Applying Biomimetic Algorithms for Extra-Terrestrial Habitat Generation

NASA Technical Reports Server (NTRS)

Birge, Brian

2012-01-01

The objective is to simulate and optimize distributed cooperation among a network of robots tasked with cooperative excavation on an extra-terrestrial surface. Additionally to examine the concept of directed Emergence among a group of limited artificially intelligent agents. Emergence is the concept of achieving complex results from very simple rules or interactions. For example, in a termite mound each individual termite does not carry a blueprint of how to make their home in a global sense, but their interactions based strictly on local desires create a complex superstructure. Leveraging this Emergence concept applied to a simulation of cooperative agents (robots) will allow an examination of the success of non-directed group strategy achieving specific results. Specifically the simulation will be a testbed to evaluate population based robotic exploration and cooperative strategies while leveraging the evolutionary teamwork approach in the face of uncertainty about the environment and partial loss of sensors. Checking against a cost function and 'social' constraints will optimize cooperation when excavating a simulated tunnel. Agents will act locally with non-local results. The rules by which the simulated robots interact will be optimized to the simplest possible for the desired result, leveraging Emergence. Sensor malfunction and line of sight issues will be incorporated into the simulation. This approach falls under Swarm Robotics, a subset of robot control concerned with finding ways to control large groups of robots. Swarm Robotics often contains biologically inspired approaches, research comes from social insect observation but also data from among groups of herding, schooling, and flocking animals. Biomimetic algorithms applied to manned space exploration is the method under consideration for further study.

Interacting scales and energy transfer in isotropic turbulence

NASA Technical Reports Server (NTRS)

Zhou, YE

1993-01-01

The dependence of the energy transfer process on the disparity of the interacting scales is investigated in the inertial and far-dissipation ranges of isotropic turbulence. The strategy for generating the simulated flow fields and the choice of a disparity parameter to characterize the scaling of the interactions is discussed. The inertial range is found to be dominated by relatively local interactions, in agreement with the Kolmogorov assumption. The far-dissipation is found to be dominated by relatively non-local interactions, supporting the classical notion that the far-dissipation range is slaved to the Kolmogorov scales. The measured energy transfer is compared with the classical models of Heisenberg, Obukhov, and the more detailed analysis of Tennekes and Lumley. The energy transfer statistics measured in the numerically simulated flows are found to be nearly self-similar for wave numbers in the inertial range. Using the self-similar form measured within the limited scale range of the simulation, an 'ideal' energy transfer function and the corresponding energy flux rate for an inertial range of infinite extent are constructed. From this flux rate, the Kolmogorov constant is calculated to be 1.5, in excellent agreement with experiments.

Solar Wind - Magnetosheath - Magnetopause Interactions in Global Hybrid-Vlasov Simulations

NASA Astrophysics Data System (ADS)

Hoilijoki, S.; Pfau-Kempf, Y.; Ganse, U.; Hietala, H.; Cassak, P.; Walsh, B.; Juusola, L.; Jarvinen, R.; von Alfthan, S.; Palmroth, M.

2017-12-01

We present results of interactions of solar wind and Earth's magnetosphere in global hybrid-Vlasov simulations carried out using the Vlasiator model. Vlasiator propagates ions as velocity distribution functions by solving the Vlasov equation and electrons are treated as charge-neutralizing massless fluid. Vlasiator simulations show a strong coupling between the ion scale and global scale physics. Global scale phenomena affect the local physics and the local phenomena impact the global system. Our results have shown that mirror mode waves growing in the quasi-perpendicular magnetosheath have an impact on the local reconnection rates at the dayside magnetopause. Furthermore, multiple X-line reconnection at the dayside magnetopause leads to the formation of magnetic islands (2D flux transfer events), which launch bow waves upstream propagating through the magnetosheath. These steep bow waves have the ability to accelerate ions in the magnetosheath. When the bow waves reach the bow shock they are able to bulge the shock locally. The bulge in the shock decreases the angle between the interplanetary magnetic field and the shock normal and allows ions to be reflected back to the solar wind along the magnetic field lines. Consequently, Vlasiator simulations show that magnetosheath fluctuations affect magnetopause reconnection and reconnection may influence particle acceleration and reflection in the magnetosheath and solar wind.

Protonation-modulated localization of excess electrons in histidine aqueous solutions revealed by ab initio molecular dynamics simulations: anion-centered versus cation-centered localization.

PubMed

Gao, Liang; Bu, Yuxiang

2017-05-31

In this work, we present an ab initio molecular dynamics simulation study on the interaction of an excess electron (EE) with histidine in its aqueous solution. Two different configurations of histidine (imidazole group protonated or not) are considered to reflect its different existing forms in neutral or slightly acidic surroundings. The simulation results indicate that localizations of EEs in different aqueous histidine solutions are quite different and are strongly affected by protonation of the side chain imidazole group and are thus pH-controlled. In neutral aqueous histidine solution, an EE localizes onto the carboxyl anionic group of the amino acid backbone after a relatively lengthy diffuse state, performing just like in an aliphatic amino acid solution. But in weakly acidic solution in which the side chain imidazole group is protonated, an EE undergoes a short lifetime diffuse state and finally localizes on the protonated imidazole group. We carefully examine these two different localization dynamics processes and analyze the competition between different dominating groups in their corresponding electron localization mechanisms. To explain the difference, we investigate the frontier molecular orbitals of these two systems and find that their energy levels and compositions are important to determine these differences. These findings can provide helpful information to understand the interaction mechanisms of low energy EEs with amino acids and even oligopeptides, especially with aromatic rings.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Molecular dynamics simulation of solute diffusion in Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Kimura, Y.; Hirota, N.

We performed a molecular dynamics (MD) simulation for a system of 5 solute molecules in 495 solvent molecules interacting through the Lennard-Jones (LJ) 12-6 potential, in order to study solvent density effects on the diffusion coefficients in supercritical fluids. The effects of the size of the solute and the strength of the solute-solvent attractive interaction on the diffusion coefficient of the solute were examined. The diffusion coefficients of the solute molecules were calculated at T = 1.5 (in the LJ reduced unit), slightly above the critical temperature, from rho = 0.1 to rho = 0.95, where rho is the number density in the LJ reduced unit. The memory function in the generalized Langevin equation was calculated, in order to know the molecular origin of the friction on a solute. The memory function is separated into fast and slow components. The former arises from the solute-solvent repulsive interaction, and is interpreted as collisional Enskog-like friction. The interaction strength dependence of the collisional friction is larger in the low- and medium-density regions, which is consistent with the 'clustering' picture, i.e., the local density enhancement due to the solute-solvent attractive interaction. However, the slow component of the memory function suppresses the effect of the local density on the diffusion coefficients, and as a result the effect of the attractive interaction is smaller on the diffusion coefficients than on the local density. Nonetheless, the solvent density dependence of the effect of the attraction on the diffusion coefficient varies with the local density, and it is concluded that the local density is the principal factor that determines the interaction strength dependence of the diffusion coefficient in the low- and medium-density regions (p < 0.6).

VASA: Interactive Computational Steering of Large Asynchronous Simulation Pipelines for Societal Infrastructure.

PubMed

Ko, Sungahn; Zhao, Jieqiong; Xia, Jing; Afzal, Shehzad; Wang, Xiaoyu; Abram, Greg; Elmqvist, Niklas; Kne, Len; Van Riper, David; Gaither, Kelly; Kennedy, Shaun; Tolone, William; Ribarsky, William; Ebert, David S

2014-12-01

We present VASA, a visual analytics platform consisting of a desktop application, a component model, and a suite of distributed simulation components for modeling the impact of societal threats such as weather, food contamination, and traffic on critical infrastructure such as supply chains, road networks, and power grids. Each component encapsulates a high-fidelity simulation model that together form an asynchronous simulation pipeline: a system of systems of individual simulations with a common data and parameter exchange format. At the heart of VASA is the Workbench, a visual analytics application providing three distinct features: (1) low-fidelity approximations of the distributed simulation components using local simulation proxies to enable analysts to interactively configure a simulation run; (2) computational steering mechanisms to manage the execution of individual simulation components; and (3) spatiotemporal and interactive methods to explore the combined results of a simulation run. We showcase the utility of the platform using examples involving supply chains during a hurricane as well as food contamination in a fast food restaurant chain.

Capturing nonlocal interaction effects in the Hubbard model: Optimal mappings and limits of applicability

NASA Astrophysics Data System (ADS)

van Loon, E. G. C. P.; Schüler, M.; Katsnelson, M. I.; Wehling, T. O.

2016-10-01

We investigate the Peierls-Feynman-Bogoliubov variational principle to map Hubbard models with nonlocal interactions to effective models with only local interactions. We study the renormalization of the local interaction induced by nearest-neighbor interaction and assess the quality of the effective Hubbard models in reproducing observables of the corresponding extended Hubbard models. We compare the renormalization of the local interactions as obtained from numerically exact determinant quantum Monte Carlo to approximate but more generally applicable calculations using dual boson, dynamical mean field theory, and the random phase approximation. These more approximate approaches are crucial for any application with real materials in mind. Furthermore, we use the dual boson method to calculate observables of the extended Hubbard models directly and benchmark these against determinant quantum Monte Carlo simulations of the effective Hubbard model.

Effects of Ignoring Item Interaction on Item Parameter Estimation and Detection of Interacting Items

ERIC Educational Resources Information Center

Chen, Cheng-Te; Wang, Wen-Chung

2007-01-01

This study explores the effects of ignoring item interaction on item parameter estimation and the efficiency of using the local dependence index Q[subscript 3] and the SAS NLMIXED procedure to detect item interaction under the three-parameter logistic model and the generalized partial credit model. Through simulations, it was found that ignoring…

Chimera regimes in a ring of oscillators with local nonlinear interaction

NASA Astrophysics Data System (ADS)

Shepelev, Igor A.; Zakharova, Anna; Vadivasova, Tatiana E.

2017-03-01

One of important problems concerning chimera states is the conditions of their existence and stability. Until now, it was assumed that chimeras could arise only in ensembles with nonlocal character of interactions. However, this assumption is not exactly right. In some special cases chimeras can be realized for local type of coupling [1-3]. We propose a simple model of ensemble with local coupling when chimeras are realized. This model is a ring of linear oscillators with the local nonlinear unidirectional interaction. Chimera structures in the ring are found using computer simulations for wide area of values of parameters. Diagram of the regimes on plane of control parameters is plotted and scenario of chimera destruction are studied when the parameters are changed.

The role of quench rate in colloidal gels.

PubMed

Royall, C Patrick; Malins, Alex

2012-01-01

Interactions between colloidal particles have hitherto usually been fixed by the suspension composition. Recent experimental developments now enable the control of interactions in situ. Here we use Brownian dynamics simulations to investigate the effect of controlling interactions upon gelation, by "quenching" the system from an equilibrium fluid to a gel. We find that, contrary to the normal case of an instantaneous quench, where the local structure of the gel is highly disordered, controlled quenching results in a gel with a much higher degree of local order. Under sufficiently slow quenching, local crystallisation is found, which is strongly enhanced when a monodisperse system is used. The higher the degree of local order, the smaller the mean squared displacement, indicating an enhancement of gel stability.

Look and Feel: Haptic Interaction for Biomedicine

DTIC Science & Technology

1995-10-01

algorithm that is evaluated within the topology of the model. During each time step, forces are summed for each mobile atom based on external forces...volumetric properties; (b) conserving computation power by rendering media local to the interaction point; and (c) evaluating the simulation within...alteration of the model topology. Simulation of the DSM state is accomplished by a multi-step algorithm that is evaluated within the topology of the

Plasphonics: local hybridization of plasmons and phonons.

PubMed

Marty, Renaud; Mlayah, Adnen; Arbouet, Arnaud; Girard, Christian; Tripathy, Sudhiranjan

2013-02-25

We show that the interaction between localized surface plasmons sustained by a metallic nano-antenna and delocalized phonons lying at the surface of an heteropolar semiconductor can generate a new class of hybrid electromagnetic modes. These plasphonic modes are investigated using an analytical model completed by accurate Green dyadic numerical simulations. When surface plasmon and surface phonon frequencies match, the optical resonances exhibit a large Rabi splitting typical of strongly interacting two-level systems. Based on numerical simulations of the electric near-field maps, we investigate the nature of the plaphonic excitations. In particular, we point out a strong local field enhancement boosted by the phononic surface. This effect is interpreted in terms of light harvesting by the plasmonic antenna from the phononic surface. We thus introduce the concept of active phononic surfaces that may be exploited for far-infared optoelectronic devices and sensors.

Ocean-Atmosphere Interactions Modulate Irrigation's Climate Impacts

NASA Technical Reports Server (NTRS)

Krakauer, Nir Y.; Puma, Michael J.; Cook, Benjamin I.; Gentine, Pierre; Nazarenko, Larissa

2016-01-01

Numerous studies have focused on the local and regional climate effects of irrigated agriculture and other land cover and land use change (LCLUC) phenomena, but there are few studies on the role of ocean- atmosphere interaction in modulating irrigation climate impacts. Here, we compare simulations with and without interactive sea surface temperatures of the equilibrium effect on climate of contemporary (year 2000) irrigation geographic extent and intensity. We find that ocean-atmosphere interaction does impact the magnitude of global-mean and spatially varying climate impacts, greatly increasing their global reach. Local climate effects in the irrigated regions remain broadly similar, while non-local effects, particularly over the oceans, tend to be larger. The interaction amplifies irrigation-driven standing wave patterns in the tropics and mid-latitudes in our simulations, approximately doubling the global-mean amplitude of surface temperature changes due to irrigation. The fractions of global area experiencing significant annual-mean surface air temperature and precipitation change also approximately double with ocean-atmosphere interaction. Subject to confirmation with other models, these findings imply that LCLUC is an important contributor to climate change even in remote areas such as the Southern Ocean, and that attribution studies should include interactive oceans and need to consider LCLUC, including irrigation, as a truly global forcing that affects climate and the water cycle over ocean as well as land areas.

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

PubMed Central

Koldsø, Heidi; Shorthouse, David; Hélie, Jean; Sansom, Mark S. P.

2014-01-01

Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins. PMID:25340788

Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

PubMed

Koldsø, Heidi; Shorthouse, David; Hélie, Jean; Sansom, Mark S P

2014-10-01

Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

Atomic quantum simulation of the lattice gauge-Higgs model: Higgs couplings and emergence of exact local gauge symmetry.

PubMed

Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

2013-09-13

Recently, the possibility of quantum simulation of dynamical gauge fields was pointed out by using a system of cold atoms trapped on each link in an optical lattice. However, to implement exact local gauge invariance, fine-tuning the interaction parameters among atoms is necessary. In the present Letter, we study the effect of violation of the U(1) local gauge invariance by relaxing the fine-tuning of the parameters and showing that a wide variety of cold atoms is still a faithful quantum simulator for a U(1) gauge-Higgs model containing a Higgs field sitting on sites. The clarification of the dynamics of this gauge-Higgs model sheds some light upon various unsolved problems, including the inflation process of the early Universe. We study the phase structure of this model by Monte Carlo simulation and also discuss the atomic characteristics of the Higgs phase in each simulator.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

PubMed Central

Chen, Yang; Zhang, Michael Q.

2018-01-01

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. PMID:29440282

Interactive Tax Reform: Simulating Impacts of Legislative Proposals.

ERIC Educational Resources Information Center

Downing, Roger H.; And Others

1985-01-01

Pennsylvania's mathematical modeling technique to evaluate tax reform proposals requires the following data: personal income at the local level and measures of the breakdown of property tax payment by land use classification. The simulation technique could be readily adapted in reorganizing educational finance systems. (MLF)

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

A Tool to Simulate the Transmission, Reception, and Execution of Interactive TV Applications

PubMed Central

Kulesza, Raoni; Rodrigues, Thiago; Machado, Felipe A. L.; Santos, Celso A. S.

2017-01-01

The emergence of Interactive Digital Television (iDTV) opened a set of technological possibilities that go beyond those offered by conventional TV. Among these opportunities we can highlight interactive contents that run together with linear TV program (television service where the viewer has to watch a scheduled TV program at the particular time it is offered and on the particular channel it is presented on). However, developing interactive contents for this new platform is not as straightforward as, for example, developing Internet applications. One of the options to make this development process easier and safer is to use an iDTV simulator. However, after having investigated some of the existing iDTV simulation environments, we have found a limitation: these simulators mainly present solutions focused on the TV receiver, whose interactive content must be loaded in advance by the programmer to a local repository (e.g., Hard Drive, USB). Therefore, in this paper, we propose a tool, named BiS (Broadcast iDTV content Simulator), which makes possible a broader solution for the simulation of interactive contents. It allows simulating the transmission of interactive content along with the linear TV program (simulating the transmission of content over the air and in broadcast to the receivers). To enable this, we defined a generic and easy-to-customize communication protocol that was implemented in the tool. The proposed environment differs from others because it allows simulating reception of both linear content and interactive content while running Java applications to allow such a content presentation. PMID:28280770

Quantum phases with differing computational power.

PubMed

Cui, Jian; Gu, Mile; Kwek, Leong Chuan; Santos, Marcelo França; Fan, Heng; Vedral, Vlatko

2012-05-01

The observation that concepts from quantum information has generated many alternative indicators of quantum phase transitions hints that quantum phase transitions possess operational significance with respect to the processing of quantum information. Yet, studies on whether such transitions lead to quantum phases that differ in their capacity to process information remain limited. Here we show that there exist quantum phase transitions that cause a distinct qualitative change in our ability to simulate certain quantum systems under perturbation of an external field by local operations and classical communication. In particular, we show that in certain quantum phases of the XY model, adiabatic perturbations of the external magnetic field can be simulated by local spin operations, whereas the resulting effect within other phases results in coherent non-local interactions. We discuss the potential implications to adiabatic quantum computation, where a computational advantage exists only when adiabatic perturbation results in coherent multi-body interactions.

Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection

PubMed Central

Alam, Maksudul; Deng, Xinwei; Philipson, Casandra; Bassaganya-Riera, Josep; Bisset, Keith; Carbo, Adria; Eubank, Stephen; Hontecillas, Raquel; Hoops, Stefan; Mei, Yongguo; Abedi, Vida; Marathe, Madhav

2015-01-01

Agent-based models (ABM) are widely used to study immune systems, providing a procedural and interactive view of the underlying system. The interaction of components and the behavior of individual objects is described procedurally as a function of the internal states and the local interactions, which are often stochastic in nature. Such models typically have complex structures and consist of a large number of modeling parameters. Determining the key modeling parameters which govern the outcomes of the system is very challenging. Sensitivity analysis plays a vital role in quantifying the impact of modeling parameters in massively interacting systems, including large complex ABM. The high computational cost of executing simulations impedes running experiments with exhaustive parameter settings. Existing techniques of analyzing such a complex system typically focus on local sensitivity analysis, i.e. one parameter at a time, or a close “neighborhood” of particular parameter settings. However, such methods are not adequate to measure the uncertainty and sensitivity of parameters accurately because they overlook the global impacts of parameters on the system. In this article, we develop novel experimental design and analysis techniques to perform both global and local sensitivity analysis of large-scale ABMs. The proposed method can efficiently identify the most significant parameters and quantify their contributions to outcomes of the system. We demonstrate the proposed methodology for ENteric Immune SImulator (ENISI), a large-scale ABM environment, using a computational model of immune responses to Helicobacter pylori colonization of the gastric mucosa. PMID:26327290

Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection.

PubMed

Alam, Maksudul; Deng, Xinwei; Philipson, Casandra; Bassaganya-Riera, Josep; Bisset, Keith; Carbo, Adria; Eubank, Stephen; Hontecillas, Raquel; Hoops, Stefan; Mei, Yongguo; Abedi, Vida; Marathe, Madhav

2015-01-01

Agent-based models (ABM) are widely used to study immune systems, providing a procedural and interactive view of the underlying system. The interaction of components and the behavior of individual objects is described procedurally as a function of the internal states and the local interactions, which are often stochastic in nature. Such models typically have complex structures and consist of a large number of modeling parameters. Determining the key modeling parameters which govern the outcomes of the system is very challenging. Sensitivity analysis plays a vital role in quantifying the impact of modeling parameters in massively interacting systems, including large complex ABM. The high computational cost of executing simulations impedes running experiments with exhaustive parameter settings. Existing techniques of analyzing such a complex system typically focus on local sensitivity analysis, i.e. one parameter at a time, or a close "neighborhood" of particular parameter settings. However, such methods are not adequate to measure the uncertainty and sensitivity of parameters accurately because they overlook the global impacts of parameters on the system. In this article, we develop novel experimental design and analysis techniques to perform both global and local sensitivity analysis of large-scale ABMs. The proposed method can efficiently identify the most significant parameters and quantify their contributions to outcomes of the system. We demonstrate the proposed methodology for ENteric Immune SImulator (ENISI), a large-scale ABM environment, using a computational model of immune responses to Helicobacter pylori colonization of the gastric mucosa.

Self-Interaction Corrected Electronic Structure and Energy Gap of CuAlO2 beyond Local Density Approximation

NASA Astrophysics Data System (ADS)

Nakanishi, Akitaka

2011-05-01

We implemented a self-interaction correction (SIC) into first-principles calculation code to go beyond local density approximation and applied it to CuAlO2. Our simulation shows that the valence band width calculated within the SIC is narrower than that calculated without the SIC because the SIC makes the d-band potential deeper. The energy gap calculated within the SIC expands and is close to experimental data.

Modeling Membrane Deformations and Lipid Demixing upon Protein-Membrane Interaction: The BAR Dimer Adsorption

PubMed Central

Khelashvili, George; Harries, Daniel; Weinstein, Harel

2009-01-01

We use a self-consistent mean-field theory, designed to investigate membrane reshaping and lipid demixing upon interaction with proteins, to explore BAR domains interacting with large patches of lipid membranes of heterogeneous compositions. The computational model includes contributions to the system free energy from electrostatic interactions and elastic energies of the membrane, as well as salt and lipid mixing entropies. The results from our simulation of a single adsorbing Amphiphysin BAR dimer indicate that it is capable of stabilizing a significantly curved membrane. However, we predict that such deformations will occur only for membrane patches that have the inherent propensity for high curvature, reflected in the tendency to create local distortions that closely match the curvature of the BAR dimer itself. Such favorable preconditioning for BAR-membrane interaction may be the result of perturbations such as local lipid demixing induced by the interaction, or of a prior insertion of the BAR domain's amphiphatic N-helix. From our simulations it appears that local segregation of charged lipids under the influence of the BAR dimer cannot produce high enough asymmetry between bilayer leaflets to induce significant bending. In the absence of additional energy contributions that favor membrane asymmetry, the membrane will remain nearly flat upon single BAR dimer adsorption, relative to the undulation expected from thermal fluctuations. Thus, we conclude that the N-helix insertions have a critical mechanistic role in the local perturbation and curving of the membrane, which is then stabilized by the electrostatic interaction with the BAR dimer. We discuss how these results can be used to estimate the tendency of BARs to bend membranes in terms of a spatially nonisotropic spontaneous curvature. PMID:19751667

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides.

PubMed

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-01-13

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

NASA Astrophysics Data System (ADS)

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-03-01

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

Molecular dynamics simulations of oxide memory resistors (memristors).

PubMed

Savel'ev, S E; Alexandrov, A S; Bratkovsky, A M; Williams, R Stanley

2011-06-24

Reversible bipolar nanoswitches that can be set and read electronically in a solid-state two-terminal device are very promising for applications. We have performed molecular dynamics simulations that mimic systems with oxygen vacancies interacting via realistic potentials and driven by an external bias voltage. The competing short- and long-range interactions among charged mobile vacancies lead to density fluctuations and short-range ordering, while illustrating some aspects of observed experimental behavior, such as memristor polarity inversion. The simulations show that the 'localized conductive filaments' and 'uniform push/pull' models for memristive switching are actually two extremes of the one stochastic mechanism.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Hao, Ming-Hong; Scheraga, Harold A.

1995-01-01

A comparative study of protein folding with an analytical theory and computer simulations, respectively, is reported. The theory is based on an improved mean-field formalism which, in addition to the usual mean-field approximations, takes into account the distributions of energies in the subsets of conformational states. Sequence-specific properties of proteins are parametrized in the theory by two sets of variables, one for the energetics of mean-field interactions and one for the distribution of energies. Simulations are carried out on model polypeptides with different sequences, with different chain lengths, and with different interaction potentials, ranging from strong biases towards certain local chain states (bond angles and torsional angles) to complete absence of local conformational preferences. Theoretical analysis of the simulation results for the model polypeptides reveals three different types of behavior in the folding transition from the statistical coiled state to the compact globular state; these include a cooperative two-state transition, a continuous folding, and a glasslike transition. It is found that, with the fitted theoretical parameters which are specific for each polypeptide under a different potential, the mean-field theory can describe the thermodynamic properties and folding behavior of the different polypeptides accurately. By comparing the theoretical descriptions with simulation results, we verify the basic assumptions of the theory and, thereby, obtain new insights about the folding transitions of proteins. It is found that the cooperativity of the first-order folding transition of the model polypeptides is determined mainly by long-range interactions, in particular the dipolar orientation; the local interactions (e.g., bond-angle and torsion-angle potentials) have only marginal effect on the cooperative characteristic of the folding, but have a large impact on the difference in energy between the folded lowest-energy structure and the unfolded conformations of a protein.

A New Kinetic Simulation Model with Self-Consistent Calculation of Regolith Layer Charging for Moon-Plasma Interactions

NASA Astrophysics Data System (ADS)

Han, D.; Wang, J.

2015-12-01

The moon-plasma interactions and the resulting surface charging have been subjects of extensive recent investigations. While many particle-in-cell (PIC) based simulation models have been developed, all existing PIC simulation models treat the surface of the Moon as a boundary condition to the plasma flow. In such models, the surface of the Moon is typically limited to simple geometry configurations, the surface floating potential is calculated from a simplified current balance condition, and the electric field inside the regolith layer cannot be resolved. This paper presents a new full particle PIC model to simulate local scale plasma flow and surface charging. A major feature of this new model is that the surface is treated as an "interface" between two mediums rather than a boundary, and the simulation domain includes not only the plasma but also the regolith layer and the bedrock underneath it. There are no limitations on the surface shape. An immersed-finite-element field solver is applied which calculates the regolith surface floating potential and the electric field inside the regolith layer directly from local charge deposition. The material property of the regolith layer is also explicitly included in simulation. This new model is capable of providing a self-consistent solution to the plasma flow field, lunar surface charging, the electric field inside the regolith layer and the bedrock for realistic surface terrain. This new model is applied to simulate lunar surface-plasma interactions and surface charging under various ambient plasma conditions. The focus is on the lunar terminator region, where the combined effects from the low sun elevation angle and the localized plasma wake generated by plasma flow over a rugged terrain can generate strongly differentially charged surfaces and complex dust dynamics. We discuss the effects of the regolith properties and regolith layer charging on the plasma flow field, dust levitation, and dust transport.

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

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

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; Giese, Timothy J.

2015-12-21

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom’s local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion andmore » dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the S{sub N}2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.« less

Non-fragile consensus algorithms for a network of diffusion PDEs with boundary local interaction

NASA Astrophysics Data System (ADS)

Xiong, Jun; Li, Junmin

2017-07-01

In this study, non-fragile consensus algorithm is proposed to solve the average consensus problem of a network of diffusion PDEs, modelled by boundary controlled heat equations. The problem deals with the case where the Neumann-type boundary controllers are corrupted by additive persistent disturbances. To achieve consensus between agents, a linear local interaction rule addressing this requirement is given. The proposed local interaction rules are analysed by applying a Lyapunov-based approach. The multiplicative and additive non-fragile feedback control algorithms are designed and sufficient conditions for the consensus of the multi-agent systems are presented in terms of linear matrix inequalities, respectively. Simulation results are presented to support the effectiveness of the proposed algorithms.

Interactions of nonlocal dark solitons under competing cubic-quintic nonlinearities.

PubMed

Chen, Wei; Shen, Ming; Kong, Qian; Shi, Jielong; Wang, Qi; Krolikowski, Wieslaw

2014-04-01

We investigate analytically and numerically the interactions of dark solitons under competing nonlocal cubic and local quintic nonlinearities. It is shown that the self-defocusing quintic nonlinearity will strengthen the attractive interaction and decrease the relative distance between solitons, whereas the self-focusing quintic nonlinearity will enhance the repulsive interaction and increase soliton separation. We demonstrate these results by approximate variational approach and direct numerical simulation.

System theoretic models for high density VLSI structures

NASA Astrophysics Data System (ADS)

Dickinson, Bradley W.; Hopkins, William E., Jr.

This research project involved the development of mathematical models for analysis, synthesis, and simulation of large systems of interacting devices. The work was motivated by problems that may become important in high density VLSI chips with characteristic feature sizes less than 1 micron: it is anticipated that interactions of neighboring devices will play an important role in the determination of circuit properties. It is hoped that the combination of high device densities and such local interactions can somehow be exploited to increase circuit speed and to reduce power consumption. To address these issues from the point of view of system theory, research was pursued in the areas of nonlinear and stochastic systems and into neural network models. Statistical models were developed to characterize various features of the dynamic behavior of interacting systems. Random process models for studying the resulting asynchronous modes of operation were investigated. The local interactions themselves may be modeled as stochastic effects. The resulting behavior was investigated through the use of various scaling limits, and by a combination of other analytical and simulation techniques. Techniques arising in a variety of disciplines where models of interaction were formulated and explored were considered and adapted for use.

Dynamics of Entangled Polymers: Role of Attractive Interactions

NASA Astrophysics Data System (ADS)

Grest, Gary S.; Koski, Jason

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. Numerical simulations of highly coarse grained models are often used to follow chain mobility from the intermediate Rouse and reptation regimes to the late time diffusive regime. In these models, purely repulsive interactions between monomers are typically used because it is less computationally expensive than including attractive interactions. The effect of including the attractive interaction on the local and macroscopic properties of entangled polymer melts is explored over a wide temperature range using large scale molecular dynamics simulations. Attractive interactions are shown to have little effect on the local packing for all temperatures T and chain mobility for T higher than about twice the glass transition Tg. For lower T, the attractive interactions play a significant role, reducing the chain mobility compared to the repulsive case. As T approaches Tg breakdown of time-temperature superposition for the stress autocorrelation function is observed. Sandia National Labs is a multiprogram laboratory managed and operated by Sandia Corporation, a Lockheed-Martin Company, for the U.S. Dept of Energy under Contract No. DEAC04-94AL85000.

Temperature-dependent errors in nuclear lattice simulations

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

Lee, Dean; Thomson, Richard

2007-06-15

We study the temperature dependence of discretization errors in nuclear lattice simulations. We find that for systems with strong attractive interactions the predominant error arises from the breaking of Galilean invariance. We propose a local 'well-tempered' lattice action which eliminates much of this error. The well-tempered action can be readily implemented in lattice simulations for nuclear systems as well as cold atomic Fermi systems.

Local structure of percolating gels at very low volume fractions

NASA Astrophysics Data System (ADS)

Griffiths, Samuel; Turci, Francesco; Royall, C. Patrick

2017-01-01

The formation of colloidal gels is strongly dependent on the volume fraction of the system and the strength of the interactions between the colloids. Here we explore very dilute solutions by the means of numerical simulations and show that, in the absence of hydrodynamic interactions and for sufficiently strong interactions, percolating colloidal gels can be realised at very low values of the volume fraction. Characterising the structure of the network of the arrested material we find that, when reducing the volume fraction, the gels are dominated by low-energy local structures, analogous to the isolated clusters of the interaction potential. Changing the strength of the interaction allows us to tune the compactness of the gel as characterised by the fractal dimension, with low interaction strength favouring more chain-like structures.

Modeling of fatigue crack induced nonlinear ultrasonics using a highly parallelized explicit local interaction simulation approach

NASA Astrophysics Data System (ADS)

Shen, Yanfeng; Cesnik, Carlos E. S.

2016-04-01

This paper presents a parallelized modeling technique for the efficient simulation of nonlinear ultrasonics introduced by the wave interaction with fatigue cracks. The elastodynamic wave equations with contact effects are formulated using an explicit Local Interaction Simulation Approach (LISA). The LISA formulation is extended to capture the contact-impact phenomena during the wave damage interaction based on the penalty method. A Coulomb friction model is integrated into the computation procedure to capture the stick-slip contact shear motion. The LISA procedure is coded using the Compute Unified Device Architecture (CUDA), which enables the highly parallelized supercomputing on powerful graphic cards. Both the explicit contact formulation and the parallel feature facilitates LISA's superb computational efficiency over the conventional finite element method (FEM). The theoretical formulations based on the penalty method is introduced and a guideline for the proper choice of the contact stiffness is given. The convergence behavior of the solution under various contact stiffness values is examined. A numerical benchmark problem is used to investigate the new LISA formulation and results are compared with a conventional contact finite element solution. Various nonlinear ultrasonic phenomena are successfully captured using this contact LISA formulation, including the generation of nonlinear higher harmonic responses. Nonlinear mode conversion of guided waves at fatigue cracks is also studied.

Molecular simulations of multimodal ligand-protein binding: elucidation of binding sites and correlation with experiments.

PubMed

Freed, Alexander S; Garde, Shekhar; Cramer, Steven M

2011-11-17

Multimodal chromatography, which employs more than one mode of interaction between ligands and proteins, has been shown to have unique selectivity and high efficacy for protein purification. To test the ability of free solution molecular dynamics (MD) simulations in explicit water to identify binding regions on the protein surface and to shed light on the "pseudo affinity" nature of multimodal interactions, we performed MD simulations of a model protein ubiquitin in aqueous solution of free ligands. Comparisons of MD with NMR spectroscopy of ubiquitin mutants in solutions of free ligands show a good agreement between the two with regard to the preferred binding region on the surface of the protein and several binding sites. MD simulations also identify additional binding sites that were not observed in the NMR experiments. "Bound" ligands were found to be sufficiently flexible and to access a number of favorable conformations, suggesting only a moderate loss of ligand entropy in the "pseudo affinity" binding of these multimodal ligands. Analysis of locations of chemical subunits of the ligand on the protein surface indicated that electrostatic interaction units were located on the periphery of the preferred binding region on the protein. The analysis of the electrostatic potential, the hydrophobicity maps, and the binding of both acetate and benzene probes were used to further study the localization of individual ligand moieties. These results suggest that water-mediated electrostatic interactions help the localization and orientation of the MM ligand to the binding region with additional stability provided by nonspecific hydrophobic interactions.

Molecular driving forces defining lipid positions around aquaporin-0

PubMed Central

Aponte-Santamaría, Camilo; Briones, Rodolfo; Schenk, Andreas D.; Walz, Thomas; de Groot, Bert L.

2012-01-01

Lipid–protein interactions play pivotal roles in biological membranes. Electron crystallographic studies of the lens-specific water channel aquaporin-0 (AQP0) revealed atomistic views of such interactions, by providing high-resolution structures of annular lipids surrounding AQP0. It remained unclear, however, whether these lipid structures are representative of the positions of unconstrained lipids surrounding an individual protein, and what molecular determinants define the lipid positions around AQP0. We addressed these questions by using molecular dynamics simulations and crystallographic refinement, and calculated time-averaged densities of dimyristoyl-phosphatidylcholine lipids around AQP0. Our simulations demonstrate that, although the experimentally determined crystallographic lipid positions are constrained by the crystal packing, they appropriately describe the behavior of unconstrained lipids around an individual AQP0 tetramer, and thus likely represent physiologically relevant lipid positions.While the acyl chains were well localized, the lipid head groups were not. Furthermore, in silico mutations showed that electrostatic interactions do not play a major role attracting these phospholipids towards AQP0. Instead, the mobility of the protein crucially modulates the lipid localization and explains the difference in lipid density between extracellular and cytoplasmic leaflets. Moreover, our simulations support a general mechanism in which membrane proteins laterally diffuse accompanied by several layers of localized lipids, with the positions of the annular lipids being influenced the most by the protein surface. We conclude that the acyl chains rather than the head groups define the positions of dimyristoyl-phosphatidylcholine lipids around AQP0. Lipid localization is largely determined by the mobility of the protein surface, whereas hydrogen bonds play an important but secondary role. PMID:22679286

Towards a bulk approach to local interactions of hydrometeors

NASA Astrophysics Data System (ADS)

Baumgartner, Manuel; Spichtinger, Peter

2018-02-01

The growth of small cloud droplets and ice crystals is dominated by the diffusion of water vapor. Usually, Maxwell's approach to growth for isolated particles is used in describing this process. However, recent investigations show that local interactions between particles can change diffusion properties of cloud particles. In this study we develop an approach for including these local interactions into a bulk model approach. For this purpose, a simplified framework of local interaction is proposed and governing equations are derived from this setup. The new model is tested against direct simulations and incorporated into a parcel model framework. Using the parcel model, possible implications of the new model approach for clouds are investigated. The results indicate that for specific scenarios the lifetime of cloud droplets in subsaturated air may be longer (e.g., for an initially water supersaturated air parcel within a downdraft). These effects might have an impact on mixed-phase clouds, for example in terms of riming efficiencies.

Soliton-cnoidal interactional wave solutions for the reduced Maxwell-Bloch equations

NASA Astrophysics Data System (ADS)

Huang, Li-Li; Qiao, Zhi-Jun; Chen, Yong

2018-02-01

Based on nonlocal symmetry method, localized excitations and interactional solutions are investigated for the reduced Maxwell-Bloch equations. The nonlocal symmetries of the reduced Maxwell-Bloch equations are obtained by the truncated Painleve expansion approach and the Mobious invariant property. The nonlocal symmetries are localized to a prolonged system by introducing suitable auxiliary dependent variables. The extended system can be closed and a novel Lie point symmetry system is constructed. By solving the initial value problems, a new type of finite symmetry transformations is obtained to derive periodic waves, Ma breathers and breathers travelling on the background of periodic line waves. Then rich exact interactional solutions are derived between solitary waves and other waves including cnoidal waves, rational waves, Painleve waves, and periodic waves through similarity reductions. In particular, several new types of localized excitations including rogue waves are found, which stem from the arbitrary function generated in the process of similarity reduction. By computer numerical simulation, the dynamics of these localized excitations and interactional solutions are discussed, which exhibit meaningful structures.

Quantum Monte Carlo calculations of neutron matter with chiral three-body forces

DOE PAGES

Tews, I.; Gandolfi, Stefano; Gezerlis, A.; ...

2016-02-02

Chiral effective field theory (EFT) enables a systematic description of low-energy hadronic interactions with controlled theoretical uncertainties. For strongly interacting systems, quantum Monte Carlo (QMC) methods provide some of the most accurate solutions, but they require as input local potentials. We have recently constructed local chiral nucleon-nucleon (NN) interactions up to next-to-next-to-leading order (N 2LO). Chiral EFT naturally predicts consistent many-body forces. In this paper, we consider the leading chiral three-nucleon (3N) interactions in local form. These are included in auxiliary field diffusion Monte Carlo (AFDMC) simulations. We present results for the equation of state of neutron matter and formore » the energies and radii of neutron drops. Specifically, we study the regulator dependence at the Hartree-Fock level and in AFDMC and find that present local regulators lead to less repulsion from 3N forces compared to the usual nonlocal regulators.« less

Close packing in curved space by simulated annealing

NASA Astrophysics Data System (ADS)

Wille, L. T.

1987-12-01

The problem of packing spheres of a maximum radius on the surface of a four-dimensional hypersphere is considered. It is shown how near-optimal solutions can be obtained by packing soft spheres, modelled as classical particles interacting under an inverse power potential, followed by a subsequent hardening of the interaction. In order to avoid trapping in high-lying local minima, the simulated annealing method is used to optimise the soft-sphere packing. Several improvements over other work (based on local optimisation of random initial configurations of hard spheres) have been found. The freezing behaviour of this system is discussed as a function of particle number, softness of the potential and cooling rate. Apart from their geometric interest, these results are useful in the study of topological frustration, metallic glasses and quasicrystals.

An individual-based modeling approach to simulate the effects of cellular nutrient competition on Escherichia coli K-12 MG1655 colony behavior and interactions in aerobic structured food systems.

PubMed

Tack, Ignace L M M; Logist, Filip; Noriega Fernández, Estefanía; Van Impe, Jan F M

2015-02-01

Traditional kinetic models in predictive microbiology reliably predict macroscopic dynamics of planktonically-growing cell cultures in homogeneous liquid food systems. However, most food products have a semi-solid structure, where microorganisms grow locally in colonies. Individual colony cells exhibit strongly different and non-normally distributed behavior due to local nutrient competition. As a result, traditional models considering average population behavior in a homogeneous system do not describe colony dynamics in full detail. To incorporate local resource competition and individual cell differences, an individual-based modeling approach has been applied to Escherichia coli K-12 MG1655 colonies, considering the microbial cell as modeling unit. The first contribution of this individual-based model is to describe single colony growth under nutrient-deprived conditions. More specifically, the linear and stationary phase in the evolution of the colony radius, the evolution from a disk-like to branching morphology, and the emergence of a starvation zone in the colony center are simulated and compared to available experimental data. These phenomena occur earlier at more severe nutrient depletion conditions, i.e., at lower nutrient diffusivity and initial nutrient concentration in the medium. Furthermore, intercolony interactions have been simulated. Higher inoculum densities lead to stronger intercolony interactions, such as colony merging and smaller colony sizes, due to nutrient competition. This individual-based model contributes to the elucidation of characteristic experimentally observed colony behavior from mechanistic information about cellular physiology and interactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration

NASA Technical Reports Server (NTRS)

Lin, Risheng; Afjeh, Abdollah A.

2003-01-01

This paper discusses the detailed design of an XML databinding framework for aircraft engine simulation. The framework provides an object interface to access and use engine data. while at the same time preserving the meaning of the original data. The Language independent representation of engine component data enables users to move around XML data using HTTP through disparate networks. The application of this framework is demonstrated via a web-based turbofan propulsion system simulation using the World Wide Web (WWW). A Java Servlet based web component architecture is used for rendering XML engine data into HTML format and dealing with input events from the user, which allows users to interact with simulation data from a web browser. The simulation data can also be saved to a local disk for archiving or to restart the simulation at a later time.

Modeling Local Interactions during the Motion of Cyanobacteria

PubMed Central

Galante, Amanda; Wisen, Susanne; Bhaya, Devaki; Levy, Doron

2012-01-01

Synechocystis sp., a common unicellular freshwater cyanobacterium, has been used as a model organism to study phototaxis, an ability to move in the direction of a light source. This microorganism displays a number of additional characteristics such as delayed motion, surface dependence, and a quasi-random motion, where cells move in a seemingly disordered fashion instead of in the direction of the light source, a global force on the system. These unexplained motions are thought to be modulated by local interactions between cells such as intercellular communication. In this paper, we consider only local interactions of these phototactic cells in order to mathematically model this quasi-random motion. We analyze an experimental data set to illustrate the presence of quasi-random motion and then derive a stochastic dynamic particle system modeling interacting phototactic cells. The simulations of our model are consistent with experimentally observed phototactic motion. PMID:22713858

Numerical simulation of magnetic interactions in polycrystalline YFeO 3

NASA Astrophysics Data System (ADS)

Lima, E.; Martins, T. B.; Rechenberg, H. R.; Goya, G. F.; Cavelius, C.; Rapalaviciute, R.; Hao, S.; Mathur, S.

The magnetic behavior of polycrystalline yttrium orthoferrite was studied from the experimental and theoretical points of view. Magnetization measurements up to 170 kOe were carried out on a single-phase YFeO 3 sample synthesized from heterobimetallic alkoxides. The complex interplay between weak-ferromagnetic and antiferromagnetic interactions, observed in the experimental M( H) curves, was successfully simulated by locally minimizing the magnetic energy of two interacting Fe sublattices. The resulting values of exchange field ( HE=5590 kOe), anisotropy field ( HA=0.5 kOe) and Dzyaloshinsky-Moriya antisymmetric field ( HD=149 kOe) are in good agreement with previous reports on this system.

Compliant energy and momentum conservation in NEGF simulation of electron-phonon scattering in semiconductor nano-wire transistors

NASA Astrophysics Data System (ADS)

Barker, J. R.; Martinez, A.; Aldegunde, M.

2012-05-01

The modelling of spatially inhomogeneous silicon nanowire field-effect transistors has benefited from powerful simulation tools built around the Keldysh formulation of non-equilibrium Green function (NEGF) theory. The methodology is highly efficient for situations where the self-energies are diagonal (local) in space coordinates. It has thus been common practice to adopt diagonality (locality) approximations. We demonstrate here that the scattering kernel that controls the self-energies for electron-phonon interactions is generally non-local on the scale of at least a few lattice spacings (and thus within the spatial scale of features in extreme nano-transistors) and for polar optical phonon-electron interactions may be very much longer. It is shown that the diagonality approximation strongly under-estimates the scattering rates for scattering on polar optical phonons. This is an unexpected problem in silicon devices but occurs due to strong polar SO phonon-electron interactions extending into a narrow silicon channel surrounded by high kappa dielectric in wrap-round gate devices. Since dissipative inelastic scattering is already a serious problem for highly confined devices it is concluded that new algorithms need to be forthcoming to provide appropriate and efficient NEGF tools.

An approach for drag correction based on the local heterogeneity for gas-solid flows

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

Li, Tingwen; Wang, Limin; Rogers, William

2016-09-22

The drag models typically used for gas-solids interaction are mainly developed based on homogeneous systems of flow passing fixed particle assembly. It has been shown that the heterogeneous structures, i.e., clusters and bubbles in fluidized beds, need to be resolved to account for their effect in the numerical simulations. Since the heterogeneity is essentially captured through the local concentration gradient in the computational cells, this study proposes a simple approach to account for the non-uniformity of solids spatial distribution inside a computational cell and its effect on the interaction between gas and solid phases. Finally, to validate this approach, themore » predicted drag coefficient has been compared to the results from direct numerical simulations. In addition, the need to account for this type of heterogeneity is discussed for a periodic riser flow simulation with highly resolved numerical grids and the impact of the proposed correction for drag is demonstrated.« less

Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces.

PubMed

Dongmo Foumthuim, Cedrix J; Corazza, Alessandra; Esposito, Gennaro; Fogolari, Federico

2017-11-21

Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.

Modeling the long-term evolution of space debris

DOEpatents

Nikolaev, Sergei; De Vries, Willem H.; Henderson, John R.; Horsley, Matthew A.; Jiang, Ming; Levatin, Joanne L.; Olivier, Scot S.; Pertica, Alexander J.; Phillion, Donald W.; Springer, Harry K.

2017-03-07

A space object modeling system that models the evolution of space debris is provided. The modeling system simulates interaction of space objects at simulation times throughout a simulation period. The modeling system includes a propagator that calculates the position of each object at each simulation time based on orbital parameters. The modeling system also includes a collision detector that, for each pair of objects at each simulation time, performs a collision analysis. When the distance between objects satisfies a conjunction criterion, the modeling system calculates a local minimum distance between the pair of objects based on a curve fitting to identify a time of closest approach at the simulation times and calculating the position of the objects at the identified time. When the local minimum distance satisfies a collision criterion, the modeling system models the debris created by the collision of the pair of objects.

Dynamic heterogeneities and non-Gaussian behavior in two-dimensional randomly confined colloidal fluids

NASA Astrophysics Data System (ADS)

Schnyder, Simon K.; Skinner, Thomas O. E.; Thorneywork, Alice L.; Aarts, Dirk G. A. L.; Horbach, Jürgen; Dullens, Roel P. A.

2017-03-01

A binary mixture of superparamagnetic colloidal particles is confined between glass plates such that the large particles become fixed and provide a two-dimensional disordered matrix for the still mobile small particles, which form a fluid. By varying fluid and matrix area fractions and tuning the interactions between the superparamagnetic particles via an external magnetic field, different regions of the state diagram are explored. The mobile particles exhibit delocalized dynamics at small matrix area fractions and localized motion at high matrix area fractions, and the localization transition is rounded by the soft interactions [T. O. E. Skinner et al., Phys. Rev. Lett. 111, 128301 (2013), 10.1103/PhysRevLett.111.128301]. Expanding on previous work, we find the dynamics of the tracers to be strongly heterogeneous and show that molecular dynamics simulations of an ideal gas confined in a fixed matrix exhibit similar behavior. The simulations show how these soft interactions make the dynamics more heterogeneous compared to the disordered Lorentz gas and lead to strong non-Gaussian fluctuations.

Communication: Polymer entanglement dynamics: Role of attractive interactions

DOE PAGES

Grest, Gary S.

2016-10-10

The coupled dynamics of entangled polymers, which span broad time and length scales, govern their unique viscoelastic properties. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes to the late time diffusive regime, highly coarse grained models with purely repulsive interactions between monomers are widely used since they are computationally the most efficient. In this paper, using large scale molecular dynamics simulations, the effect of including the attractive interaction between monomers on the dynamics of entangled polymer melts is explored for the first time over a wide temperature range. Attractive interactions have little effect onmore » the local packing for all temperatures T and on the chain mobility for T higher than about twice the glass transition T g. Finally, these results, across a broad range of molecular weight, show that to study the dynamics of entangled polymer melts, the interactions can be treated as pure repulsive, confirming a posteriori the validity of previous studies and opening the way to new large scale numerical simulations.« less

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

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

A Systematic Review of Agent-Based Modelling and Simulation Applications in the Higher Education Domain

ERIC Educational Resources Information Center

Gu, X.; Blackmore, K. L.

