the surface and aircraft measurements with considerable spatial variations resulting from urban, power plant, and industrial sources of primary pollutants. Sulfate, organic carbon, and other inorganics were the largest constituents of the predicted particulates. The predicted shortwave radiation was 30 to 40 W m-2 closer to the observations when the aerosol optical properties were incorporated into the shortwave radiation scheme; however, the predicted hourly aerosol radiative forcing was still underestimated by 10 to 50 W m-2. The predicted aerosol radiative forcing was larger over Houston and the industrial ship channel than over the rural areas, consistent with surface measurements. The differences between the observed and simulated aerosol radiative forcing resulted from transport errors, relative humidity errors in the upper convective boundary layer that affect aerosol water content, secondary organic aerosols that were not yet included in the model, and uncertainties in the primary particulate emission rates. The current model was run in a predictive mode and demonstrates the challenges of accurately simulating all of the meteorological, chemical, and aerosol parameters over urban to regional scales that can affect aerosol radiative forcing.

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

    Science.gov (United States)

    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.

  20. From the groundwater to the boundary layer: a fully-coupled hydrometeorologic modeling approach for a catchment of the Alpine foothils

    Science.gov (United States)

    Fersch, Benjamin; Kunstmann, Harald; Gochis, David

    2016-04-01

    Through capillary rise, shallow groundwater tables can considerably affect the soil moisture contents within the root layer of the vadose zone and consequently govern the exchange of moisture and energy between the land-surface and the atmospheric boundary layer. In addition, they play an important role for channel flow and substantial quantities of recharge water are subject to lateral redistribution. A combination of these processes can lead to various non-linear dependencies, feedback and back coupling. As a physically based hydrometeorologic modeling system, WRF-Hydro enables the study of the interactions between the atmospheric boundary layer and the hydrological quantities above and within the soil. However, in its current version a linear storage (bucket) model is employed to simulate the groundwater with single direction from the recharge towards the channel. For an improved representation, we present an extension to the hydrological component of WRF-Hydro that features a 2-dimensional, finite-difference, single-layer, porous groundwater flow model, a Darcy-flux parametrization of vertical water flux from and to the unsaturated zone, and a head-gradient based groundwater coupling to the river channel network. The developed model system is applied for the diverse Alpine foothill catchment of the Ammer river (650 km²), in Southern Germany, characterized by complex terrain, ranging from 550 to more than 2200 m.a.s.l. We will present an overview on the model structure and the coupling approach. Moreover, first results of the stand-alone model calibration and the fully coupled application will be shown.

  1. A fully-stochasticized, age-structured population model for population viability analysis of fish: Lower Missouri River endangered pallid sturgeon example

    Science.gov (United States)

    Wildhaber, Mark L.; Albers, Janice; Green, Nicholas; Moran, Edward H.

    2017-01-01

    We develop a fully-stochasticized, age-structured population model suitable for population viability analysis (PVA) of fish and demonstrate its use with the endangered pallid sturgeon (Scaphirhynchus albus) of the Lower Missouri River as an example. The model incorporates three levels of variance: parameter variance (uncertainty about the value of a parameter itself) applied at the iteration level, temporal variance (uncertainty caused by random environmental fluctuations over time) applied at the time-step level, and implicit individual variance (uncertainty caused by differences between individuals) applied within the time-step level. We found that population dynamics were most sensitive to survival rates, particularly age-2+ survival, and to fecundity-at-length. The inclusion of variance (unpartitioned or partitioned), stocking, or both generally decreased the influence of individual parameters on population growth rate. The partitioning of variance into parameter and temporal components had a strong influence on the importance of individual parameters, uncertainty of model predictions, and quasiextinction risk (i.e., pallid sturgeon population size falling below 50 age-1+ individuals). Our findings show that appropriately applying variance in PVA is important when evaluating the relative importance of parameters, and reinforce the need for better and more precise estimates of crucial life-history parameters for pallid sturgeon.