2015-01-01

This paper presents the results of a systematic review of agent-based modelling and simulation (ABMS) applications in the higher education (HE) domain. Agent-based modelling is a "bottom-up" modelling paradigm in which system-level behaviour (macro) is modelled through the behaviour of individual local-level agent interactions (micro).…

Evaluating average and atypical response in radiation effects simulations

NASA Astrophysics Data System (ADS)

Weller, R. A.; Sternberg, A. L.; Massengill, L. W.; Schrimpf, R. D.; Fleetwood, D. M.

2003-12-01

We examine the limits of performing single-event simulations using pre-averaged radiation events. Geant4 simulations show the necessity, for future devices, to supplement current methods with ensemble averaging of device-level responses to physically realistic radiation events. Initial Monte Carlo simulations have generated a significant number of extremal events in local energy deposition. These simulations strongly suggest that proton strikes of sufficient energy, even those that initiate purely electronic interactions, can initiate device response capable in principle of producing single event upset or microdose damage in highly scaled devices.

Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions.

PubMed

Vosmeer, C Ruben; Kooi, Derk P; Capoferri, Luigi; Terpstra, Margreet M; Vermeulen, Nico P E; Geerke, Daan P

2016-01-01

Recently an iterative method was proposed to enhance the accuracy and efficiency of ligand-protein binding affinity prediction through linear interaction energy (LIE) theory. For ligand binding to flexible Cytochrome P450s (CYPs), this method was shown to decrease the root-mean-square error and standard deviation of error prediction by combining interaction energies of simulations starting from different conformations. Thereby, different parts of protein-ligand conformational space are sampled in parallel simulations. The iterative LIE framework relies on the assumption that separate simulations explore different local parts of phase space, and do not show transitions to other parts of configurational space that are already covered in parallel simulations. In this work, a method is proposed to (automatically) detect such transitions during the simulations that are performed to construct LIE models and to predict binding affinities. Using noise-canceling techniques and splines to fit time series of the raw data for the interaction energies, transitions during simulation between different parts of phase space are identified. Boolean selection criteria are then applied to determine which parts of the interaction energy trajectories are to be used as input for the LIE calculations. Here we show that this filtering approach benefits the predictive quality of our previous CYP 2D6-aryloxypropanolamine LIE model. In addition, an analysis is performed of the gain in computational efficiency that can be obtained from monitoring simulations using the proposed filtering method and by prematurely terminating simulations accordingly.

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.

PubMed

Chikenji, George; Fujitsuka, Yoshimi; Takada, Shoji

2006-02-28

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of "chimera proteins." In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape.

Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study

PubMed Central

Chikenji, George; Fujitsuka, Yoshimi; Takada, Shoji

2006-01-01

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of “chimera proteins.” In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape. PMID:16488978

Tristan code and its application

NASA Astrophysics Data System (ADS)

Nishikawa, K.-I.

Since TRISTAN: The 3-D Electromagnetic Particle Code was introduced in 1990, it has been used for many applications including the simulations of global solar windmagnetosphere interaction. The most essential ingridients of this code have been published in the ISSS-4 book. In this abstract we describe some of issues and an application of this code for the study of global solar wind-magnetosphere interaction including a substorm study. The basic code (tristan.f) for the global simulation and a local simulation of reconnection with a Harris model (issrec2.f) are available at http:/www.physics.rutger.edu/˜kenichi. For beginners the code (isssrc2.f) with simpler boundary conditions is suitable to start to run simulations. The future of global particle simulations for a global geospace general circulation (GGCM) model with predictive capability (for Space Weather Program) is discussed.

Grid-size dependence of Cauchy boundary conditions used to simulate stream-aquifer interactions

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2010-01-01

This work examines the simulation of stream–aquifer interactions as grids are refined vertically and horizontally and suggests that traditional methods for calculating conductance can produce inappropriate values when the grid size is changed. Instead, different grid resolutions require different estimated values. Grid refinement strategies considered include global refinement of the entire model and local refinement of part of the stream. Three methods of calculating the conductance of the Cauchy boundary conditions are investigated. Single- and multi-layer models with narrow and wide streams produced stream leakages that differ by as much as 122% as the grid is refined. Similar results occur for globally and locally refined grids, but the latter required as little as one-quarter the computer execution time and memory and thus are useful for addressing some scale issues of stream–aquifer interactions. Results suggest that existing grid-size criteria for simulating stream–aquifer interactions are useful for one-layer models, but inadequate for three-dimensional models. The grid dependence of the conductance terms suggests that values for refined models using, for example, finite difference or finite-element methods, cannot be determined from previous coarse-grid models or field measurements. Our examples demonstrate the need for a method of obtaining conductances that can be translated to different grid resolutions and provide definitive test cases for investigating alternative conductance formulations.

Exploring Localization in Nuclear Spin Chains

NASA Astrophysics Data System (ADS)

Wei, Ken Xuan; Ramanathan, Chandrasekhar; Cappellaro, Paola

2018-02-01

Characterizing out-of-equilibrium many-body dynamics is a complex but crucial task for quantum applications and understanding fundamental phenomena. A central question is the role of localization in quenching thermalization in many-body systems and whether such localization survives in the presence of interactions. Probing this question in real systems necessitates the development of an experimentally measurable metric that can distinguish between different types of localization. While it is known that the localized phase of interacting systems [many-body localization (MBL)] exhibits a long-time logarithmic growth in entanglement entropy that distinguishes it from the noninteracting case of Anderson localization (AL), entanglement entropy is difficult to measure experimentally. Here, we present a novel correlation metric, capable of distinguishing MBL from AL in high-temperature spin systems. We demonstrate the use of this metric to detect localization in a natural solid-state spin system using nuclear magnetic resonance (NMR). We engineer the natural Hamiltonian to controllably introduce disorder and interactions, and observe the emergence of localization. In particular, while our correlation metric saturates for AL, it slowly keeps increasing for MBL, demonstrating analogous features to entanglement entropy, as we show in simulations. Our results show that our NMR techniques, akin to measuring out-of-time correlations, are well suited for studying localization in spin systems.

Diffusion, subdiffusion, and localization of active colloids in random post lattices

NASA Astrophysics Data System (ADS)

Morin, Alexandre; Lopes Cardozo, David; Chikkadi, Vijayakumar; Bartolo, Denis

2017-10-01

Combining experiments and theory, we address the dynamics of self-propelled particles in crowded environments. We first demonstrate that motile colloids cruising at constant speed through random lattices undergo a smooth transition from diffusive to subdiffusive to localized dynamics upon increasing the obstacle density. We then elucidate the nature of these transitions by performing extensive simulations constructed from a detailed analysis of the colloid-obstacle interactions. We evidence that repulsion at a distance and hard-core interactions both contribute to slowing down the long-time diffusion of the colloids. In contrast, the localization transition stems solely from excluded-volume interactions and occurs at the void-percolation threshold. Within this critical scenario, equivalent to that of the random Lorentz gas, genuine asymptotic subdiffusion is found only at the critical density where the motile particles explore a fractal maze.

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

NASA Astrophysics Data System (ADS)

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; Omand, Conor; Nishino, Masamichi

2016-02-01

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean-field method for a simplified model of a spin-crossover material with a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S =1 /2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley (equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shaped regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. We believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.

Long-ranged contributions to solvation free energies from theory and short-ranged models

PubMed Central

Remsing, Richard C.; Liu, Shule; Weeks, John D.

2016-01-01

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object. PMID:26929375

Capabilities of current wildfire models when simulating topographical flow

NASA Astrophysics Data System (ADS)

Kochanski, A.; Jenkins, M.; Krueger, S. K.; McDermott, R.; Mell, W.

2009-12-01

Accurate predictions of the growth, spread and suppression of wild fires rely heavily on the correct prediction of the local wind conditions and the interactions between the fire and the local ambient airflow. Resolving local flows, often strongly affected by topographical features like hills, canyons and ridges, is a prerequisite for accurate simulation and prediction of fire behaviors. In this study, we present the results of high-resolution numerical simulations of the flow over a smooth hill, performed using (1) the NIST WFDS (WUI or Wildland-Urban-Interface version of the FDS or Fire Dynamic Simulator), and (2) the LES version of the NCAR Weather Research and Forecasting (WRF-LES) model. The WFDS model is in the initial stages of development for application to wind flow and fire spread over complex terrain. The focus of the talk is to assess how well simple topographical flow is represented by WRF-LES and the current version of WFDS. If sufficient progress has been made prior to the meeting then the importance of the discrepancies between the predicted and measured winds, in terms of simulated fire behavior, will be examined.

Multiscale modeling of shock wave localization in porous energetic material

NASA Astrophysics Data System (ADS)

Wood, M. A.; Kittell, D. E.; Yarrington, C. D.; Thompson, A. P.

2018-01-01

Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (<6 GPa), atomistic simulations of pore collapse are used to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock waves interacting with pores as a function of this viscoplastic material response. We find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.

3D Hybrid Simulations of Interactions of High-Velocity Plasmoids with Obstacles

NASA Astrophysics Data System (ADS)

Omelchenko, Y. A.; Weber, T. E.; Smith, R. J.

2015-11-01

Interactions of fast plasma streams and objects with magnetic obstacles (dipoles, mirrors, etc) lie at the core of many space and laboratory plasma phenomena ranging from magnetoshells and solar wind interactions with planetary magnetospheres to compact fusion plasmas (spheromaks and FRCs) to astrophysics-in-lab experiments. Properly modeling ion kinetic, finite-Larmor radius and Hall effects is essential for describing large-scale plasma dynamics, turbulence and heating in complex magnetic field geometries. Using an asynchronous parallel hybrid code, HYPERS, we conduct 3D hybrid (particle-in-cell ion, fluid electron) simulations of such interactions under realistic conditions that include magnetic flux coils, ion-ion collisions and the Chodura resistivity. HYPERS does not step simulation variables synchronously in time but instead performs time integration by executing asynchronous discrete events: updates of particles and fields carried out as frequently as dictated by local physical time scales. Simulations are compared with data from the MSX experiment which studies the physics of magnetized collisionless shocks through the acceleration and subsequent stagnation of FRC plasmoids against a strong magnetic mirror and flux-conserving boundary.

Local condensate depletion at trap center under strong interactions

NASA Astrophysics Data System (ADS)

Yukalov, V. I.; Yukalova, E. P.

2018-04-01

Cold trapped Bose-condensed atoms, interacting via hard-sphere repulsive potentials are considered. Simple mean-field approximations show that the condensate distribution inside a harmonic trap always has the shape of a hump with the maximum condensate density occurring at the trap center. However, Monte Carlo simulations at high density and strong interactions display the condensate depletion at the trap center. The explanation of this effect of local condensate depletion at trap center is suggested in the frame of self-consistent theory of Bose-condensed systems. The depletion is shown to be due to the existence of the anomalous average that takes into account pair correlations and appears in systems with broken gauge symmetry.

Transport behaviors of locally fractional coupled Brownian motors with fluctuating interactions

NASA Astrophysics Data System (ADS)

Wang, Huiqi; Ni, Feixiang; Lin, Lifeng; Lv, Wangyong; Zhu, Hongqiang

2018-09-01

In some complex viscoelastic mediums, it is ubiquitous that absorbing and desorbing surrounding Brownian particles randomly occur in coupled systems. The conventional method is to model a variable-mass system driven by both multiplicative and additive noises. In this paper, an improved mathematical model is created based on generalized Langevin equations (GLE) to characterize the random interaction with locally fluctuating number of coupled particles in the elastically coupled factional Brownian motors (FBM). By the numerical simulations, the effect of fluctuating interactions on collective transport behaviors is investigated, and some abnormal phenomena, such as cooperative behaviors, stochastic resonance (SR) and anomalous transport, are observed in the regime of sub-diffusion.

First-Principles and Thermodynamic Simulation of Elastic Stress Effect on Energy of Hydrogen Dissolution in Alpha Iron

NASA Astrophysics Data System (ADS)

Rakitin, M. S.; Mirzoev, A. A.; Mirzaev, D. A.

2018-04-01

Mobile hydrogen, when dissolving in metals, redistributes due to the density gradients and elastic stresses, and enables destruction processes or phase transformations in local volumes of a solvent metal. It is rather important in solid state physics to investigate these interactions. The first-principle calculations performed in terms of the density functional theory, are used for thermodynamic simulation of the elastic stress effect on the energy of hydrogen dissolution in α-Fe crystal lattice. The paper presents investigations of the total energy of Fe-H system depending on the lattice parameter. As a result, the relation is obtained between the hydrogen dissolution energy and stress. A good agreement is shown between the existing data and simulation results. The extended equation is suggested for the chemical potential of hydrogen atom in iron within the local stress field. Two parameters affecting the hydrogen distribution are compared, namely local stress and phase transformations.

Molecular dynamics simulation of the partitioning of benzocaine and phenytoin into a lipid bilayer.

PubMed

Martin, Lewis J; Chao, Rebecca; Corry, Ben

2014-01-01

Molecular dynamics simulations were used to examine the partitioning behaviour of the local anaesthetic benzocaine and the anti-epileptic phenytoin into lipid bilayers, a factor that is critical to their mode of action. Free energy methods are used to quantify the thermodynamics of drug movement between water and octanol as well as for permeation across a POPC membrane. Both drugs are shown to favourably partition into the lipid bilayer from water and are likely to accumulate just inside the lipid headgroups where they may alter bilayer properties or interact with target proteins. Phenytoin experiences a large barrier to cross the centre of the bilayer due to less favourable energetic interactions in this less dense region of the bilayer. Remarkably, in our simulations both drugs are able to pull water into the bilayer, creating water chains that extend back to bulk, and which may modify the local bilayer properties. We find that the choice of atomic partial charges can have a significant impact on the quantitative results, meaning that careful validation of parameters for new drugs, such as performed here, should be performed prior to their use in biomolecular simulations. Copyright © 2013 Elsevier B.V. All rights reserved.

Asymmetric Kelvin-Helmholtz Instability at Jupiter's Magnetopause Boundary: Implications for Corotation-Dominated Systems

NASA Astrophysics Data System (ADS)

Zhang, B.; Delamere, P. A.; Ma, X.; Burkholder, B.; Wiltberger, M.; Lyon, J. G.; Merkin, V. G.; Sorathia, K. A.

2018-01-01

The multifluid Lyon-Fedder-Mobarry (MFLFM) global magnetosphere model is used to study the interactions between solar wind and rapidly rotating, internally driven Jupiter magnetosphere. The MFLFM model is the first global simulation of Jupiter magnetosphere that captures the Kelvin-Helmholtz instability (KHI) in the critically important subsolar region. Observations indicate that Kelvin-Helmholtz vortices are found predominantly in the dusk sector. Our simulations explain that this distribution is driven by the growth of KHI modes in the prenoon and subsolar region (e.g., >10 local time) that are advected by magnetospheric flows to the dusk sector. The period of density fluctuations at the dusk terminator flank (18 magnetic local time, MLT) is roughly 1.4 h compared with 7.2 h at the dawn flank (6 MLT). Although the simulations are only performed using parameters of the Jupiter's magnetosphere, the results may also have implications for solar wind-magnetosphere interactions at other corotation-dominated systems such as Saturn. For instance, the simulated average azimuthal speed of magnetosheath flows exhibit significant dawn-dusk asymmetry, consistent with recent observations at Saturn. The results are particularly relevant for the ongoing Juno mission and the analysis of dawnside magnetopause boundary crossings for other planetary missions.

Water-hammer pressure waves interaction at cross-section changes in series in viscoelastic pipes

NASA Astrophysics Data System (ADS)

Meniconi, S.; Brunone, B.; Ferrante, M.

2012-08-01

In view of scarcity of both experimental data and numerical models concerning transient behavior of cross-section area changes in pressurized liquid flow, the paper presents laboratory data and numerical simulation of the interaction of a surge wave with a partial blockage by a valve, a single pipe contraction or expansion and a series of pipe contraction/expansion in close proximity.With regard to a single change of cross-section area, laboratory data point out the completely different behavior with respect to one of the partially closed in-line valves with the same area ratio. In fact, for the former the pressure wave interaction is not regulated by the steady-state local head loss. With regard to partial blockages, transient tests have shown that the smaller the length, the more intense the overlapping of pressure waves due to the expansion and contraction in series.Numerically, the need for taking into account both the viscoelasticity and unsteady friction is demonstrated, since the classical water-hammer theory does not simulate the relevant damping of pressure peaks and gives rise to a time shifting between numerical and laboratory data. The transient behavior of a single local head loss has been checked by considering tests carried out in a system with a partially closed in-line valve. As a result, the reliability of the quasi steady-state approach for local head loss simulation has been demonstrated in viscoelastic pipes. The model parameters obtained on the basis of transients carried out in single pipe systems have then been used to simulate transients in the more complex pipe systems. These numerical experiments show the great importance of the length of the small-bore pipe with respect to one of the large-bore pipes. Precisely, until a gradually flow establishes in the small-bore pipe, the smaller such a length, the better the quality of the numerical simulation.

Quantum simulation of the Hubbard model with dopant atoms in silicon

PubMed Central

Salfi, J.; Mol, J. A.; Rahman, R.; Klimeck, G.; Simmons, M. Y.; Hollenberg, L. C. L.; Rogge, S.

2016-01-01

In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose–Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model. PMID:27094205

Mechanics Model for Simulating RC Hinges under Reversed Cyclic Loading

PubMed Central

Shukri, Ahmad Azim; Visintin, Phillip; Oehlers, Deric J.; Jumaat, Mohd Zamin

2016-01-01

Describing the moment rotation (M/θ) behavior of reinforced concrete (RC) hinges is essential in predicting the behavior of RC structures under severe loadings, such as under cyclic earthquake motions and blast loading. The behavior of RC hinges is defined by localized slip or partial interaction (PI) behaviors in both the tension and compression region. In the tension region, slip between the reinforcement and the concrete defines crack spacing, crack opening and closing, and tension stiffening. While in the compression region, slip along concrete to concrete interfaces defines the formation and failure of concrete softening wedges. Being strain-based, commonly-applied analysis techniques, such as the moment curvature approach, cannot directly simulate these PI behaviors because they are localized and displacement based. Therefore, strain-based approaches must resort to empirical factors to define behaviors, such as tension stiffening and concrete softening hinge lengths. In this paper, a displacement-based segmental moment rotation approach, which directly simulates the partial interaction behaviors in both compression and tension, is developed for predicting the M/θ response of an RC beam hinge under cyclic loading. Significantly, in order to develop the segmental approach, a partial interaction model to predict the tension stiffening load slip relationship between the reinforcement and the concrete is developed. PMID:28773430

Mechanics Model for Simulating RC Hinges under Reversed Cyclic Loading.

PubMed

Shukri, Ahmad Azim; Visintin, Phillip; Oehlers, Deric J; Jumaat, Mohd Zamin

2016-04-22

Describing the moment rotation (M/θ) behavior of reinforced concrete (RC) hinges is essential in predicting the behavior of RC structures under severe loadings, such as under cyclic earthquake motions and blast loading. The behavior of RC hinges is defined by localized slip or partial interaction (PI) behaviors in both the tension and compression region. In the tension region, slip between the reinforcement and the concrete defines crack spacing, crack opening and closing, and tension stiffening. While in the compression region, slip along concrete to concrete interfaces defines the formation and failure of concrete softening wedges. Being strain-based, commonly-applied analysis techniques, such as the moment curvature approach, cannot directly simulate these PI behaviors because they are localized and displacement based. Therefore, strain-based approaches must resort to empirical factors to define behaviors, such as tension stiffening and concrete softening hinge lengths. In this paper, a displacement-based segmental moment rotation approach, which directly simulates the partial interaction behaviors in both compression and tension, is developed for predicting the M/θ response of an RC beam hinge under cyclic loading. Significantly, in order to develop the segmental approach, a partial interaction model to predict the tension stiffening load slip relationship between the reinforcement and the concrete is developed.

Hands-On! Living in the Biosphere: Production, Pattern, Population, and Diversity. Developing Active Learning Module on the Human Dimensions of Global Change.

ERIC Educational Resources Information Center

Brown, Dwight

Biogeography examines questions of organism inventory and pattern, organisms' interactions with the environment, and the processes that create and change inventory, pattern, and interactions. This learning module uses time series maps and simple simulation models to illustrate how human actions alter biological productivity patterns at local and…

Agent-based spin model for financial markets on complex networks: Emergence of two-phase phenomena

NASA Astrophysics Data System (ADS)

Kim, Yup; Kim, Hong-Joo; Yook, Soon-Hyung

2008-09-01

We study a microscopic model for financial markets on complex networks, motivated by the dynamics of agents and their structure of interaction. The model consists of interacting agents (spins) with local ferromagnetic coupling and global antiferromagnetic coupling. In order to incorporate more realistic situations, we also introduce an external field which changes in time. From numerical simulations, we find that the model shows two-phase phenomena. When the local ferromagnetic interaction is balanced with the global antiferromagnetic interaction, the resulting return distribution satisfies a power law having a single peak at zero values of return, which corresponds to the market equilibrium phase. On the other hand, if local ferromagnetic interaction is dominant, then the return distribution becomes double peaked at nonzero values of return, which characterizes the out-of-equilibrium phase. On random networks, the crossover between two phases comes from the competition between two different interactions. However, on scale-free networks, not only the competition between the different interactions but also the heterogeneity of underlying topology causes the two-phase phenomena. Possible relationships between the critical phenomena of spin system and the two-phase phenomena are discussed.

AceCloud: Molecular Dynamics Simulations in the Cloud.

PubMed

Harvey, M J; De Fabritiis, G

2015-05-26

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

Modelling surface water-groundwater interaction with a conceptual approach: model development and application in New Zealand

NASA Astrophysics Data System (ADS)

Yang, J.; Zammit, C.; McMillan, H. K.

2016-12-01

As in most countries worldwide, water management in lowland areas is a big concern for New Zealand due to its economic importance for water related human activities. As a result, the estimation of available water resources in these areas (e.g., for irrigation and water supply purpose) is crucial and often requires an understanding of complex hydrological processes, which are often characterized by strong interactions between surface water and groundwater (usually expressed as losing and gaining rivers). These processes are often represented and simulated using integrated physically based hydrological models. However models with physically based groundwater modules typically require large amount of non-readily available geologic and aquifer information and are computationally intensive. Instead, this paper presents a conceptual groundwater model that is fully integrated into New Zealand's national hydrological model TopNet based on TopModel concepts (Beven, 1992). Within this conceptual framework, the integrated model can simulate not only surface processes, but also groundwater processes and surface water-groundwater interaction processes (including groundwater flow, river-groundwater interaction, and groundwater interaction with external watersheds). The developed model was applied to two New Zealand catchments with different hydro-geological and climate characteristics (Pareora catchment in the Canterbury Plains and Grey catchment on the West Coast). Previous studies have documented strong interactions between the river and groundwater, based on the analysis of a large number of concurrent flow measurements and associated information along the river main stem. Application of the integrated hydrological model indicates flow simulation (compared to the original hydrological model conceptualisation) during low flow conditions are significantly improved and further insights on local river dynamics are gained. Due to its conceptual characteristics and low level of data requirement, the integrated model could be used at local and national scales to improve the simulation of hydrological processes in non-topographically driven areas (where groundwater processes are important), and to assess impact of climate change on the integrated hydrological cycle in these areas.

First-principles electron dynamics control simulation of diamond under femtosecond laser pulse train irradiation.

PubMed

Wang, Cong; Jiang, Lan; Wang, Feng; Li, Xin; Yuan, Yanping; Xiao, Hai; Tsai, Hai-Lung; Lu, Yongfeng

2012-07-11

A real-time and real-space time-dependent density functional is applied to simulate the nonlinear electron-photon interactions during shaped femtosecond laser pulse train ablation of diamond. Effects of the key pulse train parameters such as the pulse separation, spatial/temporal pulse energy distribution and pulse number per train on the electron excitation and energy absorption are discussed. The calculations show that photon-electron interactions and transient localized electron dynamics can be controlled including photon absorption, electron excitation, electron density, and free electron distribution by the ultrafast laser pulse train.

Solitary solutions including spatially localized chaos and their interactions in two-dimensional Kolmogorov flow.

PubMed

Hiruta, Yoshiki; Toh, Sadayoshi

2015-12-01

Two-dimensional Kolmogorov flow in wide periodic boxes is numerically investigated. It is shown that the total flow rate in the direction perpendicular to the force controls the characteristics of the flow, especially the existence of spatially localized solitary solutions such as traveling waves, periodic solutions, and chaotic solutions, which can behave as elementary components of the flow. We propose a procedure to construct approximate solutions consisting of solitary solutions. It is confirmed by direct numerical simulations that these solutions are stable and represent interactions between elementary components such as collisions, coexistence, and collapse of chaos.

Phase Space Approach to Dynamics of Interacting Fermions

NASA Astrophysics Data System (ADS)

Davidson, Shainen; Sels, Dries; Kasper, Valentin; Polkovnikov, Anatoli

Understanding the behavior of interacting fermions is of fundamental interest in many fields ranging from condensed matter to high energy physics. Developing numerically efficient and accurate simulation methods is an indispensable part of this. Already in equilibrium, fermions are notoriously hard to handle due to the sign problem. Out of equilibrium, an important outstanding problem is the efficient numerical simulation of the dynamics of these systems. In this work we develop a new semiclassical phase-space approach (a.k.a. the truncated Wigner approximation) for simulating the dynamics of interacting lattice fermions in arbitrary dimensions. We demonstrate the strength of the method by comparing the results to exact diagonalization (ED) on small 1D and 2D systems. We furthermore present results on Many-Body Localized (MBL) systems in 1D and 2D, and demonstrate how the method can be used to determine the MBL transition.

Experimental and numerical simulation of a rotor/stator interaction event localized on a single blade within an industrial high-pressure compressor

NASA Astrophysics Data System (ADS)

Batailly, Alain; Agrapart, Quentin; Millecamps, Antoine; Brunel, Jean-François

2016-08-01

This contribution addresses a confrontation between the experimental simulation of a rotor/stator interaction case initiated by structural contacts with numerical predictions made with an in-house numerical strategy. Contrary to previous studies carried out within the low-pressure compressor of an aircraft engine, this interaction is found to be non-divergent: high amplitudes of vibration are experimentally observed and numerically predicted over a short period of time. An in-depth analysis of experimental data first allows for a precise characterization of the interaction as a rubbing event involving the first torsional mode of a single blade. Numerical results are in good agreement with experimental observations: the critical angular speed, the wear patterns on the casing as well as the blade dynamics are accurately predicted. Through out the article, the in-house numerical strategy is also confronted to another numerical strategy that may be found in the literature for the simulation of rubbing events: key differences are underlined with respect to the prediction of non-linear interaction phenomena.

Effects of doping and interchain interactions on the metal-insulator transition in trans-polyacetylene

NASA Astrophysics Data System (ADS)

Paulsson, Magnus; Stafström, Sven

1999-09-01

Using a tight-binding Hamiltonian the metal-insulator phase diagram for trans-polyacetylene was calculated as a function of doping concentration and interchain interaction strength. The phase boundary for the periodic system coincides with the gap closing, which occurs for certain combinations of critical values for the doping concentration and the interchain interaction strength. The values found are in good agreement with the experimentally observed increase in the Pauli susceptibility. To simulate disorder in the polymer, the effect of finite chain lengths was studied. This type of disorder pushes the metal/insulator phase boundary towards the metallic side of the phase diagram. An increase in the doping concentration and/or interchain interaction is shown to reduce the localizing effects of disorder effectively. For realistic values of the interchain interaction strength the number of chain breaks needed to localize the states at the Fermi energy is quite small, of the order of a few percent. The localization length is found to be substantially longer than the conjugation length of the polymer.

Multiscale modeling of shock wave localization in porous energetic material

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

Wood, M. A.; Kittell, D. E.; Yarrington, C. D.

Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (< 6 GPa), atomistic simulations of pore collapse are used here to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock wavesmore » interacting with pores as a function of this viscoplastic material response. Finally, we find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.« less

Multiscale modeling of shock wave localization in porous energetic material

DOE PAGES

Wood, M. A.; Kittell, D. E.; Yarrington, C. D.; ...

2018-01-30

Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. The shock response of hexanitrostilbene is studied through a combination of large-scale reactive molecular dynamics and mesoscale hydrodynamic simulations. In order to extend our simulation capability at the mesoscale to include weak shock conditions (< 6 GPa), atomistic simulations of pore collapse are used here to define a strain-rate-dependent strength model. Comparing these simulation methods allows us to impose physically reasonable constraints on the mesoscale model parameters. In doing so, we have been able to study shock wavesmore » interacting with pores as a function of this viscoplastic material response. Finally, we find that the pore collapse behavior of weak shocks is characteristically different than that of strong shocks.« less

Simulation of wave packet tunneling of interacting identical particles

NASA Astrophysics Data System (ADS)

Lozovik, Yu. E.; Filinov, A. V.; Arkhipov, A. S.

2003-02-01

We demonstrate a different method of simulation of nonstationary quantum processes, considering the tunneling of two interacting identical particles, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based on the Wigner representation of quantum mechanics. In the context of this method ensembles of classical trajectories are used to solve quantum Wigner-Liouville equation. These classical trajectories obey Hamiltonian-like equations, where the effective potential consists of the usual classical term and the quantum term, which depends on the Wigner function and its derivatives. The quantum term is calculated using local distribution of trajectories in phase space, therefore, classical trajectories are not independent, contrary to classical molecular dynamics. The developed WMD method takes into account the influence of exchange and interaction between particles. The role of direct and exchange interactions in tunneling is analyzed. The tunneling times for interacting particles are calculated.

LandCaRe DSS--an interactive decision support system for climate change impact assessment and the analysis of potential agricultural land use adaptation strategies.

PubMed

Wenkel, Karl-Otto; Berg, Michael; Mirschel, Wilfried; Wieland, Ralf; Nendel, Claas; Köstner, Barbara

2013-09-01

Decision support to develop viable climate change adaptation strategies for agriculture and regional land use management encompasses a wide range of options and issues. Up to now, only a few suitable tools and methods have existed for farmers and regional stakeholders that support the process of decision-making in this field. The interactive model-based spatial information and decision support system LandCaRe DSS attempts to close the existing methodical gap. This system supports interactive spatial scenario simulations, multi-ensemble and multi-model simulations at the regional scale, as well as the complex impact assessment of potential land use adaptation strategies at the local scale. The system is connected to a local geo-database and via the internet to a climate data server. LandCaRe DSS uses a multitude of scale-specific ecological impact models, which are linked in various ways. At the local scale (farm scale), biophysical models are directly coupled with a farm economy calculator. New or alternative simulation models can easily be added, thanks to the innovative architecture and design of the DSS. Scenario simulations can be conducted with a reasonable amount of effort. The interactive LandCaRe DSS prototype also offers a variety of data analysis and visualisation tools, a help system for users and a farmer information system for climate adaptation in agriculture. This paper presents the theoretical background, the conceptual framework, and the structure and methodology behind LandCaRe DSS. Scenario studies at the regional and local scale for the two Eastern German regions of Uckermark (dry lowlands, 2600 km(2)) and Weißeritz (humid mountain area, 400 km(2)) were conducted in close cooperation with stakeholders to test the functionality of the DSS prototype. The system is gradually being transformed into a web version (http://www.landcare-dss.de) to ensure the broadest possible distribution of LandCaRe DSS to the public. The system will be continuously developed, updated and used in different research projects and as a learning and knowledge-sharing tool for students. The main objective of LandCaRe DSS is to provide information on the complex long-term impacts of climate change and on potential management options for adaptation by answering "what-if" type questions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Localization of intense electromagnetic waves in a relativistically hot plasma.

PubMed

Shukla, P K; Eliasson, B

2005-02-18

We consider nonlinear interactions between intense short electromagnetic waves (EMWs) and a relativistically hot electron plasma that supports relativistic electron holes (REHs). It is shown that such EMW-REH interactions are governed by a coupled nonlinear system of equations composed of a nonlinear Schro dinger equation describing the dynamics of the EMWs and the Poisson-relativistic Vlasov system describing the dynamics of driven REHs. The present nonlinear system of equations admits both a linearly trapped discrete number of eigenmodes of the EMWs in a quasistationary REH and a modification of the REH by large-amplitude trapped EMWs. Computer simulations of the relativistic Vlasov and Maxwell-Poisson system of equations show complex interactions between REHs loaded with localized EMWs.

Equilibrium, metastability, and hysteresis in a model spin-crossover material with nearest-neighbor antiferromagnetic-like and long-range ferromagnetic-like interactions

DOE PAGES

Rikvold, Per Arne; Brown, Gregory; Miyashita, Seiji; ...

2016-02-16

Phase diagrams and hysteresis loops were obtained by Monte Carlo simulations and a mean- field method for a simplified model of a spin-crossovermaterialwith a two-step transition between the high-spin and low-spin states. This model is a mapping onto a square-lattice S = 1/2 Ising model with antiferromagnetic nearest-neighbor and ferromagnetic Husimi-Temperley ( equivalent-neighbor) long-range interactions. Phase diagrams obtained by the two methods for weak and strong long-range interactions are found to be similar. However, for intermediate-strength long-range interactions, the Monte Carlo simulations show that tricritical points decompose into pairs of critical end points and mean-field critical points surrounded by horn-shapedmore » regions of metastability. Hysteresis loops along paths traversing the horn regions are strongly reminiscent of thermal two-step transition loops with hysteresis, recently observed experimentally in several spin-crossover materials. As a result, we believe analogous phenomena should be observable in experiments and simulations for many systems that exhibit competition between local antiferromagnetic-like interactions and long-range ferromagnetic-like interactions caused by elastic distortions.« less

Diffusion Monte Carlo approach versus adiabatic computation for local Hamiltonians

NASA Astrophysics Data System (ADS)

Bringewatt, Jacob; Dorland, William; Jordan, Stephen P.; Mink, Alan

2018-02-01

Most research regarding quantum adiabatic optimization has focused on stoquastic Hamiltonians, whose ground states can be expressed with only real non-negative amplitudes and thus for whom destructive interference is not manifest. This raises the question of whether classical Monte Carlo algorithms can efficiently simulate quantum adiabatic optimization with stoquastic Hamiltonians. Recent results have given counterexamples in which path-integral and diffusion Monte Carlo fail to do so. However, most adiabatic optimization algorithms, such as for solving MAX-k -SAT problems, use k -local Hamiltonians, whereas our previous counterexample for diffusion Monte Carlo involved n -body interactions. Here we present a 6-local counterexample which demonstrates that even for these local Hamiltonians there are cases where diffusion Monte Carlo cannot efficiently simulate quantum adiabatic optimization. Furthermore, we perform empirical testing of diffusion Monte Carlo on a standard well-studied class of permutation-symmetric tunneling problems and similarly find large advantages for quantum optimization over diffusion Monte Carlo.

Entangling spin-spin interactions of ions in individually controlled potential wells

NASA Astrophysics Data System (ADS)

Wilson, Andrew; Colombe, Yves; Brown, Kenton; Knill, Emanuel; Leibfried, Dietrich; Wineland, David

2014-03-01

Physical systems that cannot be modeled with classical computers appear in many different branches of science, including condensed-matter physics, statistical mechanics, high-energy physics, atomic physics and quantum chemistry. Despite impressive progress on the control and manipulation of various quantum systems, implementation of scalable devices for quantum simulation remains a formidable challenge. As one approach to scalability in simulation, here we demonstrate an elementary building-block of a configurable quantum simulator based on atomic ions. Two ions are trapped in separate potential wells that can individually be tailored to emulate a number of different spin-spin couplings mediated by the ions' Coulomb interaction together with classical laser and microwave fields. We demonstrate deterministic tuning of this interaction by independent control of the local wells and emulate a particular spin-spin interaction to entangle the internal states of the two ions with 0.81(2) fidelity. Extension of the building-block demonstrated here to a 2D-network, which ion-trap micro-fabrication processes enable, may provide a new quantum simulator architecture with broad flexibility in designing and scaling the arrangement of ions and their mutual interactions. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), ONR, and the NIST Quantum Information Program.

Numerical simulations (2D) on the influence of pre-existing local structures and seismic source characteristics in earthquake-volcano interactions

NASA Astrophysics Data System (ADS)

Farías, Cristian; Galván, Boris; Miller, Stephen A.

2017-09-01

Earthquake triggering of hydrothermal and volcanic systems is ubiquitous, but the underlying processes driving these systems are not well-understood. We numerically investigate the influence of seismic wave interaction with volcanic systems simulated as a trapped, high-pressure fluid reservoir connected to a fluid-filled fault system in a 2-D poroelastic medium. Different orientations and earthquake magnitudes are studied to quantify dynamic and static stress, and pore pressure changes induced by a seismic event. Results show that although the response of the system is mainly dominated by characteristics of the radiated seismic waves, local structures can also play an important role on the system dynamics. The fluid reservoir affects the seismic wave front, distorts the static overpressure pattern induced by the earthquake, and concentrates the kinetic energy of the incoming wave on its boundaries. The static volumetric stress pattern inside the fault system is also affected by the local structures. Our results show that local faults play an important role in earthquake-volcanic systems dynamics by concentrating kinetic energy inside and acting as wave-guides that have a breakwater-like behavior. This generates sudden changes in pore pressure, volumetric expansion, and stress gradients. Local structures also influence the regional Coulomb yield function. Our results show that local structures affect the dynamics of volcanic and hydrothermal systems, and should be taken into account when investigating triggering of these systems from nearby or distant earthquakes.

Theory and computer simulation of relaxor ferroelectrics doped by off-center impurities

NASA Astrophysics Data System (ADS)

Su, Chin-Cheng

A family of ferroelectric materials have relaxation type dynamics. These materials, called relaxor ferroelectrics, show remarkable dielectric and electromechanical properties important for many practical applications that are different from those of normal ferroelectrics. Despite of the engineering importance of relaxor ferroelectrics, the physical origin of the relaxor behavior is not fully understood. A purpose of this thesis is to advance the theory of relaxor ferroelectrics and to develop the model, which could be used for a computer simulation of the static dielectric and dynamic properties and their relation to the concentration of dopant ions. In this thesis, a Ginzburg-Landau type theory of interaction of randomly distributed local dipoles immersed in a paraelectric crystal is developed. The interaction is caused by the polarization of the host lattice generated by these dipoles. It is long-ranged and decays proportionally to the inverse distance between the local dipoles. The obtained effective Hamiltonian of the dipole-dipole interaction is employed for both the Monte Carlo and the Master Equation simulations of the dielectric and ferroelectric properties of a system with off-center dopant ions producing local dipoles. The computer simulation shows that at low concentration of dopant ions the paraelectric state transforms into a macroscopically paraelectric state consisting of randomly oriented polar clusters. The behavior of the system is similar to that of a spin-glass system. The polar clusters amplify the effective dipole moment and significantly increase the dielectric constant. It is shown that the interaction between the clusters results in a spectrum of relaxation times and the transition to the relaxor state. The real and imaginary parts of the susceptibility of this state are calculated. The slim hysteresis loop in the polarization, which usually appears in the high temperature non-polarized relaxor ferroelectrics, is also obtained for our doped system under similar physical conditions. At intermediate dopant concentration, the material undergoes a diffuse phase transition smeared within a temperature range to a ferroelectric state. A further increase in the dopant concentration makes the transition sharper and closer to the conventional ferroelectric transition. The results obtained are compared with the behavior of the K1-xLixTaO 3 relaxor ferroelectric.

Quantum simulation of strongly correlated condensed matter systems

NASA Astrophysics Data System (ADS)

Hofstetter, W.; Qin, T.

2018-04-01

We review recent experimental and theoretical progress in realizing and simulating many-body phases of ultracold atoms in optical lattices, which gives access to analog quantum simulations of fundamental model Hamiltonians for strongly correlated condensed matter systems, such as the Hubbard model. After a general introduction to quantum gases in optical lattices, their preparation and cooling, and measurement techniques for relevant observables, we focus on several examples, where quantum simulations of this type have been performed successfully during the past years: Mott-insulator states, itinerant quantum magnetism, disorder-induced localization and its interplay with interactions, and topological quantum states in synthetic gauge fields.

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

Acciarri, R.; Adams, C.; An, R.

Here, we present several studies of convolutional neural networks applied to data coming from the MicroBooNE detector, a liquid argon time projection chamber (LArTPC). The algorithms studied include the classification of single particle images, the localization of single particle and neutrino interactions in an image, and the detection of a simulated neutrino event overlaid with cosmic ray backgrounds taken from real detector data. These studies demonstrate the potential of convolutional neural networks for particle identification or event detection on simulated neutrino interactions. Lastly, we also address technical issues that arise when applying this technique to data from a large LArTPCmore » at or near ground level.« less

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

Acciarri, R.; Adams, C.; An, R.

We present several studies of convolutional neural networks applied to data coming from the MicroBooNE detector, a liquid argon time projection chamber (LArTPC). The algorithms studied include the classification of single particle images, the localization of single particle and neutrino interactions in an image, and the detection of a simulated neutrino event overlaid with cosmic ray backgrounds taken from real detector data. These studies demonstrate the potential of convolutional neural networks for particle identification or event detection on simulated neutrino interactions. We also address technical issues that arise when applying this technique to data from a large LArTPC at ormore » near ground level.« less

Local lubrication model for spherical particles within incompressible Navier-Stokes flows.

PubMed

Lambert, B; Weynans, L; Bergmann, M

2018-03-01

The lubrication forces are short-range hydrodynamic interactions essential to describe suspension of the particles. Usually, they are underestimated in direct numerical simulations of particle-laden flows. In this paper, we propose a lubrication model for a coupled volume penalization method and discrete element method solver that estimates the unresolved hydrodynamic forces and torques in an incompressible Navier-Stokes flow. Corrections are made locally on the surface of the interacting particles without any assumption on the global particle shape. The numerical model has been validated against experimental data and performs as well as existing numerical models that are limited to spherical particles.

Electroosmotic flow and Joule heating in preparative continuous annular electrochromatography.

PubMed

Laskowski, René; Bart, Hans-Jörg

2015-09-01

An openFOAM "computational fluid dynamic" simulation model was developed for the description of local interaction of hydrodynamics and Joule heating in annular electrochromatography. A local decline of electrical conductivity of the background eluent is caused by an electrokinetic migration of ions resulting in higher Joule heat generation. The model equations consider the Navier-Stokes equation for incompressible fluids, the energy equation for stationary temperature fields, and the mass transfer equation for the electrokinetic flow. The simulations were embedded in commercial ANSYS Fluent software and in open-source environment openFOAM. The annular gap (1 mm width) contained an inorganic C8 reverse-phase monolith as stationary phase prepared by an in situ sol-gel process. The process temperature generated by Joule heating was determined by thermal camera system. The local hydrodynamics in the prototype was detected by a gravimetric contact-free measurement method and experimental and simulated values matched quite well. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

NASA Astrophysics Data System (ADS)

Lei, Qun-li; Hadinoto, Kunn; Ni, Ran

2017-10-01

Hierarchical self-assembly consisting of local associations of simple building blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building blocks, the association between hemispheres can also induce both reentrant melting and reentrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel reentrant crystallization of identical crystals, which melt only in a certain temperature range. This offers another axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

Interactions of Marine Hydrokinetic Devices in Complex Bathymetries: Numerical Simulations in the Chacao Channel in Southern Chile.

NASA Astrophysics Data System (ADS)

Soto, K. A.; Escauriaza, C. R.; Richter, D. H.

2015-12-01

Many coastal areas in the South Pacific Ocean can provide significant marine energy resources in the near future. The installation of marine hydrokinetic (MHK) devices in these regions will require new approaches to understand physical and environmental processes that are relevant for the installation of turbine arrays, which are also specific of each site. The coastal morphology of the Chacao channel in southern Chile, which separates the Chiloé island from the main continent (41º47'S, 73º31'W) stands out as an important energy resource that can potentially contribute a significant power capacity. This coastal area not only sustains delicate ecosystems with limited anthropic intervention, but it is characterized by a complex bathymetry that can have important effects on the performance of MHK devices and their local impacts. To understand the interactions of the local bathymetry and ambient turbulence with turbine arrays, we carry out a series of numerical simulations with a coherent-structure resolving turbulence model using the actuator disk parameterization. The main objective of this study is to further our understanding on the physical processes associated with the installation of the turbine arrays. We perform simulations with different geometries and inlet boundary conditions, from simple cases in a rectangular channel, to more complex cases that include the high-resolution bathymetry of an extensive area of the Chacao channel. The results show how the interactions between the MHK devices, the local flow, and the bed can affect the energy flux and potential generation in specific sites. The results also provide new insights of local impacts of MHK devices and they can also help to optimize turbine arrays in natural environments. This work has been supported by Fondecyt project 1130940, and the Marine Energy Research & Innovation Center (MERIC) financed by Corfo and based in Santiago, Chile.

Many-body matter-wave dark soliton.

PubMed

Delande, Dominique; Sacha, Krzysztof

2014-01-31

The Gross-Pitaevskii equation--which describes interacting bosons in the mean-field approximation--possesses solitonic solutions in dimension one. For repulsively interacting particles, the stationary soliton is dark, i.e., is represented by a local density minimum. Many-body effects may lead to filling of the dark soliton. Using quasiexact many-body simulations, we show that, in single realizations, the soliton appears totally dark although the single particle density tends to be uniform.

Continuum understanding of twin formation near grain boundaries of FCC metals with low stacking fault energy

NASA Astrophysics Data System (ADS)

Jung, Jaimyun; Yoon, Jae Ik; Kim, Jung Gi; Latypov, Marat I.; Kim, Jin You; Kim, Hyoung Seop

2017-12-01

Deformation twinning from grain boundaries is often observed in face-centered cubic metals with low stacking fault energy. One of the possible factors that contribute to twinning origination from grain boundaries is the intergranular interactions during deformation. Nonetheless, the influence of mechanical interaction among grains on twin evolution has not been fully understood. In spite of extensive experimental and modeling efforts on correlating microstructural features with their twinning behavior, a clear relation among the large aggregate of grains is still lacking. In this work, we characterize the micromechanics of grain-to-grain interactions that contribute to twin evolution by investigating the mechanical twins near grain boundaries using a full-field crystal plasticity simulation of a twinning-induced plasticity steel deformed in uniaxial tension at room temperature. Microstructures are first observed through electron backscatter diffraction technique to obtain data to reconstruct a statistically equivalent microstructure through synthetic microstructure building. Grain-to-grain micromechanical response is analyzed to assess the collective twinning behavior of the microstructural volume element under tensile deformation. Examination of the simulated results reveal that grain interactions are capable of changing the local mechanical behavior near grain boundaries by transferring strain across grain boundary or localizing strain near grain boundary.

Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

PubMed

Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

2017-05-04

Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C 1 mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast, the interaction energy between the cellulose and water is too weak to dissolve cellulose in water.

Accurate thermodynamics for short-ranged truncations of Coulomb interactions in site-site molecular models

NASA Astrophysics Data System (ADS)

Rodgers, Jocelyn M.; Weeks, John D.

2009-12-01

Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple analytical corrections for the thermodynamics of uniform truncated systems are possible. In particular, results for the simple point charge/extended (SPC/E) water model treated with spherically truncated Coulomb interactions suggested by local molecular field theory [J. M. Rodgers and J. D. Weeks, Proc. Natl. Acad. Sci. U.S.A. 105, 19136 (2008)] are presented. We extend the results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] so that we may treat the thermodynamics of mixtures of flexible charged and uncharged molecules simulated with spherical truncations. We show that the energy and pressure of spherically truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Furthermore, applying the pressure correction as an external pressure removes the density errors observed by other research groups in NPT simulations of spherically truncated bulk species.

Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H.

PubMed

Rausch, Felix; Schicht, Martin; Bräuer, Lars; Paulsen, Friedrich; Brandt, Wolfgang

2014-11-01

Surfactant proteins are well known from the human lung where they are responsible for the stability and flexibility of the pulmonary surfactant system. They are able to influence the surface tension of the gas-liquid interface specifically by directly interacting with single lipids. This work describes the generation of reliable protein structure models to support the experimental characterization of two novel putative surfactant proteins called SP-G and SP-H. The obtained protein models were complemented by predicted posttranslational modifications and placed in a lipid model system mimicking the pulmonary surface. Molecular dynamics simulations of these protein-lipid systems showed the stability of the protein models and the formation of interactions between protein surface and lipid head groups on an atomic scale. Thereby, interaction interface and strength seem to be dependent on orientation and posttranslational modification of the protein. The here presented modeling was fundamental for experimental localization studies and the simulations showed that SP-G and SP-H are theoretically able to interact with lipid systems and thus are members of the surfactant protein family.

Continuum Model of Gas Uptake for Inhomogeneous Fluids

DOE PAGES

Ihm, Yungok; Cooper, Valentino R.; Vlcek, Lukas; ...

2017-07-20

We describe a continuum model of gas uptake for inhomogeneous fluids (CMGIF) and use it to predict fluid adsorption in porous materials directly from gas-substrate interaction energies determined by first principles calculations or accurate effective force fields. The method uses a perturbation approach to correct bulk fluid interactions for local inhomogeneities caused by gas substrate interactions, and predicts local pressure and density of the adsorbed gas. The accuracy and limitations of the model are tested by comparison with the results of Grand Canonical Monte Carlo simulations of hydrogen uptake in metal-organic frameworks (MOFs). We show that the approach provides accuratemore » predictions at room temperature and at low temperatures for less strongly interacting materials. As a result, the speed of the CMGIF method makes it a promising candidate for high-throughput materials discovery in connection with existing databases of nano-porous materials.« less

Virtual reality to simulate large lighting with high efficiency LEDs

NASA Astrophysics Data System (ADS)

Blandet, Thierry; Coutelier, Gilles; Meyrueis, Patrick

2011-05-01

When a city or a local authority wishes to emphasize its historical heritage, for the lighting of its streets, setting up lights during the festive season, they call upon the skills of a lighting designer. The lighting designer proposes concepts, ideas, lighting, and to be able to present them, he makes use of simulation. On the other hand lighting technologies are evolving very rapidly and new lighting systems offer features that lighting designers are now integrating their projects. The street lights consume lot of energy; light projects are now taking into account the energy saving aspect. Lighting systems based on LEDs today provide good lighting needs, taking into account sustainable development issues while enabling new creative dimension. The lighting simulation can handle these parameters. Images or video simulation are no longer sufficient: stereoscopy and virtual reality techniques allow better communication and better understanding of projects. Virtual reality offers new possibilities of interaction, the freedom of movement in a scene, the presentation of variants or interactive simulations.

TRACKING SIMULATIONS NEAR HALF-INTEGER RESONANCE AT PEP-II

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

Nosochkov, Yuri

2003-05-13

Beam-beam simulations predict that PEP-II luminosity can be increased by operating the horizontal betatron tune near and above a half-integer resonance. However, effects of the resonance and its synchrotron sidebands significantly enhance betatron and chromatic perturbations which tend to reduce dynamic aperture. In the study, chromatic variation of horizontal tune near the resonance was minimized by optimizing local sextupoles in the Interaction Region. Dynamic aperture was calculated using tracking simulations in LEGO code. Dependence of dynamic aperture on the residual orbit, dispersion and {beta} distortion after correction was investigated.

Importance of tread inertia and damping on the tyre/road contact stiffness

NASA Astrophysics Data System (ADS)

Winroth, J.; Andersson, P. B. U.; Kropp, W.

2014-10-01

Predicting tyre/road interaction processes like roughness excitation, stick-slip, stick-snap, wear and traction requires detailed information about the road surface, the tyre dynamics and the local deformation of the tread at the interface. Aspects of inertia and damping when the tread is locally deformed are often neglected in many existing tyre/road interaction models. The objective of this paper is to study how the dynamic features of the tread affect contact forces and contact stiffness during local deformation. This is done by simulating the detailed contact between an elastic layer and a rough road surface using a previously developed numerical time domain contact model. Road roughness on length scales smaller than the discretisation scale is included by the addition of nonlinear contact springs between each pair of contact elements. The dynamic case, with an elastic layer impulse response extending in time, is compared with the case where the corresponding quasi-static response is used. Results highlight the difficulty of estimating a constant contact stiffness as it increases during the indentation process between the elastic layer and the rough road surface. The stiffness-indentation relation additionally depends on how rapidly the contact develops; a faster process gives a stiffer contact. Material properties like loss factor and density also alter the contact development. This work implies that dynamic properties of the local tread deformation may be of importance when simulating contact details during normal tyre/road interaction conditions. There are however indications that the significant effect of damping could approximately be included as an increased stiffness in a quasi-static tread model.

Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

NASA Astrophysics Data System (ADS)

Miceli, Giacomo; de Gironcoli, Stefano; Pasquarello, Alfredo

2015-01-01

We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers the advantage of simulating liquid water at essentially the same computational cost of standard semilocal functionals. Applied to the water dimer and to ice Ih, we find that the hydrogen-bond energy is only slightly enhanced compared to a standard semilocal functional. We simulate liquid water through molecular dynamics in the NpH statistical ensemble allowing for fluctuations of the system density. The structure of the liquid departs from that found with a semilocal functional leading to more compact structural arrangements. This indicates that the directionality of the hydrogen-bond interaction has a diminished role as compared to the overall attractions, as expected when dispersion interactions are accounted for. This is substantiated through a detailed analysis comprising the study of the partial radial distribution functions, various local order indices, the hydrogen-bond network, and the selfdiffusion coefficient. The explicit treatment of the van der Waals interactions leads to an overall improved description of liquid water.

Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

NASA Astrophysics Data System (ADS)

Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

2018-05-01

Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA Online

PubMed Central

Lehmann, Eldon D.; DeWolf, Dennis K.; Novotny, Christopher A.; Reed, Karen; Gotwals, Robert R.

2014-01-01

Background. AIDA is a widely available downloadable educational simulator of glucose-insulin interaction in diabetes. Methods. A web-based version of AIDA was developed that utilises a server-based architecture with HTML FORM commands to submit numerical data from a web-browser client to a remote web server. AIDA online, located on a remote server, passes the received data through Perl scripts which interactively produce 24 hr insulin and glucose simulations. Results. AIDA online allows users to modify the insulin regimen and diet of 40 different prestored “virtual diabetic patients” on the internet or create new “patients” with user-generated regimens. Multiple simulations can be run, with graphical results viewed via a standard web-browser window. To date, over 637,500 diabetes simulations have been run at AIDA online, from all over the world. Conclusions. AIDA online's functionality is similar to the downloadable AIDA program, but the mode of implementation and usage is different. An advantage to utilising a server-based application is the flexibility that can be offered. New modules can be added quickly to the online simulator. This has facilitated the development of refinements to AIDA online, which have instantaneously become available around the world, with no further local downloads or installations being required. PMID:24511312

Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA Online.

PubMed

Lehmann, Eldon D; Dewolf, Dennis K; Novotny, Christopher A; Reed, Karen; Gotwals, Robert R

2014-01-01

Background. AIDA is a widely available downloadable educational simulator of glucose-insulin interaction in diabetes. Methods. A web-based version of AIDA was developed that utilises a server-based architecture with HTML FORM commands to submit numerical data from a web-browser client to a remote web server. AIDA online, located on a remote server, passes the received data through Perl scripts which interactively produce 24 hr insulin and glucose simulations. Results. AIDA online allows users to modify the insulin regimen and diet of 40 different prestored "virtual diabetic patients" on the internet or create new "patients" with user-generated regimens. Multiple simulations can be run, with graphical results viewed via a standard web-browser window. To date, over 637,500 diabetes simulations have been run at AIDA online, from all over the world. Conclusions. AIDA online's functionality is similar to the downloadable AIDA program, but the mode of implementation and usage is different. An advantage to utilising a server-based application is the flexibility that can be offered. New modules can be added quickly to the online simulator. This has facilitated the development of refinements to AIDA online, which have instantaneously become available around the world, with no further local downloads or installations being required.

Local interaction simulation approach to modelling nonclassical, nonlinear elastic behavior in solids.

PubMed

Scalerandi, Marco; Agostini, Valentina; Delsanto, Pier Paolo; Van Den Abeele, Koen; Johnson, Paul A

2003-06-01

Recent studies show that a broad category of materials share "nonclassical" nonlinear elastic behavior much different from "classical" (Landau-type) nonlinearity. Manifestations of "nonclassical" nonlinearity include stress-strain hysteresis and discrete memory in quasistatic experiments, and specific dependencies of the harmonic amplitudes with respect to the drive amplitude in dynamic wave experiments, which are remarkably different from those predicted by the classical theory. These materials have in common soft "bond" elements, where the elastic nonlinearity originates, contained in hard matter (e.g., a rock sample). The bond system normally comprises a small fraction of the total material volume, and can be localized (e.g., a crack in a solid) or distributed, as in a rock. In this paper a model is presented in which the soft elements are treated as hysteretic or reversible elastic units connected in a one-dimensional lattice to elastic elements (grains), which make up the hard matrix. Calculations are performed in the framework of the local interaction simulation approach (LISA). Experimental observations are well predicted by the model, which is now ready both for basic investigations about the physical origins of nonlinear elasticity and for applications to material damage diagnostics.

Cluster Formation of Anchored Proteins Induced by Membrane-Mediated Interaction

PubMed Central

Li, Shuangyang; Zhang, Xianren; Wang, Wenchuan

2010-01-01

Abstract Computer simulations were used to study the cluster formation of anchored proteins in a membrane. The rate and extent of clustering was found to be dependent upon the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work was ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrated that only when the penetration depth of anchored proteins was larger than half the membrane thickness, could the structure of the lower monolayer be significantly deformed. Additionally, studies on the local structures of membranes indicated weak perturbation of bilayer thickness for a shallowly inserted protein, while there was significant perturbation for a more deeply inserted protein. The origin of membrane-mediated protein-protein interaction is therefore due to the local perturbation of the membrane thickness, and the entropy loss—both of which are caused by the conformation restriction on the lipid chains and the enhanced intermonolayer coupling for a deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins. PMID:20513399

The use of MR B+1 imaging for validation of FDTD electromagnetic simulations of human anatomies.

PubMed

Van den Berg, Cornelis A T; Bartels, Lambertus W; van den Bergen, Bob; Kroeze, Hugo; de Leeuw, Astrid A C; Van de Kamer, Jeroen B; Lagendijk, Jan J W

2006-10-07

In this study, MR B(+)(1) imaging is employed to experimentally verify the validity of FDTD simulations of electromagnetic field patterns in human anatomies. Measurements and FDTD simulations of the B(+)(1) field induced by a 3 T MR body coil in a human corpse were performed. It was found that MR B(+)(1) imaging is a sensitive method to measure the radiofrequency (RF) magnetic field inside a human anatomy with a precision of approximately 3.5%. A good correlation was found between the B(+)(1) measurements and FDTD simulations. The measured B(+)(1) pattern for a human pelvis consisted of a global, diagonal modulation pattern plus local B(+)(1) heterogeneties. It is believed that these local B(+)(1) field variations are the result of peaks in the induced electric currents, which could not be resolved by the FDTD simulations on a 5 mm(3) simulation grid. The findings from this study demonstrate that B(+)(1) imaging is a valuable experimental technique to gain more knowledge about the dielectric interaction of RF fields with the human anatomy.

Multi-focused geospatial analysis using probes.

PubMed

Butkiewicz, Thomas; Dou, Wenwen; Wartell, Zachary; Ribarsky, William; Chang, Remco

2008-01-01

Traditional geospatial information visualizations often present views that restrict the user to a single perspective. When zoomed out, local trends and anomalies become suppressed and lost; when zoomed in for local inspection, spatial awareness and comparison between regions become limited. In our model, coordinated visualizations are integrated within individual probe interfaces, which depict the local data in user-defined regions-of-interest. Our probe concept can be incorporated into a variety of geospatial visualizations to empower users with the ability to observe, coordinate, and compare data across multiple local regions. It is especially useful when dealing with complex simulations or analyses where behavior in various localities differs from other localities and from the system as a whole. We illustrate the effectiveness of our technique over traditional interfaces by incorporating it within three existing geospatial visualization systems: an agent-based social simulation, a census data exploration tool, and an 3D GIS environment for analyzing urban change over time. In each case, the probe-based interaction enhances spatial awareness, improves inspection and comparison capabilities, expands the range of scopes, and facilitates collaboration among multiple users.

Local Interactions of Hydrometeors by Diffusion in Mixed-Phase Clouds

NASA Astrophysics Data System (ADS)

Baumgartner, Manuel; Spichtinger, Peter

2017-04-01

Mixed-phase clouds, containing both ice particles and liquid droplets, are important for the Earth-Atmosphere system. They modulate the radiation budget by a combination of albedo effect and greenhouse effect. In contrast to liquid water clouds, the radiative impact of clouds containing ice particles is still uncertain. Scattering and absorption highly depends in microphysical properties of ice crystals, e.g. size and shape. In addition, most precipitation on Earth forms via the ice phase. Thus, better understanding of ice processes as well as their representation in models is required. A key process for determining shape and size of ice crystals is diffusional growth. Diffusion processes in mixed-phase clouds are highly uncertain; in addition they are usually highly simplified in cloud models, especially in bulk microphysics parameterizations. The direct interaction between cloud droplets and ice particles, due to spatial inhomogeneities, is ignored; the particles can only interact via their environmental conditions. Local effects as supply of supersaturation due to clusters of droplets around ice particles are usually not represented, although they form the physical basis of the Wegener-Bergeron-Findeisen process. We present direct numerical simulations of the interaction of single ice particles and droplets, especially their local competition for the available water vapor. In addition, we show an approach to parameterize local interactions by diffusion. The suggested parameterization uses local steady-state solutions of the diffusion equations for water vapor for an ice particle as well as a droplet. The individual solutions are coupled together to obtain the desired interaction. We show some results of the scheme as implemented in a parcel model.

Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

PubMed Central

Buck, Patrick M.; Bystroff, Christopher

2015-01-01

Protein folding is a hierarchical process where structure forms locally first, then globally. Some short sequence segments initiate folding through strong structural preferences that are independent of their three-dimensional context in proteins. We have constructed a knowledge-based force field in which the energy functions are conditional on local sequence patterns, as expressed in the hidden Markov model for local structure (HMMSTR). Carbon-alpha force field (CALF) builds sequence specific statistical potentials based on database frequencies for α-carbon virtual bond opening and dihedral angles, pairwise contacts and hydrogen bond donor-acceptor pairs, and simulates folding via Brownian dynamics. We introduce hydrogen bond donor and acceptor potentials as α-carbon probability fields that are conditional on the predicted local sequence. Constant temperature simulations were carried out using 27 peptides selected as putative folding initiation sites, each 12 residues in length, representing several different local structure motifs. Each 0.6 μs trajectory was clustered based on structure. Simulation convergence or representativeness was assessed by subdividing trajectories and comparing clusters. For 21 of the 27 sequences, the largest cluster made up more than half of the total trajectory. Of these 21 sequences, 14 had cluster centers that were at most 2.6 Å root mean square deviation (RMSD) from their native structure in the corresponding full-length protein. To assess the adequacy of the energy function on nonlocal interactions, 11 full length native structures were relaxed using Brownian dynamics simulations. Equilibrated structures deviated from their native states but retained their overall topology and compactness. A simple potential that folds proteins locally and stabilizes proteins globally may enable a more realistic understanding of hierarchical folding pathways. PMID:19137613

Intracellular Electric Field and pH Optimize Protein Localization and Movement

PubMed Central

Cunningham, Jessica; Estrella, Veronica; Lloyd, Mark; Gillies, Robert; Frieden, B. Roy; Gatenby, Robert

2012-01-01

Mammalian cell function requires timely and accurate transmission of information from the cell membrane (CM) to the nucleus (N). These pathways have been intensively investigated and many critical components and interactions have been identified. However, the physical forces that control movement of these proteins have received scant attention. Thus, transduction pathways are typically presented schematically with little regard to spatial constraints that might affect the underlying dynamics necessary for protein-protein interactions and molecular movement from the CM to the N. We propose messenger protein localization and movements are highly regulated and governed by Coulomb interactions between: 1. A recently discovered, radially directed E-field from the NM into the CM and 2. Net protein charge determined by its isoelectric point, phosphorylation state, and the cytosolic pH. These interactions, which are widely applied in elecrophoresis, provide a previously unknown mechanism for localization of messenger proteins within the cytoplasm as well as rapid shuttling between the CM and N. Here we show these dynamics optimize the speed, accuracy and efficiency of transduction pathways even allowing measurement of the location and timing of ligand binding at the CM –previously unknown components of intracellular information flow that are, nevertheless, likely necessary for detecting spatial gradients and temporal fluctuations in ligand concentrations within the environment. The model has been applied to the RAF-MEK-ERK pathway and scaffolding protein KSR1 using computer simulations and in-vitro experiments. The computer simulations predicted distinct distributions of phosphorylated and unphosphorylated components of this transduction pathway which were experimentally confirmed in normal breast epithelial cells (HMEC). PMID:22623963

Navier-Stokes Simulation of UH-60A Rotor/Wake Interaction Using Adaptive Mesh Refinement

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

2017-01-01

High-resolution simulations of rotor/vortex-wake interaction for a UH60-A rotor under BVI and dynamic stallconditions were carried out with the OVERFLOW Navier-Stokes code.a. The normal force and pitching moment variation with azimuth angle were in good overall agreementwith flight-test data, similar to other CFD results reported in the literature.b. The wake-grid resolution did not have a significant effect on the rotor-blade airloads. This surprisingresult indicates that a wake grid spacing of (Delta)S=10% ctip is sufficient for engineering airloads predictionfor hover and forward flight. This assumes high-resolution body grids, high-order spatial accuracy, anda hybrid RANS/DDES turbulence model.c. Three-dimensional dynamic stall was found to occur due the presence of blade-tip vortices passing overa rotor blade on the retreating side. This changed the local airfoil angle of attack, causing stall, unlikethe 2D perspective of pure pitch oscillation of the local airfoil section.

Chemo-mechanical modeling of tumor growth in elastic epithelial tissue

NASA Astrophysics Data System (ADS)

Bratsun, Dmitry A.; Zakharov, Andrey P.; Pismen, Len

2016-08-01

We propose a multiscale chemo-mechanical model of the cancer tumor development in the epithelial tissue. The epithelium is represented by an elastic 2D array of polygonal cells with its own gene regulation dynamics. The model allows the simulation of the evolution of multiple cells interacting via the chemical signaling or mechanically induced strain. The algorithm includes the division and intercalation of cells as well as the transformation of normal cells into a cancerous state triggered by a local failure of the spatial synchronization of the cellular rhythms driven by transcription/translation processes. Both deterministic and stochastic descriptions of the system are given for chemical signaling. The transformation of cells means the modification of their respective parameters responsible for chemo-mechanical interactions. The simulations reproduce a distinct behavior of invasive and localized carcinoma. Generally, the model is designed in such a way that it can be readily modified to take account of any newly understood gene regulation processes and feedback mechanisms affecting chemo-mechanical properties of cells.

Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

DOE PAGES

Giera, Brian; Lawrence Livermore National Lab.; Henson, Neil; ...

2015-02-27

We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drivemore » strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.« less

ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging

PubMed Central

Ovesný, Martin; Křížek, Pavel; Borkovec, Josef; Švindrych, Zdeněk; Hagen, Guy M.

2014-01-01

Summary: ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy. ThunderSTORM offers an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data. ThunderSTORM also offers a set of tools for creation of simulated data and quantitative performance evaluation of localization algorithms using Monte Carlo simulations. Availability and implementation: ThunderSTORM and the online documentation are both freely accessible at https://code.google.com/p/thunder-storm/ Contact: guy.hagen@lf1.cuni.cz Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24771516

The Alfvénic nature of energy transfer mediation in localized, strongly nonlinear Alfvén wavepacket collisions

NASA Astrophysics Data System (ADS)

Verniero, J. L.; Howes, G. G.

2018-02-01

In space and astrophysical plasmas, violent events or instabilities inject energy into turbulent motions at large scales. Nonlinear interactions among the turbulent fluctuations drive a cascade of energy to small perpendicular scales at which the energy is ultimately converted into plasma heat. Previous work with the incompressible magnetohydrodynamic (MHD) equations has shown that this turbulent energy cascade is driven by the nonlinear interaction between counterpropagating Alfvén waves - also known as Alfvén wave collisions. Direct numerical simulations of weakly collisional plasma turbulence enables deeper insight into the nature of the nonlinear interactions underlying the turbulent cascade of energy. In this paper, we directly compare four cases: both periodic and localized Alfvén wave collisions in the weakly and strongly nonlinear limits. Our results reveal that in the more realistic case of localized Alfvén wave collisions (rather than the periodic case), all nonlinearly generated fluctuations are Alfvén waves, which mediates nonlinear energy transfer to smaller perpendicular scales.

Variation Process of Radiation Belt Electron Fluxes due to Interaction With Chorus and EMIC Rising-tone Emissions Localized in Longitude

NASA Astrophysics Data System (ADS)

Kubota, Y.; Omura, Y.

2017-12-01

Using results of test particle simulations of a large number of electrons interacting with a pair of chorus emissions, we create Green's functions to model the electron distribution function after all of the possible interactions with the waves [Omura et al., 2015]. Assuming that the waves are generated in a localized range of longitudes in the dawn side, we repeat taking the convolution integral of the Green's function with the distribution function of the electrons injected into the generation region of the localized waves. From numerical and theoretical analyses, we find that electron acceleration process only takes place efficiently below 4 MeV. Because extremely relativistic electrons go through the wave generation region rapidly due to grad-B0 and curvature drift, they don't have enough interaction time to be accelerated. In setting up the electrons after all interaction with chorus emissions as initial electron distribution function, we also compute the loss process of radiation belt electron fluxes due to interaction with EMIC rising-tone emissions generated in a localized range of longitudes in the dusk side [Kubota and Omura,2017]. References: (1) Omura, Y., Y. Miyashita, M. Yoshikawa, D. Summers, M. Hikishima, Y. Ebihara, and Y. Kubota (2015), Formation process of relativistic electron flux through interaction with chorus emissions in the Earth's inner magnetosphere, J. Geophys. Res. Space Physics, 120, 9545-9562, doi:10.1002/2015JA021563. (2) Kubota, Y., and Y. Omura (2017), Rapid precipitation of radiation belt electrons induced by EMIC rising tone emissions localized in longitude inside and outside the plasmapause, J. Geophys. Res. Space Physics, 122, 293-309, doi:10.1002/2016JA023267.

Extratropical Respones to Amazon Deforestation

NASA Astrophysics Data System (ADS)

Badger, A.; Dirmeyer, P.

2014-12-01

Land-use change (LUC) is known to impact local climate conditions through modifications of land-atmosphere interactions. Large-scale LUC, such as Amazon deforestation, could have a significant effect on the local and regional climates. The question remains as to what the global impact of large-scale LUC could be, as previous modeling studies have shown non-local responses due to Amazon deforestation. A common shortcoming in many previous modeling studies is the use of prescribed ocean conditions, which can act as a boundary condition to dampen the global response with respect to changes in the mean and variability. Using fully coupled modeling simulations with the Community Earth System Model version 1.2.0, the Amazon rainforest has been replaced with a distribution of representative tropical crops. Through the modifications of local land-atmosphere interactions, a significant change in the region, both at the surface and throughout the atmosphere, can be quantified. Accompanying these local changes are significant changes to the atmospheric circulation across all scales, thus modifying regional climates in other locales. Notable impacts include significant changes in precipitation, surface fluxes, basin-wide sea surface temperatures and ENSO behavior.

Molecular dynamics simulation of the local concentration and structure in multicomponent aerosol nanoparticles under atmospheric conditions.

PubMed

Karadima, Katerina S; Mavrantzas, Vlasis G; Pandis, Spyros N

2017-06-28

Molecular dynamics (MD) simulations were employed to investigate the local structure and local concentration in atmospheric nanoparticles consisting of an organic compound (cis-pinonic acid or n-C 30 H 62 ), sulfate and ammonium ions, and water. Simulations in the isothermal-isobaric (NPT) statistical ensemble under atmospheric conditions with a prespecified number of molecules of the abovementioned compounds led to the formation of a nanoparticle. Calculations of the density profiles of all the chemical species in the nanoparticle, the corresponding radial pair distribution functions, and their mobility inside the nanoparticle revealed strong interactions developing between sulfate and ammonium ions. However, sulfate and ammonium ions prefer to populate the central part of the nanoparticle under the simulated conditions, whereas organic molecules like to reside at its outer surface. Sulfate and ammonium ions were practically immobile; in contrast, the organic molecules exhibited appreciable mobility at the outer surface of the nanoparticle. When the organic compound was a normal alkane (e.g. n-C 30 H 62 ), a well-organized (crystalline-like) phase was rapidly formed at the free surface of the nanoparticle and remained separate from the rest of the species.

Simulating the interaction of the heliosphere with the local interstellar medium: MHD results from a finite volume approach, first bidimensional results

NASA Technical Reports Server (NTRS)

Chanteur, G.; Khanfir, R.

1995-01-01

We have designed a full compressible MHD code working on unstructured meshes in order to be able to compute accurately sharp structures embedded in large scale simulations. The code is based on a finite volume method making use of a kinetic flux splitting. A bidimensional version of the code has been used to simulate the interaction of a moving interstellar medium, magnetized or unmagnetized with a rotating and magnetized heliopspheric plasma source. Being aware that these computations are not realistic due to the restriction to two dimensions, we present it to demonstrate the ability of this new code to handle this problem. An axisymetric version, now under development, will be operational in a few months. Ultimately we plan to run a full 3d version.

Tunable spin-spin interactions and entanglement of ions in separate potential wells.

PubMed

Wilson, A C; Colombe, Y; Brown, K R; Knill, E; Leibfried, D; Wineland, D J

2014-08-07

Quantum simulation--the use of one quantum system to simulate a less controllable one--may provide an understanding of the many quantum systems which cannot be modelled using classical computers. Considerable progress in control and manipulation has been achieved for various quantum systems, but one of the remaining challenges is the implementation of scalable devices. In this regard, individual ions trapped in separate tunable potential wells are promising. Here we implement the basic features of this approach and demonstrate deterministic tuning of the Coulomb interaction between two ions, independently controlling their local wells. The scheme is suitable for emulating a range of spin-spin interactions, but to characterize the performance of our set-up we select one that entangles the internal states of the two ions with a fidelity of 0.82(1) (the digit in parentheses shows the standard error of the mean). Extension of this building block to a two-dimensional network, which is possible using ion-trap microfabrication processes, may provide a new quantum simulator architecture with broad flexibility in designing and scaling the arrangement of ions and their mutual interactions. To perform useful quantum simulations, including those of condensed-matter phenomena such as the fractional quantum Hall effect, an array of tens of ions might be sufficient.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

Convolutional neural networks applied to neutrino events in a liquid argon time projection chamber

NASA Astrophysics Data System (ADS)

Acciarri, R.; Adams, C.; An, R.; Asaadi, J.; Auger, M.; Bagby, L.; Baller, B.; Barr, G.; Bass, M.; Bay, F.; Bishai, M.; Blake, A.; Bolton, T.; Bugel, L.; Camilleri, L.; Caratelli, D.; Carls, B.; Castillo Fernandez, R.; Cavanna, F.; Chen, H.; Church, E.; Cianci, D.; Collin, G. H.; Conrad, J. M.; Convery, M.; Crespo-Anadón, J. I.; Del Tutto, M.; Devitt, D.; Dytman, S.; Eberly, B.; Ereditato, A.; Escudero Sanchez, L.; Esquivel, J.; Fleming, B. T.; Foreman, W.; Furmanski, A. P.; Garvey, G. T.; Genty, V.; Goeldi, D.; Gollapinni, S.; Graf, N.; Gramellini, E.; Greenlee, H.; Grosso, R.; Guenette, R.; Hackenburg, A.; Hamilton, P.; Hen, O.; Hewes, J.; Hill, C.; Ho, J.; Horton-Smith, G.; James, C.; de Vries, J. Jan; Jen, C.-M.; Jiang, L.; Johnson, R. A.; Jones, B. J. P.; Joshi, J.; Jostlein, H.; Kaleko, D.; Karagiorgi, G.; Ketchum, W.; Kirby, B.; Kirby, M.; Kobilarcik, T.; Kreslo, I.; Laube, A.; Li, Y.; Lister, A.; Littlejohn, B. R.; Lockwitz, S.; Lorca, D.; Louis, W. C.; Luethi, M.; Lundberg, B.; Luo, X.; Marchionni, A.; Mariani, C.; Marshall, J.; Martinez Caicedo, D. A.; Meddage, V.; Miceli, T.; Mills, G. B.; Moon, J.; Mooney, M.; Moore, C. D.; Mousseau, J.; Murrells, R.; Naples, D.; Nienaber, P.; Nowak, J.; Palamara, O.; Paolone, V.; Papavassiliou, V.; Pate, S. F.; Pavlovic, Z.; Porzio, D.; Pulliam, G.; Qian, X.; Raaf, J. L.; Rafique, A.; Rochester, L.; von Rohr, C. Rudolf; Russell, B.; Schmitz, D. W.; Schukraft, A.; Seligman, W.; Shaevitz, M. H.; Sinclair, J.; Snider, E. L.; Soderberg, M.; Söldner-Rembold, S.; Soleti, S. R.; Spentzouris, P.; Spitz, J.; St. John, J.; Strauss, T.; Szelc, A. M.; Tagg, N.; Terao, K.; Thomson, M.; Toups, M.; Tsai, Y.-T.; Tufanli, S.; Usher, T.; Van de Water, R. G.; Viren, B.; Weber, M.; Weston, J.; Wickremasinghe, D. A.; Wolbers, S.; Wongjirad, T.; Woodruff, K.; Yang, T.; Zeller, G. P.; Zennamo, J.; Zhang, C.

2017-03-01

We present several studies of convolutional neural networks applied to data coming from the MicroBooNE detector, a liquid argon time projection chamber (LArTPC). The algorithms studied include the classification of single particle images, the localization of single particle and neutrino interactions in an image, and the detection of a simulated neutrino event overlaid with cosmic ray backgrounds taken from real detector data. These studies demonstrate the potential of convolutional neural networks for particle identification or event detection on simulated neutrino interactions. We also address technical issues that arise when applying this technique to data from a large LArTPC at or near ground level.

Investigation of the effect of sealed surfaces on local climate in urban areas

NASA Astrophysics Data System (ADS)

Weihs, Philipp; Hasel, Stefan; Mursch-Radlgruber, Erich; Gützer, Christian; Krispel, Stefan; Peyerl, Martin; Trimmel, Heidi

2015-04-01

Local climate is driven by the interaction between energy balance and energy transported by advected air. Short-wave and long-wave radiation are major components in this interaction. Some few studies (e.g. Santamouris et al.) showed that adjusting the grade of reflection of surfaces is an efficient way to influence temperature. The present study investigates the influence of high albedo concrete surfaces on local climate. The first step of the study consisted of experimental investigations: routine measurements of the short and longwave radiation balance, of the ground and of the air temperature and humidity at different heights above 6 different types of sealed surfaces were performed. During this measurement campaign the above mentioned components were measured over a duration of 4 months above two conventional asphalt surfaces, one conventional concrete and three newly developed concrete surfaces with increased reflectances. Measured albedo values amounted to 0.12±0.02 for the asphalt surfaces and to maximum values of 0.56 for high albedo concrete. The maximum difference in surface temperature between the asphalt surfaces and the high albedo concrete surfaces amounted to 15°C. In addition the emission constants of the different sealed surfaces were also determined and were compared to values from literature.. In a second step the urban energy balance model Envi_Met was used to simulate the surface temperature of the six surfaces. The simulated surface temperatures were compared to the measured surface temperatures and statements as to uncertainties of the model simulations were made In a third step, Envi_Met was used to simulate the local climate of an urban district in Vienna. The surface and air temperature and the SW, LW fluxes were calculated for different types of sealed surfaces. By performing calculations of thermal stress indices (UTCI, PMV), statements as to the influence of the type of sealed surface on thermal stress on humans was made.

A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes.

PubMed Central

Klenin, K; Merlitz, H; Langowski, J

1998-01-01

For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps. PMID:9533691

RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Guan, W.; Cheng, X.; Huang, J.; Huber, G.; Li, W.; McCammon, J. A.; Zhang, B.

2018-06-01

RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) (Greengard and Rokhlin, 1997) where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library (DeBuhr et al., 2016, 2018). Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12,288 cores, while achieving approximately 54% strong-scaling efficiency.

Inhomogeneity of PAGs in resist film studied by molecular-dynamics simulations for EUV lithography

NASA Astrophysics Data System (ADS)

Toriumi, Minoru; Itani, Toshiro

2014-03-01

EUV resist materials are requested simultaneously to improve the resolution, line-edge roughness (LER), and sensitivity (RLS). In a resist film inhomogeneous structures in nanometer region may have large effects on directly the resolution and LER and indirectly on sensitivity. Inhomogeneity of PAGs in a hybrid resist for EUV lithography was investigated using molecular dynamics simulations. The hybrid resist film showed the inhomogeneous positions and motions of PAG cations and anions. Free volumes in resist matrix influence the motions of PAGs. Molecular structure such as bulky phenyl groups of a PAG cation localize the positions and reduce the motion of a cation. Chemical properties such as ionic interactions and lone-pair interaction also play an important role to determine the inhomogeneity of PAGs. Fluorine interaction enables active motions of PAG anions.

Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins.

PubMed

Deb, Pranab; Haldar, Tapas; Kashid, Somnath M; Banerjee, Subhrashis; Chakrabarty, Suman; Bagchi, Sayan

2016-05-05

Noncovalent interactions, in particular the hydrogen bonds and nonspecific long-range electrostatic interactions are fundamental to biomolecular functions. A molecular understanding of the local electrostatic environment, consistently for both specific (hydrogen-bonding) and nonspecific electrostatic (local polarity) interactions, is essential for a detailed understanding of these processes. Vibrational Stark Effect (VSE) has proven to be an extremely useful method to measure the local electric field using infrared spectroscopy of carbonyl and nitrile based probes. The nitrile chemical group would be an ideal choice because of its absorption in an infrared spectral window transparent to biomolecules, ease of site-specific incorporation into proteins, and common occurrence as a substituent in various drug molecules. However, the inability of VSE to describe the dependence of IR frequency on electric field for hydrogen-bonded nitriles to date has severely limited nitrile's utility to probe the noncovalent interactions. In this work, using infrared spectroscopy and atomistic molecular dynamics simulations, we have reported for the first time a linear correlation between nitrile frequencies and electric fields in a wide range of hydrogen-bonding environments that may bridge the existing gap between VSE and H-bonding interactions. We have demonstrated the robustness of this field-frequency correlation for both aromatic nitriles and sulfur-based nitriles in a wide range of molecules of varying size and compactness, including small molecules in complex solvation environments, an amino acid, disordered peptides, and structured proteins. This correlation, when coupled to VSE, can be used to quantify noncovalent interactions, specific or nonspecific, in a consistent manner.

An integrative model of the cardiac ventricular myocyte incorporating local control of Ca2+ release.

PubMed Central

Greenstein, Joseph L; Winslow, Raimond L

2002-01-01

The local control theory of excitation-contraction (EC) coupling in cardiac muscle asserts that L-type Ca(2+) current tightly controls Ca(2+) release from the sarcoplasmic reticulum (SR) via local interaction of closely apposed L-type Ca(2+) channels (LCCs) and ryanodine receptors (RyRs). These local interactions give rise to smoothly graded Ca(2+)-induced Ca(2+) release (CICR), which exhibits high gain. In this study we present a biophysically detailed model of the normal canine ventricular myocyte that conforms to local control theory. The model formulation incorporates details of microscopic EC coupling properties in the form of Ca(2+) release units (CaRUs) in which individual sarcolemmal LCCs interact in a stochastic manner with nearby RyRs in localized regions where junctional SR membrane and transverse-tubular membrane are in close proximity. The CaRUs are embedded within and interact with the global systems of the myocyte describing ionic and membrane pump/exchanger currents, SR Ca(2+) uptake, and time-varying cytosolic ion concentrations to form a model of the cardiac action potential (AP). The model can reproduce both the detailed properties of EC coupling, such as variable gain and graded SR Ca(2+) release, and whole-cell phenomena, such as modulation of AP duration by SR Ca(2+) release. Simulations indicate that the local control paradigm predicts stable APs when the L-type Ca(2+) current is adjusted in accord with the balance between voltage- and Ca(2+)-dependent inactivation processes as measured experimentally, a scenario where common pool models become unstable. The local control myocyte model provides a means for studying the interrelationship between microscopic and macroscopic behaviors in a manner that would not be possible in experiments. PMID:12496068

Science and Policy Interactions: A Case Study with Acid Rain

EPA Science Inventory

Management of air pollution has a long history in the United States. A succession of laws, with the first Federal law, passed in 1955, has lead to substantial reductions in emissions and improvements in air quality. These laws were simulated originally by acute local effects on ...

Interaction of magnetic resonators studied by the magnetic field enhancement

NASA Astrophysics Data System (ADS)

Hou, Yumin

2013-12-01

It is the first time that the magnetic field enhancement (MFE) is used to study the interaction of magnetic resonators (MRs), which is more sensitive than previous parameters-shift and damping of resonance frequency. To avoid the coherence of lattice and the effect of Bloch wave, the interaction is simulated between two MRs with same primary phase when the distance is changed in the range of several resonance wavelengths, which is also compared with periodic structure. The calculated MFE oscillating and decaying with distance with the period equal to resonance wavelength directly shows the retardation effect. Simulation also shows that the interaction at normal incidence is sensitive to the phase correlation which is related with retardation effect and is ultra-long-distance interaction when the two MRs are strongly localized. When the distance is very short, the amplitude of magnetic resonance is oppressed by the strong interaction and thus the MFE can be much lower than that of single MR. This study provides the design rules of metamaterials for engineering resonant properties of MRs.

Particle Trapping Mechanisms Are Different in Spatially Ordered and Disordered Interacting Gels.

PubMed

Hansing, Johann; Netz, Roland R

2018-06-05

Using stochastic simulations, we study the influence of spatial disorder on the diffusion of a single particle through a gel that consists of rigid, straight fibers. The interaction between the particle and the gel fibers consists of an invariant short-range repulsion, the steric part, and an interaction part that can be attractive or repulsive and of varying range. The effect that spatial disorder of the gel structure has on the particle diffusivity depends crucially on the presence of nonsteric interactions. For attractive interactions, disorder slows down diffusion, because in disordered gels, the particle becomes strongly trapped in regions of locally increased fiber density. For repulsive interactions, the diffusivity is minimal for intermediate disorder strength, because highly disordered lattices exhibit abundant passageways of locally low fiber density. The comparison with experimental data on protein and fluorophore diffusion through various hydrogels is favorable. Our findings shed light on particle-diffusion mechanisms in biogels and thus on biological barrier properties, which can be helpful for the optimal design of synthetic diffusors as well as synthetic mucus constructs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Stability and dynamics of membrane-spanning DNA nanopores

NASA Astrophysics Data System (ADS)

Maingi, Vishal; Burns, Jonathan R.; Uusitalo, Jaakko J.; Howorka, Stefan; Marrink, Siewert J.; Sansom, Mark S. P.

2017-03-01

Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

Plasmonics simulations including nonlocal effects using a boundary element method approach

NASA Astrophysics Data System (ADS)

Trügler, Andreas; Hohenester, Ulrich; García de Abajo, F. Javier

2017-09-01

Spatial nonlocality in the photonic response of metallic nanoparticles is actually known to produce near-field quenching and significant plasmon frequency shifts relative to local descriptions. As the control over size and morphology of fabricated nanostructures is truly reaching the nanometer scale, understanding and accounting for nonlocal phenomena is becoming increasingly important. Recent advances clearly point out the need to go beyond the local theory. We here present a general formalism for incorporating spatial dispersion effects through the hydrodynamic model and generalizations for arbitrary surface morphologies. Our method relies on the boundary element method, which we supplement with a nonlocal interaction potential. We provide numerical examples in excellent agreement with the literature for individual and paired gold nanospheres, and critically examine the accuracy of our approach. The present method involves marginal extra computational cost relative to local descriptions and facilitates the simulation of spatial dispersion effects in the photonic response of complex nanoplasmonic structures.

Decentralized control experiments on NASA's flexible grid

NASA Technical Reports Server (NTRS)

Ozguner, U.; Yurkowich, S.; Martin, J., III; Al-Abbass, F.

1986-01-01

Methods arising from the area of decentralized control are emerging for analysis and control synthesis for large flexible structures. In this paper the control strategy involves a decentralized model reference adaptive approach using a variable structure control. Local models are formulated based on desired damping and response time in a model-following scheme for various modal configurations. Variable structure controllers are then designed employing co-located angular rate and position feedback. In this scheme local control forces the system to move on a local sliding mode in some local error space. An important feature of this approach is that the local subsystem is made insensitive to dynamical interactions with other subsystems once the sliding surface is reached. Experiments based on the above have been performed for NASA's flexible grid experimental apparatus. The grid is designed to admit appreciable low-frequency structural dynamics, and allows for implementation of distributed computing components, inertial sensors, and actuation devices. A finite-element analysis of the grid provides the model for control system design and simulation; results of several simulations are reported on here, and a discussion of application experiments on the apparatus is presented.

Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wood, Irene; Martini, M. Florencia; Pickholz, Mónica

2013-08-01

In this work, we report a molecular dynamics (MD) simulations study of relevant biological molecules as serotonin (neutral and protonated) and its precursors, tryptophan and 5-hydroxy-tryptophan, in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC). The simulations were carried out at the fluid lamellar phase of POPC at constant pressure and temperature conditions. Two guest molecules of each type were initially placed at the water phase. We have analyzed, the main localization, preferential orientation and specific interactions of the guest molecules within the bilayer. During the simulation run, the four molecules were preferentially found at the water-lipid interphase. We found that the interactions that stabilized the systems are essentially hydrogen bonds, salt bridges and cation-π. None of the guest molecules have access to the hydrophobic region of the bilayer. Besides, zwitterionic molecules have access to the water phase, while protonated serotonin is anchored in the interphase. Even taking into account that these simulations were done using a model membrane, our results suggest that the studied molecules could not cross the blood brain barrier by diffusion. These results are in good agreement with works that show that serotonin and Trp do not cross the BBB by simple diffusion.

Structuring Light to Manipulate Multipolar Resonances for Metamaterial Applications

NASA Astrophysics Data System (ADS)

Das, Tanya

Multipolar electromagnetic phenomena in sub-wavelength resonators are at the heart of metamaterial science and technology. Typically, researchers engineer multipolar light-matter interactions by modifying the size, shape, and composition of the resonators. Here, we instead engineer multipolar interactions by modifying properties of the incident radiation. In this dissertation, we propose a new framework for determining the scattering response of resonators based on properties of the local excitation field. First, we derive an analytical theory to determine the scattering response of spherical nanoparticles under any type of illumination. Using this theory, we demonstrate the ability to drastically manipulate the scattering properties of a spherical nanoparticle by varying the illumination and demonstrate excitation of a longitudinal quadrupole mode that cannot be accessed with conventional illumination. Next, we investigate the response of dielectric dimer structures illuminated by cylindrical vector beams. Using finite-difference time-domain simulations, we demonstrate significant modification of the scattering spectra of dimer antennas and reveal how the illumination condition gives rise to these spectra through manipulation of electric and magnetic mode hybridization. Finally, we present a simple and efficient numerical simulation based on local field principles for extracting the multipolar response of any resonator under illumination by structured light. This dissertation enhances the understanding of fundamental light-matter interactions in metamaterials and lays the foundation for researchers to identify, quantify, and manipulate multipolar light-matter interactions through optical beam engineering.

Elucidation of the binding sites of sodium dodecyl sulfate to β-lactoglobulin using hydrogen/deuterium exchange mass spectrometry combined with docking simulation.

PubMed

Hu, Wenbing; Liu, Jianan; Luo, Qun; Han, Yumiao; Wu, Kui; Lv, Shuang; Xiong, Shaoxiang; Wang, Fuyi

2011-05-30

Hydrogen/deuterium exchange mass spectrometry (H/DX MS) has become a powerful tool to investigate protein-protein and protein-ligand interactions, but it is still challenging to localize the interaction regions/sites of ligands with pepsin-resistant proteins such as lipocalins. β-Lactoglobulin (BLG), a member of the lipocalin family, can bind a variety of small hydrophobic molecules including retinols, retinoic acids, and long linear fatty acids. However, whether the binding site of linear molecules locates in the external groove or internal cavity of BLG is controversial. In this study we used H/DX MS combined with docking simulation to localize the interaction sites of a tested ligand, sodium dodecyl sulfate (SDS), binding to BLG. H/DX MS results indicated that SDS can bind to both the external and the internal sites in BLG. However, neither of the sites is saturated with SDS, allowing a dynamic ligand exchange to occur between the sites at equilibrium state. Docking studies revealed that SDS forms H-bonds with Lys69 in the internal site and Lys138 and Lys141 in the external site in BLG via the sulfate group, and interacts with the hydrophobic residues valine, leucine, isoleucine and methionine within both of the sites via its hydrocarbon tail, stabilizing the BLG-SDS complex. Copyright © 2011 John Wiley & Sons, Ltd.

Investigating the effects of tropomyosin mutations on its flexibility and interactions with filamentous actin using molecular dynamics simulation.

PubMed

Zheng, Wenjun; Hitchcock-DeGregori, Sarah E; Barua, Bipasha

2016-10-01

Tropomyosin (Tpm) is a two-chained α-helical coiled-coil protein that binds to filamentous actin (F-actin), and regulates its interactions with myosin by occupying three average positions on F-actin (blocked, closed, and open). Mutations in the Tpm are linked to heart diseases including hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). To elucidate the molecular mechanisms of Tpm mutations (including DCM mutation E54K, HCM mutations E62Q, A63V, K70T, V95A, D175N, E180G, L185R, E192K, and a designed synthetic mutation D137L) in terms of their effects on Tpm flexibility and its interactions with F-actin, we conducted extensive molecular dynamics simulations for the wild-type and mutant Tpm in complex with F-actin (total simulation time 160 ns per mutant). The mutants exhibited distinct changes (i.e., increase or decrease) in the overall and local flexibility of the Tpm coiled-coil, with each mutation causing both local and long-range modifications of the Tpm flexibility. In addition, our binding calculations revealed weakened Tpm-F-actin interactions (except for L185R, D137L and A63V) involving five periods of Tpm, which correlate with elevated fluctuation of Tpm relative to the blocked position on F-actin that may lead to easier activation and increased Ca 2+ -sensitivity. We also simulated the αβ/βα-Tpm heterodimer in comparison with the αα-Tpm homodimer, which revealed greater flexibility and weaker actin binding in the heterodimer. Our findings are consistent with a complex mechanism underlying how different Tpm mutations perturb the Tpm function in distinct ways (e.g., by affecting specific sites of Tpm), which bear no simple links to the disease phenotypes (e.g., HCM vs. DCM).

Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines.

PubMed

Li, Yang; Xu, Weixin; Mu, Yuguang; Zhang, John Z H

2013-08-07

The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent β-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.

Topological frustration in βα-repeat proteins: sequence diversity modulates the conserved folding mechanisms of α/β/α sandwich proteins

PubMed Central

Hills, Ronald D.; Kathuria, Sagar V.; Wallace, Louise A.; Day, Iain J.; Brooks, Charles L.; Matthews, C. Robert

2010-01-01

The thermodynamic hypothesis of Anfinsen postulates that structures and stabilities of globular proteins are determined by their amino acid sequences. Chain topology, however, is known to influence the folding reaction, in that motifs with a preponderance of local interactions typically fold more rapidly than those with a larger fraction of non-local interactions. Together, the topology and sequence can modulate the energy landscape and influence the rate at which the protein folds to the native conformation. To explore the relationship of sequence and topology in the folding of βα–repeat proteins, which are dominated by local interactions, a combined experimental and simulation analysis was performed on two members of the flavodoxin-like, α/β/α sandwich fold. Spo0F and the N-terminal receiver domain of NtrC (NT-NtrC) have similar topologies but low sequence identity, enabling a test of the effects of sequence on folding. Experimental results demonstrated that both response-regulator proteins fold via parallel channels through highly structured sub-millisecond intermediates before accessing their cis prolyl peptide bond-containing native conformations. Global analysis of the experimental results preferentially places these intermediates off the productive folding pathway. Sequence-sensitive Gō-model simulations conclude that frustration in the folding in Spo0F, corresponding to the appearance of the off-pathway intermediate, reflects competition for intra-subdomain van der Waals contacts between its N- and C-terminal subdomains. The extent of transient, premature structure appears to correlate with the number of isoleucine, leucine and valine (ILV) side-chains that form a large sequence-local cluster involving the central β-sheet and helices α2, α3 and α4. The failure to detect the off-pathway species in the simulations of NT-NtrC may reflect the reduced number of ILV side-chains in its corresponding hydrophobic cluster. The location of the hydrophobic clusters in the structure may also be related to the differing functional properties of these response regulators. Comparison with the results of previous experimental and simulation analyses on the homologous CheY argues that prematurely-folded unproductive intermediates are a common property of the βα-repeat motif. PMID:20226790

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

NASA Astrophysics Data System (ADS)

Sanyal, Tanmoy; Shell, M. Scott

2016-07-01

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions

PubMed Central

Vagenende, Vincent; Han, Alvin X.; Pek, Han B.; Loo, Bernard L. W.

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments. PMID:23696727

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

PubMed

Vagenende, Vincent; Han, Alvin X; Pek, Han B; Loo, Bernard L W

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

Numerical studies of the KP line-solitons

NASA Astrophysics Data System (ADS)

Chakravarty, S.; McDowell, T.; Osborne, M.

2017-03-01

The Kadomtsev-Petviashvili (KP) equation admits a class of solitary wave solutions localized along distinct rays in the xy-plane, called the line-solitons, which describe the interaction of shallow water waves on a flat surface. These wave interactions have been observed on long, flat beaches, as well as have been recreated in laboratory experiments. In this paper, the line-solitons are investigated via direct numerical simulations of the KP equation, and the interactions of the evolved solitary wave patterns are studied. The objective is to obtain greater insight into solitary wave interactions in shallow water and to determine the extent the KP equation is a good model in describing these nonlinear interactions.

Influence of coupling on atmosphere, sea ice and ocean regional models in the Ross Sea sector, Antarctica

NASA Astrophysics Data System (ADS)

Jourdain, Nicolas C.; Mathiot, Pierre; Gallée, Hubert; Barnier, Bernard

2011-04-01

Air-sea ice-ocean interactions in the Ross Sea sector form dense waters that feed the global thermohaline circulation. In this paper, we develop the new limited-area ocean-sea ice-atmosphere coupled model TANGO to simulate the Ross Sea sector. TANGO is built up by coupling the atmospheric limited-area model MAR to a regional configuration of the ocean-sea ice model NEMO. A method is then developed to identify the mechanisms by which local coupling affects the simulations. TANGO is shown to simulate realistic sea ice properties and atmospheric surface temperatures. These skills are mostly related to the skills of the stand alone atmospheric and oceanic models used to build TANGO. Nonetheless, air temperatures over ocean and winter sea ice thickness are found to be slightly improved in coupled simulations as compared to standard stand alone ones. Local atmosphere ocean feedbacks over the open ocean are found to significantly influence ocean temperature and salinity. In a stand alone ocean configuration, the dry and cold air produces an ocean cooling through sensible and latent heat loss. In a coupled configuration, the atmosphere is in turn moistened and warmed by the ocean; sensible and latent heat loss is therefore reduced as compared to the stand alone simulations. The atmosphere is found to be less sensitive to local feedbacks than the ocean. Effects of local feedbacks are increased in the coastal area because of the presence of sea ice. It is suggested that slow heat conduction within sea ice could amplify the feedbacks. These local feedbacks result in less sea ice production in polynyas in coupled mode, with a subsequent reduction in deep water formation.