  2. Implementation of a fully 3D system model for brain SPECT with fan- beam-collimator OSEM reconstruction with 3D total variation regularization

    Science.gov (United States)

    Ye, Hongwei; Krol, Andrzej; Lipson, Edward D.; Lu, Yao; Xu, Yuesheng; Lee, Wei; Feiglin, David H.

    2007-03-01

    In order to improve tomographically reconstructed image quality, we have implemented a fully 3D reconstruction, using an ordered subsets expectation maximization (OSEM) algorithm for fan-beam collimator (FBC) SPECT, along with a volumetric system model-fan-volume system model (FVSM), a modified attenuation compensation, a 3D depth- and angle-dependent resolution and sensitivity correction, and a 3D total variation (TV) regularization. SPECT data were acquired in a 128x64 matrix, in 120 views with a circular orbit. The numerical Zubal brain phantom was used to simulate a FBC HMPAO Tc-99m brain SPECT scan, and a low noise and scatter-free projection dataset was obtained using the SimSET Monte Carlo package. A SPECT scan for a mini-Defrise phantom and brain HMPAO SPECT scans for five patients were acquired with a triple-head gamma camera (Triad 88) equipped with a low-energy high-resolution (LEHR) FBC. The reconstructed images, obtained using clinical filtered back projection (FBP), OSEM with a line-length system model (LLSM) and 3D TV regularization, and OSEM with FVSM and 3D TV regularization were quantitatively studied. Overall improvement in the image quality has been observed, including better axial and transaxial resolution, better integral uniformity, higher contrast-to-noise ration between the gray matter and the white matter, and better accuracy and lower bias in OSEM-FVSM, compared with OSEM-LLSM and clinical FBP.

  3. Atomistic simulations of jog migration on extended screw dislocations

    DEFF Research Database (Denmark)

    Vegge, T.; Leffers, T.; Pedersen, O.B.;

    2001-01-01

    We have performed large-scale atomistic simulations of the migration of elementary jogs on dissociated screw dislocations in Cu. The local crystalline configurations, transition paths. effective masses. and migration barriers for the jogs are determined using an interatomic potential based on the...

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

    NARCIS (Netherlands)

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

    2014-01-01

    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 coa

  5. Cascade defect evolution processes: Comparison of atomistic methods

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Haixuan, E-mail: xuh1@ornl.gov; Stoller, Roger E.; Osetsky, Yury N.

    2013-11-15

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

  6. Definition and detection of contact in atomistic simulations

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    2015-01-01

    In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

  7. Definition and detection of contact in atomistic simulations

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    2015-01-01

    In atomistic simulations, contact depends on the accurate detection of contacting atoms as well as their contact area. While it is common to define contact between atoms based on the so-called ‘contact distance’ where the interatomic potential energy reaches its minimum, this discounts, for example,

  8. Atomistic understanding of hydrogen loading phenomenon into palladium cathode: A simple nanocluster approach and electrochemical evidence

    Indian Academy of Sciences (India)

    Mohsen Lashgari; Davood Matloubi

    2015-03-01

    The inherent potency of palladium to sorb hydrogen atoms was examined empirically and theoretically through various electrochemical methods and high-level quantum chemical calculations (HSE06) based on cluster model (CM) and density functional theory (DFT). The CM-DFT approach using QZVP/cc-PV6Z basis sets revealed a strong attraction between Pd nanoclusters and H atoms that generates some charged entities. This atomistically justifies why the electrochemical impedance of the system becomes less by the loading phenomenon. It is concluded that hydrogen atoms enter the palladium subsurface through hollow and bridge sites by diffusing as proton-like species and get loaded predominantly in the octahedral voids.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    McCarty, Keven F. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Zhou, Xiaowang [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ward, Donald K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schultz, Peter A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Foster, Michael E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bartelt, Norman Charles [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

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

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

    Science.gov (United States)

    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