New insights into chromatin folding and dynamics from multi-scale modeling

NASA Astrophysics Data System (ADS)

Olson, Wilma

The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes-the familiar assemblies of roughly 150 DNA base pairs and eight histone proteins-found on chromatin fibers. We have developed a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs with 3-25 evenly spaced nucleosomes. The correspondence between the predicted and observed effects of nucleosome composition, spacing, and numbers on long-range communication between regulatory proteins bound to the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We have extracted effective nucleosome-nucleosome potentials from the mesoscale simulations and introduced the potentials in a larger scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable influence of nucleosome spacing on chromatin flexibility. Small changes in the length of the DNA fragments linking successive nucleosomes introduce marked changes in the local interactions of the nucleosomes and in the spatial configurations of the fiber as a whole. The changes in nucleosome positioning influence the statistical properties of longer chromatin constructs with 100-10,000 nucleosomes. We are investigating the extent to which the `local' interactions of regularly spaced nucleosomes contribute to the corresponding interactions in chains with mixed spacings as a step toward the treatment of fibers with nucleosomes positioned at the sites mapped at base-pair resolution on genomic sequences. Support of the work by USPHS R01 GM 34809 is gratefully acknowledged.

Self-Consistent Monte Carlo Study of the Coulomb Interaction under Nano-Scale Device Structures

NASA Astrophysics Data System (ADS)

Sano, Nobuyuki

2011-03-01

It has been pointed that the Coulomb interaction between the electrons is expected to be of crucial importance to predict reliable device characteristics. In particular, the device performance is greatly degraded due to the plasmon excitation represented by dynamical potential fluctuations in high-doped source and drain regions by the channel electrons. We employ the self-consistent 3D Monte Carlo (MC) simulations, which could reproduce both the correct mobility under various electron concentrations and the collective plasma waves, to study the physical impact of dynamical potential fluctuations on device performance under the Double-gate MOSFETs. The average force experienced by an electron due to the Coulomb interaction inside the device is evaluated by performing the self-consistent MC simulations and the fixed-potential MC simulations without the Coulomb interaction. Also, the band-tailing associated with the local potential fluctuations in high-doped source region is quantitatively evaluated and it is found that the band-tailing becomes strongly dependent of position in real space even inside the uniform source region. This work was partially supported by Grants-in-Aid for Scientific Research B (No. 2160160) from the Ministry of Education, Culture, Sports, Science and Technology in Japan.

Regularization method for large eddy simulations of shock-turbulence interactions

NASA Astrophysics Data System (ADS)

Braun, N. O.; Pullin, D. I.; Meiron, D. I.

2018-05-01

The rapid change in scales over a shock has the potential to introduce unique difficulties in Large Eddy Simulations (LES) of compressible shock-turbulence flows if the governing model does not sufficiently capture the spectral distribution of energy in the upstream turbulence. A method for the regularization of LES of shock-turbulence interactions is presented which is constructed to enforce that the energy content in the highest resolved wavenumbers decays as k - 5 / 3, and is computed locally in physical-space at low computational cost. The application of the regularization to an existing subgrid scale model is shown to remove high wavenumber errors while maintaining agreement with Direct Numerical Simulations (DNS) of forced and decaying isotropic turbulence. Linear interaction analysis is implemented to model the interaction of a shock with isotropic turbulence from LES. Comparisons to analytical models suggest that the regularization significantly improves the ability of the LES to predict amplifications in subgrid terms over the modeled shockwave. LES and DNS of decaying, modeled post shock turbulence are also considered, and inclusion of the regularization in shock-turbulence LES is shown to improve agreement with lower Reynolds number DNS.

Number-squeezed and fragmented states of strongly interacting bosons in a double well

NASA Astrophysics Data System (ADS)

Corbo, Joel C.; DuBois, Jonathan L.; Whaley, K. Birgitta

2017-11-01

We present a systematic study of the phenomena of number squeezing and fragmentation for a repulsive Bose-Einstein condensate (BEC) in a three-dimensional double-well potential over a range of interaction strengths and barrier heights, including geometries that exhibit appreciable overlap in the one-body wave functions localized in the left and right wells. We compute the properties of the condensate with numerically exact, full-dimensional path-integral ground-state (PIGS) quantum Monte Carlo simulations and compare with results obtained from using two- and eight-mode truncated basis models. The truncated basis models are found to agree with the numerically exact PIGS simulations for weak interactions, but fail to correctly predict the amount of number squeezing and fragmentation exhibited by the PIGS simulations for strong interactions. We find that both number squeezing and fragmentation of the BEC show nonmonotonic behavior at large values of interaction strength a . The number squeezing shows a universal scaling with the product of number of particles and interaction strength (N a ), but no such universal behavior is found for fragmentation. Detailed analysis shows that the introduction of repulsive interactions not only suppresses number fluctuations to enhance number squeezing, but can also enhance delocalization across wells and tunneling between wells, each of which may suppress number squeezing. This results in a dynamical competition whose resolution shows a complex dependence on all three physical parameters defining the system: interaction strength, number of particles, and barrier height.

Interaction of Kelvin waves and nonlocality of energy transfer in superfluids

NASA Astrophysics Data System (ADS)

Laurie, Jason; L'Vov, Victor S.; Nazarenko, Sergey; Rudenko, Oleksii

2010-03-01

We argue that the physics of interacting Kelvin Waves (KWs) is highly nontrivial and cannot be understood on the basis of pure dimensional reasoning. A consistent theory of KW turbulence in superfluids should be based upon explicit knowledge of their interactions. To achieve this, we present a detailed calculation and comprehensive analysis of the interaction coefficients for KW turbuelence, thereby, resolving previous mistakes stemming from unaccounted contributions. As a first application of this analysis, we derive a local nonlinear (partial differential) equation. This equation is much simpler for analysis and numerical simulations of KWs than the Biot-Savart equation, and in contrast to the completely integrable local induction approximation (in which the energy exchange between KWs is absent), describes the nonlinear dynamics of KWs. Second, we show that the previously suggested Kozik-Svistunov energy spectrum for KWs, which has often been used in the analysis of experimental and numerical data in superfluid turbulence, is irrelevant, because it is based upon an erroneous assumption of the locality of the energy transfer through scales. Moreover, we demonstrate the weak nonlocality of the inverse cascade spectrum with a constant particle-number flux and find resulting logarithmic corrections to this spectrum.

Efficacy of computer-based video and simulation in ultrasound-guided regional anesthesia training.

PubMed

Woodworth, Glenn E; Chen, Elliza M; Horn, Jean-Louis E; Aziz, Michael F

2014-05-01

To determine the effectiveness of a short educational video and simulation on improvement of ultrasound (US) image acquisition and interpretation skills. Prospective, randomized study. University medical center. 28 anesthesia residents and community anesthesiologists with varied ultrasound experience were randomized to teaching video with interactive simulation or sham video groups. Participants were assessed preintervention and postintervention on their ability to identify the sciatic nerve and other anatomic structures on static US images, as well as their ability to locate the sciatic nerve with US on live models. Pretest written test scores correlated with reported US block experience (Kendall tau rank r = 0.47) and with live US scanning scores (r = 0.64). The teaching video and simulation significantly improved scores on the written examination (P < 0.001); however, they did not significantly improve live US scanning skills. A short educational video with interactive simulation significantly improved knowledge of US anatomy, but failed to improve hands-on performance of US scanning to localize the nerve. Copyright © 2014 Elsevier Inc. All rights reserved.

Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Smith, Grant D.

1994-01-01

The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.

Interactions of localized wave structures and dynamics in the defocusing coupled nonlinear Schrödinger equations.

PubMed

Zhang, Guoqiang; Yan, Zhenya; Wen, Xiao-Yong; Chen, Yong

2017-04-01

We investigate the defocusing coupled nonlinear Schrödinger equations from a 3×3 Lax pair. The Darboux transformations with the nonzero plane-wave solutions are presented to derive the newly localized wave solutions including dark-dark and bright-dark solitons, breather-breather solutions, and different types of new vector rogue wave solutions, as well as interactions between distinct types of localized wave solutions. Moreover, we analyze these solutions by means of parameters modulation. Finally, the perturbed wave propagations of some obtained solutions are explored by means of systematic simulations, which demonstrates that nearly stable and strongly unstable solutions. Our research results could constitute a significant contribution to explore the distinct nonlinear waves (e.g., dark solitons, breather solutions, and rogue wave solutions) dynamics of the coupled system in related fields such as nonlinear optics, plasma physics, oceanography, and Bose-Einstein condensates.

From homeostasis to behavior: Balanced activity in an exploration of embodied dynamic environmental-neural interaction.

PubMed

Hellyer, Peter John; Clopath, Claudia; Kehagia, Angie A; Turkheimer, Federico E; Leech, Robert

2017-08-01

In recent years, there have been many computational simulations of spontaneous neural dynamics. Here, we describe a simple model of spontaneous neural dynamics that controls an agent moving in a simple virtual environment. These dynamics generate interesting brain-environment feedback interactions that rapidly destabilize neural and behavioral dynamics demonstrating the need for homeostatic mechanisms. We investigate roles for homeostatic plasticity both locally (local inhibition adjusting to balance excitatory input) as well as more globally (regional "task negative" activity that compensates for "task positive", sensory input in another region) balancing neural activity and leading to more stable behavior (trajectories through the environment). Our results suggest complementary functional roles for both local and macroscale mechanisms in maintaining neural and behavioral dynamics and a novel functional role for macroscopic "task-negative" patterns of activity (e.g., the default mode network).

Multistability of second-order competitive neural networks with nondecreasing saturated activation functions.

PubMed

Nie, Xiaobing; Cao, Jinde

2011-11-01

In this paper, second-order interactions are introduced into competitive neural networks (NNs) and the multistability is discussed for second-order competitive NNs (SOCNNs) with nondecreasing saturated activation functions. Firstly, based on decomposition of state space, Cauchy convergence principle, and inequality technique, some sufficient conditions ensuring the local exponential stability of 2N equilibrium points are derived. Secondly, some conditions are obtained for ascertaining equilibrium points to be locally exponentially stable and to be located in any designated region. Thirdly, the theory is extended to more general saturated activation functions with 2r corner points and a sufficient criterion is given under which the SOCNNs can have (r+1)N locally exponentially stable equilibrium points. Even if there is no second-order interactions, the obtained results are less restrictive than those in some recent works. Finally, three examples with their simulations are presented to verify the theoretical analysis.

Evaluation of the HadGEM3-A simulations in view of detection and attribution of human influence on extreme events in Europe

NASA Astrophysics Data System (ADS)

Vautard, Robert; Christidis, Nikolaos; Ciavarella, Andrew; Alvarez-Castro, Carmen; Bellprat, Omar; Christiansen, Bo; Colfescu, Ioana; Cowan, Tim; Doblas-Reyes, Francisco; Eden, Jonathan; Hauser, Mathias; Hegerl, Gabriele; Hempelmann, Nils; Klehmet, Katharina; Lott, Fraser; Nangini, Cathy; Orth, René; Radanovics, Sabine; Seneviratne, Sonia I.; van Oldenborgh, Geert Jan; Stott, Peter; Tett, Simon; Wilcox, Laura; Yiou, Pascal

2018-04-01

A detailed analysis is carried out to assess the HadGEM3-A global atmospheric model skill in simulating extreme temperatures, precipitation and storm surges in Europe in the view of their attribution to human influence. The analysis is performed based on an ensemble of 15 atmospheric simulations forced with observed sea surface temperature of the 54 year period 1960-2013. These simulations, together with dual simulations without human influence in the forcing, are intended to be used in weather and climate event attribution. The analysis investigates the main processes leading to extreme events, including atmospheric circulation patterns, their links with temperature extremes, land-atmosphere and troposphere-stratosphere interactions. It also compares observed and simulated variability, trends and generalized extreme value theory parameters for temperature and precipitation. One of the most striking findings is the ability of the model to capture North-Atlantic atmospheric weather regimes as obtained from a cluster analysis of sea level pressure fields. The model also reproduces the main observed weather patterns responsible for temperature and precipitation extreme events. However, biases are found in many physical processes. Slightly excessive drying may be the cause of an overestimated summer interannual variability and too intense heat waves, especially in central/northern Europe. However, this does not seem to hinder proper simulation of summer temperature trends. Cold extremes appear well simulated, as well as the underlying blocking frequency and stratosphere-troposphere interactions. Extreme precipitation amounts are overestimated and too variable. The atmospheric conditions leading to storm surges were also examined in the Baltics region. There, simulated weather conditions appear not to be leading to strong enough storm surges, but winds were found in very good agreement with reanalyses. The performance in reproducing atmospheric weather patterns indicates that biases mainly originate from local and regional physical processes. This makes local bias adjustment meaningful for climate change attribution.

Computational modeling of chemo-electro-mechanical coupling: A novel implicit monolithic finite element approach

PubMed Central

Wong, J.; Göktepe, S.; Kuhl, E.

2014-01-01

Summary Computational modeling of the human heart allows us to predict how chemical, electrical, and mechanical fields interact throughout a cardiac cycle. Pharmacological treatment of cardiac disease has advanced significantly over the past decades, yet it remains unclear how the local biochemistry of an individual heart cell translates into global cardiac function. Here we propose a novel, unified strategy to simulate excitable biological systems across three biological scales. To discretize the governing chemical, electrical, and mechanical equations in space, we propose a monolithic finite element scheme. We apply a highly efficient and inherently modular global-local split, in which the deformation and the transmembrane potential are introduced globally as nodal degrees of freedom, while the chemical state variables are treated locally as internal variables. To ensure unconditional algorithmic stability, we apply an implicit backward Euler finite difference scheme to discretize the resulting system in time. To increase algorithmic robustness and guarantee optimal quadratic convergence, we suggest an incremental iterative Newton-Raphson scheme. The proposed algorithm allows us to simulate the interaction of chemical, electrical, and mechanical fields during a representative cardiac cycle on a patient-specific geometry, robust and stable, with calculation times on the order of four days on a standard desktop computer. PMID:23798328

NEUTRAL ATOM PROPERTIES IN THE DIRECTION OF THE IBEX RIBBON

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

Heerikhuisen, Jacob; Pogorelov, Nikolai V.; Gamayunov, Konstantin V.

2016-11-10

In this paper, we present results from our three-dimensional (3D) simulations of the interaction between the solar wind and local interstellar medium with an emphasis on the phase-space properties of energetic neutral atoms (ENAs) along a sight line that intersects the ribbon of enhanced ENA flux seen by NASA’s Interstellar Boundary EXplorer spacecraft. The majority of these ENAs have velocities directed away from the heliosphere, but it is believed that interactions between heliospheric ENAs and ions outside the heliosphere may result in a population of secondary ENAs that return to the heliosphere and generate the ribbon. While we do notmore » consider the ion dynamics that result in secondary ENAs, our analysis is of key importance to the process since the heliospheric ENAs we consider form the source population for those ions. We present the moments of the hydrogen distribution, along with moments parallel and perpendicular to the local magnetic field for the pick-up ions (PUIs) that these neutrals generate. Finally, we present gyro-averaged velocity distributions relative to the local magnetic field for the PUIs created from our simulated H-atoms, along with analytic fits to these distributions in the secondary ENA source region just beyond the heliopause.« less

The effect of individual variation on the structure and function of interaction networks in harvester ants

PubMed Central

Pinter-Wollman, Noa; Wollman, Roy; Guetz, Adam; Holmes, Susan; Gordon, Deborah M.

2011-01-01

Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant's interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow. PMID:21490001

Strong inter-population cooperation leads to partner intermixing in microbial communities

DOE PAGES

Momeni, Babak; Brileya, Kristen A.; Fields, Matthew W.; ...

2013-01-22

Patterns of spatial positioning of individuals within microbial communities are often critical to community function. However, understanding patterning in natural communities is hampered by the multitude of cell–cell and cell–environment interactions as well as environmental variability. Here, through simulations and experiments on communities in defined environments, we examined how ecological interactions between two distinct partners impacted community patterning. We found that in strong cooperation with spatially localized large fitness benefits to both partners, a unique pattern is generated: partners spatially intermixed by appearing successively on top of each other, insensitive to initial conditions and interaction dynamics. Intermixing was experimentally observedmore » in two obligatory cooperative systems: an engineered yeast community cooperating through metabolite-exchanges and a methane-producing community cooperating through redox-coupling. Even in simulated communities consisting of several species, most of the strongly-cooperating pairs appeared intermixed. Thus, when ecological interactions are the major patterning force, strong cooperation leads to partner intermixing.« less

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

PubMed

Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David; Luthey-Schulten, Zaida; Gruebele, Martin

2017-09-14

U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.

Convolutional neural networks applied to neutrino events in a liquid argon time projection chamber

DOE PAGES

Acciarri, R.; Adams, C.; An, R.; ...

2017-03-14

Here, we present several studies of convolutional neural networks applied to data coming from the MicroBooNE detector, a liquid argon time projection chamber (LArTPC). The algorithms studied include the classification of single particle images, the localization of single particle and neutrino interactions in an image, and the detection of a simulated neutrino event overlaid with cosmic ray backgrounds taken from real detector data. These studies demonstrate the potential of convolutional neural networks for particle identification or event detection on simulated neutrino interactions. Lastly, we also address technical issues that arise when applying this technique to data from a large LArTPCmore » at or near ground level.« less

Cluster dynamics and cluster size distributions in systems of self-propelled particles

NASA Astrophysics Data System (ADS)

Peruani, F.; Schimansky-Geier, L.; Bär, M.

2010-12-01

Systems of self-propelled particles (SPP) interacting by a velocity alignment mechanism in the presence of noise exhibit rich clustering dynamics. Often, clusters are responsible for the distribution of (local) information in these systems. Here, we investigate the properties of individual clusters in SPP systems, in particular the asymmetric spreading behavior of clusters with respect to their direction of motion. In addition, we formulate a Smoluchowski-type kinetic model to describe the evolution of the cluster size distribution (CSD). This model predicts the emergence of steady-state CSDs in SPP systems. We test our theoretical predictions in simulations of SPP with nematic interactions and find that our simple kinetic model reproduces qualitatively the transition to aggregation observed in simulations.

Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex.

PubMed

Wang, Jingwen; Zhao, Yuqi; Wang, Yanjie; Huang, Jingfei

2013-01-16

Coevolution between proteins is crucial for understanding protein-protein interaction. Simultaneous changes allow a protein complex to maintain its overall structural-functional integrity. In this study, we combined statistical coupling analysis (SCA) and molecular dynamics simulations on the CDK6-CDKN2A protein complex to evaluate coevolution between proteins. We reconstructed an inter-protein residue coevolution network, consisting of 37 residues and 37 interactions. It shows that most of the coevolved residue pairs are spatially proximal. When the mutations happened, the stable local structures were broken up and thus the protein interaction was decreased or inhibited, with a following increased risk of melanoma. The identification of inter-protein coevolved residues in the CDK6-CDKN2A complex can be helpful for designing protein engineering experiments. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Water resources planning based on complex system dynamics: A case study of Tianjin city

NASA Astrophysics Data System (ADS)

Zhang, X. H.; Zhang, H. W.; Chen, B.; Chen, G. Q.; Zhao, X. H.

2008-12-01

A complex system dynamic (SD) model focusing on water resources, termed as TianjinSD, is developed for the integrated and scientific management of the water resources of Tianjin, which contains information feedback that governs interactions in the system and is capable of synthesizing component-level knowledge into system behavior simulation at an integrated level, thus presenting reasonable predictive results for policy-making on water resources allocation and management. As for the Tianjin city, interactions among 96 components for 12 years are explored and four planning alternatives are chosen, one of which is based on the conventional mode assuming that the existing pattern of human activities will be prevailed, while the others are alternative planning designs based on the interaction of local authorities and planning researchers. Optimal mode is therefore obtained according to different scenarios when compared the simulation results for evaluation of different decisions and dynamic consequences.

Model of mobile agents for sexual interactions networks

NASA Astrophysics Data System (ADS)

González, M. C.; Lind, P. G.; Herrmann, H. J.

2006-02-01

We present a novel model to simulate real social networks of complex interactions, based in a system of colliding particles (agents). The network is build by keeping track of the collisions and evolves in time with correlations which emerge due to the mobility of the agents. Therefore, statistical features are a consequence only of local collisions among its individual agents. Agent dynamics is realized by an event-driven algorithm of collisions where energy is gained as opposed to physical systems which have dissipation. The model reproduces empirical data from networks of sexual interactions, not previously obtained with other approaches.

Computational and theoretical approaches for studies of a lipid recognition protein on biological membranes

PubMed Central

Yamamoto, Eiji

2017-01-01

Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes. Multiscale molecular dynamics simulations using combinations of atomistic and coarse-grained models yielded results comparable to those of actual experiments and could be used to elucidate the molecular mechanisms of the formation of protein/lipid complexes on membrane surfaces, which are often difficult to obtain using experimental techniques. Simulations revealed some modes of membrane localization and interactions of PH domains with membranes in addition to the canonical binding mode. In the last part of this review, I address the dynamics of PH domains on the membrane surface. Local PIP clusters formed around the proteins exhibit anomalous fluctuations. This dynamic change in protein-lipid interactions cause temporally fluctuating diffusivity of proteins, i.e., the short-term diffusivity of the bound protein changes substantially with time, and may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:29159013

Time-Domain Modeling of RF Antennas and Plasma-Surface Interactions

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, David N.

2017-10-01

Recent advances in finite-difference time-domain (FDTD) modeling techniques allow plasma-surface interactions such as sheath formation and sputtering to be modeled concurrently with the physics of antenna near- and far-field behavior and ICRF power flow. Although typical sheath length scales (micrometers) are much smaller than the wavelengths of fast (tens of cm) and slow (millimeter) waves excited by the antenna, sheath behavior near plasma-facing antenna components can be represented by a sub-grid kinetic sheath boundary condition, from which RF-rectified sheath potential variation over the surface is computed as a function of current flow and local plasma parameters near the wall. These local time-varying sheath potentials can then be used, in tandem with particle-in-cell (PIC) models of the edge plasma, to study sputtering effects. Particle strike energies at the wall can be computed more accurately, consistent with their passage through the known potential of the sheath, such that correspondingly increased accuracy of sputtering yields and heat/particle fluxes to antenna surfaces is obtained. The new simulation capabilities enable time-domain modeling of plasma-surface interactions and ICRF physics in realistic experimental configurations at unprecedented spatial resolution. We will present results/animations from high-performance (10k-100k core) FDTD/PIC simulations of Alcator C-Mod antenna operation.

Synthesis, characterization and computational study of the newly synthetized sulfonamide molecule

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Suchetan, P. A.; Giri, L.; Rao, R. Sreenivasa

2018-02-01

A new compound N-(2,5-dimethyl-4-nitrophenyl)-4-methylbenzenesulfonamide (NDMPMBS) has been derived from 2,5-dimethyl-4-nitroaniline and 4-methylbenzene-1-sulfonyl chloride. Structure was characterized by SCXRD studies and spectroscopic tools. Compound crystallized in the monoclinic crystal system with P21/c space group a = 10.0549, b = 18.967, c = 8.3087, β = 103.18 and Z = 4. Type and nature of intermolecular interaction in crystal state investigated by 3D-Hirshfeld surface and 2D-finger print plots revealed that title compound stabilized by several interactions. The structural and electronic properties of title compound have been calculated at DFT/B3LYP/6-311G++(d,p) level of theory. Computationally obtained spectral data was compared with experimental results, showing excellent mutual agreement. Assignment of each vibrational wave number was done on the basis of potential energy distribution (PED). Investigation of local reactivity descriptors encompassed visualization of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) surfaces, visualization of Fukui functions, natural bond order (NBO) analysis, bond dissociation energies for hydrogen abstraction (H-BDE) and radial distribution functions (RDF) after molecular dynamics (MD) simulations. MD simulations were also used in order to investigate interaction of NDMPMBS molecule with 1WKR and 3ETT proteins protein.

Using Nucleon Multiplicities to Analyze Anti-Neutrino Interactions with Nuclei

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

Elkins, Miranda J.

The most commonly used, simple interaction models have not accurately described the nuclear effects on either neutrino-nucleus or anti-neutrino-nucleus interactions. Comparison of data collected by the MINERvA experiment and these models shows a discrepancy in the reconstructed hadronic energy distribution at momentum transfers below 0.8 GeV. Two nuclear model effects that were previously not modeled are possible culprits of this discrepancy. The first is known as random-phase-approximation and the second is the addition of a meson exchange current process, also known as two-particle two-hole due to its result in two particles leaving the nucleus with two holes left in theirmore » place. For the first time a neutron counting software algorithm has been created and used to compare the multiplicity and spatial distributions of neutrons between the simulation and data. There is localized sensitivity to the RPA and 2p2h effects and both help the simulation better describe the data. Ad ditional systematic or model effects are present which cause the simulation to overproduce neutrons, and potential causes are discussed.« less

Real fuel effects on flame extinction and re-ignition

NASA Astrophysics Data System (ADS)

Zhao, Xinyu; Wu, Bifen; Xu, Chao; Lu, Tianfeng; Chen, Jacqueline H.

2016-11-01

Flame-vortex interactions have significant implications in studying combustion in practical aeronautical engines, and can be used to facilitate the model development in capturing local extinction and re-ignition. To study the interactions between the complex fuel and the intense turbulence that are commonly encountered in engines, direct numerical simulations of the interactions between a flame and a vortex pair are carried out using a recently-developed 24-species reduced chemistry for n-dodecane. Both non-premixed and premixed flames with different initial and inlet thermochemical conditions are studied. Parametric studies of different vortex strengths and orientations are carried out to induce maximum local extinction and re-ignition. Chemical-explosive-mode-analysis based flame diagnostic tools are used to identify different modes of combustion, including auto-ignition and extinction. Results obtained from the reduced chemistry are compared with those obtained from one-step chemistry to quantify the effect of fuel pyrolysis on the extinction limit. Effects of flame curvature, heat loss and unsteadiness on flame extinction are also explored. Finally, the validity of current turbulent combustion models to capture the local extinction and re-ignition will be discussed.

Collective Behavior of Water on Platinum

NASA Astrophysics Data System (ADS)

Limmer, David; Willard, Adam; Chandler, David

2012-02-01

We present the results of molecular dynamics simulations of a interface between water and a platinum electrode. Using importance sampling techniques we probe a variety of collective phenomenon that emerge at the interface. We consider platinum electrodes with two different geometries and discuss how different behaviors result from a competition between geometrical frustration and favorable local interactions.

Plastic deformation and failure mechanisms in nano-scale notched metallic glass specimens under tensile loading

NASA Astrophysics Data System (ADS)

Dutta, Tanmay; Chauniyal, Ashish; Singh, I.; Narasimhan, R.; Thamburaja, P.; Ramamurty, U.

2018-02-01

In this work, numerical simulations using molecular dynamics and non-local plasticity based finite element analysis are carried out on tensile loading of nano-scale double edge notched metallic glass specimens. The effect of acuteness of notches as well as the metallic glass chemical composition or internal material length scale on the plastic deformation response of the specimens are studied. Both MD and FE simulations, in spite of the fundamental differences in their nature, indicate near-identical deformation features. Results show two distinct transitions in the notch tip deformation behavior as the acuity is increased, first from single shear band dominant plastic flow localization to ligament necking, and then to double shear banding in notches that are very sharp. Specimens with moderately blunt notches and composition showing wider shear bands or higher material length scale characterizing the interaction stress associated with flow defects display profuse plastic deformation and failure by ligament necking. These results are rationalized from the role of the interaction stress and development of the notch root plastic zones.

Interaction of viscous and inviscid instability modes in separation-bubble transition

NASA Astrophysics Data System (ADS)

Brinkerhoff, Joshua R.; Yaras, Metin I.

2011-12-01

This paper describes numerical simulations that are used to examine the interaction of viscous and inviscid instability modes in laminar-to-turbulent transition in a separation bubble. The results of a direct numerical simulation are presented in which separation of a laminar boundary-layer occurs in the presence of an adverse streamwise pressure gradient. The simulation is performed at low freestream-turbulence levels and at a flow Reynolds number and pressure distribution approximating those typically encountered on the suction side of low-pressure turbine blades in a gas-turbine engine. The simulation results reveal the development of a viscous instability upstream of the point of separation which produces streamwise-oriented vortices in the attached laminar boundary layer. These vortices remain embedded in the flow downstream of separation and are carried into the separated shear layer, where they are amplified by the local adverse pressure-gradient and contribute to the formation of coherent hairpin-like vortices. A strong interaction is observed between these vortices and the inviscid instability that typically dominates the shear layer in the separated zone. The interaction is noted to determine the spanwise extent of the vortical flow structures that periodically shed from the downstream end of the separated shear layer. The structure of the shed vortical flow structures is examined and compared with the coherent structures typically observed within turbulent boundary layers.

Screen-Space Normal Distribution Function Caching for Consistent Multi-Resolution Rendering of Large Particle Data.

PubMed

Ibrahim, Mohamed; Wickenhauser, Patrick; Rautek, Peter; Reina, Guido; Hadwiger, Markus

2018-01-01

Molecular dynamics (MD) simulations are crucial to investigating important processes in physics and thermodynamics. The simulated atoms are usually visualized as hard spheres with Phong shading, where individual particles and their local density can be perceived well in close-up views. However, for large-scale simulations with 10 million particles or more, the visualization of large fields-of-view usually suffers from strong aliasing artifacts, because the mismatch between data size and output resolution leads to severe under-sampling of the geometry. Excessive super-sampling can alleviate this problem, but is prohibitively expensive. This paper presents a novel visualization method for large-scale particle data that addresses aliasing while enabling interactive high-quality rendering. We introduce the novel concept of screen-space normal distribution functions (S-NDFs) for particle data. S-NDFs represent the distribution of surface normals that map to a given pixel in screen space, which enables high-quality re-lighting without re-rendering particles. In order to facilitate interactive zooming, we cache S-NDFs in a screen-space mipmap (S-MIP). Together, these two concepts enable interactive, scale-consistent re-lighting and shading changes, as well as zooming, without having to re-sample the particle data. We show how our method facilitates the interactive exploration of real-world large-scale MD simulation data in different scenarios.

The effect of interacting dark energy on local measurements of the Hubble constant

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

Odderskov, Io; Baldi, Marco; Amendola, Luca, E-mail: isho07@phys.au.dk, E-mail: marco.baldi5@unibo.it, E-mail: l.amendola@thphys.uni-heidelberg.de

2016-05-01

In the current state of cosmology, where cosmological parameters are being measured to percent accuracy, it is essential to understand all sources of error to high precision. In this paper we present the results of a study of the local variations in the Hubble constant measured at the distance scale of the Coma Cluster, and test the validity of correcting for the peculiar velocities predicted by gravitational instability theory. The study is based on N-body simulations, and includes models featuring a coupling between dark energy and dark matter, as well as two ΛCDM simulations with different values of σ{sub 8}.more » It is found that the variance in the local flows is significantly larger in the coupled models, which increases the uncertainty in the local measurements of the Hubble constant in these scenarios. By comparing the results from the different simulations, it is found that most of the effect is caused by the higher value of σ{sub 8} in the coupled cosmologies, though this cannot account for all of the additional variance. Given the discrepancy between different estimates of the Hubble constant in the universe today, cosmological models causing a greater cosmic variance is something that we should be aware of.« less

A case study of the fluid structure interaction of a Francis turbine

NASA Astrophysics Data System (ADS)

Müller, C.; Staubli, T.; Baumann, R.; Casartelli, E.

2014-03-01

The Francis turbine runners of the Grimsel 2 pump storage power plant showed repeatedly cracks during the last decade. It is assumed that these cracks were caused by flow induced forces acting on blades and eventual resonant runner vibrations lead to high stresses in the blade root areas. The eigenfrequencies of the runner were simulated in water using acoustic elements and compared to experimental data. Unsteady blades pressure distribution determined by a transient CFD simulation of the turbine were coupled to a FEM simulation. The FEM simulation enabled analyzing the stresses in the runner and the eigenmodes of the runner vibrations. For a part-load operating point, transient CFD simulations of the entire turbine, including the spiral case, the runner and the draft tube were carried out. The most significant loads on the turbine runner resulted from the centrifugal forces and the fluid forces. Such forces effect temporally invariant runner blades loads, in contrast rotor stator interaction or draft tube instabilities induce pressure fluctuations which cause the temporally variable forces. The blades pressure distribution resulting from the flow simulation was coupled by unidirectional-harmonic FEM simulation. The dominant transient blade pressure distribution of the CFD simulation were Fourier transformed, and the static and harmonic portion assigned to the blade surfaces in the FEM model. The evaluation of the FEM simulation showed that the simulated part load operating point do not cause critical stress peaks in the crack zones. The pressure amplitudes and frequencies are very small and interact only locally with the runner blades. As the frequencies are far below the modal frequencies of the turbine runner, resonant vibrations obviously are not excited.

On the chain length dependence of local correlations in polymer melts and a perturbation theory of symmetric polymer blends.

PubMed

Morse, David C; Chung, Jun Kyung

2009-06-14

The self-consistent field (SCF) approach to the thermodynamics of dense polymer liquids is based on the idea that short-range correlations in a polymer liquid are almost independent of how monomers are connected into polymers over larger scales. Some limits of this idea are explored in the context of a perturbation theory for symmetric polymer blends. We consider mixtures of two structurally identical polymers, A and B, in which the AB monomer pair interaction differs slightly from the AA and BB interactions by an amount proportional to a parameter alpha. An expansion of the free energy to first order in alpha yields an excess free energy of mixing per monomer of the form alphaz(N)phi(A)phi(B) in both lattice and continuum models, where z(N) is a measure of the number of intermolecular near neighbors per monomer in a one-component (alpha=0) reference liquid with chains of length N. The quantity z(N) decreases slightly with increasing N because the concentration of intramolecular near neighbors is slightly higher for longer chains, creating a slightly deeper intermolecular correlation hole. We predict that z(N)=z(infinity)[1+betaN(-1/2)], where N is an invariant degree of polymerization and beta=(6/pi)(3/2) is a universal coefficient. This and related predictions about the slight N dependence of local correlations are confirmed by comparison to simulations of a continuum bead-spring model and to published lattice Monte Carlo simulations. We show that a renormalized one-loop theory for blends correctly describes this N dependence of local liquid structure. We also propose a way to estimate the effective interaction parameter appropriate for comparisons of simulation data to SCF theory and to coarse-grained theories of corrections to SCF theory, which is based on an extrapolation of perturbation theory to the limit N-->infinity.

Land-Atmosphere Interactions: Successes, Problems and Prospects

NASA Technical Reports Server (NTRS)

Sud, Y. C.; Mocko, D. M.

1999-01-01

After two decades of active research, a much better understanding of the broader role of biospheric processes on the local climate has emerged. A surface-albedo increase, particularly in desert border regions of the subtropics (as well as the deforested tropical regions), leads to a net surface energy deficit, which in turn leads to a relative sinking and reduced rainfall. On the other hand, studies of the influence of altered ratios of evapotranspiration and sensible fluxes, in situations where the net solar income is unchanged, show that evapotranspiration is a more desirable flux for increased precipitation and vitality of the biosphere. Besides providing water vapor and convective available potential energy (CAPE) to the lower troposphere, evapotranspiration helps in building larger CAPE before "turning on" the moist-convection. Larger CAPE in the lower troposphere enables convection to reach into the deeper atmosphere thereby heating the upper troposphere; indeed, moist-convection is also accompanied by the evaporation of falling precipitation that cools and moistens the lower atmosphere. While convective, as opposed to stratiform, precipitation reduces the fractional cloud cover; it also allows more solar radiation to reach the surface thereby invigorating surface fluxes. These, together with moist convection and associated downdrafts help to maintain the characteristic upper temperature limit(s) of the moist-land as well as oceanic regions. Regardless of the above understanding, several important problems continue to hinder the accurate simulation of a realistic land atmosphere interaction in a numerical model (both GCM and/or Meso-scale models). Among the unsolved problems are parameterization of sub-grid scale land processes that include small-scale variability of soil moisture, snow-cover and snow-physics, the biodiversity of the biosphere, orography, local drainage characteristics under natural conditions, and surface flow over the natural terrain. A well-known non-linear response of surface fluxes to these variations makes the problem of parameterizing land-atmosphere interaction processes hard-to-address and simulate, particularly in a GCM. In our presentation, we will discuss how orographic, snow-cover, and water table interactions can be included into a Simple Biosphere Model such as SiB/SSiB. Figure I shows how, in the Russian region, spring snowmelt affects the soil moisture profile. Corresponding figure 2 shows how interaction with the water table decreases the natural evapotranspiration in the Sahel region simulation. While these simulations need better validation with data, the simulations reveal that surface processes are sensitive to these parameterizations. With these developments, we continue to advance our understanding of the interaction of land with the atmosphere aloft, but the intrinsic variability of the newer parameters, e. g., hydraulic properties of the soil, diminish the positive influences of these advances on the improved climate simulation with GCMs.

Ocean eddies and climate predictability

NASA Astrophysics Data System (ADS)

Kirtman, Ben P.; Perlin, Natalie; Siqueira, Leo

2017-12-01

A suite of coupled climate model simulations and experiments are used to examine how resolved mesoscale ocean features affect aspects of climate variability, air-sea interactions, and predictability. In combination with control simulations, experiments with the interactive ensemble coupling strategy are used to further amplify the role of the oceanic mesoscale field and the associated air-sea feedbacks and predictability. The basic intent of the interactive ensemble coupling strategy is to reduce the atmospheric noise at the air-sea interface, allowing an assessment of how noise affects the variability, and in this case, it is also used to diagnose predictability from the perspective of signal-to-noise ratios. The climate variability is assessed from the perspective of sea surface temperature (SST) variance ratios, and it is shown that, unsurprisingly, mesoscale variability significantly increases SST variance. Perhaps surprising is the fact that the presence of mesoscale ocean features even further enhances the SST variance in the interactive ensemble simulation beyond what would be expected from simple linear arguments. Changes in the air-sea coupling between simulations are assessed using pointwise convective rainfall-SST and convective rainfall-SST tendency correlations and again emphasize how the oceanic mesoscale alters the local association between convective rainfall and SST. Understanding the possible relationships between the SST-forced signal and the weather noise is critically important in climate predictability. We use the interactive ensemble simulations to diagnose this relationship, and we find that the presence of mesoscale ocean features significantly enhances this link particularly in ocean eddy rich regions. Finally, we use signal-to-noise ratios to show that the ocean mesoscale activity increases model estimated predictability in terms of convective precipitation and atmospheric upper tropospheric circulation.

Ocean eddies and climate predictability.

PubMed

Kirtman, Ben P; Perlin, Natalie; Siqueira, Leo

2017-12-01

A suite of coupled climate model simulations and experiments are used to examine how resolved mesoscale ocean features affect aspects of climate variability, air-sea interactions, and predictability. In combination with control simulations, experiments with the interactive ensemble coupling strategy are used to further amplify the role of the oceanic mesoscale field and the associated air-sea feedbacks and predictability. The basic intent of the interactive ensemble coupling strategy is to reduce the atmospheric noise at the air-sea interface, allowing an assessment of how noise affects the variability, and in this case, it is also used to diagnose predictability from the perspective of signal-to-noise ratios. The climate variability is assessed from the perspective of sea surface temperature (SST) variance ratios, and it is shown that, unsurprisingly, mesoscale variability significantly increases SST variance. Perhaps surprising is the fact that the presence of mesoscale ocean features even further enhances the SST variance in the interactive ensemble simulation beyond what would be expected from simple linear arguments. Changes in the air-sea coupling between simulations are assessed using pointwise convective rainfall-SST and convective rainfall-SST tendency correlations and again emphasize how the oceanic mesoscale alters the local association between convective rainfall and SST. Understanding the possible relationships between the SST-forced signal and the weather noise is critically important in climate predictability. We use the interactive ensemble simulations to diagnose this relationship, and we find that the presence of mesoscale ocean features significantly enhances this link particularly in ocean eddy rich regions. Finally, we use signal-to-noise ratios to show that the ocean mesoscale activity increases model estimated predictability in terms of convective precipitation and atmospheric upper tropospheric circulation.

The Impacts of Miyun Reservoirs on Local Climate: A Modeling Study Using WRF-Lake Model

NASA Astrophysics Data System (ADS)

Wang, F.; Xing, Y.; Sun, T.; Ni, G.

2016-12-01

Large reservoirs, where a great volume of water is stored for various purposes (e.g. hydropower generation, irrigation, transportation, recreation, etc.), play a key role in regional hydrological cycles as well as in modulating the local climate. In particular, to understand the impacts of reservoirs on local climate, numeric simulations are widely conducted using different weather prediction (NWP) models. However, some of these NWP models treat reservoirs as water surfaces with prescribed surface temperatures and thus the hydrothermal dynamics within water bodies are missing. In this study, we use the Weather Research Forecasting (WRF) model coupled with a lake module, which is equipped with the ability to simulate full thermal dynamics of water, to examine the impacts of Miyun Reservoir, the largest reservoir in Beijing, on the local climate. Simulations are conducted from July 1 to August 1, 2010 in a one-way nesting mode of three spatial resolutions (i.e., 9 km, 3 km and 1 km). Comparison between the simulation results and observations shows a general agreement and demonstrates the ability of WRF-Lake in simulating the summertime climate in the study area. The simulation results indicate the Miyun Reservoir significantly reduces daytime air temperature at 2 m above the water surface and its surroundings by a maximum of 4 K as compared with the case without a reservoir, and such impacts diminish at a distance of 90 km from the reservoir center (a decrease of 0.2 K). At night, a maximum increase of 1.4 K is simulated for the air temperature above the reservoir, but the influencing area is very limited. The reservoir also increases the local air specific humidity by 0.0025 kg kg-1. In addition to near surface meteorology, surface energy balance is remarkably changed as compared to the case without a reservoir: a daytime decrease of 100 W m-2 and a nighttime increase of 15 W m-2are simulated for the sensible heat flux. It is noteworthy that the latent heat flux decreases in the daytime and slightly increases at night. It should also be noted that the influencing area is strongly dependent on the wind direction. This study provides a better understanding of the water-atmosphere interactions by reservoirs and their impacts on local climate.

Experimental observation of spatially localized dynamo magnetic fields.

PubMed

Gallet, B; Aumaître, S; Boisson, J; Daviaud, F; Dubrulle, B; Bonnefoy, N; Bourgoin, M; Odier, Ph; Pinton, J-F; Plihon, N; Verhille, G; Fauve, S; Pétrélis, F

2012-04-06

We report the first experimental observation of a spatially localized dynamo magnetic field, a common feature of astrophysical dynamos and convective dynamo simulations. When the two propellers of the von Kármán sodium experiment are driven at frequencies that differ by 15%, the mean magnetic field's energy measured close to the slower disk is nearly 10 times larger than the one close to the faster one. This strong localization of the magnetic field when a symmetry of the forcing is broken is in good agreement with a prediction based on the interaction between a dipolar and a quadrupolar magnetic mode. © 2012 American Physical Society

SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation.

PubMed

Schmit, Jeremy D; Kariyawasam, Nilusha L; Needham, Vince; Smith, Paul E

2018-04-10

An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number of ions in the simulation box to capture screening effects. However, the number of ions that should be added to the box is seldom given by the bulk salt concentration because a charged biomolecule solute will perturb the local solvent environment. We present a simple method for calculating the number of ions that requires only the total solute charge, solvent volume, and bulk salt concentration as inputs. We show that the most commonly used method for adding salt to a simulation results in an effective salt concentration that is too high. These findings are confirmed using simulations of lysozyme. We have established a web server where these calculations can be readily performed to aid simulation setup.

Astrophysical uncertainties on the local dark matter distribution and direct detection experiments

NASA Astrophysics Data System (ADS)

Green, Anne M.

2017-08-01

The differential event rate in weakly interacting massive particle (WIMP) direct detection experiments depends on the local dark matter density and velocity distribution. Accurate modelling of the local dark matter distribution is therefore required to obtain reliable constraints on the WIMP particle physics properties. Data analyses typically use a simple standard halo model which might not be a good approximation to the real Milky Way (MW) halo. We review observational determinations of the local dark matter density, circular speed and escape speed and also studies of the local dark matter distribution in simulated MW-like galaxies. We discuss the effects of the uncertainties in these quantities on the energy spectrum and its time and direction dependence. Finally, we conclude with an overview of various methods for handling these astrophysical uncertainties.

Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation

PubMed Central

Hanson, Sonya M.; Newstead, Simon; Swartz, Kenton J.; Sansom, Mark S.P.

2015-01-01

Transient receptor potential vanilloid subtype 1 (TRPV1) is a heat-sensitive ion channel also involved in pain sensation, and is the receptor for capsaicin, the active ingredient of hot chili peppers. The recent structures of TRPV1 revealed putative ligand density within the S1 to S4 voltage-sensor-like domain of the protein. However, questions remain regarding the dynamic role of the lipid bilayer in ligand binding to TRPV1. Molecular dynamics simulations were used to explore behavior of capsaicin in a 1-palmitoyl-2-oleoyl phosphatidylcholine bilayer and with the target S1–S4 transmembrane helices of TRPV1. Equilibrium simulations reveal a preferred interfacial localization for capsaicin. We also observed a capsaicin molecule flipping from the extracellular to the intracellular leaflet, and subsequently able to access the intracellular TRPV1 binding site. Calculation of the potential of mean force (i.e., free energy profile) of capsaicin along the bilayer normal confirms that it prefers an interfacial localization. The free energy profile indicates that there is a nontrivial but surmountable barrier to the flipping of capsaicin between opposing leaflets of the bilayer. Molecular dynamics of the S1–S4 transmembrane helices of the TRPV1 in a lipid bilayer confirm that Y511, known to be crucial to capsaicin binding, has a distribution along the bilayer normal similar to that of the aromatic group of capsaicin. Simulations were conducted of the TRPV1 S1–S4 transmembrane helices in the presence of capsaicin placed in the aqueous phase, in the lipid, or docked to the protein. No stable interaction between ligand and protein was seen for simulations initiated with capsaicin in the bilayer. However, interactions were seen between TRPV1 and capsaicin starting from the cytosolic aqueous phase, and capsaicin remained stable in the majority of simulations from the docked pose. We discuss the significance of capsaicin flipping from the extracellular to the intracellular leaflet and mechanisms of binding site access by capsaicin. PMID:25809255

Examination of ductile spall failure through direct numerical simulation

NASA Astrophysics Data System (ADS)

Becker, Richard

2017-06-01

Direct numerical simulation is used to examine the growth and coalescence of a random population of voids leading to spall failure. Void nucleating particles are explicitly represented in the initial geometry, and the arbitrary Lagrange-Eulerian finite element code tracks the void evolution to create the spall surface. The flow fields capture strain localization associated with void interaction at low porosities and ligament necking at final coalescence. Simulations are run to assess the influence of material strain hardening and strain rate sensitivity on void growth and coalescence. These analyses also provide the evolution of longitudinal stress and the energy dissipated, and they reveal a length scale associated with the spall. Additional calculations are performed to examine the influence of loading pulse shape on spall behavior for triangular shaped pressure loading. A dependence of spall scab thickness on pulse shape is determined. These results show localization delayed until porosities reach a few percent and they demonstrate a consistent stress versus porosity relation. The simulations also provide a direct correlation between the spall stress history and the free surface velocity, which can aid in understanding stress corrections applied to experimental data.

Dependence of radiation belt simulations to assumed radial diffusion rates

NASA Astrophysics Data System (ADS)

Drozdov, A.; Shprits, Y.; Aseev, N.; Kellerman, A. C.; Reeves, G. D.

2017-12-01

Radial diffusion is one of the dominant physical mechanisms that drives acceleration and loss of the radiation belt electrons due to wave-particle interaction with ultra low frequency (ULF) waves, which makes it very important for radiation belt modeling and forecasting. We investigate the sensitivity of several parameterizations of the radial diffusion including Brautigam and Albert [2000], Ozeke et al. [2014] and Ali et al. [2016] on long-term radiation belt modeling using the Versatile Electron Radiation Belt (VERB). Following previous studies, we first perform 1-D radial diffusion simulations. To take into account effects of local acceleration and loss, we perform additional 3-D simulations, including pitch-angle, energy and mixed diffusion. The obtained result demonstrates that the inclusion of local acceleration and pitch-angle diffusion can provide a negative feedback effect, such that the result is largely indistinguishable between simulations conducted with different radial diffusion parameterizations. We also perform a number of sensitivity tests by multiplying radial diffusion rates by constant factors and show that such an approach leads to unrealistic predictions of radiation belt dynamics.

Average structure and local configuration of excess oxygen in UO(2+x).

PubMed

Wang, Jianwei; Ewing, Rodney C; Becker, Udo

2014-03-19

Determination of the local configuration of interacting defects in a crystalline, periodic solid is problematic because defects typically do not have a long-range periodicity. Uranium dioxide, the primary fuel for fission reactors, exists in hyperstoichiometric form, UO(2+x). Those excess oxygen atoms occur as interstitial defects, and these defects are not random but rather partially ordered. The widely-accepted model to date, the Willis cluster based on neutron diffraction, cannot be reconciled with the first-principles molecular dynamics simulations present here. We demonstrate that the Willis cluster is a fair representation of the numerical ratio of different interstitial O atoms; however, the model does not represent the actual local configuration. The simulations show that the average structure of UO(2+x) involves a combination of defect structures including split di-interstitial, di-interstitial, mono-interstitial, and the Willis cluster, and the latter is a transition state that provides for the fast diffusion of the defect cluster. The results provide new insights in differentiating the average structure from the local configuration of defects in a solid and the transport properties of UO(2+x).

Is the impact of eutrophication on phytoplankton diversity dependent on lake volume/ecosystem size?

USGS Publications Warehouse

Baho, Didier L.; Drakare, Stina; Johnson, Richard K.; Allen, Craig R.; Angeler, David G.

2017-01-01

Research focusing on biodiversity responses to the interactions of ecosystem size and anthropogenic stressors are based mainly on correlative gradient studies, and may therefore confound size-stress relationships due to spatial context and differences in local habitat features across ecosystems. We investigated how local factors related to anthropogenic stressors (e.g.,eutrophication) interact with ecosystem size to influence species diversity. In this study, constructed lake mesocosms (with two contrasting volumes: 1020 (shallow mesocosms) and 2150 (deep mesocosms) litres) were used to simulate ecosystems of different size and manipulated nutrient levels to simulate mesotrophic and hypertrophic conditions. Using a factorial design, we assessed how the interaction between ecosystem size and nutrients influences phytoplankton diversity. We assessed community metrics (richness, diversity, evenness and total biovolumes) and multivariate community structure over a growing season (May to early November 2011). Different community structures were found between deep and shallow mescosoms with nutrient enrichment: Cyanobacteria dominated in the deep and Charophyta in the shallow mesocosms. In contrast, phytoplankton communities were more similar to each other in the low nutrient treatments; only Chlorophyta had generally a higher biovolume in the shallow compared to the deep mesocosms. These results suggest that ecosystem size is not only a determinant of species diversity, but that it can mediate the influence of anthropogenic effects on biodiversity. Such interactions increase the uncertainty of global change outcomes, and should therefore not be ignored in risk/impact assessment and management.

Simulation-Based Approach for Site-Specific Optimization of Hydrokinetic Turbine Arrays

NASA Astrophysics Data System (ADS)

Sotiropoulos, F.; Chawdhary, S.; Yang, X.; Khosronejad, A.; Angelidis, D.

2014-12-01

A simulation-based approach has been developed to enable site-specific optimization of tidal and current turbine arrays in real-life waterways. The computational code is based on the St. Anthony Falls Laboratory Virtual StreamLab (VSL3D), which is able to carry out high-fidelity simulations of turbulent flow and sediment transport processes in rivers and streams taking into account the arbitrary geometrical complexity characterizing natural waterways. The computational framework can be used either in turbine-resolving mode, to take into account all geometrical details of the turbine, or with the turbines parameterized as actuator disks or actuator lines. Locally refined grids are employed to dramatically increase the resolution of the simulation and enable efficient simulations of multi-turbine arrays. Turbine/sediment interactions are simulated using the coupled hydro-morphodynamic module of VSL3D. The predictive capabilities of the resulting computational framework will be demonstrated by applying it to simulate turbulent flow past a tri-frame configuration of hydrokinetic turbines in a rigid-bed turbulent open channel flow as well as turbines mounted on mobile bed open channels to investigate turbine/sediment interactions. The utility of the simulation-based approach for guiding the optimal development of turbine arrays in real-life waterways will also be discussed and demonstrated. This work was supported by NSF grant IIP-1318201. Simulations were carried out at the Minnesota Supercomputing Institute.

Local communities obstruct global consensus: Naming game on multi-local-world networks

NASA Astrophysics Data System (ADS)

Lou, Yang; Chen, Guanrong; Fan, Zhengping; Xiang, Luna

2018-02-01

Community structure is essential for social communications, where individuals belonging to the same community are much more actively interacting and communicating with each other than those in different communities within the human society. Naming game, on the other hand, is a social communication model that simulates the process of learning a name of an object within a community of humans, where the individuals can generally reach global consensus asymptotically through iterative pair-wise conversations. The underlying network indicates the relationships among the individuals. In this paper, three typical topologies, namely random-graph, small-world and scale-free networks, are employed, which are embedded with the multi-local-world community structure, to study the naming game. Simulations show that (1) the convergence process to global consensus is getting slower as the community structure becomes more prominent, and eventually might fail; (2) if the inter-community connections are sufficiently dense, neither the number nor the size of the communities affects the convergence process; and (3) for different topologies with the same (or similar) average node-degree, local clustering of individuals obstruct or prohibit global consensus to take place. The results reveal the role of local communities in a global naming game in social network studies.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

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

Sanyal, Tanmoy; Shell, M. Scott, E-mail: shell@engineering.ucsb.edu

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one atmore » which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.« less

Spatially cascading effect of perturbations in experimental meta-ecosystems.

PubMed

Harvey, Eric; Gounand, Isabelle; Ganesanandamoorthy, Pravin; Altermatt, Florian

2016-09-14

Ecosystems are linked to neighbouring ecosystems not only by dispersal, but also by the movement of subsidy. Such subsidy couplings between ecosystems have important landscape-scale implications because perturbations in one ecosystem may affect community structure and functioning in neighbouring ecosystems via increased/decreased subsidies. Here, we combine a general theoretical approach based on harvesting theory and a two-patch protist meta-ecosystem experiment to test the effect of regional perturbations on local community dynamics. We first characterized the relationship between the perturbation regime and local population demography on detritus production using a mathematical model. We then experimentally simulated a perturbation gradient affecting connected ecosystems simultaneously, thus altering cross-ecosystem subsidy exchanges. We demonstrate that the perturbation regime can interact with local population dynamics to trigger unexpected temporal variations in subsidy pulses from one ecosystem to another. High perturbation intensity initially led to the highest level of subsidy flows; however, the level of perturbation interacted with population dynamics to generate a crash in subsidy exchange over time. Both theoretical and experimental results show that a perturbation regime interacting with local community dynamics can induce a collapse in population levels for recipient ecosystems. These results call for integrative management of human-altered landscapes that takes into account regional dynamics of both species and resource flows. © 2016 The Author(s).

Local/non-local regularized image segmentation using graph-cuts: application to dynamic and multispectral MRI.

PubMed

Hanson, Erik A; Lundervold, Arvid

2013-11-01

Multispectral, multichannel, or time series image segmentation is important for image analysis in a wide range of applications. Regularization of the segmentation is commonly performed using local image information causing the segmented image to be locally smooth or piecewise constant. A new spatial regularization method, incorporating non-local information, was developed and tested. Our spatial regularization method applies to feature space classification in multichannel images such as color images and MR image sequences. The spatial regularization involves local edge properties, region boundary minimization, as well as non-local similarities. The method is implemented in a discrete graph-cut setting allowing fast computations. The method was tested on multidimensional MRI recordings from human kidney and brain in addition to simulated MRI volumes. The proposed method successfully segment regions with both smooth and complex non-smooth shapes with a minimum of user interaction.

Size-Tuned Plastic Flow Localization in Irradiated Materials at the Submicron Scale

NASA Astrophysics Data System (ADS)

Cui, Yinan; Po, Giacomo; Ghoniem, Nasr

2018-05-01

Three-dimensional discrete dislocation dynamics (3D-DDD) simulations reveal that, with reduction of sample size in the submicron regime, the mechanism of plastic flow localization in irradiated materials transitions from irradiation-controlled to an intrinsic dislocation source controlled. Furthermore, the spatial correlation of plastic deformation decreases due to weaker dislocation interactions and less frequent cross slip as the system size decreases, thus manifesting itself in thinner dislocation channels. A simple model of discrete dislocation source activation coupled with cross slip channel widening is developed to reproduce and physically explain this transition. In order to quantify the phenomenon of plastic flow localization, we introduce a "deformation localization index," with implications to the design of radiation-resistant materials.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

PubMed

Wall, Michael E

2018-03-01

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

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

Wall, Michael E.

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.

2018-01-25

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

Tamm, A.; Samolyuk, G.; Correa, A. A.; ...

2016-07-14

Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

Effects of reaction control system jet flow field interactions on the aerodynamic characteristics of a 0.010-scale space shuttle orbiter model in the Langley Research Center 31 inch CFHT (OA85)

NASA Technical Reports Server (NTRS)

Daileda, J. J.; Marroquin, J.

1974-01-01

An experimental investigation was conducted to obtain detailed effects on supersonic vehicle hypersonic aerodynamic and stability and control characteristics of reaction control system jet flow field interactions with the local vehicle flow field. A 0.010-scale model was used. Six-component force data and wing, elevon, and body flap surface pressure data were obtained through an angle-of-attack range of -10 to +35 degrees with 0 deg angle of sideslip. The test was conducted with yaw, pitch and roll jet simulation at a free-stream Mach number of 10.3 and reaction control system plume simulation of flight dynamic pressures of 5, 10 and 20 PSF.

Reinventing atomic magnetic simulations with spin-orbit coupling

DOE PAGES

Perera, Meewanage Dilina N.; Eisenbach, Markus; Nicholson, Don M.; ...

2016-02-10

We propose a powerful extension to the combined molecular and spin dynamics method that fully captures the coupling between the atomic and spin subsystems via spin-orbit interactions. Moreover, the foundation of this method lies in the inclusion of the local magnetic anisotropies that arise as a consequence of the lattice symmetry breaking due to phonons or crystallographic defects. By using canonical simulations of bcc iron with the system coupled to a phonon heat bath, we show that our extension enables the previously unachievable angular momentum exchange between the atomic and spin degrees of freedom.

Sensor Fusion of Gaussian Mixtures for Ballistic Target Tracking in the Re-Entry Phase

PubMed Central

Lu, Kelin; Zhou, Rui

2016-01-01

A sensor fusion methodology for the Gaussian mixtures model is proposed for ballistic target tracking with unknown ballistic coefficients. To improve the estimation accuracy, a track-to-track fusion architecture is proposed to fuse tracks provided by the local interacting multiple model filters. During the fusion process, the duplicate information is removed by considering the first order redundant information between the local tracks. With extensive simulations, we show that the proposed algorithm improves the tracking accuracy in ballistic target tracking in the re-entry phase applications. PMID:27537883

Sensor Fusion of Gaussian Mixtures for Ballistic Target Tracking in the Re-Entry Phase.

PubMed

Lu, Kelin; Zhou, Rui

2016-08-15

A sensor fusion methodology for the Gaussian mixtures model is proposed for ballistic target tracking with unknown ballistic coefficients. To improve the estimation accuracy, a track-to-track fusion architecture is proposed to fuse tracks provided by the local interacting multiple model filters. During the fusion process, the duplicate information is removed by considering the first order redundant information between the local tracks. With extensive simulations, we show that the proposed algorithm improves the tracking accuracy in ballistic target tracking in the re-entry phase applications.

Anion-π Catalysis on Fullerenes.

PubMed

López-Andarias, Javier; Frontera, Antonio; Matile, Stefan

2017-09-27

Anion-π interactions on fullerenes are about as poorly explored as the use of fullerenes in catalysis. However, strong exchange-correlation contributions and the localized π holes on their surface promise unique selectivities. To elaborate on this promise, tertiary amines are attached nearby. Dependent on their positioning, the resulting stabilization of anionic transition states on fullerenes is shown to accelerate disfavored enolate addition and exo Diels-Alder reactions enantioselectively. The found selectivities are consistent with computational simulations, particularly concerning the discrimination of differently planarized and charge-delocalized enolate tautomers by anion-π interactions. Enolate-π interactions on fullerenes are much shorter than standard π-π interactions and anion-π interactions on planar surfaces, and alternative cation-π interactions are not observed. These findings open new perspectives with regard to anion-π interactions in general and the use of carbon allotropes in catalysis.

Modeling the Population Dynamics of Antibiotic-Resistant Bacteria:. AN Agent-Based Approach

NASA Astrophysics Data System (ADS)

Murphy, James T.; Walshe, Ray; Devocelle, Marc

The response of bacterial populations to antibiotic treatment is often a function of a diverse range of interacting factors. In order to develop strategies to minimize the spread of antibiotic resistance in pathogenic bacteria, a sound theoretical understanding of the systems of interactions taking place within a colony must be developed. The agent-based approach to modeling bacterial populations is a useful tool for relating data obtained at the molecular and cellular level with the overall population dynamics. Here we demonstrate an agent-based model, called Micro-Gen, which has been developed to simulate the growth and development of bacterial colonies in culture. The model also incorporates biochemical rules and parameters describing the kinetic interactions of bacterial cells with antibiotic molecules. Simulations were carried out to replicate the development of methicillin-resistant S. aureus (MRSA) colonies growing in the presence of antibiotics. The model was explored to see how the properties of the system emerge from the interactions of the individual bacterial agents in order to achieve a better mechanistic understanding of the population dynamics taking place. Micro-Gen provides a good theoretical framework for investigating the effects of local environmental conditions and cellular properties on the response of bacterial populations to antibiotic exposure in the context of a simulated environment.

Vortex jump behavior in coupled nanomagnetic heterostructures

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

Zhang, S.; Phatak, C., E-mail: cd@anl.gov; Petford-Long, A. K.

2014-11-24

The spin configuration and magnetic behavior in patterned nanostructures can be controlled by manipulating the interplay between the competing energy terms. This in turn requires fundamental knowledge of the magnetic interactions at the local nanometer scale. Here, we report on the spin structure and magnetization behavior of patterned discs containing exchange coupled ferromagnetic layers with additional exchange bias to an antiferromagnetic layer. The magnetization reversal was explored by direct local visualization of the domain behavior using in-situ Lorentz transmission electron microscopy, from which quantitative magnetic induction maps were reconstructed. The roles of the main competing energy terms were elucidated andmore » the reversal mechanism was identified as a coupled phenomenon of incoherent rotation in the exchange-biased layer and localized vortex nucleation and discontinuous propagation in the free layer, including an anomalous jump in the trajectory. The observations were supported by micromagnetic simulations and modeled phase shift simulations. The work presented here provides fundamental insights into opportunities for macroscopic control of the energy landscape of magnetic heterostructures for functional applications.« less

Three-Dimensional Direct Numerical Simulation of Methane-Air Turbulent Premixed Flames with Reduced Kinetic Mechanism

NASA Astrophysics Data System (ADS)

Tanahashi, Mamoru; Kikuta, Satoshi; Miyauchi, Toshio

2004-11-01

Three-dimensional DNS of methane-air turbulent premixed flames have been conducted to investigate local extinction mechanism of turbulent premixed flames. A reduced kinetic mechanism (MeCH-19), which is created from GRI-Mech. 2.11 and includes 23 reactive species and 19 step reactions, are used to simulate CH_4-O_2-N2 reaction in turbulence. The effectiveness of this reduced kinetic mechanism has been conformed by preliminary two-dimensional DNS with the reduced kinetic mechanism and two detailed kinetic mechanisms; GRI-Mech. 2.11 and Miller & Bowman. Flame structures of methane-air turbulent premixed flames are compared with those of hydrogen-air turbulent premixed flames which have been obtained by 3D-DNS with a detailed kinetic mechanism in our previous study. Local extinctions occur in methane-air turbulent premixed flames, whereas no extinction is observed for hydrogen-air flames in nearly same turbulence condition. The local extinction mechanism is discussed based on eddy/flame interaction in small scales.

Vortex jump behavior in coupled nanomagnetic heterostructures

NASA Astrophysics Data System (ADS)

Zhang, S.; Petford-Long, A. K.; Heinonen, O.; Phatak, C.

2014-11-01

The spin configuration and magnetic behavior in patterned nanostructures can be controlled by manipulating the interplay between the competing energy terms. This in turn requires fundamental knowledge of the magnetic interactions at the local nanometer scale. Here, we report on the spin structure and magnetization behavior of patterned discs containing exchange coupled ferromagnetic layers with additional exchange bias to an antiferromagnetic layer. The magnetization reversal was explored by direct local visualization of the domain behavior using in-situ Lorentz transmission electron microscopy, from which quantitative magnetic induction maps were reconstructed. The roles of the main competing energy terms were elucidated and the reversal mechanism was identified as a coupled phenomenon of incoherent rotation in the exchange-biased layer and localized vortex nucleation and discontinuous propagation in the free layer, including an anomalous jump in the trajectory. The observations were supported by micromagnetic simulations and modeled phase shift simulations. The work presented here provides fundamental insights into opportunities for macroscopic control of the energy landscape of magnetic heterostructures for functional applications.

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium-Ion Battery Electrolytes.

PubMed

Shakourian-Fard, Mehdi; Kamath, Ganesh; Sankaranarayanan, Subramanian K R S

2016-09-19

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li(+) with pure carbonates and ethylene carbonate (EC)-based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06-2X/6-311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li-ion solvation in carbonates and EC-based mixtures. A strong local tetrahedral order involving four carbonates around the Li(+) was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li(+) ion with carbonates are negative and suggested the ion-carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li(+) interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO-EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li(+) ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO-EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li-ion batteries, which complies with experiments and other theoretical results. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An efficient and scalable deformable model for virtual reality-based medical applications.

PubMed

Choi, Kup-Sze; Sun, Hanqiu; Heng, Pheng-Ann

2004-09-01

Modeling of tissue deformation is of great importance to virtual reality (VR)-based medical simulations. Considerable effort has been dedicated to the development of interactively deformable virtual tissues. In this paper, an efficient and scalable deformable model is presented for virtual-reality-based medical applications. It considers deformation as a localized force transmittal process which is governed by algorithms based on breadth-first search (BFS). The computational speed is scalable to facilitate real-time interaction by adjusting the penetration depth. Simulated annealing (SA) algorithms are developed to optimize the model parameters by using the reference data generated with the linear static finite element method (FEM). The mechanical behavior and timing performance of the model have been evaluated. The model has been applied to simulate the typical behavior of living tissues and anisotropic materials. Integration with a haptic device has also been achieved on a generic personal computer (PC) platform. The proposed technique provides a feasible solution for VR-based medical simulations and has the potential for multi-user collaborative work in virtual environment.

Numerical Study of Richtmyer-Meshkov Instability with Re-Shock

NASA Astrophysics Data System (ADS)

Wong, Man Long; Livescu, Daniel; Lele, Sanjiva

2017-11-01

The interaction of a Mach 1.45 shock wave with a perturbed planar interface between two gases with an Atwood number 0.68 is studied through 2D and 3D shock-capturing adaptive mesh refinement (AMR) simulations with physical diffusive and viscous terms. The simulations have initial conditions similar to those in the actual experiment conducted by Poggi et al. [1998]. The development of the flow and evolution of mixing due to the interactions with the first shock and the re-shock are studied together with the sensitivity of various global parameters to the properties of the initial perturbation. Grid resolutions needed for fully resolved and 2D and 3D simulations are also evaluated. Simulations are conducted with an in-house AMR solver HAMeRS built on the SAMRAI library. The code utilizes the high-order localized dissipation weighted compact nonlinear scheme [Wong and Lele, 2017] for shock-capturing and different sensors including the wavelet sensor [Wong and Lele, 2016] to identify regions for grid refinement. First and third authors acknowledge the project sponsor LANL.

Molecular dynamics study of solid-liquid heat transfer and passive liquid flow

NASA Astrophysics Data System (ADS)

Yesudasan Daisy, Sumith

High heat flux removal is a challenging problem in boilers, electronics cooling, concentrated photovoltaic and other power conversion devices. Heat transfer by phase change is one of the most efficient mechanisms for removing heat from a solid surface. Futuristic electronic devices are expected to generate more than 1000 W/cm2 of heat. Despite the advancements in microscale and nanoscale manufacturing, the maximum passive heat flux removal has been 300 W/cm2 in pool boiling. Such limitations can be overcome by developing nanoscale thin-film evaporation based devices, which however require a better understanding of surface interactions and liquid vapor phase change process. Evaporation based passive flow is an inspiration from the transpiration process that happens in trees. If we can mimic this process and develop heat removal devices, then we can develop efficient cooling devices. The existing passive flow based cooling devices still needs improvement to meet the future demands. To improve the efficiency and capacity of these devices, we need to explore and quantify the passive flow happening at nanoscales. Experimental techniques have not advanced enough to study these fundamental phenomena at the nanoscale, an alternative method is to perform theoretical study at nanoscales. Molecular dynamics (MD) simulation is a widely accepted powerful tool for studying a range of fundamental and engineering problems. MD simulations can be utilized to study the passive flow mechanism and heat transfer due to it. To study passive flow using MD, apart from the conventional methods available in MD, we need to have methods to simulate the heat transfer between solid and liquid, local pressure, surface tension, density, temperature calculation methods, realistic boundary conditions, etc. Heat transfer between solid and fluids has been a challenging area in MD simulations, and has only been minimally explored (especially for a practical fluid like water). Conventionally, an equilibrium canonical ensemble (NVT) is simulated using thermostat algorithms. For research in heat transfer involving solid liquid interaction, we need to perform non equilibrium MD (NEMD) simulations. In such NEMD simulations, the methods used for simulating heating from a surface is very important and must capture proper physics and thermodynamic properties. Development of MD simulation techniques to simulate solid-liquid heating and the study of fundamental mechanism of passive flow is the main focus of this thesis. An accurate surface-heating algorithm was developed for water which can now allow the study of a whole new set of fundamental heat transfer problems at the nanoscale like surface heating/cooling of droplets, thin-films, etc. The developed algorithm is implemented in the in-house developed C++ MD code. A direct two dimensional local pressure estimation algorithm is also formulated and implemented in the code. With this algorithm, local pressure of argon and platinum interaction is studied. Also, the surface tension of platinum-argon (solid-liquid) was estimated directly from the MD simulations for the first time. Contact angle estimation studies of water on platinum, and argon on platinum were also performed. A thin film of argon is kept above platinum plate and heated in the middle region, leading to the evaporation and pressure reduction thus creating a strong passive flow in the near surface region. This observed passive liquid flow is characterized by estimating the pressure, density, velocity and surface tension using Eulerian mapping method. Using these simulation, we have demonstrated the fundamental nature and origin of surface-driven passive flow. Heat flux removed from the surface is also estimated from the results, which shows a significant improvement can be achieved in thermal management of electronic devices by taking advantage of surface-driven strong passive liquid flow. Further, the local pressure of water on silicon di-oxide surface is estimated using the LAMMPS atomic to continuum (ATC) package towards the goal of simulating the passive flow in water.

Insights into enzyme point mutation effect by molecular simulation: phenylethylamine oxidation catalyzed by monoamine oxidase A.

PubMed

Oanca, Gabriel; Purg, Miha; Mavri, Janez; Shih, Jean C; Stare, Jernej

2016-05-21

The I335Y point mutation effect on the kinetics of phenylethylamine decomposition catalyzed by monoamine oxidase A was elucidated by means of molecular simulation. The established empirical valence bond methodology was used in conjunction with the free energy perturbation sampling technique and a classical force field representing the state of reactants and products. The methodology allows for the simulation of chemical reactions, in the present case the breaking of the α-C-H bond in a phenylethylamine substrate and the subsequent hydrogen transfer to the flavin cofactor, resulting in the formation of the N-H bond on flavin. The empirical parameters were calibrated against the experimental data for the simulated reaction in a wild type protein and then used for the calculation of the reaction free energy profile in the I335Y mutant. In very good agreement with the measured kinetic data, mutation increases the free energy barrier for the rate limiting step by slightly more than 1 kcal mol(-1) and consequently decreases the rate constant by about an order of magnitude. The magnitude of the computed effect slightly varies with simulation settings, but always remains in reasonable agreement with the experiment. Analysis of trajectories reveals a major change in the interaction between phenyl rings of the substrate and the neighboring Phe352 residue upon the I335Y mutation due to the increased local polarity, leading to an attenuated quadrupole interaction between the rings and destabilization of the transition state. Additionally, the increased local polarity in the mutant allows for a larger number of water molecules to be present near the active site, effectively shielding the catalytic effect of the enzyme and contributing to the increased barrier.

Scale Dependence of Land Atmosphere Interactions in Wet and Dry Regions as Simulated with NU-WRF over the Southwestern and Southeast US

NASA Technical Reports Server (NTRS)

Zhou, Yaping; Wu, Di; Lau, K.- M.; Tao, Wei-Kuo

2016-01-01

Large-scale forcing and land-atmosphere interactions on precipitation are investigated with NASA-Unified WRF (NU-WRF) simulations during fast transitions of ENSO phases from spring to early summer of 2010 and 2011. The model is found to capture major precipitation episodes in the 3-month simulations without resorting to nudging. However, the mean intensity of the simulated precipitation is underestimated by 46% and 57% compared with the observations in dry and wet regions in the southwestern and south-central United States, respectively. Sensitivity studies show that large-scale atmospheric forcing plays a major role in producing regional precipitation. A methodology to account for moisture contributions to individual precipitation events, as well as total precipitation, is presented under the same moisture budget framework. The analysis shows that the relative contributions of local evaporation and large-scale moisture convergence depend on the dry/wet regions and are a function of temporal and spatial scales. While the ratio of local and large-scale moisture contributions vary with domain size and weather system, evaporation provides a major moisture source in the dry region and during light rain events, which leads to greater sensitivity to soil moisture in the dry region and during light rain events. The feedback of land surface processes to large-scale forcing is well simulated, as indicated by changes in atmospheric circulation and moisture convergence. Overall, the results reveal an asymmetrical response of precipitation events to soil moisture, with higher sensitivity under dry than wet conditions. Drier soil moisture tends to suppress further existing below-normal precipitation conditions via a positive soil moisture-land surface flux feedback that could worsen drought conditions in the southwestern United States.

Gas-Expanded Liquids: Synergism of Experimental and Computational Determinations of Local Structure

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

Charles A. Eckert; Charles L. Liotta; Rigoberto Hernandez

2007-06-26

This project focuses on the characterization of a new class of solvent systems called gas-expanded liquids (GXLs), targeted for green-chemistry processing. The collaboration has adopted a synergistic approach combining elements of molecular dynamics (MD) simulation and spectroscopic experiments to explore the local solvent behavior that could not be studied by simulation or experiment alone. The major accomplishments from this project are: • Applied MD simulations to explore the non-uniform structure of CO2/methanol and CO2/acetone GXLs and studied their dynamic behavior with self-diffusion coefficients and correlation functions • Studied local solvent structure and solvation behavior with a combination of spectroscopy andmore » MD simulations • Measured transport properties of heterocyclic solutes in GXLs through Taylor-Aris diffusion techniques and compared these findings to those of MD simulations • Probed local polarity and specific solute-solvent interactions with Diels-Alder and SN2 reaction studies The broader scientific impact resulting from the research activities of this contract have been recognized by two recent awards: the Presidential Green Chemistry Award (Eckert & Liotta) and a fellowship in the American Association for the Advancement of Science (Hernandez). In addition to the technical aspects of this contract, the investigators have been engaged in a number of programs extending the broader impacts of this project. The project has directly supported the development of two postdoctoral researcher, four graduate students, and five undergraduate students. Several of the undergraduate students were co-funded by a Georgia Tech program, the Presidential Undergraduate Research Award. The other student, an African-American female graduated from Georgia Tech in December 2005, and was co-funded through an NSF Research and Education for Undergraduates (REU) award.« less

Images of turbulent, absorbing-emitting atmospheres and their application to windshear detection

NASA Astrophysics Data System (ADS)

Watt, David W.; Philbrick, Daniel A.

1991-03-01

The simulation of images generated by thermally-radiating, optically- thick turbulent media are discussed and the time-dependent evolution of these images is modeled. This characteristics of these images are particularly applicable to the atmosphere in the 13-15 mm band and their behavior may have application in detecting aviation hazards. The image is generated by volumetric thermal emission by atmospheric constituents within the field-of-view of the detector. The structure of the turbulent temperature field and the attenuating properties of the atmosphere interact with the field-of-view's geometry to produce a localized region which dominates the optical flow of the image. The simulations discussed in this paper model the time-dependent behavior of images generated by atmospheric flows viewed from an airborne platform. The images ar modelled by (1) generating a random field of temperature fluctuations have the proper spatial structure, (2) adding these fluctuation to the baseline temperature field of the atmospheric event, (3) accumulating the image on the detector from radiation emitted in the imaging volume, (4) allowing the individual radiating points within the imaging volume to move with the local velocity, (5) recalculating the thermal field and generating a new image. This approach was used to simulate the images generated by the temperature and velocity fields of a windshear. The simulation generated pais of images separated by a small time interval. These image paris were analyzed by image cross-correlation. The displacement of the cross-correlation peak was used to infer the velocity at the localized region. The localized region was found to depend weakly on the shape of the velocity profile. Prediction of the localized region, the effects of imaging from a moving platform, alternative image analysis schemes, and possible application to aviation hazards are discussed.

Numerical Simulation of the Vortex-Induced Vibration of A Curved Flexible Riser in Shear Flow

NASA Astrophysics Data System (ADS)

Zhu, Hong-jun; Lin, Peng-zhi

2018-06-01

A series of fully three-dimensional (3D) numerical simulations of flow past a free-to-oscillate curved flexible riser in shear flow were conducted at Reynolds number of 185-1015. The numerical results obtained by the two-way fluid-structure interaction (FSI) simulations are in good agreement with the experimental results reported in the earlier study. It is further found that the frequency transition is out of phase not only in the inline (IL) and crossflow (CF) directions but also along the span direction. The mode competition leads to the non-zero nodes of the rootmean- square (RMS) amplitude and the relatively chaotic trajectories. The fluid-structure interaction is to some extent reflected by the transverse velocity of the ambient fluid, which reaches the maximum value when the riser reaches the equilibrium position. Moreover, the local maximum transverse velocities occur at the peak CF amplitudes, and the values are relatively large when the vibration is in the resonance regions. The 3D vortex columns are shed nearly parallel to the axis of the curved flexible riser. As the local Reynolds number increases from 0 at the bottom of the riser to the maximum value at the top, the wake undergoes a transition from a two-dimensional structure to a 3D one. More irregular small-scale vortices appeared at the wake region of the riser, undergoing large amplitude responses.

Modeling of episodic particulate matter events using a 3-D air quality model with fine grid: Applications to a pair of cities in the US/Mexico border

NASA Astrophysics Data System (ADS)

Choi, Yu-Jin; Hyde, Peter; Fernando, H. J. S.

High (episodic) particulate matter (PM) events over the sister cities of Douglas (AZ) and Agua Prieta (Sonora), located in the US-Mexico border, were simulated using the 3D Eulerian air quality model, MODELS-3/CMAQ. The best available input information was used for the simulations, with pollution inventory specified on a fine grid. In spite of inherent uncertainties associated with the emission inventory as well as the chemistry and meteorology of the air quality simulation tool, model evaluations showed acceptable PM predictions, while demonstrating the need for including the interaction between meteorology and emissions in an interactive mode in the model, a capability currently unavailable in MODELS-3/CMAQ when dealing with PM. Sensitivity studies on boundary influence indicate an insignificant regional (advection) contribution of PM to the study area. The contribution of secondary particles to the occurrence of high PM events was trivial. High PM episodes in the study area, therefore, are purely local events that largely depend on local meteorological conditions. The major PM emission sources were identified as vehicular activities on unpaved/paved roads and wind-blown dust. The results will be of immediate utility in devising PM mitigation strategies for the study area, which is one of the US EPA-designated non-attainment areas with respect to PM.

Local phase separation of co-solvents enhances pretreatment of biomass for bioenergy applications

DOE PAGES

Mostofian, Barmak; Cai, Charles M.; Smith, Micholas Dean; ...

2016-08-02

Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. Here, to elucidate the mechanism of the THF water interactions with cellulose, we pair simulation and experimental data demonstrating that enhancedmore » solubilization of cellulose can be achieved by the THF water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method.« less

Estimation of effective brain connectivity with dual Kalman filter and EEG source localization methods.

PubMed

Rajabioun, Mehdi; Nasrabadi, Ali Motie; Shamsollahi, Mohammad Bagher

2017-09-01

Effective connectivity is one of the most important considerations in brain functional mapping via EEG. It demonstrates the effects of a particular active brain region on others. In this paper, a new method is proposed which is based on dual Kalman filter. In this method, firstly by using a brain active localization method (standardized low resolution brain electromagnetic tomography) and applying it to EEG signal, active regions are extracted, and appropriate time model (multivariate autoregressive model) is fitted to extracted brain active sources for evaluating the activity and time dependence between sources. Then, dual Kalman filter is used to estimate model parameters or effective connectivity between active regions. The advantage of this method is the estimation of different brain parts activity simultaneously with the calculation of effective connectivity between active regions. By combining dual Kalman filter with brain source localization methods, in addition to the connectivity estimation between parts, source activity is updated during the time. The proposed method performance has been evaluated firstly by applying it to simulated EEG signals with interacting connectivity simulation between active parts. Noisy simulated signals with different signal to noise ratios are used for evaluating method sensitivity to noise and comparing proposed method performance with other methods. Then the method is applied to real signals and the estimation error during a sweeping window is calculated. By comparing proposed method results in different simulation (simulated and real signals), proposed method gives acceptable results with least mean square error in noisy or real conditions.

RURALSIM: the design and implementation of a rural EMS simulator.

PubMed

Shuman, L J; Wolfe, H; Gunter, M J

1992-01-01

Why were these applications of simulation technology unsuccessful? Parochialism, the volunteer nature of EMS planning, and limited regional commitment to resolve such complex problems at the local level all combined to present significant barriers to implementation. Political factors which posed the most significant barriers included: conservative attitudes concerning the funding and regulation of EMS activities by local governments; general opposition to governmental intervention in the private sector; strong resistance to mandatory standards for EMS; jurisdictional disputes between EMS-related agencies; lack of cooperation between the local governments; competition between prehospital-care providers and between hospitals; overemphasis on local jurisdictional boundaries in the planning and delivery of services; and the allocation of EMS resources, such as ambulances, according to political priorities, rather than more objective criteria. Based upon the results of the four field tests, the following observations are relevant: 1. RURALSIM is a very complex simulator. While every effort was made to assure generalizability, for any given situation, it required extensive modification and tailoring. The result was a model capable of handling a rather diverse set of situations, but one that could not be turned over to the general public for use. To implement RURALSIM required the participation of the University of Pittsburgh research team. The newer simulation languages now available alleviate this problem somewhat. 2. RURALSIM's complexity was needed to examine the different alternatives proposed by local planners. It was particularly needed in order to simulate each region's existing system. Such "base-line" simulations were required in order to achieve face validity and provide a basis for comparing alternatives. 3. With hindsight, a major weakness was the limited amount of face-to-face interaction between local planners and decision makers and the University of Pittsburgh staff. Only two trips to the region were budgeted. This proved to be insufficient and placed too much responsibility for model interpretation and analysis on the local contractors. 4. In none of the four test sites did the contractors and/or local health planners have the authority, influence and/or incentives necessary to develop regional EMS systems. In particular, none of the contractors were in the position to be decision makers, nor was there ever only one decision maker. This is not a criticism of the contractors, who did their best under difficult circumstances. Rather, it is a criticism of the state of eMS system development in the US in the early 1980s. There were few examples where regional systems developed successfully in the face of serious opposition from local interests.(ABSTRACT TRUNCATED AT 400 WORDS)

Event-chain Monte Carlo algorithms for three- and many-particle interactions

NASA Astrophysics Data System (ADS)

Harland, J.; Michel, M.; Kampmann, T. A.; Kierfeld, J.

2017-02-01

We generalize the rejection-free event-chain Monte Carlo algorithm from many-particle systems with pairwise interactions to systems with arbitrary three- or many-particle interactions. We introduce generalized lifting probabilities between particles and obtain a general set of equations for lifting probabilities, the solution of which guarantees maximal global balance. We validate the resulting three-particle event-chain Monte Carlo algorithms on three different systems by comparison with conventional local Monte Carlo simulations: i) a test system of three particles with a three-particle interaction that depends on the enclosed triangle area; ii) a hard-needle system in two dimensions, where needle interactions constitute three-particle interactions of the needle end points; iii) a semiflexible polymer chain with a bending energy, which constitutes a three-particle interaction of neighboring chain beads. The examples demonstrate that the generalization to many-particle interactions broadens the applicability of event-chain algorithms considerably.

Consequences of localized frustration for the folding mechanism of the IM7 protein

PubMed Central

Sutto, Ludovico; Lätzer, Joachim; Hegler, Joseph A.; Ferreiro, Diego U.; Wolynes, Peter G.

2007-01-01

In the laboratory, IM7 has been found to have an unusual folding mechanism in which an “on-pathway” intermediate with nonnative interactions is formed. We show that this intermediate is a consequence of an unusual cluster of highly frustrated interactions in the native structure. This cluster is involved in the binding of IM7 to its target, Colicin E7. Redesign of residues in this cluster to eliminate frustration is predicted by simulations to lead to faster folding without the population of an intermediate ensemble. PMID:18077415

Emulation of simulations of atmospheric dispersion at Fukushima for Sobol' sensitivity analysis

NASA Astrophysics Data System (ADS)

Girard, Sylvain; Korsakissok, Irène; Mallet, Vivien

2015-04-01

Polyphemus/Polair3D, from which derives IRSN's operational model ldX, was used to simulate the atmospheric dispersion at the Japan scale of radionuclides after the Fukushima disaster. A previous study with the screening method of Morris had shown that - The sensitivities depend a lot on the considered output; - Only a few of the inputs are non-influential on all considered outputs; - Most influential inputs have either non-linear effects or are interacting. These preliminary results called for a more detailed sensitivity analysis, especially regarding the characterization of interactions. The method of Sobol' allows for a precise evaluation of interactions but requires large simulation samples. Gaussian process emulators for each considered outputs were built in order to relieve this computational burden. Globally aggregated outputs proved to be easy to emulate with high accuracy, and associated Sobol' indices are in broad agreement with previous results obtained with the Morris method. More localized outputs, such as temporal averages of gamma dose rates at measurement stations, resulted in lesser emulator performances: tests simulations could not satisfactorily be reproduced by some emulators. These outputs are of special interest because they can be compared to available observations, for instance for calibration purpose. A thorough inspection of prediction residuals hinted that the model response to wind perturbations often behaved in very distinct regimes relatively to some thresholds. Complementing the initial sample with wind perturbations set to the extreme values allowed for sensible improvement of some of the emulators while other remained too unreliable to be used in a sensitivity analysis. Adaptive sampling or regime-wise emulation could be tried to circumvent this issue. Sobol' indices for local outputs revealed interesting patterns, mostly dominated by the winds, with very high interactions. The emulators will be useful for subsequent studies. Indeed, our goal is to characterize the model output uncertainty but too little information is available about input uncertainties. Hence, calibration of the input distributions with observation and a Bayesian approach seem necessary. This would probably involve methods such as MCMC which would be intractable without emulators.

Understanding the complex dynamics of stock markets through cellular automata

NASA Astrophysics Data System (ADS)

Qiu, G.; Kandhai, D.; Sloot, P. M. A.

2007-04-01

We present a cellular automaton (CA) model for simulating the complex dynamics of stock markets. Within this model, a stock market is represented by a two-dimensional lattice, of which each vertex stands for a trader. According to typical trading behavior in real stock markets, agents of only two types are adopted: fundamentalists and imitators. Our CA model is based on local interactions, adopting simple rules for representing the behavior of traders and a simple rule for price updating. This model can reproduce, in a simple and robust manner, the main characteristics observed in empirical financial time series. Heavy-tailed return distributions due to large price variations can be generated through the imitating behavior of agents. In contrast to other microscopic simulation (MS) models, our results suggest that it is not necessary to assume a certain network topology in which agents group together, e.g., a random graph or a percolation network. That is, long-range interactions can emerge from local interactions. Volatility clustering, which also leads to heavy tails, seems to be related to the combined effect of a fast and a slow process: the evolution of the influence of news and the evolution of agents’ activity, respectively. In a general sense, these causes of heavy tails and volatility clustering appear to be common among some notable MS models that can confirm the main characteristics of financial markets.

Nonlinear dispersion effects in elastic plates: numerical modelling and validation

NASA Astrophysics Data System (ADS)

Kijanka, Piotr; Radecki, Rafal; Packo, Pawel; Staszewski, Wieslaw J.; Uhl, Tadeusz; Leamy, Michael J.

2017-04-01

Nonlinear features of elastic wave propagation have attracted significant attention recently. The particular interest herein relates to complex wave-structure interactions, which provide potential new opportunities for feature discovery and identification in a variety of applications. Due to significant complexity associated with wave propagation in nonlinear media, numerical modeling and simulations are employed to facilitate design and development of new measurement, monitoring and characterization systems. However, since very high spatio- temporal accuracy of numerical models is required, it is critical to evaluate their spectral properties and tune discretization parameters for compromise between accuracy and calculation time. Moreover, nonlinearities in structures give rise to various effects that are not present in linear systems, e.g. wave-wave interactions, higher harmonics generation, synchronism and | recently reported | shifts to dispersion characteristics. This paper discusses local computational model based on a new HYBRID approach for wave propagation in nonlinear media. The proposed approach combines advantages of the Local Interaction Simulation Approach (LISA) and Cellular Automata for Elastodynamics (CAFE). The methods are investigated in the context of their accuracy for predicting nonlinear wavefields, in particular shifts to dispersion characteristics for finite amplitude waves and secondary wavefields. The results are validated against Finite Element (FE) calculations for guided waves in copper plate. Critical modes i.e., modes determining accuracy of a model at given excitation frequency - are identified and guidelines for numerical model parameters are proposed.

Simulation of the Atmospheric Boundary Layer for Wind Energy Applications

NASA Astrophysics Data System (ADS)

Marjanovic, Nikola

Energy production from wind is an increasingly important component of overall global power generation, and will likely continue to gain an even greater share of electricity production as world governments attempt to mitigate climate change and wind energy production costs decrease. Wind energy generation depends on wind speed, which is greatly influenced by local and synoptic environmental forcings. Synoptic forcing, such as a cold frontal passage, exists on a large spatial scale while local forcing manifests itself on a much smaller scale and could result from topographic effects or land-surface heat fluxes. Synoptic forcing, if strong enough, may suppress the effects of generally weaker local forcing. At the even smaller scale of a wind farm, upstream turbines generate wakes that decrease the wind speed and increase the atmospheric turbulence at the downwind turbines, thereby reducing power production and increasing fatigue loading that may damage turbine components, respectively. Simulation of atmospheric processes that span a considerable range of spatial and temporal scales is essential to improve wind energy forecasting, wind turbine siting, turbine maintenance scheduling, and wind turbine design. Mesoscale atmospheric models predict atmospheric conditions using observed data, for a wide range of meteorological applications across scales from thousands of kilometers to hundreds of meters. Mesoscale models include parameterizations for the major atmospheric physical processes that modulate wind speed and turbulence dynamics, such as cloud evolution and surface-atmosphere interactions. The Weather Research and Forecasting (WRF) model is used in this dissertation to investigate the effects of model parameters on wind energy forecasting. WRF is used for case study simulations at two West Coast North American wind farms, one with simple and one with complex terrain, during both synoptically and locally-driven weather events. The model's performance with different grid nesting configurations, turbulence closures, and grid resolutions is evaluated by comparison to observation data. Improvement to simulation results from the use of more computationally expensive high resolution simulations is only found for the complex terrain simulation during the locally-driven event. Physical parameters, such as soil moisture, have a large effect on locally-forced events, and prognostic turbulence kinetic energy (TKE) schemes are found to perform better than non-local eddy viscosity turbulence closure schemes. Mesoscale models, however, do not resolve turbulence directly, which is important at finer grid resolutions capable of resolving wind turbine components and their interactions with atmospheric turbulence. Large-eddy simulation (LES) is a numerical approach that resolves the largest scales of turbulence directly by separating large-scale, energetically important eddies from smaller scales with the application of a spatial filter. LES allows higher fidelity representation of the wind speed and turbulence intensity at the scale of a wind turbine which parameterizations have difficulty representing. Use of high-resolution LES enables the implementation of more sophisticated wind turbine parameterizations to create a robust model for wind energy applications using grid spacing small enough to resolve individual elements of a turbine such as its rotor blades or rotation area. Generalized actuator disk (GAD) and line (GAL) parameterizations are integrated into WRF to complement its real-world weather modeling capabilities and better represent wind turbine airflow interactions, including wake effects. The GAD parameterization represents the wind turbine as a two-dimensional disk resulting from the rotation of the turbine blades. Forces on the atmosphere are computed along each blade and distributed over rotating, annular rings intersecting the disk. While typical LES resolution (10-20 m) is normally sufficient to resolve the GAD, the GAL parameterization requires significantly higher resolution (1-3 m) as it does not distribute the forces from the blades over annular elements, but applies them along lines representing individual blades. In this dissertation, the GAL is implemented into WRF and evaluated against the GAD parameterization from two field campaigns that measured the inflow and near-wake regions of a single turbine. The data-sets are chosen to allow validation under the weakly convective and weakly stable conditions characterizing most turbine operations. The parameterizations are evaluated with respect to their ability to represent wake wind speed, variance, and vorticity by comparing fine-resolution GAD and GAL simulations along with coarse-resolution GAD simulations. Coarse-resolution GAD simulations produce aggregated wake characteristics similar to both GAD and GAL simulations (saving on computational cost), while the GAL parameterization enables resolution of near wake physics (such as vorticity shedding and wake expansion) for high fidelity applications. (Abstract shortened by ProQuest.).

Transient shocks beyond the heliopause

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

Fermo, R. L.; Pogorelov, N. V.; Burlaga, L. F.

The heliopause is a rich, dynamic surface affected by the time-dependent solar wind. Stream interactions due to coronal mass ejections (CMEs), corotating interaction regions (CIRs), and other transient phenomena are known to merge producing global merged interaction regions (GMIRs). Numerical simulations of the solar wind interaction with the local interstellar medium (LISM) show that GMIRs, as well other time-dependent structures in the solar wind, may produce compression/rarefaction waves and shocks in the LISM behind the heliopause. These shocks may initiate wave activity observed by the Voyager spacecraft. The magnetometer onboard Voyager 1 indeed observed a few structures that may bemore » interpreted as shocks. We present numerical simulations of such shocks in the year of 2000, when both Voyager spacecraft were in the supersonic solar wind region, and in 2012, when Voyager 1 observed traveling shocks. In the former case, Voyager observations themselves provide time- dependent boundary conditions in the solar wind. In the latter case, we use OMNI data at 1 AU to analyze the plasma and magnetic field behavior after Voyager 1 crossed the heliospheric boundary. Numerical results are compared with spacecraft observations.« less

Transient shocks beyond the heliopause

DOE PAGES

Fermo, R. L.; Pogorelov, N. V.; Burlaga, L. F.

2015-09-30

The heliopause is a rich, dynamic surface affected by the time-dependent solar wind. Stream interactions due to coronal mass ejections (CMEs), corotating interaction regions (CIRs), and other transient phenomena are known to merge producing global merged interaction regions (GMIRs). Numerical simulations of the solar wind interaction with the local interstellar medium (LISM) show that GMIRs, as well other time-dependent structures in the solar wind, may produce compression/rarefaction waves and shocks in the LISM behind the heliopause. These shocks may initiate wave activity observed by the Voyager spacecraft. The magnetometer onboard Voyager 1 indeed observed a few structures that may bemore » interpreted as shocks. We present numerical simulations of such shocks in the year of 2000, when both Voyager spacecraft were in the supersonic solar wind region, and in 2012, when Voyager 1 observed traveling shocks. In the former case, Voyager observations themselves provide time- dependent boundary conditions in the solar wind. In the latter case, we use OMNI data at 1 AU to analyze the plasma and magnetic field behavior after Voyager 1 crossed the heliospheric boundary. Numerical results are compared with spacecraft observations.« less

Non-filamentated ultra-intense and ultra-short pulse fronts in three-dimensional Raman seed amplification

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

Lehmann, G.; Spatschek, K. H.

Ultra-intense and ultra-short laser pulses may be generated up to the exawatt-zetawatt regime due to parametric processes in plasmas. The minimization of unwanted plasma processes leads to operational limits which are discussed here with respect to filamentation. Transverse filamentation, which originally was derived for plane waves, is being investigated for seed pulse propagation in the so called π-pulse limit. A three-dimensional (3D) three-wave-interaction model is the basis of the present investigation. To demonstrate the applicability of the three-wave-interaction model, the 1D pulse forms are compared with those obtained from 1D particle in cell and Vlasov simulations. Although wave-breaking may occur,more » the kinetic simulations show that the leading pumped pulse develops a form similar to that obtained from the three-wave-interaction model. In the main part, 2D and 3D filamentation processes of (localized) pulses are investigated with the three-wave-interaction model. It is shown that the leading pulse front can stay filamentation-free, whereas the rear parts show transverse modulations.« less

Chromatic patchy particles: Effects of specific interactions on liquid structure

DOE PAGES

Vasilyev, Oleg A.; Tkachenko, Alexei V.; Klumov, Boris A.

2015-07-13

We study the structural and thermodynamic properties of patchy particle liquids, with a special focus on the role of “color,” i.e., specific interactions between individual patches. A possible experimental realization of such “chromatic” interactions is by decorating the particle patches with single-stranded DNA linkers. The complementarity of the linkers can promote selective bond formation between predetermined pairs of patches. By using MD simulations, we compare the local connectivity, the bond orientation order, and other structural properties of the aggregates formed by the “colored” and “colorless” systems. The analysis is done for spherical particles with two different patch arrangements (tetrahedral andmore » cubic). It is found that the aggregated (liquid) phase of the “colorless” patchy particles is better connected, denser and typically has stronger local order than the corresponding “colored” one. This, in turn, makes the colored liquid less stable thermodynamically. Specifically, we predict that in a typical case the chromatic interactions should increase the relative stability of the crystalline phase with respect to the disordered liquid, thus expanding its region in the phase diagram.« less

Atomistic understanding of cation exchange in PbS nanocrystals using simulations with pseudoligands

PubMed Central

Fan, Zhaochuan; Lin, Li-Chiang; Buijs, Wim; Vlugt, Thijs J. H.; van Huis, Marijn A.

2016-01-01

Cation exchange is a powerful tool for the synthesis of nanostructures such as core–shell nanocrystals, however, the underlying mechanism is poorly understood. Interactions of cations with ligands and solvent molecules are systematically ignored in simulations. Here, we introduce the concept of pseudoligands to incorporate cation-ligand-solvent interactions in molecular dynamics. This leads to excellent agreement with experimental data on cation exchange of PbS nanocrystals, whereby Pb ions are partially replaced by Cd ions from solution. The temperature and the ligand-type control the exchange rate and equilibrium composition of cations in the nanocrystal. Our simulations reveal that Pb ions are kicked out by exchanged Cd interstitials and migrate through interstitial sites, aided by local relaxations at core–shell interfaces and point defects. We also predict that high-pressure conditions facilitate strongly enhanced cation exchange reactions at elevated temperatures. Our approach is easily extendable to other semiconductor compounds and to other families of nanocrystals. PMID:27160371

Trading Speed and Accuracy by Coding Time: A Coupled-circuit Cortical Model

PubMed Central

Standage, Dominic; You, Hongzhi; Wang, Da-Hui; Dorris, Michael C.

2013-01-01

Our actions take place in space and time, but despite the role of time in decision theory and the growing acknowledgement that the encoding of time is crucial to behaviour, few studies have considered the interactions between neural codes for objects in space and for elapsed time during perceptual decisions. The speed-accuracy trade-off (SAT) provides a window into spatiotemporal interactions. Our hypothesis is that temporal coding determines the rate at which spatial evidence is integrated, controlling the SAT by gain modulation. Here, we propose that local cortical circuits are inherently suited to the relevant spatial and temporal coding. In simulations of an interval estimation task, we use a generic local-circuit model to encode time by ‘climbing’ activity, seen in cortex during tasks with a timing requirement. The model is a network of simulated pyramidal cells and inhibitory interneurons, connected by conductance synapses. A simple learning rule enables the network to quickly produce new interval estimates, which show signature characteristics of estimates by experimental subjects. Analysis of network dynamics formally characterizes this generic, local-circuit timing mechanism. In simulations of a perceptual decision task, we couple two such networks. Network function is determined only by spatial selectivity and NMDA receptor conductance strength; all other parameters are identical. To trade speed and accuracy, the timing network simply learns longer or shorter intervals, driving the rate of downstream decision processing by spatially non-selective input, an established form of gain modulation. Like the timing network's interval estimates, decision times show signature characteristics of those by experimental subjects. Overall, we propose, demonstrate and analyse a generic mechanism for timing, a generic mechanism for modulation of decision processing by temporal codes, and we make predictions for experimental verification. PMID:23592967

Justification for, and design of, an economical programmable multiple flight simulator

NASA Technical Reports Server (NTRS)

Kreifeldt, J. G.; Wittenber, J.; Macdonald, G.

1981-01-01

The considered research interests in air traffic control (ATC) studies revolve about the concept of distributed ATC management based on the assumption that the pilot has a cockpit display of traffic and navigation information (CDTI) via CRT graphics. The basic premise is that a CDTI equipped pilot can, in coordination with a controller, manage a part of his local traffic situation thereby improving important aspects of ATC performance. A modularly designed programmable flight simulator system is prototyped as a means of providing an economical facility of up to eight simulators to interface with a mainframe/graphics system for ATC experimentation, particularly CDTI-distributed management in which pilot-pilot interaction can have a determining effect on system performance. Need for a multiman simulator facility is predicted on results from an earlier three simulator facility.

Effects of mass loading on dayside solar wind-magnetosphere interactions

NASA Astrophysics Data System (ADS)

Zhang, B.; Brambles, O.; Wiltberger, M. J.; Lyon, J.; Lotko, W.

2016-12-01

Satellite observations have shown that terrestrial-sourced plasmas mass load the dayside magnetopause and cause reductions in local reconnection rates. Whether the integrated dayside reconnection rate is affected by these local mass-loading processes is still an open question. Several mechanisms have been proposed to describe the control of dayside reconnection, including the local-control and global-control hypotheses. We have conducted a series of controlled numerical simulations to investigate the response of dayside solar wind-magnetopshere (SW-M) coupling to mass loading processes. Our simulation results show that the coupled SW-M system may exhibit both local and global control behaviors depending on the amount of mass loading. With a small amount of mass loading, the changes in the local reconnection rate does not affect magnetosheath properties and the geoeffective length in the upstream solar wind, resulting in the same integrated dayside reconnection rate. With a large amount of mass loading, the magnetosheath properties and the geoeffective length are significantly modified by slowing down the local reconnection rate, resulting in a significant reduction in the integrated dayside reconnection rate. The response of magnetosheath properties to mass loading is expected from the Cassak-Shay asymmetric reconnection theory through conservation of energy. The physical origin of the transition regime between local and global control is qualitatively explained. The parameters that determine the transition regime depend on the location, spatial extension and density of the mass loading process.

NMR investigations of molecular dynamics

NASA Astrophysics Data System (ADS)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

On the local relaxation of solid neon upon Rydberg excitation of a NO impurity: the role of the NO(A)-Ne interaction potential and zero-point quantum delocalization.

PubMed

Pajón-Suárez, Pedro; Rojas-Lorenzo, Germán A; Rubayo-Soneira, Jesús; Hernández-Lamoneda, Ramón; Larrégaray, Pascal

2009-12-31

The local relaxation of solid neon subsequent to the impulsive excitation of the NO chromophore to its A(3s sigma) Ryberg state is investigated using molecular dynamics simulations. This study makes use of empirical NO(X,A)-Ne isotropic pair potentials as well as a recently developed ab initio triatomic potential energy surface for the excited state. The role of these interaction potentials is analyzed, including many-body effects. In particular, empirical potentials, designed to reproduce correctly both the NO X-A steady-state absorption and emission bands, are shown to lead to a good description of the subpicosecond relaxation dynamics. The 600 fs expansion of the electronic bubble fairly agrees with experimental data. This relatively long time scale with respect to solid Argon, which was previously attributed to the range of the NO(A)-Ne interaction, is presumably related to the quantum nature of the medium. The time-resolved local relaxation of the Ne solid is understandably intermediate between that of classical solids (e.g., Ar) and that of quantum solids (e.g., H(2)).

A 2D modeling approach for fluid propagation during FE-forming simulation of continuously reinforced composites in wet compression moulding

NASA Astrophysics Data System (ADS)

Poppe, Christian; Dörr, Dominik; Henning, Frank; Kärger, Luise

2018-05-01

Wet compression moulding (WCM) provides large-scale production potential for continuously fiber reinforced components as a promising alternative to resin transfer moulding (RTM). Lower cycle times are possible due to parallelization of the process steps draping, infiltration and curing during moulding (viscous draping). Experimental and theoretical investigations indicate a strong mutual dependency between the physical mechanisms, which occur during draping and mould filling (fluid-structure-interaction). Thus, key process parameters, like fiber orientation, fiber volume fraction, cavity pressure and the amount and viscosity of the resin are physically coupled. To enable time and cost efficient product and process development throughout all design stages, accurate process simulation tools are desirable. Separated draping and mould filling simulation models, as appropriate for the sequential RTM-process, cannot be applied for the WCM process due to the above outlined physical couplings. Within this study, a two-dimensional Darcy-Propagation-Element (DPE-2D) based on a finite element formulation with additional control volumes (FE/CV) is presented, verified and applied to forming simulation of a generic geometry, as a first step towards a fluid-structure-interaction model taking into account simultaneous resin infiltration and draping. The model is implemented in the commercial FE-Solver Abaqus by means of several user subroutines considering simultaneous draping and 2D-infiltration mechanisms. Darcy's equation is solved with respect to a local fiber orientation. Furthermore, the material model can access the local fluid domain properties to update the mechanical forming material parameter, which enables further investigations on the coupled physical mechanisms.

Plant and Animal Gravitational Biology. Part 1

NASA Technical Reports Server (NTRS)

1997-01-01

Session TA2 includes short reports covering: (1) The Interaction of Microgravity and Ethylene on Soybean Growth and Metabolism; (2) Structure and G-Sensitivity of Root Statocytes under Different Mass Acceleration; (3) Extracellular Production of Taxanes on Cell Surfaces in Simulated Microgravity and Hypergravity; (4) Current Problems of Space Cell Phytobiology; (5) Biological Consequences of Microgravity-Induced Alterations in Water Metabolism of Plant Cells; (6) Localization of Calcium Ions in Chlorella Cells Under Clinorotation; (7) Changes of Fatty Acids Content of Plant Cell Plasma Membranes under Altered Gravity; (8) Simulation of Gravity by Non-Symmetrical Vibrations and Ultrasound; and (9) Response to Simulated weightlessness of In Vitro Cultures of Differentiated Epithelial Follicular Cells from Thyroid.

Acidic pH retards the fibrillization of human islet amyloid polypeptide due to electrostatic repulsion of histidines

NASA Astrophysics Data System (ADS)

Li, Yang; Xu, Weixin; Mu, Yuguang; Zhang, John Z. H.

2013-08-01

The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], 10.1021/ja205007j, which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent β-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.

Numerical Methods of Computational Electromagnetics for Complex Inhomogeneous Systems

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

Cai, Wei

Understanding electromagnetic phenomena is the key in many scientific investigation and engineering designs such as solar cell designs, studying biological ion channels for diseases, and creating clean fusion energies, among other things. The objectives of the project are to develop high order numerical methods to simulate evanescent electromagnetic waves occurring in plasmon solar cells and biological ion-channels, where local field enhancement within random media in the former and long range electrostatic interactions in the latter are of major challenges for accurate and efficient numerical computations. We have accomplished these objectives by developing high order numerical methods for solving Maxwell equationsmore » such as high order finite element basis for discontinuous Galerkin methods, well-conditioned Nedelec edge element method, divergence free finite element basis for MHD, and fast integral equation methods for layered media. These methods can be used to model the complex local field enhancement in plasmon solar cells. On the other hand, to treat long range electrostatic interaction in ion channels, we have developed image charge based method for a hybrid model in combining atomistic electrostatics and continuum Poisson-Boltzmann electrostatics. Such a hybrid model will speed up the molecular dynamics simulation of transport in biological ion-channels.« less

Multi-A Graph Patrolling and Partitioning

NASA Astrophysics Data System (ADS)

Elor, Y.; Bruckstein, A. M.

2012-12-01

We introduce a novel multi agent patrolling algorithm inspired by the behavior of gas filled balloons. Very low capability ant-like agents are considered with the task of patrolling an unknown area modeled as a graph. While executing the proposed algorithm, the agents dynamically partition the graph between them using simple local interactions, every agent assuming the responsibility for patrolling his subgraph. Balanced graph partition is an emergent behavior due to the local interactions between the agents in the swarm. Extensive simulations on various graphs (environments) showed that the average time to reach a balanced partition is linear with the graph size. The simulations yielded a convincing argument for conjecturing that if the graph being patrolled contains a balanced partition, the agents will find it. However, we could not prove this. Nevertheless, we have proved that if a balanced partition is reached, the maximum time lag between two successive visits to any vertex using the proposed strategy is at most twice the optimal so the patrol quality is at least half the optimal. In case of weighted graphs the patrol quality is at least (1)/(2){lmin}/{lmax} of the optimal where lmax (lmin) is the longest (shortest) edge in the graph.

Organization of the cytokeratin network in an epithelial cell.

PubMed

Portet, Stéphanie; Arino, Ovide; Vassy, Jany; Schoëvaërt, Damien

2003-08-07

The cytoskeleton is a dynamic three-dimensional structure mainly located in the cytoplasm. It is involved in many cell functions such as mechanical signal transduction and maintenance of cell integrity. Among the three cytoskeletal components, intermediate filaments (the cytokeratin in epithelial cells) are the best candidates for this mechanical role. A model of the establishment of the cytokeratin network of an epithelial cell is proposed to study the dependence of its structural organization on extracellular mechanical environment. To implicitly describe the latter and its effects on the intracellular domain, we use mechanically regulated protein synthesis. Our model is a hybrid of a partial differential equation of parabolic type, governing the evolution of the concentration of cytokeratin, and a set of stochastic differential equations describing the dynamics of filaments. Each filament is described by a stochastic differential equation that reflects both the local interactions with the environment and the non-local interactions via the past history of the filament. A three-dimensional simulation model is derived from this mathematical model. This simulation model is then used to obtain examples of cytokeratin network architectures under given mechanical conditions, and to study the influence of several parameters.

STAR FORMATION IN DISK GALAXIES. III. DOES STELLAR FEEDBACK RESULT IN CLOUD DEATH?

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

Tasker, Elizabeth J.; Wadsley, James; Pudritz, Ralph

2015-03-01

Stellar feedback, star formation, and gravitational interactions are major controlling forces in the evolution of giant molecular clouds (GMCs). To explore their relative roles, we examine the properties and evolution of GMCs forming in an isolated galactic disk simulation that includes both localized thermal feedback and photoelectric heating. The results are compared with the three previous simulations in this series, which consists of a model with no star formation, star formation but no form of feedback, and star formation with photoelectric heating in a set with steadily increasing physical effects. We find that the addition of localized thermal feedback greatlymore » suppresses star formation but does not destroy the surrounding GMC, giving cloud properties closely resembling the run in which no stellar physics is included. The outflows from the feedback reduce the mass of the cloud but do not destroy it, allowing the cloud to survive its stellar children. This suggests that weak thermal feedback such as the lower bound expected for a supernova may play a relatively minor role in the galactic structure of quiescent Milky-Way-type galaxies, compared to gravitational interactions and disk shear.« less

The complex nature of calcium cation interactions with phospholipid bilayers

PubMed Central

Melcrová, Adéla; Pokorna, Sarka; Pullanchery, Saranya; Kohagen, Miriam; Jurkiewicz, Piotr; Hof, Martin; Jungwirth, Pavel; Cremer, Paul S.; Cwiklik, Lukasz

2016-01-01

Understanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments. To gain additional atomic-level information, the experiments are complemented by molecular simulations that utilize an accurate force field for calcium ions with scaled charges effectively accounting for electronic polarization effects. We demonstrate that lipid membranes have substantial calcium-binding capacity, with several types of binding sites present. Significantly, the binding mode depends on calcium concentration with important implications for calcium buffering, synaptic plasticity, and protein-membrane association. PMID:27905555

Translating statistical species-habitat models to interactive decision support tools

USGS Publications Warehouse

Wszola, Lyndsie S.; Simonsen, Victoria L.; Stuber, Erica F.; Gillespie, Caitlyn R.; Messinger, Lindsey N.; Decker, Karie L.; Lusk, Jeffrey J.; Jorgensen, Christopher F.; Bishop, Andrew A.; Fontaine, Joseph J.

2017-01-01

Understanding species-habitat relationships is vital to successful conservation, but the tools used to communicate species-habitat relationships are often poorly suited to the information needs of conservation practitioners. Here we present a novel method for translating a statistical species-habitat model, a regression analysis relating ring-necked pheasant abundance to landcover, into an interactive online tool. The Pheasant Habitat Simulator combines the analytical power of the R programming environment with the user-friendly Shiny web interface to create an online platform in which wildlife professionals can explore the effects of variation in local landcover on relative pheasant habitat suitability within spatial scales relevant to individual wildlife managers. Our tool allows users to virtually manipulate the landcover composition of a simulated space to explore how changes in landcover may affect pheasant relative habitat suitability, and guides users through the economic tradeoffs of landscape changes. We offer suggestions for development of similar interactive applications and demonstrate their potential as innovative science delivery tools for diverse professional and public audiences.

Interactive visualization and analysis of multimodal datasets for surgical applications.

PubMed

Kirmizibayrak, Can; Yim, Yeny; Wakid, Mike; Hahn, James

2012-12-01

Surgeons use information from multiple sources when making surgical decisions. These include volumetric datasets (such as CT, PET, MRI, and their variants), 2D datasets (such as endoscopic videos), and vector-valued datasets (such as computer simulations). Presenting all the information to the user in an effective manner is a challenging problem. In this paper, we present a visualization approach that displays the information from various sources in a single coherent view. The system allows the user to explore and manipulate volumetric datasets, display analysis of dataset values in local regions, combine 2D and 3D imaging modalities and display results of vector-based computer simulations. Several interaction methods are discussed: in addition to traditional interfaces including mouse and trackers, gesture-based natural interaction methods are shown to control these visualizations with real-time performance. An example of a medical application (medialization laryngoplasty) is presented to demonstrate how the combination of different modalities can be used in a surgical setting with our approach.

Translating statistical species-habitat models to interactive decision support tools.

PubMed

Wszola, Lyndsie S; Simonsen, Victoria L; Stuber, Erica F; Gillespie, Caitlyn R; Messinger, Lindsey N; Decker, Karie L; Lusk, Jeffrey J; Jorgensen, Christopher F; Bishop, Andrew A; Fontaine, Joseph J

2017-01-01

Understanding species-habitat relationships is vital to successful conservation, but the tools used to communicate species-habitat relationships are often poorly suited to the information needs of conservation practitioners. Here we present a novel method for translating a statistical species-habitat model, a regression analysis relating ring-necked pheasant abundance to landcover, into an interactive online tool. The Pheasant Habitat Simulator combines the analytical power of the R programming environment with the user-friendly Shiny web interface to create an online platform in which wildlife professionals can explore the effects of variation in local landcover on relative pheasant habitat suitability within spatial scales relevant to individual wildlife managers. Our tool allows users to virtually manipulate the landcover composition of a simulated space to explore how changes in landcover may affect pheasant relative habitat suitability, and guides users through the economic tradeoffs of landscape changes. We offer suggestions for development of similar interactive applications and demonstrate their potential as innovative science delivery tools for diverse professional and public audiences.

Translating statistical species-habitat models to interactive decision support tools

PubMed Central

Simonsen, Victoria L.; Stuber, Erica F.; Gillespie, Caitlyn R.; Messinger, Lindsey N.; Decker, Karie L.; Lusk, Jeffrey J.; Jorgensen, Christopher F.; Bishop, Andrew A.; Fontaine, Joseph J.

2017-01-01

Understanding species-habitat relationships is vital to successful conservation, but the tools used to communicate species-habitat relationships are often poorly suited to the information needs of conservation practitioners. Here we present a novel method for translating a statistical species-habitat model, a regression analysis relating ring-necked pheasant abundance to landcover, into an interactive online tool. The Pheasant Habitat Simulator combines the analytical power of the R programming environment with the user-friendly Shiny web interface to create an online platform in which wildlife professionals can explore the effects of variation in local landcover on relative pheasant habitat suitability within spatial scales relevant to individual wildlife managers. Our tool allows users to virtually manipulate the landcover composition of a simulated space to explore how changes in landcover may affect pheasant relative habitat suitability, and guides users through the economic tradeoffs of landscape changes. We offer suggestions for development of similar interactive applications and demonstrate their potential as innovative science delivery tools for diverse professional and public audiences. PMID:29236707

The complex nature of calcium cation interactions with phospholipid bilayers

NASA Astrophysics Data System (ADS)

Melcrová, Adéla; Pokorna, Sarka; Pullanchery, Saranya; Kohagen, Miriam; Jurkiewicz, Piotr; Hof, Martin; Jungwirth, Pavel; Cremer, Paul S.; Cwiklik, Lukasz

2016-12-01

Understanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments. To gain additional atomic-level information, the experiments are complemented by molecular simulations that utilize an accurate force field for calcium ions with scaled charges effectively accounting for electronic polarization effects. We demonstrate that lipid membranes have substantial calcium-binding capacity, with several types of binding sites present. Significantly, the binding mode depends on calcium concentration with important implications for calcium buffering, synaptic plasticity, and protein-membrane association.

Coevolving complex networks in the model of social interactions

NASA Astrophysics Data System (ADS)

Raducha, Tomasz; Gubiec, Tomasz

2017-04-01

We analyze Axelrod's model of social interactions on coevolving complex networks. We introduce four extensions with different mechanisms of edge rewiring. The models are intended to catch two kinds of interactions-preferential attachment, which can be observed in scientists or actors collaborations, and local rewiring, which can be observed in friendship formation in everyday relations. Numerical simulations show that proposed dynamics can lead to the power-law distribution of nodes' degree and high value of the clustering coefficient, while still retaining the small-world effect in three models. All models are characterized by two phase transitions of a different nature. In case of local rewiring we obtain order-disorder discontinuous phase transition even in the thermodynamic limit, while in case of long-distance switching discontinuity disappears in the thermodynamic limit, leaving one continuous phase transition. In addition, we discover a new and universal characteristic of the second transition point-an abrupt increase of the clustering coefficient, due to formation of many small complete subgraphs inside the network.

Relativistic laser-plasma interactions in the quantum regime.

PubMed

Eliasson, Bengt; Shukla, P K

2011-04-01

We consider nonlinear interactions between a relativistically strong laser beam and a plasma in the quantum regime. The collective behavior of electrons is modeled by a Klein-Gordon equation, which is nonlinearly coupled with the electromagnetic wave through the Maxwell and Poisson equations. This allows us to study nonlinear interactions between arbitrarily large-amplitude electromagnetic waves and a quantum plasma. We have used our system of nonlinear equations to study theoretically the parametric instabilities involving stimulated Raman scattering and modulational instabilities. A model for quasi-steady-state propagating electromagnetic wave packets is also derived, and which shows possibility of localized solitary structures in a quantum plasma. Numerical simulations demonstrate collapse and acceleration of electrons in the nonlinear stage of the modulational instability, as well as possibility of the wake-field acceleration of electrons to relativistic speeds by short laser pulses at nanometer length scales. Our study is relevant for understanding the localization of intense electromagnetic pulses in a quantum plasma with extremely high electron densities and relatively low temperature.

Energy exchange and transition to localization in the asymmetric Fermi-Pasta-Ulam oscillatory chain

NASA Astrophysics Data System (ADS)

Smirnov, Valeri V.; Shepelev, Denis S.; Manevitch, Leonid I.

2013-01-01

A finite (periodic) FPU chain is chosen as a convenient model for investigating the energy exchange phenomenon in nonlinear oscillatory systems. As we have recently shown, this phenomenon may occur as a consequence of the resonant interaction between high-frequency nonlinear normal modes. This interaction determines both the complete energy exchange between different parts of the chain and the transition to energy localization in an excited group of particles. In the paper, we demonstrate that this mechanism can exist in realistic (asymmetric) models of atomic or molecular oscillatory chains. Also, we study the resonant interaction of conjugated nonlinear normal modes and prove a possibility of linearization of the equations of motion. The theoretical constructions developed in this paper are based on the concepts of "effective particles" and Limiting Phase Trajectories. In particular, an analytical description of energy exchange between the "effective particles" in the terms of non-smooth functions is presented. The analytical results are confirmed with numerical simulations.

An Investigation of Topography Modulated Low Level Moisture Convergence Patterns in the Southern Appalachians Using WRF

NASA Astrophysics Data System (ADS)

Wilson, A. M.; Duan, Y.; Barros, A.

2015-12-01

The Southern Appalachian Mountains (SAM) region is a biodiversity hot-spot that is vulnerable to land use/land cover changes due to its proximity to the rapidly growing population in the Southeast U.S. Persistent near surface moisture and associated microclimates observed in this region have been documented since the colonization of the area. The landform in this area, in particular in the inner mountain region, is highly complex with nested valleys and ridges. The geometry of the terrain causes distinct diurnal and seasonal local flow patterns that result in highly complex interactions of this low level moisture with meso- and synoptic-scale cyclones passing through the region. The Weather Research and Forecasting model (WRF) was used to conduct high resolution simulations of several case studies of warm season precipitation in the SAM with different synoptic-scale conditions to investigate this interaction between local and larger-scale flow patterns. The aim is to elucidate the microphysical interactions among these shallow orographic clouds and preexisting precipitating cloud systems and identify uncertainties in the model microphysics using in situ measurements. Findings show that ridge-valley precipitation gradients, in particular the "reverse" to the classical orographic effect observed in inner mountain valleys, is linked to horizontal heterogeneity in the vertical structure of low level cloud and precipitation promoted through landform controls on local flow. Moisture convergence patterns follow the peaks and valleys as represented by WRF terrain, and the topography effectively controls their timing and spatial structure. The simulations support the hypothesis that ridge-valley precipitation gradients, and in particular the reverse orographic enhancement effect in inner mountain valleys, is linked to horizontal heterogeneity in the vertical structure of low level clouds and precipitation promoted through landform controls on moisture convergence.

Frequency Response of a Protein to Local Conformational Perturbations

PubMed Central

Eren, Dilek; Alakent, Burak

2013-01-01

Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as Cα atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (<∼0.8 ns−1) not to attenuate the propagating signal and enhance the contribution of the side-chains to the dissipation of the signals. Employing Discrete Fourier Transform (DFT) to TMD simulation trajectories of 16 cycles of conformational transitions at periods of 1.2 to 5 ns yielded Cα displacements consistent with those obtained from crystal structures. Identification of the perturbed atomic variables by statistical t-tests on log-log scale spectral densities revealed the extent of signal propagation in PTP1B, while phase angles of the filtered trajectories at the fundamental frequency were used to cluster collectively fluctuating elements. Hydrophobic interactions were found to have a higher contribution to signal transduction between side-chains compared to the role of polar interactions. Most of in-phase fluctuating residues on the signaling pathway were found to have high identity among PTP domains, and located over a wide region of PTP1B including the allosteric site. Due to its simplicity and efficiency, the suggested technique may find wide applications in identification of signaling pathways of different proteins. PMID:24086121

Applicability of WRF-Lake System in Studying Reservoir-Induced Impacts on Local Climate: Case Study of Two Reservoirs with Contrasting Characteristics

NASA Astrophysics Data System (ADS)

Wang, F.; Zhu, D.; Ni, G.; Sun, T.

2017-12-01

Large reservoirs play a key role in regional hydrological cycles as well as in modulating the local climate. The emerging large reservoirs in concomitant with rapid hydropower exploitation in southwestern China warrant better understanding of their impacts on local and regional climates. One of the crucial pathways through which reservoirs impact the climate is lake-atmospheric interaction. Although such interactions have been widely studied with numeric weather prediction (NWP) models, an outstanding limitation across various NWPs resides on the poor thermodynamic representation of lakes. The recent version of Weather Research and Forecasting (WRF) system has been equipped with a one-dimensional lake model to better represent the thermodynamics of large water body and has been shown to enhance the its predication skill in the lake-atmospheric interaction. In this study, we further explore the applicability of the WRF-Lake system in two reservoirs with contrasting characteristics: Miyun Reservoir with an average depth of 30 meters in North China Plain, and Nuozhadu Reservoir with an average depth of 200 meters in the Tibetan Plateau Region. Driven by the high spatiotemporal resolution meteorological forcing data, the WRF-Lake system is used to simulate the water temperature and surface energy budgets of the two reservoirs after the evaluation against temperature observations. The simulated results show the WRF-Lake model can well predict the vertical profile of water temperature in Miyun Reservoir, but underestimates deep water temperature and overestimates surface temperature in the deeper Nuozhadu Reservoir. In addition, sensitivity analysis indicates the poor performance of the WRF-Lake system in Nuozhadu Reservoir could be attributed to the weak vertical mixing in the model, which can be improved by tuning the eddy diffusion coefficient ke . Keywords: reservoir-induced climatic impact; lake-atmospheric interaction; WRF-Lake system; hydropower exploitation

Kinetic Monte Carlo simulations of travelling pulses and spiral waves in the lattice Lotka-Volterra model.

PubMed

Makeev, Alexei G; Kurkina, Elena S; Kevrekidis, Ioannis G

2012-06-01

Kinetic Monte Carlo simulations are used to study the stochastic two-species Lotka-Volterra model on a square lattice. For certain values of the model parameters, the system constitutes an excitable medium: travelling pulses and rotating spiral waves can be excited. Stable solitary pulses travel with constant (modulo stochastic fluctuations) shape and speed along a periodic lattice. The spiral waves observed persist sometimes for hundreds of rotations, but they are ultimately unstable and break-up (because of fluctuations and interactions between neighboring fronts) giving rise to complex dynamic behavior in which numerous small spiral waves rotate and interact with each other. It is interesting that travelling pulses and spiral waves can be exhibited by the model even for completely immobile species, due to the non-local reaction kinetics.

Control Mechanisms of the Electron Heat Flux in the Solar Wind: Observations in Comparison to Numerical Simulations

NASA Astrophysics Data System (ADS)

Stverak, S.; Hellinger, P.; Landi, S.; Travnicek, P. M.; Maksimovic, M.

2017-12-01

Recent understanding of the heat transport and dissipation in the expanding solar wind propose number of complex control mechanisms down to the electron kinetic scales. We investigate the evolution of electron heat flux properties and constraints along the expansion using in situ observations from Helios spacecraft in comparison to numerical kinetic simulations. In particular we focus on the roles of Coulomb collisions and wave-particle interactions in shaping the electron velocity distribution functions and thus controlling the heat transported by the electron heat flux. We show the general evolution of the electron heat flux to be driven namely by the Coulomb collisions. Locally we demonstrate the wave-particle interactions related to the kinetic plasma instabilities to be providing effective constraints in case of extreme heat flux levels.

Anatomical education and surgical simulation based on the Chinese Visible Human: a three-dimensional virtual model of the larynx region.

PubMed

Liu, Kaijun; Fang, Binji; Wu, Yi; Li, Ying; Jin, Jun; Tan, Liwen; Zhang, Shaoxiang

2013-09-01

Anatomical knowledge of the larynx region is critical for understanding laryngeal disease and performing required interventions. Virtual reality is a useful method for surgical education and simulation. Here, we assembled segmented cross-section slices of the larynx region from the Chinese Visible Human dataset. The laryngeal structures were precisely segmented manually as 2D images, then reconstructed and displayed as 3D images in the virtual reality Dextrobeam system. Using visualization and interaction with the virtual reality modeling language model, a digital laryngeal anatomy instruction was constructed using HTML and JavaScript languages. The volume larynx models can thus display an arbitrary section of the model and provide a virtual dissection function. This networked teaching system of the digital laryngeal anatomy can be read remotely, displayed locally, and manipulated interactively.

Nonlinear interaction of kinetic Alfven wave and whistler: Turbulent spectra and anisotropic scaling

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

Kumar Dwivedi, Navin; Sharma, R. P.

2013-04-15

In this work, we are presenting the excitation of oblique propagating whistler wave as a consequence of nonlinear interaction between whistler wave and kinetic Alfven wave (KAW) in intermediate beta plasmas. Numerical simulation has been done to study the transient evolution of magnetic field structures of KAW when the nonlinearity arises due to ponderomotive effects by taking the adiabatic response of the background density. Weak oblique propagating whistler signals in these nonlinear plasma density filaments (produced by KAW localization) get amplified. The spectral indices of the power spectrum at different times are calculated with given initial conditions of the simulations.more » Anisotropic scaling laws for KAW and whistlers are presented. The relevance of the present investigation to solar wind turbulence and its acceleration is also pointed out.« less

Particle in cell simulation on plasma grating contrast enhancement induced by infrared laser pulse

NASA Astrophysics Data System (ADS)

Li, M.; Yuan, T.; Xu, Y. X.; Wang, J. X.; Luo, S. N.

2018-05-01

The dynamics of plasma grating contrast enhancement (PGCE) irradiated by an infrared laser pulse is investigated with one dimensional particle-in-cell simulation where field ionization and impact ionization are simultaneously considered for the first time. The numeric results show that the impact ionization dominates the PGCE process. Upon the interaction with the laser pulse, abundant free electrons are efficiently accelerated and subsequently triggered massive impact ionizations in the density ridges of the plasma grating for the higher local plasma energy density, which efficiently enhances the grating contrast. Besides the dynamic analysis of PGCE, we explore the parameter space of the incident infrared laser pulse to optimize the PGCE effect, which can provide useful guidance to experiments related to laser-plasma-grating interactions and may find applications in prolonging the duration of the plasma grating.

Consensus for linear multi-agent system with intermittent information transmissions using the time-scale theory

NASA Astrophysics Data System (ADS)

Taousser, Fatima; Defoort, Michael; Djemai, Mohamed

2016-01-01

This paper investigates the consensus problem for linear multi-agent system with fixed communication topology in the presence of intermittent communication using the time-scale theory. Since each agent can only obtain relative local information intermittently, the proposed consensus algorithm is based on a discontinuous local interaction rule. The interaction among agents happens at a disjoint set of continuous-time intervals. The closed-loop multi-agent system can be represented using mixed linear continuous-time and linear discrete-time models due to intermittent information transmissions. The time-scale theory provides a powerful tool to combine continuous-time and discrete-time cases and study the consensus protocol under a unified framework. Using this theory, some conditions are derived to achieve exponential consensus under intermittent information transmissions. Simulations are performed to validate the theoretical results.

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

Gu, L. L.; Guo, X. G., E-mail: xgguo@mail.sim.ac.cn; Fu, Z. L.

Strong and sharp photocurrent peak at longitudinal optical (LO) phonon frequency (8.87 THz) is found in GaAs/(Al,Ga)As terahertz quantum-well photodetectors (QWPs). Two mesa-structure terahertz QWPs with and without one-dimensional metal grating are fabricated to investigate the behavior of such photoresponse peak. The experimental and simulation results indicate that the photocurrent peak originates from a two-step process. First, at the LO phonon frequency, a large number of non-equilibrium LO phonons are excited by the incident electromagnetic field, and the electromagnetic energy is localized and enhanced in the thin multi-quantum-well layer. Second, through the Frohlich interaction, the localized electrons are excited tomore » continuum states by absorbing the non-equilibrium LO phonons, which leads to the strong photoresponse peak. This finding is useful for exploring strong light-matter interaction and realizing high sensitive terahertz photodetectors.« less

Solar wind/local interstellar medium interaction including charge exchange with neural hydrogen

NASA Technical Reports Server (NTRS)

Pauls, H. Louis; Zank, Gary P.

1995-01-01

We present results from a hydrodynamic model of the interaction of the solar wind with the local interstellar medium (LISM), self-consistently taking into account the effects of charge exchange between the plasma component and the interstellar neutrals. The simulation is fully time dependent, and is carried out in two or three dimensions, depending on whether the helio-latitudinal dependence of the solar wind speed and number density (both giving rise to three dimensional effects) are included. As a first approximation it is assumed that the neutral component of the flow can be described by a single, isotropic fluid. Clearly, this is not the actual situation, since charge exchange with the supersonic solar wind plasma in the region of the nose results in a 'second' neutral fluid propagating in the opposite direction as that of the LISM neutrals.

Complexity Induced Anisotropic Bimodal Intermittent Turbulence in Space Plasmas

NASA Technical Reports Server (NTRS)

Chang, Tom; Tam, Sunny W. Y.; Wu, Cheng-Chin

2004-01-01

The "physics of complexity" in space plasmas is the central theme of this exposition. It is demonstrated that the sporadic and localized interactions of magnetic coherent structures arising from the plasma resonances can be the source for the coexistence of nonpropagating spatiotemporal fluctuations and propagating modes. Non-Gaussian probability distribution functions of the intermittent fluctuations from direct numerical simulations are obtained and discussed. Power spectra and local intermittency measures using the wavelet analyses are presented to display the spottiness of the small-scale turbulent fluctuations and the non-uniformity of coarse-grained dissipation that can lead to magnetic topological reconfigurations. The technique of the dynamic renormalization group is applied to the study of the scaling properties of such type of multiscale fluctuations. Charged particle interactions with both the propagating and nonpropagating portions of the intermittent turbulence are also described.

Potential energy surface fitting by a statistically localized, permutationally invariant, local interpolating moving least squares method for the many-body potential: Method and application to N{sub 4}

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

Bender, Jason D.; Doraiswamy, Sriram; Candler, Graham V., E-mail: truhlar@umn.edu, E-mail: candler@aem.umn.edu

2014-02-07

Fitting potential energy surfaces to analytic forms is an important first step for efficient molecular dynamics simulations. Here, we present an improved version of the local interpolating moving least squares method (L-IMLS) for such fitting. Our method has three key improvements. First, pairwise interactions are modeled separately from many-body interactions. Second, permutational invariance is incorporated in the basis functions, using permutationally invariant polynomials in Morse variables, and in the weight functions. Third, computational cost is reduced by statistical localization, in which we statistically correlate the cutoff radius with data point density. We motivate our discussion in this paper with amore » review of global and local least-squares-based fitting methods in one dimension. Then, we develop our method in six dimensions, and we note that it allows the analytic evaluation of gradients, a feature that is important for molecular dynamics. The approach, which we call statistically localized, permutationally invariant, local interpolating moving least squares fitting of the many-body potential (SL-PI-L-IMLS-MP, or, more simply, L-IMLS-G2), is used to fit a potential energy surface to an electronic structure dataset for N{sub 4}. We discuss its performance on the dataset and give directions for further research, including applications to trajectory calculations.« less

Gyrokinetic turbulence: between idealized estimates and a detailed analysis of nonlinear energy transfers

NASA Astrophysics Data System (ADS)

Teaca, Bogdan; Jenko, Frank; Told, Daniel

2017-04-01

Using large resolution numerical simulations of gyrokinetic (GK) turbulence, spanning an interval ranging from the end of the fluid scales to the electron gyroradius, we study the energy transfers in the perpendicular direction for a proton-electron plasma in a slab equilibrium magnetic geometry. The plasma parameters employed here are relevant to kinetic Alfvén wave turbulence in solar wind conditions. In addition, we use an idealized test representation for the energy transfers between two scales, to aid our understanding of the diagnostics applicable to the nonlinear cascade in an infinite inertial range. For GK turbulence, a detailed analysis of nonlinear energy transfers that account for the separation of energy exchanging scales is performed. Starting from the study of the energy cascade and the scale locality problem, we show that the general nonlocal nature of GK turbulence, captured via locality functions, contains a subset of interactions that are deemed local, are scale invariant (i.e. a sign of asymptotic locality) and possess a locality exponent that can be recovered directly from measurements on the energy cascade. It is the first time that GK turbulence is shown to possess an asymptotic local component, even if the overall locality of interactions is nonlocal. The results presented here and their implications are discussed from the perspective of previous findings reported in the literature and the idea of universality of GK turbulence.

A DGTD method for the numerical modeling of the interaction of light with nanometer scale metallic structures taking into account non-local dispersion effects

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

Schmitt, Nikolai; Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder; Scheid, Claire

2016-07-01

The interaction of light with metallic nanostructures is increasingly attracting interest because of numerous potential applications. Sub-wavelength metallic structures, when illuminated with a frequency close to the plasma frequency of the metal, present resonances that cause extreme local field enhancements. Exploiting the latter in applications of interest requires a detailed knowledge about the occurring fields which can actually not be obtained analytically. For the latter mentioned reason, numerical tools are thus an absolute necessity. The insight they provide is very often the only way to get a deep enough understanding of the very rich physics at play. For the numericalmore » modeling of light-structure interaction on the nanoscale, the choice of an appropriate material model is a crucial point. Approaches that are adopted in a first instance are based on local (i.e. with no interaction between electrons) dispersive models, e.g. Drude or Drude–Lorentz models. From the mathematical point of view, when a time-domain modeling is considered, these models lead to an additional system of ordinary differential equations coupled to Maxwell's equations. However, recent experiments have shown that the repulsive interaction between electrons inside the metal makes the response of metals intrinsically non-local and that this effect cannot generally be overlooked. Technological achievements have enabled the consideration of metallic structures in a regime where such non-localities have a significant influence on the structures' optical response. This leads to an additional, in general non-linear, system of partial differential equations which is, when coupled to Maxwell's equations, significantly more difficult to treat. Nevertheless, dealing with a linearized non-local dispersion model already opens the route to numerous practical applications of plasmonics. In this work, we present a Discontinuous Galerkin Time-Domain (DGTD) method able to solve the system of Maxwell's equations coupled to a linearized non-local dispersion model relevant to plasmonics. While the method is presented in the general 3D case, numerical results are given for 2D simulation settings.« less

The Stokesian hydrodynamics of flexing, stretching filaments

NASA Astrophysics Data System (ADS)

Shelley, Michael J.; Ueda, Tetsuji

2000-11-01

A central element of many fundamental problems in physics and biology lies in the interaction of a viscous fluid with slender, elastic filaments. Examples arise in the dynamics of biological fibers, the motility of microscopic organisms, and in phase transitions of liquid crystals. When considering the dynamics on the scale of a single filament, the surrounding fluid can often be assumed to be inertialess and hence governed by the Stokes’ equations. A typical simplification then is to assume a local relation, along the filament, between the force per unit length exerted by the filament upon the fluid and the velocity of the filament. While this assumption can be justified through slender-body theory as the leading-order effect, this approximation is only logarithmically separated (in aspect ratio) from the next-order contribution capturing the first effects of non-local interactions mediated by the surrounding fluid; non-local interactions become increasingly important as a filament comes within proximity to itself, or another filament. Motivated by a pattern forming system in isotropic to smectic-A phase transitions, we consider the non-local Stokesian dynamics of a growing elastica immersed in a fluid. The non-local interactions of the filament with itself are included using a modification of the slender-body theory of Keller and Rubinow. This modification is asymptotically equivalent, and removes an instability of their formulation at small, unphysical length-scales. Within this system, the filament lives on a marginal stability boundary, driven by a continual process of growth and buckling. Repeated bucklings result in filament flex, which, coupled to the non-local interactions and mediated by elastic response, leads to the development of space-filling patterns. We develop numerical methods to solve this system accurately and efficiently, even in the presence of temporal stiffness and the close self-approach of the filament. While we have ignored many of the thermodynamic aspects of this system, our simulations show good qualitative agreement with experimental observations. Our results also suggest that non-locality, induced by the surrounding fluid, will be important to understanding the dynamics of related filament systems.

Examining System-Wide Impacts of Solar PV Control Systems with a Power Hardware-in-the-Loop Platform

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

Williams, Tess L.; Fuller, Jason C.; Schneider, Kevin P.

2014-06-08

High penetration levels of distributed solar PV power generation can lead to adverse power quality impacts, such as excessive voltage rise, voltage flicker, and reactive power values that result in unacceptable voltage levels. Advanced inverter control schemes have been developed that have the potential to mitigate many power quality concerns. However, local closed-loop control may lead to unintended behavior in deployed systems as complex interactions can occur between numerous operating devices. To enable the study of the performance of advanced control schemes in a detailed distribution system environment, a test platform has been developed that integrates Power Hardware-in-the-Loop (PHIL) withmore » concurrent time-series electric distribution system simulation. In the test platform, GridLAB-D, a distribution system simulation tool, runs a detailed simulation of a distribution feeder in real-time mode at the Pacific Northwest National Laboratory (PNNL) and supplies power system parameters at a point of common coupling. At the National Renewable Energy Laboratory (NREL), a hardware inverter interacts with grid and PV simulators emulating an operational distribution system. Power output from the inverters is measured and sent to PNNL to update the real-time distribution system simulation. The platform is described and initial test cases are presented. The platform is used to study the system-wide impacts and the interactions of inverter control modes—constant power factor and active Volt/VAr control—when integrated into a simulated IEEE 8500-node test feeder. We demonstrate that this platform is well-suited to the study of advanced inverter controls and their impacts on the power quality of a distribution feeder. Additionally, results are used to validate GridLAB-D simulations of advanced inverter controls.« less

Hands on + hands free: simulated on-call interaction.

PubMed

Fisher, James; Martin, Richard; Tate, David

2014-10-01

In hospital, doctors and nurses frequently discuss acutely unwell patients via the telephone. Telephone communication can be challenging, yet medical students receive little training in how to conduct such interactions. We aimed to provide a simple, innovative, simulation session to address this learning need for third-year medical students at Newcastle University. Groups of students were given a pager and a supervising tutor. Students responded to a 'bleep' from a nurse practitioner in a different room, who role-played a ward nurse concerned about a patient. Speakerphones were used, allowing the entire conversation to be audible. After the call, a student-led debriefing session took place. After the debriefing another student 'held' the bleep and a different scenario ensued. Following a resuscitation scenario, students made telephone contact with the medical registrar to hand over information pertaining to the case. Before and after the session, students rated their confidence in telephone interaction and handover using a 10-point Likert scale. Students also completed a feedback questionnaire. Fifty-four students attended the session. A statistically significant improvement in student confidence in telephone communication and handover was seen after the session. Free-text feedback highlighted that students had not received teaching on this previously, and that they welcomed opportunities to practise such skills within a controlled, safe environment. Simulation training can be costly, but speakerphones are cheap and readily available. Given the frequency of telephone interaction in hospital, we believe all medical students should receive telephone communication training. Locally, our department has now incorporated these teaching methods into simulation sessions elsewhere in the curriculum. Medical students receive little training in how to conduct [telephone] interactions. © 2014 John Wiley & Sons Ltd.

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

NASA Astrophysics Data System (ADS)

Rino, José Pedro; Borges, Denilson; Mota, Rita C.; Silva, Maurício A. P.

2008-05-01

Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.

Multilevel discretized random field models with 'spin' correlations for the simulation of environmental spatial data

NASA Astrophysics Data System (ADS)

Žukovič, Milan; Hristopulos, Dionissios T.

2009-02-01

A current problem of practical significance is how to analyze large, spatially distributed, environmental data sets. The problem is more challenging for variables that follow non-Gaussian distributions. We show by means of numerical simulations that the spatial correlations between variables can be captured by interactions between 'spins'. The spins represent multilevel discretizations of environmental variables with respect to a number of pre-defined thresholds. The spatial dependence between the 'spins' is imposed by means of short-range interactions. We present two approaches, inspired by the Ising and Potts models, that generate conditional simulations of spatially distributed variables from samples with missing data. Currently, the sampling and simulation points are assumed to be at the nodes of a regular grid. The conditional simulations of the 'spin system' are forced to respect locally the sample values and the system statistics globally. The second constraint is enforced by minimizing a cost function representing the deviation between normalized correlation energies of the simulated and the sample distributions. In the approach based on the Nc-state Potts model, each point is assigned to one of Nc classes. The interactions involve all the points simultaneously. In the Ising model approach, a sequential simulation scheme is used: the discretization at each simulation level is binomial (i.e., ± 1). Information propagates from lower to higher levels as the simulation proceeds. We compare the two approaches in terms of their ability to reproduce the target statistics (e.g., the histogram and the variogram of the sample distribution), to predict data at unsampled locations, as well as in terms of their computational complexity. The comparison is based on a non-Gaussian data set (derived from a digital elevation model of the Walker Lake area, Nevada, USA). We discuss the impact of relevant simulation parameters, such as the domain size, the number of discretization levels, and the initial conditions.

ARC+(Registered Trademark) and ARC PC Welding Simulators: Teach Welders with Virtual Interactive 3D Technologies

NASA Technical Reports Server (NTRS)

Choquet, Claude

2011-01-01

123 Certification Inc., a Montreal based company, has developed an innovative hands-on welding simulator solution to help build the welding workforce in the most simple way. The solution lies in virtual reality technology, which has been fully tested since the early 90's. President and founder of 123 Certification Inc., Mr. Claude Choquet Ing. Msc. IWE. acts as a bridge between the welding and the programming world. Working in these fields for more than 20 years. he has filed 12 patents world-wide for a gesture control platform with leading edge hardware related to simulation. In the summer of 2006. Mr Choquet was proud to be invited to the annual IIW International Weld ing Congress in Quebec City to launch the ARC+ welding simulator. A 100% virtual reality system and web based training center was developed to simulate multi process. multi-materiaL multi-position and multi pass welding. The simulator is intended to train welding students and apprentices in schools or industries. The welding simulator is composed of a real welding e[eetrode holder (SMAW-GTAW) and gun (GMAW-FCAW). a head mounted display (HMD), a 6 degrees of freedom tracking system for interaction between the user's hands and head. as well as external audio speakers. Both guns and HMD are interacting online and simultaneously. The welding simulation is based on the law of physics and empirical results from detailed analysis of a series of welding tests based on industrial applications tested over the last 20 years. The simulation runs in real-time, using a local logic network to determine the quality and shape of the created weld. These results are based on the orientation distance. and speed of the welding torch and depth of penetration. The welding process and resulting weld bc.1d are displayed in a virtual environment with screenplay interactive training modules. For review. weld quality and recorded process values can be displayed and diagnosed after welding. To help in the le.tming process, a learning curve for each student and each Virtual Welding Class'" can be plotted, for an instructor's review or a required third party evaluation.

Quenching and ram pressure stripping of simulated Milky Way satellite galaxies

NASA Astrophysics Data System (ADS)

Simpson, Christine; Grand, Robert; Gomez, Facundo; Marinacci, Federico; Pakmor, Rüdiger; Springel, Volker; Campbell, David; Frenk, Carlos; Auriga Project, Virgo Consortium

2018-01-01

We present predictions for the quenching of star formation in satellite galaxies of the Local Group from a suite of 30 cosmological zoom simulations of Milky Way-like host galaxies. The Auriga simulations resolve satellites down to the luminosity of the classical dwarf spheroidal galaxies of the Milky Way. We find strong mass-dependent and distance-dependent quenching signals, where dwarf systems beyond 600 kpc are only strongly quenched below a stellar mass of 107 M⊙. Ram pressure stripping appears to be the dominant quenching mechanism and 50% of quenched systems cease star formation within 1 Gyr of first infall. We demonstrate that systems within a host galaxy's R200 radius are comprised of two populations: (i) a first infall population that has entered the host halo within the past few Gyrs and (ii) a population of returning `backsplash' systems that have had a much more extended interaction with the host. Backsplash galaxies that do not return to the host galaxy by redshift zero exhibit quenching properties similar to galaxies within R200 and are distinct from other external systems. The simulated quenching trend with stellar mass has some tension with observations, but our simulations are able reproduce the range of quenching times measured from resolved stellar populations of Local Group dwarf galaxies.

Quenching and ram pressure stripping of simulated Milky Way satellite galaxies

NASA Astrophysics Data System (ADS)

Simpson, Christine M.; Grand, Robert J. J.; Gómez, Facundo A.; Marinacci, Federico; Pakmor, Rüdiger; Springel, Volker; Campbell, David J. R.; Frenk, Carlos S.

2018-07-01

We present predictions for the quenching of star formation in satellite galaxies of the Local Group from a suite of 30 cosmological zoom simulations of Milky Way-like host galaxies. The Auriga simulations resolve satellites down to the luminosity of the classical dwarf spheroidal galaxies of the Milky Way. We find strong mass-dependent and distance-dependent quenching signals, where dwarf systems beyond 600 kpc are only strongly quenched below a stellar mass of 107 M⊙. Ram pressure stripping appears to be the dominant quenching mechanism and 50 per cent of quenched systems cease star formation within 1 Gyr of first infall. We demonstrate that systems within a host galaxy's R200 radius are comprised of two populations: (i) a first infall population that has entered the host halo within the past few Gyrs and (ii) a population of returning `backsplash' systems that have had a much more extended interaction with the host. Backsplash galaxies that do not return to the host galaxy by redshift zero exhibit quenching properties similar to galaxies within R200 and are distinct from other external systems. The simulated quenching trend with stellar mass has some tension with observations, but our simulations are able reproduce the range of quenching times measured from resolved stellar populations of Local Group dwarf galaxies.

Quenching and ram pressure stripping of simulated Milky Way satellite galaxies

NASA Astrophysics Data System (ADS)

Simpson, Christine M.; Grand, Robert J. J.; Gómez, Facundo A.; Marinacci, Federico; Pakmor, Rüdiger; Springel, Volker; Campbell, David J. R.; Frenk, Carlos S.

2018-03-01

We present predictions for the quenching of star formation in satellite galaxies of the Local Group from a suite of 30 cosmological zoom simulations of Milky Way-like host galaxies. The Auriga simulations resolve satellites down to the luminosity of the classical dwarf spheroidal galaxies of the Milky Way. We find strong mass-dependent and distance-dependent quenching signals, where dwarf systems beyond 600 kpc are only strongly quenched below a stellar mass of 107 M⊙. Ram pressure stripping appears to be the dominant quenching mechanism and 50% of quenched systems cease star formation within 1 Gyr of first infall. We demonstrate that systems within a host galaxy's R200 radius are comprised of two populations: (i) a first infall population that has entered the host halo within the past few Gyrs and (ii) a population of returning `backsplash' systems that have had a much more extended interaction with the host. Backsplash galaxies that do not return to the host galaxy by redshift zero exhibit quenching properties similar to galaxies within R200 and are distinct from other external systems. The simulated quenching trend with stellar mass has some tension with observations, but our simulations are able reproduce the range of quenching times measured from resolved stellar populations of Local Group dwarf galaxies.

Estimating net drawdown resulting from episodic withdrawals at six well fields in the coastal plain physiographic province of Virginia

USGS Publications Warehouse

Focazio, M.J.; Speiran, G.K.

1993-01-01

The groundwater-flow system of the Virginia Coastal Plain consists of areally extensive and interconnected aquifers. Large, regionally coalescing cones of depression that are caused by large withdrawals of water are found in these aquifers. Local groundwater systems are affected by regional pumping, because of the interactions within the system of aquifers. Accordingly, these local systems are affected by regional groundwater flow and by spatial and temporal differences in withdrawals by various users. A geographic- information system was used to refine a regional groundwater-flow model around selected withdrawal centers. A method was developed in which drawdown maps that were simulated by the regional groundwater-flow model and the principle of superposition could be used to estimate drawdown at local sites. The method was applied to create drawdown maps in the Brightseat/Upper Potomac Aquifer for periods of 3, 6, 9, and 12 months for Chesapeake, Newport News, Norfolk, Portsmouth, Suffolk, and Virginia Beach, Virginia. Withdrawal rates were supplied by the individual localities and remained constant for each simulation period. This provides an efficient method by which the individual local groundwater users can determine the amount of drawdown produced by their wells in a groundwater system that is a water source for multiple users and that is affected by regional-flow systems.

Real-time ab initio KMC simulation of the self-assembly and sintering of bimetallic epitaxial nanoclusters: Au + Ag on Ag(100).

PubMed

Han, Yong; Liu, Da-Jiang; Evans, James W

2014-08-13

Far-from-equilibrium shape and structure evolution during formation and post-assembly sintering of bimetallic nanoclusters is extremely sensitive to the periphery diffusion and intermixing kinetics. Precise characterization of the many distinct local-environment-dependent diffusion barriers is achieved for epitaxial nanoclusters using density functional theory to assess interaction energies both with atoms at adsorption sites and at transition states. Kinetic Monte Carlo simulation incorporating these barriers then captures structure evolution on the appropriate time scale for two-dimensional core-ring and intermixed Au-Ag nanoclusters on Ag(100).

Real-Time Ab Initio KMC Simulation of the Self-Assembly and Sintering of Bimetallic Epitaxial Nanoclusters: Au + Ag on Ag(100)

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

Han, Yong; Liu, Da-Jiang; Evans, James W

2014-08-13

Far-from-equilibrium shape and structure evolution during formation and post-assembly sintering of bimetallic nanoclusters is extremely sensitive to the periphery diffusion and intermixing kinetics. Precise characterization of the many distinct local-environment-dependent diffusion barriers is achieved for epitaxial nanoclusters using density functional theory to assess interaction energies both with atoms at adsorption sites and at transition states. Kinetic Monte Carlo simulation incorporating these barriers then captures structure evolution on the appropriate time scale for two-dimensional core-ring and intermixed Au-Ag nanoclusters on Ag(100).

CesrTA Retarding Field Analyzer Modeling Results

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

Calvey, J.R.; Celata, C.M.; Crittenden, J.A.

2010-05-23

Retarding field analyzers (RFAs) provide an effective measure of the local electron cloud density and energy distribution. Proper interpretation of RFA data can yield information about the behavior of the cloud, as well as the surface properties of the instrumented vacuum chamber. However, due to the complex interaction of the cloud with the RFA itself, understanding these measurements can be nontrivial. This paper examines different methods for interpreting RFA data via cloud simulation programs. Techniques include postprocessing the output of a simulation code to predict the RFA response; and incorporating an RFA model into the cloud modeling program itself.

Tip-induced reduction of the resonant tunneling current on semiconductor surfaces.

PubMed

Jelínek, Pavel; Svec, Martin; Pou, Pablo; Perez, Ruben; Cháb, Vladimír

2008-10-24

We report scanning tunneling microscope measurements showing a substantial decrease of the current, almost to zero, on the Si(111)-(7x7) reconstruction in the near-to-contact region under low bias conditions. First principles simulations for the tip-sample interaction and transport calculations show that this effect is driven by the substantial local modification of the atomic and electronic structure of the surface. The chemical reactivity of the adatom dangling bond states that dominate the electronic density of states close to the Fermi level and their spatial localization result in a strong modification of the electronic current.

A Parallel Sliding Region Algorithm to Make Agent-Based Modeling Possible for a Large-Scale Simulation: Modeling Hepatitis C Epidemics in Canada.

PubMed

Wong, William W L; Feng, Zeny Z; Thein, Hla-Hla

2016-11-01

Agent-based models (ABMs) are computer simulation models that define interactions among agents and simulate emergent behaviors that arise from the ensemble of local decisions. ABMs have been increasingly used to examine trends in infectious disease epidemiology. However, the main limitation of ABMs is the high computational cost for a large-scale simulation. To improve the computational efficiency for large-scale ABM simulations, we built a parallelizable sliding region algorithm (SRA) for ABM and compared it to a nonparallelizable ABM. We developed a complex agent network and performed two simulations to model hepatitis C epidemics based on the real demographic data from Saskatchewan, Canada. The first simulation used the SRA that processed on each postal code subregion subsequently. The second simulation processed the entire population simultaneously. It was concluded that the parallelizable SRA showed computational time saving with comparable results in a province-wide simulation. Using the same method, SRA can be generalized for performing a country-wide simulation. Thus, this parallel algorithm enables the possibility of using ABM for large-scale simulation with limited computational resources.

Connection of the solar wind with the interstellar medium through numerical modeling

DOE PAGES

Heerikhuisen, J.; Zirnstein, E.; Kawamura, A. D.; ...

2013-06-13

In this article we investigate the interaction between the solar wind (SW) and the local interstellar medium (LISM) using spacecraft data and numerical simulations. In particular, we focus on neutral atom results from NASA's Interstellar Boundary EXplorer (IBEX) mission, and compare these with implementations of our neutral atom models that look at both the energetic neutral atoms (ENAs) which are created as hydrogen of LISM origin interacts with the heliosphere, as well as the transmission of interstellar Oxygen through the heliospheric interface. Lastly, the goal of this work is to better understand the global structure of the heliosphere and itsmore » interaction with the galaxy.« less

Structural transitions in vortex systems with anisotropic interactions

DOE PAGES

Olszewski, Maciej W.; Eskildsen, M. R.; Reichhardt, Charles; ...

2017-12-29

We introduce a model of vortices in type-II superconductors with a four-fold anisotropy in the vortex–vortex interaction potential. Using numerical simulations we show that the vortex lattice undergoes structural transitions as the anisotropy is increased, with a triangular lattice at low anisotropy, a rhombic intermediate state, and a square lattice for high anisotropy. In some cases we observe a multi-q state consisting of an Archimedean tiling that combines square and triangular local ordering. At very high anisotropy, domains of vortex chain states appear. We discuss how this model can be generalized to higher order anisotropy as well as its applicabilitymore » to other particle-based systems with anisotropic particle–particle interactions.« less

3D Geovisualization & Stylization to Manage Comprehensive and Participative Local Urban Plans

NASA Astrophysics Data System (ADS)

Brasebin, M.; Christophe, S.; Jacquinod, F.; Vinesse, A.; Mahon, H.

2016-10-01

3D geo-visualization is more and more used and appreciated to support public participation, and is generally used to present predesigned planned projects. Nevertheless, other participatory processes may benefit from such technology such as the elaboration of urban planning documents. In this article, we present one of the objectives of the PLU++ project: the design of a 3D geo-visualization system that eases the participation concerning local urban plans. Through a pluridisciplinary approach, it aims at covering the different aspects of such a system: the simulation of built configurations to represent regulation information, the efficient stylization of these objects to make people understand their meanings and the interaction between 3D simulation and stylization. The system aims at being adaptive according to the participation context and to the dynamic of the participation. It will offer the possibility to modify simulation results and the rendering styles of the 3D representations to support participation. The proposed 3D rendering styles will be used in a set of practical experiments in order to test and validate some hypothesis from past researches of the project members about 3D simulation, 3D semiotics and knowledge about uses.

Field-scale and wellbore modeling of compaction-induced casing failures

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

Hilbert, L.B. Jr.; Gwinn, R.L.; Moroney, T.A.

1999-06-01

Presented in this paper are the results and verification of field- and wellbore-scale large deformation, elasto-plastic, geomechanical finite element models of reservoir compaction and associated casing damage. The models were developed as part of a multidisciplinary team project to reduce the number of costly well failures in the diatomite reservoir of the South Belridge Field near Bakersfield, California. Reservoir compaction of high porosity diatomite rock induces localized shearing deformations on horizontal weak-rock layers and geologic unconformities. The localized shearing deformations result in casing damage or failure. Two-dimensional, field-scale finite element models were used to develop relationships between field operations, surfacemore » subsidence, and shear-induced casing damage. Pore pressures were computed for eighteen years of simulated production and water injection, using a three-dimensional reservoir simulator. The pore pressures were input to the two-dimensional geomechanical field-scale model. Frictional contact surfaces were used to model localized shear deformations. To capture the complex casing-cement-rock interaction that governs casing damage and failure, three-dimensional models of a wellbore were constructed, including a frictional sliding surface to model localized shear deformation. Calculations were compared to field data for verification of the models.« less

Local numerical modelling of ultrasonic guided waves in linear and nonlinear media

NASA Astrophysics Data System (ADS)

Packo, Pawel; Radecki, Rafal; Kijanka, Piotr; Staszewski, Wieslaw J.; Uhl, Tadeusz; Leamy, Michael J.

2017-04-01

Nonlinear ultrasonic techniques provide improved damage sensitivity compared to linear approaches. The combination of attractive properties of guided waves, such as Lamb waves, with unique features of higher harmonic generation provides great potential for characterization of incipient damage, particularly in plate-like structures. Nonlinear ultrasonic structural health monitoring techniques use interrogation signals at frequencies other than the excitation frequency to detect changes in structural integrity. Signal processing techniques used in non-destructive evaluation are frequently supported by modeling and numerical simulations in order to facilitate problem solution. This paper discusses known and newly-developed local computational strategies for simulating elastic waves, and attempts characterization of their numerical properties in the context of linear and nonlinear media. A hybrid numerical approach combining advantages of the Local Interaction Simulation Approach (LISA) and Cellular Automata for Elastodynamics (CAFE) is proposed for unique treatment of arbitrary strain-stress relations. The iteration equations of the method are derived directly from physical principles employing stress and displacement continuity, leading to an accurate description of the propagation in arbitrarily complex media. Numerical analysis of guided wave propagation, based on the newly developed hybrid approach, is presented and discussed in the paper for linear and nonlinear media. Comparisons to Finite Elements (FE) are also discussed.

Using the Weak-Temperature Gradient Approximation to Evaluate Parameterizations: An Example of the Transition From Suppressed to Active Convection

NASA Astrophysics Data System (ADS)

Daleu, C. L.; Plant, R. S.; Woolnough, S. J.

2017-10-01

Two single-column models are fully coupled via the weak-temperature gradient approach. The coupled-SCM is used to simulate the transition from suppressed to active convection under the influence of an interactive large-scale circulation. The sensitivity of this transition to the value of mixing entrainment within the convective parameterization is explored. The results from these simulations are compared with those from equivalent simulations using coupled cloud-resolving models. Coupled-column simulations over nonuniform surface forcing are used to initialize the simulations of the transition, in which the column with suppressed convection is forced to undergo a transition to active convection by changing the local and/or remote surface forcings. The direct contributions from the changes in surface forcing are to induce a weakening of the large-scale circulation which systematically modulates the transition. In the SCM, the contributions from the large-scale circulation are dominated by the heating effects, while in the CRM the heating and moistening effects are about equally divided. A transition time is defined as the time when the rain rate in the dry column is halfway to the value at equilibrium after the transition. For the control value of entrainment, the order of the transition times is identical to that obtained in the CRM, but the transition times are markedly faster. The locally forced transition is strongly delayed by a higher entrainment. A consequence is that for a 50% higher entrainment the transition times are reordered. The remotely forced transition remains fast while the locally forced transition becomes slow, compared to the CRM.

Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations.

PubMed

Saeedi, Marzieh; Lyubartsev, Alexander P; Jalili, Seifollah

2017-07-01

To provide insight into the molecular mechanisms of local anesthetic action, we have carried out an extensive investigation of two amide type local anesthetics, lidocaine and articaine in both charged and uncharged forms, interacting with DMPC lipid membrane. We have applied both standard molecular dynamics simulations and metadynamics simulations to provide a detailed description of the free energy landscape of anesthetics embedded in the lipid bilayer. The global minimum of the free energy surface (equilibrium position of anesthetics in the lipid membrane) occurred around 1nm of the bilayer center. The uncharged anesthetics show more affinity to bind to this region compared to the charged drugs. The binding free energy of uncharged lidocaine in the membrane (-30.3kJ/mol) is higher than uncharged articaine (-24.0kJ/mol), which is in good agreement with higher lipid solubility of lidocaine relative to the articaine. The octanol/water partition coefficient of uncharged drugs was also investigated using expanded ensemble simulations. In addition, complementary standard MD simulations were carried out to study the partitioning behavior of multiple anesthetics inside the lipid bilayer. The results obtained here are in line with previously reported simulations and suggest that the different forms of anesthetics induce different structural modifications in the lipid bilayer, which can provide new insights into their complex membrane translocation phenomena. Copyright © 2017 Elsevier B.V. All rights reserved.

Photonic simulation of entanglement growth and engineering after a spin chain quench.

PubMed

Pitsios, Ioannis; Banchi, Leonardo; Rab, Adil S; Bentivegna, Marco; Caprara, Debora; Crespi, Andrea; Spagnolo, Nicolò; Bose, Sougato; Mataloni, Paolo; Osellame, Roberto; Sciarrino, Fabio

2017-11-17

The time evolution of quantum many-body systems is one of the most important processes for benchmarking quantum simulators. The most curious feature of such dynamics is the growth of quantum entanglement to an amount proportional to the system size (volume law) even when interactions are local. This phenomenon has great ramifications for fundamental aspects, while its optimisation clearly has an impact on technology (e.g., for on-chip quantum networking). Here we use an integrated photonic chip with a circuit-based approach to simulate the dynamics of a spin chain and maximise the entanglement generation. The resulting entanglement is certified by constructing a second chip, which measures the entanglement between multiple distant pairs of simulated spins, as well as the block entanglement entropy. This is the first photonic simulation and optimisation of the extensive growth of entanglement in a spin chain, and opens up the use of photonic circuits for optimising quantum devices.

Tunable Electron-Electron Interactions in LaAlO 3 / SrTiO 3 Nanostructures

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

Cheng, Guanglei; Tomczyk, Michelle; Tacla, Alexandre B.

The interface between the two complex oxides LaAlO 3 and SrTiO 3 has remarkable properties that can be locally reconfigured between conducting and insulating states using a conductive atomic force microscope. Prior investigations of “sketched” quantum dot devices revealed a phase in which electrons form pairs, implying a strongly attractive electron-electron interaction. Here, we show that these devices with strong electron-electron interactions can exhibit a gate-tunable transition from a pair-tunneling regime to a single-electron (Andreev bound state) tunneling regime where the interactions become repulsive. The electron-electron interaction sign change is associated with a Lifshitz transition where the d xz andmore » d yz bands start to become occupied. This electronically tunable electron-electron interaction, combined with the nanoscale reconfigurability of this system, provides an interesting starting point towards solid-state quantum simulation.« less

Dark and antidark soliton interactions in the nonlocal nonlinear Schrödinger equation with the self-induced parity-time-symmetric potential.

PubMed

Li, Min; Xu, Tao

2015-03-01

Via the Nth Darboux transformation, a chain of nonsingular localized-wave solutions is derived for a nonlocal nonlinear Schrödinger equation with the self-induced parity-time (PT) -symmetric potential. It is found that the Nth iterated solution in general exhibits a variety of elastic interactions among 2N solitons on a continuous-wave background and each interacting soliton could be the dark or antidark type. The interactions with an arbitrary odd number of solitons can also be obtained under different degenerate conditions. With N=1 and 2, the two-soliton and four-soliton interactions and their various degenerate cases are discussed in the asymptotic analysis. Numerical simulations are performed to support the analytical results, and the stability analysis indicates that the PT-symmetry breaking can also destroy the stability of the soliton interactions.

Tunable Electron-Electron Interactions in LaAlO 3 / SrTiO 3 Nanostructures

DOE PAGES

Cheng, Guanglei; Tomczyk, Michelle; Tacla, Alexandre B.; ...

2016-12-01

The interface between the two complex oxides LaAlO 3 and SrTiO 3 has remarkable properties that can be locally reconfigured between conducting and insulating states using a conductive atomic force microscope. Prior investigations of “sketched” quantum dot devices revealed a phase in which electrons form pairs, implying a strongly attractive electron-electron interaction. Here, we show that these devices with strong electron-electron interactions can exhibit a gate-tunable transition from a pair-tunneling regime to a single-electron (Andreev bound state) tunneling regime where the interactions become repulsive. The electron-electron interaction sign change is associated with a Lifshitz transition where the d xz andmore » d yz bands start to become occupied. This electronically tunable electron-electron interaction, combined with the nanoscale reconfigurability of this system, provides an interesting starting point towards solid-state quantum simulation.« less

The Umbra Simulation and Integration Framework Applied to Emergency Response Training

NASA Technical Reports Server (NTRS)

Hamilton, Paul Lawrence; Britain, Robert

2010-01-01

The Mine Emergency Response Interactive Training Simulation (MERITS) is intended to prepare personnel to manage an emergency in an underground coal mine. The creation of an effective training environment required realistic emergent behavior in response to simulation events and trainee interventions, exploratory modification of miner behavior rules, realistic physics, and incorporation of legacy code. It also required the ability to add rich media to the simulation without conflicting with normal desktop security settings. Our Umbra Simulation and Integration Framework facilitated agent-based modeling of miners and rescuers and made it possible to work with subject matter experts to quickly adjust behavior through script editing, rather than through lengthy programming and recompilation. Integration of Umbra code with the WebKit browser engine allowed the use of JavaScript-enabled local web pages for media support. This project greatly extended the capabilities of Umbra in support of training simulations and has implications for simulations that combine human behavior, physics, and rich media.

TRENTOOL: A Matlab open source toolbox to analyse information flow in time series data with transfer entropy

PubMed Central

2011-01-01

Background Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present. Results In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected. Conclusions TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox. PMID:22098775

TRENTOOL: a Matlab open source toolbox to analyse information flow in time series data with transfer entropy.

PubMed

Lindner, Michael; Vicente, Raul; Priesemann, Viola; Wibral, Michael

2011-11-18

Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present. In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected. TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox.

Premelting, fluctuations, and coarse-graining of water-ice interfaces.

PubMed

Limmer, David T; Chandler, David

2014-11-14

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Premelting, fluctuations, and coarse-graining of water-ice interfaces

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2014-11-01

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Correlation range in a supercooled liquid via Green-Kubo expression for viscosity, local atomic stresses, and MD simulations

NASA Astrophysics Data System (ADS)

Levashov, Valentin A.; Egami, Takeshi; Morris, James R.

2009-03-01

We present a new approach to the issue of correlation range in supercooled liquids based on Green-Kubo expression for viscosity. The integrand of this expression is the average stress-stress autocorrelation function. This correlation function could be rewritten in terms of correlations among local atomic stresses at different times and distances. The features of the autocorrelation function decay with time depend on temperature and correlation range. Through this approach we can study the development of spatial correlation with time, thus directly addressing the question of dynamic heterogeneity. We performed MD simulations on a single component system of particles interacting through short range pair potential. Our results indicate that even above the crossover temperature correlations extend well beyond the nearest neighbors. Surprisingly we found that the system size effects exist even on relatively large systems. We also address the role of diffusion in decay of stress-stress correlation function.

Researching a local heroin market as a complex adaptive system.

PubMed

Hoffer, Lee D; Bobashev, Georgiy; Morris, Robert J

2009-12-01

This project applies agent-based modeling (ABM) techniques to better understand the operation, organization, and structure of a local heroin market. The simulation detailed was developed using data from an 18-month ethnographic case study. The original research, collected in Denver, CO during the 1990s, represents the historic account of users and dealers who operated in the Larimer area heroin market. Working together, the authors studied the behaviors of customers, private dealers, street-sellers, brokers, and the police, reflecting the core elements pertaining to how the market operated. After evaluating the logical consistency between the data and agent behaviors, simulations scaled-up interactions to observe their aggregated outcomes. While the concept and findings from this study remain experimental, these methods represent a novel way in which to understand illicit drug markets and the dynamic adaptations and outcomes they generate. Extensions of this research perspective, as well as its strengths and limitations, are discussed.

Fast numerical methods for simulating large-scale integrate-and-fire neuronal networks.

PubMed

Rangan, Aaditya V; Cai, David

2007-02-01

We discuss numerical methods for simulating large-scale, integrate-and-fire (I&F) neuronal networks. Important elements in our numerical methods are (i) a neurophysiologically inspired integrating factor which casts the solution as a numerically tractable integral equation, and allows us to obtain stable and accurate individual neuronal trajectories (i.e., voltage and conductance time-courses) even when the I&F neuronal equations are stiff, such as in strongly fluctuating, high-conductance states; (ii) an iterated process of spike-spike corrections within groups of strongly coupled neurons to account for spike-spike interactions within a single large numerical time-step; and (iii) a clustering procedure of firing events in the network to take advantage of localized architectures, such as spatial scales of strong local interactions, which are often present in large-scale computational models-for example, those of the primary visual cortex. (We note that the spike-spike corrections in our methods are more involved than the correction of single neuron spike-time via a polynomial interpolation as in the modified Runge-Kutta methods commonly used in simulations of I&F neuronal networks.) Our methods can evolve networks with relatively strong local interactions in an asymptotically optimal way such that each neuron fires approximately once in [Formula: see text] operations, where N is the number of neurons in the system. We note that quantifications used in computational modeling are often statistical, since measurements in a real experiment to characterize physiological systems are typically statistical, such as firing rate, interspike interval distributions, and spike-triggered voltage distributions. We emphasize that it takes much less computational effort to resolve statistical properties of certain I&F neuronal networks than to fully resolve trajectories of each and every neuron within the system. For networks operating in realistic dynamical regimes, such as strongly fluctuating, high-conductance states, our methods are designed to achieve statistical accuracy when very large time-steps are used. Moreover, our methods can also achieve trajectory-wise accuracy when small time-steps are used.

Simulating highly nonlocal Hamiltonians with less nonlocal Hamiltonians

NASA Astrophysics Data System (ADS)

Subasi, Yigit; Jarzynski, Christopher

The need for Hamiltonians with many-body interactions arises in various applications of quantum computing. However, interactions beyond two-body are difficult to realize experimentally. Perturbative gadgets were introduced to obtain arbitrary many-body effective interactions using Hamiltonians with two-body interactions only. Although valid for arbitrary k-body interactions, their use is limited to small k because the strength of interaction is k'th order in perturbation theory. Here we develop a nonperturbative technique for obtaining effective k-body interactions using Hamiltonians consisting of at most l-body interactions with l < k . This technique works best for Hamiltonians with a few interactions with very large k and can be used together with perturbative gadgets to embed Hamiltonians of considerable complexity in proper subspaces of two-local Hamiltonians. We describe how our technique can be implemented in a hybrid (gate-based and adiabatic) as well as solely adiabatic quantum computing scheme. We gratefully acknowledge financial support from the Lockheed Martin Corporation under Contract U12001C.

Toward Rigorous Parameterization of Underconstrained Neural Network Models Through Interactive Visualization and Steering of Connectivity Generation

PubMed Central

Nowke, Christian; Diaz-Pier, Sandra; Weyers, Benjamin; Hentschel, Bernd; Morrison, Abigail; Kuhlen, Torsten W.; Peyser, Alexander

2018-01-01

Simulation models in many scientific fields can have non-unique solutions or unique solutions which can be difficult to find. Moreover, in evolving systems, unique final state solutions can be reached by multiple different trajectories. Neuroscience is no exception. Often, neural network models are subject to parameter fitting to obtain desirable output comparable to experimental data. Parameter fitting without sufficient constraints and a systematic exploration of the possible solution space can lead to conclusions valid only around local minima or around non-minima. To address this issue, we have developed an interactive tool for visualizing and steering parameters in neural network simulation models. In this work, we focus particularly on connectivity generation, since finding suitable connectivity configurations for neural network models constitutes a complex parameter search scenario. The development of the tool has been guided by several use cases—the tool allows researchers to steer the parameters of the connectivity generation during the simulation, thus quickly growing networks composed of multiple populations with a targeted mean activity. The flexibility of the software allows scientists to explore other connectivity and neuron variables apart from the ones presented as use cases. With this tool, we enable an interactive exploration of parameter spaces and a better understanding of neural network models and grapple with the crucial problem of non-unique network solutions and trajectories. In addition, we observe a reduction in turn around times for the assessment of these models, due to interactive visualization while the simulation is computed. PMID:29937723

How curvature-generating proteins build scaffolds on membrane nanotubes

PubMed Central

Evergren, Emma; Golushko, Ivan; Prévost, Coline; Renard, Henri-François; Johannes, Ludger; McMahon, Harvey T.; Lorman, Vladimir; Voth, Gregory A.; Bassereau, Patricia

2016-01-01

Bin/Amphiphysin/Rvs (BAR) domain proteins control the curvature of lipid membranes in endocytosis, trafficking, cell motility, the formation of complex subcellular structures, and many other cellular phenomena. They form 3D assemblies that act as molecular scaffolds to reshape the membrane and alter its mechanical properties. It is unknown, however, how a protein scaffold forms and how BAR domains interact in these assemblies at protein densities relevant for a cell. In this work, we use various experimental, theoretical, and simulation approaches to explore how BAR proteins organize to form a scaffold on a membrane nanotube. By combining quantitative microscopy with analytical modeling, we demonstrate that a highly curving BAR protein endophilin nucleates its scaffolds at the ends of a membrane tube, contrary to a weaker curving protein centaurin, which binds evenly along the tube’s length. Our work implies that the nature of local protein–membrane interactions can affect the specific localization of proteins on membrane-remodeling sites. Furthermore, we show that amphipathic helices are dispensable in forming protein scaffolds. Finally, we explore a possible molecular structure of a BAR-domain scaffold using coarse-grained molecular dynamics simulations. Together with fluorescence microscopy, the simulations show that proteins need only to cover 30–40% of a tube’s surface to form a rigid assembly. Our work provides mechanical and structural insights into the way BAR proteins may sculpt the membrane as a high-order cooperative assembly in important biological processes. PMID:27655892

Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

NASA Astrophysics Data System (ADS)

Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

2011-09-01

Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

Differential influences of local subpopulations on regional diversity and differentiation for greater sage-grouse (Centrocercus urophasianus)

USGS Publications Warehouse

Row, Jeffery R.; Oyler-McCance, Sara J.; Fedy, Brad C.

2016-01-01

The distribution of spatial genetic variation across a region can shape evolutionary dynamics and impact population persistence. Local population dynamics and among-population dispersal rates are strong drivers of this spatial genetic variation, yet for many species we lack a clear understanding of how these population processes interact in space to shape within-species genetic variation. Here, we used extensive genetic and demographic data from 10 subpopulations of greater sage-grouse to parameterize a simulated approximate Bayesian computation (ABC) model and (i) test for regional differences in population density and dispersal rates for greater sage-grouse subpopulations in Wyoming, and (ii) quantify how these differences impact subpopulation regional influence on genetic variation. We found a close match between observed and simulated data under our parameterized model and strong variation in density and dispersal rates across Wyoming. Sensitivity analyses suggested that changes in dispersal (via landscape resistance) had a greater influence on regional differentiation, whereas changes in density had a greater influence on mean diversity across all subpopulations. Local subpopulations, however, varied in their regional influence on genetic variation. Decreases in the size and dispersal rates of central populations with low overall and net immigration (i.e. population sources) had the greatest negative impact on genetic variation. Overall, our results provide insight into the interactions among demography, dispersal and genetic variation and highlight the potential of ABC to disentangle the complexity of regional population dynamics and project the genetic impact of changing conditions.

Complexity and Intermittent Turbulence in Space Plasmas

NASA Technical Reports Server (NTRS)

Chang, Tom; Tam, Sunny W. Y.; Wu, Cheng-Chin

2004-01-01

Sporadic and localized interactions of coherent structures arising from plasma resonances can be the origin of "complexity" of the coexistence of non- propagating spatiotemporal fluctuations and propagating modes in space plasmas. Numerical simulation results are presented to demonstrate the intermittent character of the non-propagating fluctuations. The technique of the dynamic renormalization-group is introduced and applied to the study of scale invariance of such type of multiscale fluctuations. We also demonstrate that the particle interactions with the intermittent turbulence can lead to the efficient energization of the plasma populations. An example related to the ion acceleration processes in the auroral zone is provided.

Discrete Particle Method for Simulating Hypervelocity Impact Phenomena.

PubMed

Watson, Erkai; Steinhauser, Martin O

2017-04-02

In this paper, we introduce a computational model for the simulation of hypervelocity impact (HVI) phenomena which is based on the Discrete Element Method (DEM). Our paper constitutes the first application of DEM to the modeling and simulating of impact events for velocities beyond 5 kms -1 . We present here the results of a systematic numerical study on HVI of solids. For modeling the solids, we use discrete spherical particles that interact with each other via potentials. In our numerical investigations we are particularly interested in the dynamics of material fragmentation upon impact. We model a typical HVI experiment configuration where a sphere strikes a thin plate and investigate the properties of the resulting debris cloud. We provide a quantitative computational analysis of the resulting debris cloud caused by impact and a comprehensive parameter study by varying key parameters of our model. We compare our findings from the simulations with recent HVI experiments performed at our institute. Our findings are that the DEM method leads to very stable, energy-conserving simulations of HVI scenarios that map the experimental setup where a sphere strikes a thin plate at hypervelocity speed. Our chosen interaction model works particularly well in the velocity range where the local stresses caused by impact shock waves markedly exceed the ultimate material strength.

Discrete Particle Method for Simulating Hypervelocity Impact Phenomena

PubMed Central

Watson, Erkai; Steinhauser, Martin O.

2017-01-01

In this paper, we introduce a computational model for the simulation of hypervelocity impact (HVI) phenomena which is based on the Discrete Element Method (DEM). Our paper constitutes the first application of DEM to the modeling and simulating of impact events for velocities beyond 5 kms−1. We present here the results of a systematic numerical study on HVI of solids. For modeling the solids, we use discrete spherical particles that interact with each other via potentials. In our numerical investigations we are particularly interested in the dynamics of material fragmentation upon impact. We model a typical HVI experiment configuration where a sphere strikes a thin plate and investigate the properties of the resulting debris cloud. We provide a quantitative computational analysis of the resulting debris cloud caused by impact and a comprehensive parameter study by varying key parameters of our model. We compare our findings from the simulations with recent HVI experiments performed at our institute. Our findings are that the DEM method leads to very stable, energy–conserving simulations of HVI scenarios that map the experimental setup where a sphere strikes a thin plate at hypervelocity speed. Our chosen interaction model works particularly well in the velocity range where the local stresses caused by impact shock waves markedly exceed the ultimate material strength. PMID:28772739

Introducing seasonal hydro-meteorological forecasts in local water management. First reflections from the Messara site, Crete, Greece.

NASA Astrophysics Data System (ADS)

Koutroulis, Aristeidis; Grillakis, Manolis; Tsanis, Ioannis

2017-04-01

Seasonal prediction is recently at the center of the forecasting research efforts, especially for regions that are projected to be severely affected by global warming. The value of skillful seasonal forecasts can be considerable for many sectors and especially for the agricultural in which water users and managers can benefit to better anticipate against drought conditions. Here we present the first reflections from the user/stakeholder interactions and the design of a tailored drought decision support system in an attempt to bring seasonal predictions into local practice for the Messara valley located in the central-south area of Crete, Greece. Findings from interactions with the users and stakeholders reveal that although long range and seasonal predictions are not used, there is a strong interest for this type of information. The increase in the skill of short range weather predictions is also of great interest. The drought monitoring and prediction tool under development that support local water and agricultural management will include (a) sources of skillful short to medium term forecast information, (b) tailored drought monitoring and forecasting indices for the local groundwater aquifer and rain-fed agriculture, and (c) seasonal inflow forecasts for the local dam through hydrologic simulation to support management of freshwater resources and drought impacts on irrigated agriculture.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Regional Climate Simulations over North America: Interaction of Local Processes with Improved Large-Scale Flow.

NASA Astrophysics Data System (ADS)

Miguez-Macho, Gonzalo; Stenchikov, Georgiy L.; Robock, Alan

2005-04-01

The reasons for biases in regional climate simulations were investigated in an attempt to discern whether they arise from deficiencies in the model parameterizations or are due to dynamical problems. Using the Regional Atmospheric Modeling System (RAMS) forced by the National Centers for Environmental Prediction-National Center for Atmospheric Research reanalysis, the detailed climate over North America at 50-km resolution for June 2000 was simulated. First, the RAMS equations were modified to make them applicable to a large region, and its turbulence parameterization was corrected. The initial simulations showed large biases in the location of precipitation patterns and surface air temperatures. By implementing higher-resolution soil data, soil moisture and soil temperature initialization, and corrections to the Kain-Fritch convective scheme, the temperature biases and precipitation amount errors could be removed, but the precipitation location errors remained. The precipitation location biases could only be improved by implementing spectral nudging of the large-scale (wavelength of 2500 km) dynamics in RAMS. This corrected for circulation errors produced by interactions and reflection of the internal domain dynamics with the lateral boundaries where the model was forced by the reanalysis.

Molecular Dynamics Simulations of KirBac1.1 Mutants Reveal Global Gating Changes of Kir Channels.

PubMed

Linder, Tobias; Wang, Shizhen; Zangerl-Plessl, Eva-Maria; Nichols, Colin G; Stary-Weinzinger, Anna

2015-04-27

Prokaryotic inwardly rectifying (KirBac) potassium channels are homologous to mammalian Kir channels. Their activity is controlled by dynamical conformational changes that regulate ion flow through a central pore. Understanding the dynamical rearrangements of Kir channels during gating requires high-resolution structure information from channels crystallized in different conformations and insight into the transition steps, which are difficult to access experimentally. In this study, we use MD simulations on wild type KirBac1.1 and an activatory mutant to investigate activation gating of KirBac channels. Full atomistic MD simulations revealed that introducing glutamate in position 143 causes significant widening at the helix bundle crossing gate, enabling water flux into the cavity. Further, global rearrangements including a twisting motion as well as local rearrangements at the subunit interface in the cytoplasmic domain were observed. These structural rearrangements are similar to recently reported KirBac3.1 crystal structures in closed and open conformation, suggesting that our simulations capture major conformational changes during KirBac1.1 opening. In addition, an important role of protein-lipid interactions during gating was observed. Slide-helix and C-linker interactions with lipids were strengthened during activation gating.

Deformation of Soft Tissue and Force Feedback Using the Smoothed Particle Hydrodynamics

PubMed Central

Liu, Xuemei; Wang, Ruiyi; Li, Yunhua; Song, Dongdong

2015-01-01

We study the deformation and haptic feedback of soft tissue in virtual surgery based on a liver model by using a force feedback device named PHANTOM OMNI developed by SensAble Company in USA. Although a significant amount of research efforts have been dedicated to simulating the behaviors of soft tissue and implementing force feedback, it is still a challenging problem. This paper introduces a kind of meshfree method for deformation simulation of soft tissue and force computation based on viscoelastic mechanical model and smoothed particle hydrodynamics (SPH). Firstly, viscoelastic model can present the mechanical characteristics of soft tissue which greatly promotes the realism. Secondly, SPH has features of meshless technique and self-adaption, which supply higher precision than methods based on meshes for force feedback computation. Finally, a SPH method based on dynamic interaction area is proposed to improve the real time performance of simulation. The results reveal that SPH methodology is suitable for simulating soft tissue deformation and force feedback calculation, and SPH based on dynamic local interaction area has a higher computational efficiency significantly compared with usual SPH. Our algorithm has a bright prospect in the area of virtual surgery. PMID:26417380

Hybrid local-order mechanism for inversion symmetry breaking

NASA Astrophysics Data System (ADS)

Wolpert, Emma H.; Overy, Alistair R.; Thygesen, Peter M. M.; Simonov, Arkadiy; Senn, Mark S.; Goodwin, Andrew L.

2018-04-01

Using classical Monte Carlo simulations, we study a simple statistical mechanical model of relevance to the emergence of polarization from local displacements on the square and cubic lattices. Our model contains two key ingredients: a Kitaev-like orientation-dependent interaction between nearest neighbors and a steric term that acts between next-nearest neighbors. Taken by themselves, each of these two ingredients is incapable of driving long-range symmetry breaking, despite the presence of a broad feature in the corresponding heat-capacity functions. Instead, each component results in a "hidden" transition on cooling to a manifold of degenerate states; the two manifolds are different in the sense that they reflect distinct types of local order. Remarkably, their intersection, i.e., the ground state when both interaction terms are included in the Hamiltonian, supports a spontaneous polarization. In this way, our study demonstrates how local-order mechanisms might be combined to break global inversion symmetry in a manner conceptually similar to that operating in the "hybrid" improper ferroelectrics. We discuss the relevance of our analysis to the emergence of spontaneous polarization in well-studied ferroelectrics such as BaTiO3 and KNbO3.

Galaxy properties and the cosmic web in simulations

NASA Astrophysics Data System (ADS)

Metuki, Ofer; Libeskind, Noam I.; Hoffman, Yehuda; Crain, Robert A.; Theuns, Tom

2015-01-01

We seek to understand the relationship between galaxy properties and their local environment, which calls for a proper formulation of the notion of environment. We analyse the Galaxies-Intergalactic Medium Interaction Calculation suite of cosmological hydrodynamical simulations within the framework of the cosmic web as formulated by Hoffman et al., focusing on properties of simulated dark matter haloes and luminous galaxies with respect to voids, sheets, filaments, and knots - the four elements of the cosmic web. We find that the mass functions of haloes depend on environment, which drives other environmental dependence of galaxy formation. The web shapes the halo mass function, and through the strong dependence of the galaxy properties on the mass of their host haloes, it also shapes the galaxy-(web) environment dependence.

A comparison of random draw and locally neutral models for the avifauna of an English woodland.

PubMed

Dolman, Andrew M; Blackburn, Tim M

2004-06-03

Explanations for patterns observed in the structure of local assemblages are frequently sought with reference to interactions between species, and between species and their local environment. However, analyses of null models, where non-interactive local communities are assembled from regional species pools, have demonstrated that much of the structure of local assemblages remains in simulated assemblages where local interactions have been excluded. Here we compare the ability of two null models to reproduce the breeding bird community of Eastern Wood, a 16-hectare woodland in England, UK. A random draw model, in which there is complete annual replacement of the community by immigrants from the regional pool, is compared to a locally neutral community model, in which there are two additional parameters describing the proportion of the community replaced annually (per capita death rate) and the proportion of individuals recruited locally rather than as immigrants from the regional pool. Both the random draw and locally neutral model are capable of reproducing with significant accuracy several features of the observed structure of the annual Eastern Wood breeding bird community, including species relative abundances, species richness and species composition. The two additional parameters present in the neutral model result in a qualitatively more realistic representation of the Eastern Wood breeding bird community, particularly of its dynamics through time. The fact that these parameters can be varied, allows for a close quantitative fit between model and observed communities to be achieved, particularly with respect to annual species richness and species accumulation through time. The presence of additional free parameters does not detract from the qualitative improvement in the model and the neutral model remains a model of local community structure that is null with respect to species differences at the local scale. The ability of this locally neutral model to describe a larger number of woodland bird communities with either little variation in its parameters or with variation explained by features local to the woods themselves (such as the area and isolation of a wood) will be a key subsequent test of its relevance.

A local quasicontinuum method for 3D multilattice crystalline materials: Application to shape-memory alloys

NASA Astrophysics Data System (ADS)

Sorkin, V.; Elliott, R. S.; Tadmor, E. B.

2014-07-01

The quasicontinuum (QC) method, in its local (continuum) limit, is applied to materials with a multilattice crystal structure. Cauchy-Born (CB) kinematics, which accounts for the shifts of the crystal motif, is used to relate atomic motions to continuum deformation gradients. To avoid failures of CB kinematics, QC is augmented with a phonon stability analysis that detects lattice period extensions and identifies the minimum required periodic cell size. This approach is referred to as Cascading Cauchy-Born kinematics (CCB). In this paper, the method is described and developed. It is then used, along with an effective interaction potential (EIP) model for shape-memory alloys, to simulate the shape-memory effect and pseudoelasticity in a finite specimen. The results of these simulations show that (i) the CCB methodology is an essential tool that is required in order for QC-type simulations to correctly capture the first-order phase transitions responsible for these material behaviors, and (ii) that the EIP model adopted in this work coupled with the QC/CCB methodology is capable of predicting the characteristic behavior found in shape-memory alloys.

Vortex jump behavior in coupled nanomagnetic heterostructures

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

Zhang, S.; Petford-Long, A. K.; Heinonen, O.

2014-11-26

The spin configuration and magnetic behavior in patterned nanostructures can be controlled by manipulating the interplay between the competing energy terms. This in turn requires fundamental knowledge of the magnetic interactions at the local nanometer scale. Here in this article, we report on the spin structure and magnetization behavior of patterned discs containing exchange coupled ferromagnetic layers with additional exchange bias to an antiferromagnetic layer. The magnetization reversal was explored by direct local visualization of the domain behavior using in-situ Lorentz transmission electron microscopy, from which quantitative magnetic induction maps were reconstructed. The roles of the main competing energy termsmore » were elucidated and the reversal mechanism was identified as a coupled phenomenon of incoherent rotation in the exchange-biased layer and localized vortex nucleation and discontinuous propagation in the free layer, including an anomalous jump in the trajectory. The observations were supported by micromagnetic simulations and modeled phase shift simulations. In conclusion, the work presented here provides fundamental insights into opportunities for macroscopic control of the energy landscape of magnetic heterostructures for functional applications.« less

Direct numerical simulations of flow-chemistry interactions in statistically turbulent premixed flames

NASA Astrophysics Data System (ADS)

Arias, Paul; Uranakar, Harshavardhana; Chaudhuri, Swetaprovo; Im, Hong

2015-11-01

The effects of Damköhler number and Karlovitz number on the flame dynamics of three-dimensional statistically planar turbulent premixed flames are investigated by direct numerical simulation incorporating detailed chemistry and transport for a hydrogen-air mixture. The mean inlet velocity was dynamically adjusted to ensure a stable flame within the computational domain, allowing the investigation of time-averaged quantities of interest. A particular interest was on understanding the effects of turbulence on the displacement speed of the flame relative to the local fluid flow. Results show a linear dependence on the displacement speed as a function of total strain, consistent with earlier work on premixed-laminar flames. Additional analysis on the local flame thickness reveals that the effect of turbulence is twofold: (1) the increase in mixing results in flame thinning due to the enhancement of combustion at early onset of the flame, and (2) for large Reynolds number flows, the penetration of the turbulence far into the preheat zone and into the reaction zone results in localized flame broadening.

Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

NASA Astrophysics Data System (ADS)

Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

2016-05-01

Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

Mechanical heterogeneity in ionic liquids

NASA Astrophysics Data System (ADS)

Veldhorst, Arno A.; Ribeiro, Mauro C. C.

2018-05-01

Molecular dynamics (MD) simulations of five ionic liquids based on 1-alkyl-3-methylimidazolium cations, [CnC1im]+, have been performed in order to calculate high-frequency elastic moduli and to evaluate heterogeneity of local elastic moduli. The MD simulations of [CnC1im][NO3], n = 2, 4, 6, and 8, assessed the effect of domain segregation when the alkyl chain length increases, and [C8C1im][PF6] assessed the effect of strength of anion-cation interaction. Dispersion curves of excitation energies of longitudinal and transverse acoustic, LA and TA, modes were obtained from time correlation functions of mass currents at different wavevectors. High-frequency sound velocity of LA modes depends on the alkyl chain length, but sound velocity for TA modes does not. High-frequency bulk and shear moduli, K∞ and G∞, depend on the alkyl chain length because of a density effect. Both K∞ and G∞ are strongly dependent on the anion. The calculation of local bulk and shear moduli was accomplished by performing bulk and shear deformations of the systems cooled to 0 K. The simulations showed a clear connection between structural and elastic modulus heterogeneities. The development of nano-heterogeneous structure with increasing length of the alkyl chain in [CnC1im][NO3] implies lower values for local bulk and shear moduli in the non-polar domains. The mean value and the standard deviations of distributions of local elastic moduli decrease when [NO3]- is replaced by the less coordinating [PF6]- anion.

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

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

Bzowski, M.; Kubiak, M. A.; Sokol, J. M.

Because of its high ionization potential and weak interaction with hydrogen, neutral interstellar helium (NISHe) is almost unaffected at the heliospheric interface with the interstellar medium and freely enters the solar system. This second most abundant species provides some of the best information on the characteristics of the interstellar gas in the local interstellar cloud. The Interstellar Boundary Explorer (IBEX) is the second mission to directly detect NISHe. We present a comparison between recent IBEX NISHe observations and simulations carried out using a well-tested quantitative simulation code. Simulation and observation results compare well for times when measured fluxes are dominatedmore » by NISHe (and contributions from other species are small). Differences between simulations and observations indicate a previously undetected secondary population of neutral helium, likely produced by interaction of interstellar helium with plasma in the outer heliosheath. Interstellar neutral parameters are statistically different from previous in situ results obtained mostly from the GAS/Ulysses experiment, but they do agree with the local interstellar flow vector obtained from studies of interstellar absorption: the newly established flow direction is ecliptic longitude 79.{sup 0}2, latitude -5.{sup 0}1, the velocity is {approx}22.8 km s{sup -1}, and the temperature is 6200 K. These new results imply a markedly lower absolute velocity of the gas and thus significantly lower dynamic pressure on the boundaries of the heliosphere and different orientation of the Hydrogen Deflection Plane compared to prior results from Ulysses. A different orientation of this plane also suggests a new geometry of the interstellar magnetic field, and the lower dynamic pressure calls for a compensation by other components of the pressure balance, most likely a higher density of interstellar plasma and strength of interstellar magnetic field.« less

Slow dynamics in translation-invariant quantum lattice models

NASA Astrophysics Data System (ADS)

Michailidis, Alexios A.; Žnidarič, Marko; Medvedyeva, Mariya; Abanin, Dmitry A.; Prosen, Tomaž; Papić, Z.

2018-03-01

Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.

Estimating the mass of the Local Group using machine learning applied to numerical simulations

NASA Astrophysics Data System (ADS)

McLeod, M.; Libeskind, N.; Lahav, O.; Hoffman, Y.

2017-12-01

We present a new approach to calculating the combined mass of the Milky Way (MW) and Andromeda (M31), which together account for the bulk of the mass of the Local Group (LG). We base our work on an ensemble of 30,190 halo pairs from the Small MultiDark simulation, assuming a ΛCDM (Cosmological Constant and Cold Dark Matter) cosmology. This is used in conjunction with machine learning methods (artificial neural networks, ANN) to investigate the relationship between the mass and selected parameters characterising the orbit and local environment of the binary. ANN are employed to take account of additional physics arising from interactions with larger structures or dynamical effects which are not analytically well understood. Results from the ANN are most successful when the velocity shear is provided, which demonstrates the flexibility of machine learning to model physical phenomena and readily incorporate new information. The resulting estimate for the Local Group mass, when shear information is included, is 4.9×1012Msolar, with an error of ±0.8×1012Msolar from the 68% uncertainty in observables, and a r.m.s. scatter interval of +1.7‑1.3×1012Msolar estimated scatter from the differences between the model estimates and simulation masses for a testing sample of halo pairs. We also consider a recently reported large relative transverse velocity of M31 and the Milky Way, and produce an alternative mass estimate of 3.6±0.3+2.1‑1.3×1012Msolar. Although the methods used predict similar values for the most likely mass of the LG, application of ANN compared to the traditional Timing Argument reduces the scatter in the log mass by approximately half when tested on samples from the simulation.

Measurements of localized core turbulence & turbulence suppression on DIII-D

NASA Astrophysics Data System (ADS)

Shafer, Morgan W.

The crucial dynamics of turbulent-driven cross-field transport in tokamak plasmas reside in the two-dimensional (2D) radial/poloidal plane. Thus, 2D measurements of turbulence are needed to test theoretical models and validate sophisticated gyrokinetic codes. Furthermore, measurements are important for understanding the role of turbulence suppression in enhanced confinement regimes. The Beam Emission Spectroscopy (BES) diagnostic on the DIII-D tokamak measures localized, long-wavelength (k⊥rho i≤1) density fluctuations in the 2D radial/poloidal plane and is suitable for these studies. Measurements of turbulence amplitude, S(kr,k theta) spectra, correlation lengths, decorrelation rates and group velocities are obtained via BES in the core (0.3< r/a <0.9) and compared to nonlinear gyrokinetic simulations from the GYRO code. The 2D measurements show a tilted eddy structure in the core that is consistent with ExB shear. The S(kr,ktheta) spectra are directly compared to GYRO simulations. These comparisons show the 2D structure is in reasonable agreement at r/a = 0.5 where the predicted turbulence amplitude and heat flux agree well with the measurements. However, the simulations show a strongly tilted eddy structure that extends to high-kr at r/a = 0.75, where the simulations under-predict the turbulence amplitude and heat flux. This is not observed in the experiment and suggests a possible over-exaggeration of an ExB or zonal flow shearing mechanism in the simulations. Measurements demonstrate local turbulence suppression near low-order rational q-surfaces at low magnetic shear. This interaction can lead to an Internal Transport Barrier (ITB) provided sufficient equilibrium ExB shear (largely due to the toroidal rotation of neutral beam heated rotating plasmas) sustains the barrier. Related GYRO simulations suggest these ITBs are triggered by zonal flows that form near the q = 2 surface. Consistent with the simulations, localized measurements demonstrate increased shear in the poloidal turbulence velocity. The resulting shear rate transiently exceeds the decorrelation rate, causing a reduction in turbulence and radial correlation length. The layer of suppressed turbulence moves radially outward, nearly coincident with integer q-surfaces.

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

Omelchenko, Yuri A.

Global interactions of energetic ions with magnetoplasmas and neutral gases lie at the core of many space and laboratory plasma phenomena ranging from solar wind entry into and transport within planetary magnetospheres and exospheres to fast-ion driven instabilities in fusion devices to astrophysics-in-lab experiments. The ability of computational models to properly account for physical effects that underlie such interactions, namely ion kinetic, ion cyclotron, Hall, collisional and ionization processes is important for the success and planning of experimental research in plasma physics. Understanding the physics of energetic ions, in particular their nonlinear resonance interactions with Alfvén waves, is central tomore » improving the heating performance of magnetically confined plasmas for future energy generation. Fluid models are not adequate for high-beta plasmas as they cannot fully capture ion kinetic and cyclotron physics (e.g., ion behavior in the presence of magnetic nulls, shock structures, plasma interpenetration, etc.). Recent results from global reconnection simulations show that even in a MHD-like regime there may be significant differences between kinetic and MHD simulations. Therefore, kinetic modeling becomes essential for meeting modern day challenges in plasma physics. The hybrid approximation is an intermediate approximation between the fluid and fully kinetic approximations. It eliminates light waves, removes the electron inertial temporal and spatial scales from the problem and enables full-orbit ion kinetics. As a result, hybrid codes have become effective tools for exploring ion-scale driven phenomena associated with ion beams, shocks, reconnection and turbulence that control the large-scale behavior of laboratory and space magnetoplasmas. A number of numerical issues, however, make three-dimensional (3D) large-scale hybrid simulations of inhomogeneous magnetized plasmas prohibitively expensive or even impossible. To resolve these difficulties we have developed a novel Event-driven Multiscale Asynchronous Parallel Simulation (EMAPS) technology that replaces time stepping with self-adaptive update events. Local calculations are carried out only on an “as needed basis”. EMAPS (i) guarantees accurate and stable processing of physical variables in time accurate simulations, and (ii) eliminates unnecessary computation. Applying EMAPS to the hybrid model has resulted in the development of a unique parallel code, dimension-independent (compile-time-configurable) HYPERS (Hybrid Parallel Event-Resolved Simulator) that scales to hundreds of thousands of parallel processors. HYPERS advances electromagnetic fields and particles asynchronously on time scales determined by local physical laws and mesh properties. To achieve high computational accuracy in complex device geometries, HYPERS employs high-fidelity Cartesian grids with masked conductive cells. The HYPERS model includes multiple ion species, energy and momentum conserving ion-ion collisions, and provides a number of approximations for plasma resistivity and vacuum regions. Both local and periodic boundary conditions are allowed. The HYPERS solver preserves zero divergence of magnetic field. The project has demonstrated HYPERS capabilities on a number of applications of interest to fusion and astrophysical plasma physics applications listed below. 1. Theta-pinch formation of FRCs The formation, spontaneous spin-up, and stability of theta-pinch formed field-reversed configurations have been studied self-consistently in 3D. The end-to-end hybrid simulations reveal poloidal profiles of implosion-driven fast toroidal plasma rotation and demonstrate three discharge regimes as a function of experimental parameters: the decaying stable configuration, the tilt unstable configuration, and the nonlinear evolution of a fast growing tearing mode. 2. FRC collisions with magnetic mirrors Interactions of fast plasma streams and objects with magnetic obstacles (dipoles, mirrors, etc) lie at the core of many space and laboratory plasma phenomena ranging from magnetoshells and solar wind interactions with planetary magnetospheres to compact fusion plasmas. HYPERS simulations are compared with data from the MSX experiment (LANL) that focuses on the physics of magnetized collisionless shocks through the acceleration and subsequent stagnation of FRC plasmoids against a strong magnetic mirrors and flux-conserving boundaries. 3. Exploding magnetoplasmas Results from hybrid simulations of two experiments at the LAPD and Nevada Terawatt Facility are discussed where short-pulse lasers are used to ablate solid targets to produce plasmas that expand across external magnetic fields. The first simulation recreates flutelike density striations observed at the leading edge of a carbon plasma and predicts an early destruction of the magnetic cavity in agreement with experimental evidence. In the second simulation a polyethylene target is ablated into a mixture of protons and carbon ions. A mechanism is demonstrated that allows protons to penetrate the magnetic field in the form of a collimated flow. The results are compared to experimental data and single-fluid MHD simulations. The EMAPS framework has the potential for wide application in many other engineering and scientific fields, such as climate models, biological systems, electronic devices, seismic events, oil reservation simulators that all involve advancing solutions of partial differential equations in time where the rate of activity can be adapted widely over the spatial domain depending on locally space/time phenomena (“events”).« less

Reorientation Motion and Preferential Interactions of a Peptide in Denaturants and Osmolyte.

PubMed

Jas, Gouri S; Rentchler, Eric C; Słowicka, Agnieszka M; Hermansen, John R; Johnson, Carey K; Middaugh, C Russell; Kuczera, Krzysztof

2016-03-31

Fluorescence anisotropy decay measurements and all atom molecular dynamics simulations are used to characterize the orientational motion and preferential interaction of a peptide, N-acetyl-tryptophan-amide (NATA) containing two peptide bonds, in aqueous, urea, guanidinium chloride (GdmCl), and proline solution. Anisotropy decay measurements as a function of temperature and concentration showed moderate slowing of reorientations in urea and GdmCl and very strong slowing in proline solution, relative to water. These effects deviate significantly from simple proportionality of peptide tumbling time to solvent viscosity, leading to the investigation of microscopic preferential interaction behavior through molecular dynamics simulations. Examination of the interactions of denaturants and osmolyte with the peptide backbone uncovers the presence of strongest interaction with urea, intermediate with proline, and weakest with GdmCl. In contrast, the strongest preferential solvation of the peptide side chain is by the nonpolar part of the proline zwitterion, followed by urea, and GdmCl. Interestingly, the local density of urea around the side chain is higher, but the GdmCl distribution is more organized. Thus, the computed preferential solvation of the side chain by the denaturants and osmolyte can account for the trend in reorientation rates. Analysis of water structure and its dynamics uncovered underlying differences between urea, GdmCl, and proline. Urea exerted the smallest perturbation of water behavior. GdmCl had a larger effect on water, slowing kinetics and stabilizing interactions. Proline had the largest overall interactions, exhibiting a strong stabilizing effect on both water-water and water-peptide hydrogen bonds. The results for this elementary peptide system demonstrate significant differences in microscopic behavior of the examined solvent environments. For the commonly used denaturants, urea tends to form disorganized local aggregates around the peptide groups and has little influence on water, while GdmCl only forms specific interactions with the side chain and tends to destabilize water structure. The protective osmolyte proline has the strongest and most specific interactions with the tryptophan side chain, and also stabilizes both water-water and water-peptide hydrogen bonds. Our results strongly suggest protein or peptide denaturation triggered by urea occurs by direct interaction, whereas GdmCl interacts favorably with side chains and destabilizes peptide-water hydrogen bonds. The stabilization of biopolymers by an osmolyte such as proline is governed by favorable preferential interaction with the side chains and stabilization of water.

Simulation of glioblastoma multiforme (GBM) tumor cells using ising model on the Creutz Cellular Automaton

NASA Astrophysics Data System (ADS)

Züleyha, Artuç; Ziya, Merdan; Selçuk, Yeşiltaş; Kemal, Öztürk M.; Mesut, Tez

2017-11-01

Computational models for tumors have difficulties due to complexity of tumor nature and capacities of computational tools, however, these models provide visions to understand interactions between tumor and its micro environment. Moreover computational models have potential to develop strategies for individualized treatments for cancer. To observe a solid brain tumor, glioblastoma multiforme (GBM), we present a two dimensional Ising Model applied on Creutz cellular automaton (CCA). The aim of this study is to analyze avascular spherical solid tumor growth, considering transitions between non tumor cells and cancer cells are like phase transitions in physical system. Ising model on CCA algorithm provides a deterministic approach with discrete time steps and local interactions in position space to view tumor growth as a function of time. Our simulation results are given for fixed tumor radius and they are compatible with theoretical and clinic data.

Analysis and observation of moving domain fronts in a ring of coupled electronic self-oscillators

NASA Astrophysics Data System (ADS)

English, L. Q.; Zampetaki, A.; Kevrekidis, P. G.; Skowronski, K.; Fritz, C. B.; Abdoulkary, Saidou

2017-10-01

In this work, we consider a ring of coupled electronic (Wien-bridge) oscillators from a perspective combining modeling, simulation, and experimental observation. Following up on earlier work characterizing the pairwise interaction of Wien-bridge oscillators by Kuramoto-Sakaguchi phase dynamics, we develop a lattice model for a chain thereof, featuring an exponentially decaying spatial kernel. We find that for certain values of the Sakaguchi parameter α, states of traveling phase-domain fronts involving the coexistence of two clearly separated regions of distinct dynamical behavior, can establish themselves in the ring lattice. Experiments and simulations show that stationary coexistence domains of synchronization only manifest themselves with the introduction of a local impurity; here an incoherent cluster of oscillators can arise reminiscent of the chimera states in a range of systems with homogeneous oscillators and suitable nonlocal interactions between them.

Quantum annealing with all-to-all connected nonlinear oscillators

PubMed Central

Puri, Shruti; Andersen, Christian Kraglund; Grimsmo, Arne L.; Blais, Alexandre

2017-01-01

Quantum annealing aims at solving combinatorial optimization problems mapped to Ising interactions between quantum spins. Here, with the objective of developing a noise-resilient annealer, we propose a paradigm for quantum annealing with a scalable network of two-photon-driven Kerr-nonlinear resonators. Each resonator encodes an Ising spin in a robust degenerate subspace formed by two coherent states of opposite phases. A fully connected optimization problem is mapped to local fields driving the resonators, which are connected with only local four-body interactions. We describe an adiabatic annealing protocol in this system and analyse its performance in the presence of photon loss. Numerical simulations indicate substantial resilience to this noise channel, leading to a high success probability for quantum annealing. Finally, we propose a realistic circuit QED implementation of this promising platform for implementing a large-scale quantum Ising machine. PMID:28593952

Electrophysiological models of neural processing.

PubMed

Nelson, Mark E

2011-01-01

The brain is an amazing information processing system that allows organisms to adaptively monitor and control complex dynamic interactions with their environment across multiple spatial and temporal scales. Mathematical modeling and computer simulation techniques have become essential tools in understanding diverse aspects of neural processing ranging from sub-millisecond temporal coding in the sound localization circuity of barn owls to long-term memory storage and retrieval in humans that can span decades. The processing capabilities of individual neurons lie at the core of these models, with the emphasis shifting upward and downward across different levels of biological organization depending on the nature of the questions being addressed. This review provides an introduction to the techniques for constructing biophysically based models of individual neurons and local networks. Topics include Hodgkin-Huxley-type models of macroscopic membrane currents, Markov models of individual ion-channel currents, compartmental models of neuronal morphology, and network models involving synaptic interactions among multiple neurons.

Atomic-scale investigation of point defects and hydrogen-solute atmospheres on the edge dislocation mobility in alpha iron

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

Bhatia, M. A.; Solanki, K. N., E-mail: kiran.solanki@asu.edu; Groh, S.

2014-08-14

In this study, we present atomistic mechanisms of 1/2 [111](11{sup ¯}0) edge dislocation interactions with point defects (hydrogen and vacancies) and hydrogen solute atmospheres in body centered cubic (bcc) iron. In metals such as iron, increases in hydrogen concentration can increase dislocation mobility and/or cleavage-type decohesion. Here, we first investigate the dislocation mobility in the presence of various point defects, i.e., change in the frictional stress as the edge dislocation interacts with (a) vacancy, (b) substitutional hydrogen, (c) one substitutional and one interstitial hydrogen, (d) interstitial hydrogen, (e) vacancy and interstitial hydrogen, and (f) two interstitial hydrogen. Second, we examinemore » the role of a hydrogen-solute atmosphere on the rate of local dislocation velocity. The edge dislocation simulation with a vacancy in the compression side of the dislocation and an interstitial hydrogen atom at the tension side exhibit the strongest mechanical response, suggesting a higher potential barrier and hence, the higher frictional stress (i.e., ∼83% higher than the pure iron Peierls stress). In the case of a dislocation interacting with a vacancy on the compressive side, the vacancy binds with the edge dislocation, resulting in an increase in the friction stress of about 28% when compared with the Peierls stress of an edge dislocation in pure iron. Furthermore, as the applied strain increases, the vacancy migrates through a dislocation transportation mechanism by attaining a velocity of the same order as the dislocation velocity. For the case of the edge dislocation interacting with interstitial hydrogen on the tension side, the hydrogen atom jumps through one layer perpendicular to the glide plane during the pinning-unpinning process. Finally, our simulation of dislocation interactions with hydrogen show first an increase in the local dislocation velocity followed by a pinning of the dislocation core in the atmosphere, resulting in resistance to dislocation motion as the dislocation moves though the hydrogen-solute atmospheres. With this systematic, atomistic study of the edge dislocation with various point defects, we show significant increase in obstacle strengths in addition to an increase in the local dislocation velocity during interaction with solute atmospheres. The results have implications for constitutive development and modeling of the hydrogen effect on dislocation mobility and deformation in metals.« less

Density functional theory versus quantum Monte Carlo simulations of Fermi gases in the optical-lattice arena★

NASA Astrophysics Data System (ADS)

Pilati, Sebastiano; Zintchenko, Ilia; Troyer, Matthias; Ancilotto, Francesco

2018-04-01

We benchmark the ground state energies and the density profiles of atomic repulsive Fermi gases in optical lattices (OLs) computed via density functional theory (DFT) against the results of diffusion Monte Carlo (DMC) simulations. The main focus is on a half-filled one-dimensional OLs, for which the DMC simulations performed within the fixed-node approach provide unbiased results. This allows us to demonstrate that the local spin-density approximation (LSDA) to the exchange-correlation functional of DFT is very accurate in the weak and intermediate interactions regime, and also to underline its limitations close to the strongly-interacting Tonks-Girardeau limit and in very deep OLs. We also consider a three-dimensional OL at quarter filling, showing also in this case the high accuracy of the LSDA in the moderate interaction regime. The one-dimensional data provided in this study may represent a useful benchmark to further develop DFT methods beyond the LSDA and they will hopefully motivate experimental studies to accurately measure the equation of state of Fermi gases in higher-dimensional geometries. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjb/e2018-90021-1.

Interactions of oxytetracycline with a smectite clay: a spectroscopic study with molecular simulations.

PubMed

Aristilde, Ludmilla; Marichal, Claire; Miéhé-Brendlé, Jocelyne; Lanson, Bruno; Charlet, Laurent

2010-10-15

Binding of antibiotics to clay minerals can decrease both their physical and biological availability in soils. To elucidate the binding mechanisms of tetracycline antibiotics on smectite clays as a function of pH, we probed the interactions of oxytetracycline (OTC) with Na-montmorillonite (MONT) using X-ray diffraction (XRD), infrared (IR), and solid-state nuclear magnetic resonance (NMR) spectroscopies, and Monte Carlo molecular simulations. The XRD patterns demonstrate the presence of OTC in the MONT interlayer space at acidic pH whereas complexation of OTC by external basal and edge sites seems to prevail at pH 8. At both pH, the (1)H-(13)C NMR profile indicates restricted mobility of the adsorbed OTC species; and, -CH(3) deformation and C-N stretching IR vibration bands confirm a binding mechanism involving the protonated dimethylamino group of OTC. Changes in the (23)Na NMR environments are consistent with cation-exchange and cation complexation reactions at the different sites of adsorption. Molecular simulations indicate that MONT interlayer spacing and structural charge localization dictate favorable binding conformations of the intercalated OTC, facilitating multiple interactions in agreement with the spectroscopic data. Our results present complementary insights into the mechanisms of adsorption of TETs on smectites important for their retention in natural and engineered soil environments.

Free energy landscape of a minimalist salt bridge model.

PubMed

Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

2016-01-01

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

Interaction between mantle and crustal detachments: a non-linear system controlling lithospheric extension

NASA Astrophysics Data System (ADS)

Rosenbaum, G.; Regenauer-Lieb, K.; Weinberg, R. F.

2009-12-01

We use numerical modelling to investigate the development of crustal and mantle detachment faults during lithospheric extension. Our models simulate a wide range of rift systems with varying values of crustal thickness and heat flow, showing how strain localization in the mantle interacts with localization in the upper crust and controls the evolution of extensional systems. Model results reveal a richness of structures and deformation styles, which grow in response to a self-organized mechanism that minimizes the internal stored energy of the system by localizing deformation at different levels of the lithosphere. Crustal detachment faults are well developed during extension of overthickened (60 km) continental crust, even when the initial heat flow is relatively low (50 mW/m2). In contrast, localized mantle deformation is most pronounced when the extended lithosphere has a normal crustal thickness (30-40 km) and an intermediate (60-70 mW/m2) heat flow. Results show a non-linear response to subtle changes in crustal thickness or heat flow, characterized by abrupt and sometime unexpected switches in extension modes (e.g. from diffuse rifting to effective lithospheric-scale rupturing) or from mantle- to crust-dominated strain localization. We interpret this non-linearity to result from the interference of doming wavelengths. Disharmony of crust and mantle doming wavelengths results in efficient communication between shear zones at different lithospheric levels, leading to rupturing of the whole lithosphere. In contrast, harmonious crust and mantle doming inhibits interaction of shear zones across the lithosphere and results in a prolonged rifting history prior to continental breakup.

Interaction between mantle and crustal detachments: A nonlinear system controlling lithospheric extension

NASA Astrophysics Data System (ADS)

Rosenbaum, Gideon; Regenauer-Lieb, Klaus; Weinberg, Roberto F.

2010-11-01

We use numerical modeling to investigate the development of crustal and mantle detachments during lithospheric extension. Our models simulate a wide range of extensional systems with varying values of crustal thickness and heat flow, showing how strain localization in the mantle interacts with localization in the upper crust and controls the evolution of extensional systems. Model results reveal a richness of structures and deformation styles as a response to a self-organized mechanism that minimizes the internal stored energy of the system by localizing deformation. Crustal detachments, here referred as low-angle normal decoupling horizons, are well developed during extension of overthickened (60 km) continental crust, even when the initial heat flow is relatively low (50 mW m-2). In contrast, localized mantle deformation is most pronounced when the extended lithosphere has a normal crustal thickness (30-40 km) and an intermediate heat flow (60-70 mW m-2). Results show a nonlinear response to subtle changes in crustal thickness or heat flow, characterized by abrupt and sometimes unexpected switches in extension modes (e.g., from diffuse extensional deformation to effective lithospheric-scale rupturing) or from mantle- to crust-dominated strain localization. We interpret this nonlinearity to result from the interference of doming wavelengths in the presence of multiple necking instabilities. Disharmonic crust and mantle doming wavelengths results in efficient communication between shear zones at different lithospheric levels, leading to rupturing of the whole lithosphere. In contrast, harmonic crust and mantle doming inhibits interaction of shear zones across the lithosphere and results in a prolonged history of extension prior to continental breakup.

A structural perspective on the interactions of TRAF6 and Basigin during the onset of melanoma: A molecular dynamics simulation study.

PubMed

Biswas, Ria; Ghosh, Semanti; Bagchi, Angshuman

2017-11-01

Metastatic melanoma is the most fatal type of skin cancer. The roles of matrix metalloproteinases (MMPs) have well been established in the onset of melanoma. Basigin (BSG) belongs to the immunoglobulin superfamily and is critical for induction of extracellular MMPs during the onset of various cancers including melanoma. Tumor necrosis factor receptor-associated factor 6 (TRAF6) is an E3-ligase that interacts with BSG and mediates its membrane localization, which leads to MMP expression in melanoma cells. This makes TRAF6 a potential therapeutic target in melanoma. We here conducted protein-protein interaction studies on TRAF6 and BSG to get molecular level insights of the reactions. The structure of human BSG was constructed by protein threading. Molecular-docking method was applied to develop the TRAF6-BSG complex. The refined docked complex was further optimized by molecular dynamics simulations. Results from binding free energy, surface properties, and electrostatic interaction analysis indicate that Lys340 and Glu417 of TRAF6 play as the anchor residues in the protein interaction interface. The current study will be helpful in designing specific modulators of TRAF6 to control melanoma metastasis. Copyright © 2017 John Wiley & Sons, Ltd.

Response of radiation belt simulations to different radial diffusion coefficients for relativistic and ultra-relativistic electrons

NASA Astrophysics Data System (ADS)

Drozdov, Alexander; Mann, Ian; Baker, Daniel N.; Subbotin, Dmitriy; Ozeke, Louis; Shprits, Yuri; Kellerman, Adam

Two parameterizations of the resonant wave-particle interactions of electrons with ULF waves in the magnetosphere by Brautigam and Albert [2000] and Ozeke et al. [2012] are evaluated using the Versatile Electron Radiation Belt (VERB) diffusion code to estimate the effect of changing a diffusion coefficient on the radiation belt simulation. The period of investigation includes geomagnetically quiet and active time. The simulations take into account wave-particle interactions represented by radial diffusion transport, local acceleration, losses due to pitch-angle diffusion, and mixed diffusion. 1. Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999JA900344 2. Ozeke, L. G., I. R. Mann, K. R. Murphy, I. J. Rae, D. K. Milling, S. R. Elkington, A. A. Chan, and H. J. Singer (2012), ULF wave derived radiation belt radial diffusion coefficients, J. Geophys. Res., 117, A04222, doi:10.1029/2011JA017463.

Dynamics of Magnetopause Reconnection in Response to Variable Solar Wind Conditions

NASA Astrophysics Data System (ADS)

Berchem, J.; Richard, R. L.; Escoubet, C. P.; Pitout, F.

2017-12-01

Quantifying the dynamics of magnetopause reconnection in response to variable solar wind driving is essential to advancing our predictive understanding of the interaction of the solar wind/IMF with the magnetosphere. To this end we have carried out numerical studies that combine global magnetohydrodynamic (MHD) and Large-Scale Kinetic (LSK) simulations to identify and understand the effects of solar wind/IMF variations. The use of the low dissipation, high resolution UCLA MHD code incorporating a non-linear local resistivity allows the representation of the global configuration of the dayside magnetosphere while the use of LSK ion test particle codes with distributed particle detectors allows us to compare the simulation results with spacecraft observations such as ion dispersion signatures observed by the Cluster spacecraft. We present the results of simulations that focus on the impacts of relatively simple solar wind discontinuities on the magnetopause and examine how the recent history of the interaction of the magnetospheric boundary with solar wind discontinuities can modify the dynamics of magnetopause reconnection in response to the solar wind input.

Application of a lower-upper implicit scheme and an interactive grid generation for turbomachinery flow field simulations

NASA Technical Reports Server (NTRS)

Choo, Yung K.; Soh, Woo-Yung; Yoon, Seokkwan

1989-01-01

A finite-volume lower-upper (LU) implicit scheme is used to simulate an inviscid flow in a tubine cascade. This approximate factorization scheme requires only the inversion of sparse lower and upper triangular matrices, which can be done efficiently without extensive storage. As an implicit scheme it allows a large time step to reach the steady state. An interactive grid generation program (TURBO), which is being developed, is used to generate grids. This program uses the control point form of algebraic grid generation which uses a sparse collection of control points from which the shape and position of coordinate curves can be adjusted. A distinct advantage of TURBO compared with other grid generation programs is that it allows the easy change of local mesh structure without affecting the grid outside the domain of independence. Sample grids are generated by TURBO for a compressor rotor blade and a turbine cascade. The turbine cascade flow is simulated by using the LU implicit scheme on the grid generated by TURBO.

Geometrical and Mechanical Properties Control Actin Filament Organization

PubMed Central

Ennomani, Hajer; Théry, Manuel; Nedelec, Francois; Blanchoin, Laurent

2015-01-01

The different actin structures governing eukaryotic cell shape and movement are not only determined by the properties of the actin filaments and associated proteins, but also by geometrical constraints. We recently demonstrated that limiting nucleation to specific regions was sufficient to obtain actin networks with different organization. To further investigate how spatially constrained actin nucleation determines the emergent actin organization, we performed detailed simulations of the actin filament system using Cytosim. We first calibrated the steric interaction between filaments, by matching, in simulations and experiments, the bundled actin organization observed with a rectangular bar of nucleating factor. We then studied the overall organization of actin filaments generated by more complex pattern geometries used experimentally. We found that the fraction of parallel versus antiparallel bundles is determined by the mechanical properties of actin filament or bundles and the efficiency of nucleation. Thus nucleation geometry, actin filaments local interactions, bundle rigidity, and nucleation efficiency are the key parameters controlling the emergent actin architecture. We finally simulated more complex nucleation patterns and performed the corresponding experiments to confirm the predictive capabilities of the model. PMID:26016478

A new approach to fluid-structure interaction within graphics hardware accelerated smooth particle hydrodynamics considering heterogeneous particle size distribution

NASA Astrophysics Data System (ADS)

Eghtesad, Adnan; Knezevic, Marko

2018-07-01

A corrective smooth particle method (CSPM) within smooth particle hydrodynamics (SPH) is used to study the deformation of an aircraft structure under high-velocity water-ditching impact load. The CSPM-SPH method features a new approach for the prediction of two-way fluid-structure interaction coupling. Results indicate that the implementation is well suited for modeling the deformation of structures under high-velocity impact into water as evident from the predicted stress and strain localizations in the aircraft structure as well as the integrity of the impacted interfaces, which show no artificial particle penetrations. To reduce the simulation time, a heterogeneous particle size distribution over a complex three-dimensional geometry is used. The variable particle size is achieved from a finite element mesh with variable element size and, as a result, variable nodal (i.e., SPH particle) spacing. To further accelerate the simulations, the SPH code is ported to a graphics processing unit using the OpenACC standard. The implementation and simulation results are described and discussed in this paper.

A new approach to fluid-structure interaction within graphics hardware accelerated smooth particle hydrodynamics considering heterogeneous particle size distribution

NASA Astrophysics Data System (ADS)

Eghtesad, Adnan; Knezevic, Marko

2017-12-01

A corrective smooth particle method (CSPM) within smooth particle hydrodynamics (SPH) is used to study the deformation of an aircraft structure under high-velocity water-ditching impact load. The CSPM-SPH method features a new approach for the prediction of two-way fluid-structure interaction coupling. Results indicate that the implementation is well suited for modeling the deformation of structures under high-velocity impact into water as evident from the predicted stress and strain localizations in the aircraft structure as well as the integrity of the impacted interfaces, which show no artificial particle penetrations. To reduce the simulation time, a heterogeneous particle size distribution over a complex three-dimensional geometry is used. The variable particle size is achieved from a finite element mesh with variable element size and, as a result, variable nodal (i.e., SPH particle) spacing. To further accelerate the simulations, the SPH code is ported to a graphics processing unit using the OpenACC standard. The implementation and simulation results are described and discussed in this paper.

Impact of red giant/AGB winds on active galactic nucleus jet propagation

NASA Astrophysics Data System (ADS)

Perucho, M.; Bosch-Ramon, V.; Barkov, M. V.

2017-10-01

Context. Dense stellar winds may mass-load the jets of active galactic nuclei, although it is unclear on what time and spatial scales the mixing takes place. Aims: Our aim is to study the first steps of the interaction between jets and stellar winds, and also the scales on which the stellar wind mixes with the jet and mass-loads it. Methods: We present a detailed 2D simulation - including thermal cooling - of a bubble formed by the wind of a star designed to study the initial stages of jet-star interaction. We also study the first interaction of the wind bubble with the jet using a 3D simulation in which the star enters the jet. Stability analysis is carried out for the shocked wind structure to evaluate the distances over which the jet-dragged wind, which forms a tail, can propagate without mixing with the jet flow. Results.The 2D simulations point to quick wind bubble expansion and fragmentation after about one bubble shock crossing time. Three-dimensional simulations and stability analysis point to local mixing in the case of strong perturbations and relatively low density ratios between the jet and the jet dragged-wind, and to a possibly more stable shocked wind structure at the phase of maximum tail mass flux. Analytical estimates also indicate that very early stages of the star jet-penetration time may be also relevant for mass-loading. The combination of these and previous results from the literature suggests highly unstable interaction structures and efficient wind-jet flow mixing on the scale of the jet interaction height. Conclusions: The winds of stars with strong mass loss can efficiently mix with jets from active galactic nuclei. In addition, the initial wind bubble shocked by the jet leads to a transient, large interaction surface. The interaction between jets and stars can produce strong inhomogeneities within the jet. As mixing is expected to be effective on large scales, even individual asymptotic giant branch stars can significantly contribute to the mass-load of the jet and thus affect its dynamics. Shear layer mass-entrainment could be important. The interaction structure can be a source of significant non-thermal emission.

Influence of adhesion and friction on the geometry of packings of spherical particles

NASA Astrophysics Data System (ADS)

Martin, C. L.; Bordia, R. K.

2008-03-01

We study the effect of both adhesion and friction on the geometry of monosized packings of spheres by means of discrete element simulations. We use elastic properties that are characteristic of materials typically used for particulate processing (Young’s modulus in the range 20-200 GPa). The geometrical features, both global and local, of the packings are studied using a variety of approaches in order to investigate their ability to quantify the effect of adhesion and/or friction. We show that both adhesion and friction interaction decrease the packing fraction. The very localized ordering that adhesion triggers is particularly investigated by use of the radial distribution function, the ordering parameter Q6 , and four triclinic cells that allow a description of the microstructure at the local level. We show that the probability of occurrence of these triclinic cells is approximately proportional to their degree of freedom when neither adhesion nor friction plays a role. We find that the introduction of adhesive interactions increases the probability of occurrence of those cells that have the lowest degree of freedom.

Global Particle-in-Cell Simulations of Mercury's Magnetosphere

NASA Astrophysics Data System (ADS)

Schriver, D.; Travnicek, P. M.; Lapenta, G.; Amaya, J.; Gonzalez, D.; Richard, R. L.; Berchem, J.; Hellinger, P.

2017-12-01

Spacecraft observations of Mercury's magnetosphere have shown that kinetic ion and electron particle effects play a major role in the transport, acceleration, and loss of plasma within the magnetospheric system. Kinetic processes include reconnection, the breakdown of particle adiabaticity and wave-particle interactions. Because of the vast range in spatial scales involved in magnetospheric dynamics, from local electron Debye length scales ( meters) to solar wind/planetary magnetic scale lengths (tens to hundreds of planetary radii), fully self-consistent kinetic simulations of a global planetary magnetosphere remain challenging. Most global simulations of Earth's and other planet's magnetosphere are carried out using MHD, enhanced MHD (e.g., Hall MHD), hybrid, or a combination of MHD and particle in cell (PIC) simulations. Here, 3D kinetic self-consistent hybrid (ion particle, electron fluid) and full PIC (ion and electron particle) simulations of the solar wind interaction with Mercury's magnetosphere are carried out. Using the implicit PIC and hybrid simulations, Mercury's relatively small, but highly kinetic magnetosphere will be examined to determine how the self-consistent inclusion of electrons affects magnetic reconnection, particle transport and acceleration of plasma at Mercury. Also the spatial and energy profiles of precipitating magnetospheric ions and electrons onto Mercury's surface, which can strongly affect the regolith in terms of space weathering and particle outflow, will be examined with the PIC and hybrid codes. MESSENGER spacecraft observations are used both to initiate and validate the global kinetic simulations to achieve a deeper understanding of the role kinetic physics play in magnetospheric dynamics.

Spatially Probed Plasmonic Photothermic Nanoheater Enhanced Hybrid Polymeric-Metallic PVDF-Ag Nanogenerator.

PubMed

Liow, Chi Hao; Lu, Xin; Tan, Chuan Fu; Chan, Kwok Hoe; Zeng, Kaiyang; Li, Shuzhou; Ho, Ghim Wei

2018-02-01

Surface plasmon-based photonics offers exciting opportunities to enable fine control of the site, span, and extent of mechanical harvesting. However, the interaction between plasmonic photothermic and piezoresponse still remains underexplored. Here, spatially localized and controllable piezoresponse of a hybrid self-polarized polymeric-metallic system that correlates to plasmonic light-to-heat modulation of the local strain is demonstrated. The piezoresponse is associated to the localized plasmons that serve as efficient nanoheaters leading to self-regulated strain via thermal expansion of the electroactive polymer. Moreover, the finite-difference time-domain simulation and linear thermal model also deduce the local strain to the surface plasmon heat absorption. The distinct plasmonic photothermic-piezoelectric phenomenon mediates not only localized external stimulus light response but also enhances dynamic piezoelectric energy harvesting. The present work highlights a promising surface plasmon coordinated piezoelectric response which underpins energy localization and transfer for diversified design of unique photothermic-piezotronic technology. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

2015-12-01

A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

Pilot-in-the Loop CFD Method Development

DTIC Science & Technology

2016-10-20

State University. All software supporting piloted simulations must run at real time speeds or faster. This requirement drives the number of...objects in the environment. In turn, this flowfield affects the local aerodynamics of the main rotor blade sections, affecting blade air loads, and...model, empirical models of ground effect and rotor / airframe interactions) are disabled when running in fully coupled mode, so as to not “double count

Dynamics of bulk electron heating and ionization in solid density plasmas driven by ultra-short relativistic laser pulses

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

Huang, L. G., E-mail: lingen.huang@hzdr.de; Kluge, T.; Cowan, T. E.

The dynamics of bulk heating and ionization is investigated both in simulations and theory, which determines the crucial plasma parameters such as plasma temperature and density in ultra-short relativistic laser-solid target interactions. During laser-plasma interactions, the solid density plasma absorbs a fraction of laser energy and converts it into kinetic energy of electrons. A portion of the electrons with relativistic kinetic energy goes through the solid density plasma and transfers energy into the bulk electrons, which results in bulk electron heating. The bulk electron heating is finally translated into the processes of bulk collisional ionization inside the solid target. Amore » simple model based on the Ohmic heating mechanism indicates that the local and temporal profile of bulk return current is essential to determine the temporal evolution of bulk electron temperature. A series of particle-in-cell simulations showing the local heating model is robust in the cases of target with a preplasma and without a preplasma. Predicting the bulk electron heating is then benefit for understanding the collisional ionization dynamics inside the solid targets. The connection of the heating and ionization inside the solid target is further studied using Thomas-Fermi model.« less

Dissipative NEGF methodology to treat short range Coulomb interaction: Current through a 1D nanostructure.

PubMed

Martinez, Antonio; Barker, John R; Di Prieto, Riccardo

2018-06-13

A methodology describing Coulomb blockade in the Non-equilibrium Green Function formalism is presented. We carried out ballistic and dissipative simulations through a 1D quantum dot using an Einstein phonon model. Inelastic phonons with different energies have been considered. The methodology incorporates the short-range Coulomb interaction between two electrons through the use of a two-particle Green's function. Unlike previous work, the quantum dot has spatial resolution i.e. it is not just parameterized by the energy level and coupling constants of the dot. Our method intends to describe the effect of electron localization while maintaining an open boundary or extended wave function. The formalism conserves the current through the nanostructure. A simple 1D model is used to explain the increase of mobility in semi-crystalline polymers as a function of the electron concentration. The mechanism suggested is based on the lifting of energy levels into the transmission window as a result of the local electron-electron repulsion inside a crystalline domain. The results are aligned with recent experimental findings. Finally, as a proof of concept, we present a simulation of a low temperature resonant structure showing the stability diagram in the Coulomb blockade regime. . © 2018 IOP Publishing Ltd.

Reduced-order prediction of rogue waves in two-dimensional deep-water waves

NASA Astrophysics Data System (ADS)

Farazmand, Mohammad; Sapsis, Themistoklis P.

2017-07-01

We consider the problem of large wave prediction in two-dimensional water waves. Such waves form due to the synergistic effect of dispersive mixing of smaller wave groups and the action of localized nonlinear wave interactions that leads to focusing. Instead of a direct simulation approach, we rely on the decomposition of the wave field into a discrete set of localized wave groups with optimal length scales and amplitudes. Due to the short-term character of the prediction, these wave groups do not interact and therefore their dynamics can be characterized individually. Using direct numerical simulations of the governing envelope equations we precompute the expected maximum elevation for each of those wave groups. The combination of the wave field decomposition algorithm, which provides information about the statistics of the system, and the precomputed map for the expected wave group elevation, which encodes dynamical information, allows (i) for understanding of how the probability of occurrence of rogue waves changes as the spectrum parameters vary, (ii) the computation of a critical length scale characterizing wave groups with high probability of evolving to rogue waves, and (iii) the formulation of a robust and parsimonious reduced-order prediction scheme for large waves. We assess the validity of this scheme in several cases of ocean wave spectra.

Symmetry lowering of pentacene molecular states interacting with a Cu surface

NASA Astrophysics Data System (ADS)

Baldacchini, Chiara; Mariani, Carlo; Betti, Maria Grazia; Vobornik, Ivana; Fujii, Jun; Annese, Emilia; Rossi, Giorgio; Ferretti, Andrea; Calzolari, Arrigo; di Felice, Rosa; Ruini, Alice; Molinari, Elisa

2007-12-01

Pentacene adsorbed on the Cu(119) vicinal surface forms long-range ordered chain structures. Photoemission spectroscopy measurements and ab initio density functional theory simulations provide consistent evidences that pentacene molecular orbitals mix with the copper bands, giving rise to interaction states localized at the interface. Angular-resolved and polarization dependent photoemission spectroscopy shows that most of the pentacene derived intensity is strongly dichroic. The symmetry of the molecular states of the free pentacene molecules is reduced upon adsorption on Cu(119), as a consequence of the molecule-metal interaction. Theoretical results show a redistribution of the charge density in π molecular states close to the Fermi level, consistent with the photoemission intensities (density of states) and polarization dependence (orbital symmetry).

Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions.

PubMed

Schnyder, Simon K; Horbach, Jürgen

2018-02-16

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

The paradox of enrichment in phytoplankton by induced competitive interactions

PubMed Central

Tubay, Jerrold M.; Ito, Hiromu; Uehara, Takashi; Kakishima, Satoshi; Morita, Satoru; Togashi, Tatsuya; Tainaka, Kei-ichi; Niraula, Mohan P.; Casareto, Beatriz E.; Suzuki, Yoshimi; Yoshimura, Jin

2013-01-01

The biodiversity loss of phytoplankton with eutrophication has been reported in many aquatic ecosystems, e.g., water pollution and red tides. This phenomenon seems similar, but different from the paradox of enrichment via trophic interactions, e.g., predator-prey systems. We here propose the paradox of enrichment by induced competitive interactions using multiple contact process (a lattice Lotka-Volterra competition model). Simulation results demonstrate how eutrophication invokes more competitions in a competitive ecosystem resulting in the loss of phytoplankton diversity in ecological time. The paradox is enhanced under local interactions, indicating that the limited dispersal of phytoplankton reduces interspecific competition greatly. Thus, the paradox of enrichment appears when eutrophication destroys an ecosystem either by elevated interspecific competition within a trophic level and/or destabilization by trophic interactions. Unless eutrophication due to human activities is ceased, the world's aquatic ecosystems will be at risk. PMID:24089056

Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions

NASA Astrophysics Data System (ADS)

Schnyder, Simon K.; Horbach, Jürgen

2018-02-01

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

A new parameter-free soft-core potential for silica and its application to simulation of silica anomalies

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

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M.

2015-12-28

A core-softening of the effective interaction between oxygen atoms in water and silica systems and its role in developing anomalous thermodynamic, transport, and structural properties have been extensively debated. For silica, the progress with addressing these issues has been hampered by a lack of effective interaction models with explicit core-softening. In this work, we present an extension of a two-body soft-core interatomic force field for silica recently reported by us [S. Izvekov and B. M. Rice, J. Chem. Phys. 136(13), 134508 (2012)] to include three-body forces. Similar to two-body interaction terms, the three-body terms are derived using parameter-free force-matching ofmore » the interactions from ab initio MD simulations of liquid silica. The derived shape of the O–Si–O three-body potential term affirms the existence of repulsion softening between oxygen atoms at short separations. The new model shows a good performance in simulating liquid, amorphous, and crystalline silica. By comparing the soft-core model and a similar model with the soft-core suppressed, we demonstrate that the topology reorganization within the local tetrahedral network and the O–O core-softening are two competitive mechanisms responsible for anomalous thermodynamic and kinetic behaviors observed in liquid and amorphous silica. The studied anomalies include the temperature of density maximum locus and anomalous diffusivity in liquid silica, and irreversible densification of amorphous silica. We show that the O–O core-softened interaction enhances the observed anomalies primarily through two mechanisms: facilitating the defect driven structural rearrangements of the silica tetrahedral network and modifying the tetrahedral ordering induced interactions toward multiple characteristic scales, the feature which underlies the thermodynamic anomalies.« less

Numerical analysis on interactions of vortex, shock wave, and exothermal reaction in a supersonic planar shear layer laden with droplets

NASA Astrophysics Data System (ADS)

Ren, Zhaoxin; Wang, Bing; Zheng, Longxi

2018-03-01

The analysis on the interactions of a large-scale shearing vortex, an incident oblique shock wave, and a chemical reaction in a planar shear layer is performed by numerical simulations. The reacting flows are obtained by directly solving the multi-species Navier-Stokes equations in the Eulerian frame, and the motions of individual point-mass fuel droplets are tracked in the Lagrangian frame considering the two-way coupling. The influences of shock strength and spray equivalence ratio on the shock-vortex interaction and the induced combustion are further studied. Under the present conditions, the incident shock is distorted by the vortex evolution to form the complicated waves including an incident shock wave, a multi-refracted wave, a reflected wave, and a transmitted wave. The local pressure and temperature are elevated by the shock impingement on the shearing vortex, which carries flammable mixtures. The chemical reaction is mostly accelerated by the refracted shock across the vortex. Two different exothermal reaction modes could be distinguished during the shock-vortex interaction as a thermal mode, due to the additional energy from the incident shock, and a local quasi detonation mode, due to the coupling of the refracted wave with reaction. The former mode detaches the flame and shock wave, whereas the latter mode tends to occur when the incident shock strength is higher and local equivalence ratio is higher approaching to the stoichiometric value. The numerical results illustrate that those two modes by shock-vortex interaction depend on the structure of the post-shock flame kernel, which may be located either in the vortex-braids of post-shock flows or in the shock-vortex interaction regime.

Re-forming supercritical quasi-parallel shocks. I - One- and two-dimensional simulations

NASA Technical Reports Server (NTRS)

Thomas, V. A.; Winske, D.; Omidi, N.

1990-01-01

The process of reforming supercritical quasi-parallel shocks is investigated using one-dimensional and two-dimensional hybrid (particle ion, massless fluid electron) simulations both of shocks and of simpler two-stream interactions. It is found that the supercritical quasi-parallel shock is not steady. Instread of a well-defined shock ramp between upstream and downstream states that remains at a fixed position in the flow, the ramp periodically steepens, broadens, and then reforms upstream of its former position. It is concluded that the wave generation process is localized at the shock ramp and that the reformation process proceeds in the absence of upstream perturbations intersecting the shock.

Multicomponent long-wave-short-wave resonance interaction system: Bright solitons, energy-sharing collisions, and resonant solitons.

PubMed

Sakkaravarthi, K; Kanna, T; Vijayajayanthi, M; Lakshmanan, M

2014-11-01

We consider a general multicomponent (2+1)-dimensional long-wave-short-wave resonance interaction (LSRI) system with arbitrary nonlinearity coefficients, which describes the nonlinear resonance interaction of multiple short waves with a long wave in two spatial dimensions. The general multicomponent LSRI system is shown to be integrable by performing the Painlevé analysis. Then we construct the exact bright multisoliton solutions by applying the Hirota's bilinearization method and study the propagation and collision dynamics of bright solitons in detail. Particularly, we investigate the head-on and overtaking collisions of bright solitons and explore two types of energy-sharing collisions as well as standard elastic collision. We have also corroborated the obtained analytical one-soliton solution by direct numerical simulation. Also, we discuss the formation and dynamics of resonant solitons. Interestingly, we demonstrate the formation of resonant solitons admitting breather-like (localized periodic pulse train) structure and also large amplitude localized structures akin to rogue waves coexisting with solitons. For completeness, we have also obtained dark one- and two-soliton solutions and studied their dynamics briefly.

Modeling of the energetic ion observations in the vicinity of Rhea and Dione

NASA Astrophysics Data System (ADS)

Kotova, Anna; Roussos, Elias; Krupp, Norbert; Dandouras, Iannis

2015-09-01

During several flybys of the Cassini spacecraft by the saturnian moons Rhea and Dione the energetic particle detector MIMI/LEMMS measured a significant reduction of energetic ion fluxes (20-300 keV) in their vicinity, which is caused by the absorption of those ions at the moon surfaces. In order to simulate the observed depletion profiles we developed an energetic particle tracer, which can be used to simulate the charged particle trajectories considering different models of the saturnian magnetosphere. This particle tracer is using an adaptive fourth order Gauss Runge-Kutta calculation method and its background magnetospheric model can be varied from that of a simple dipole, to a more complex one that includes also non-dipolar perturbations. The electromagnetic environment of each local, moon-magnetosphere interaction region is modeled through a hybrid plasma simulation code. Using this energetic particle tracer we explore which of these magnetospheric characteristics are more important in shaping the MIMI/LEMMS ion profiles. We also examine if MIMI/LEMMS responds primarily to protons (as typically assumed in many studies) or also to heavier ions, using calibration information, observations of the energy flux spectrum by the MIMI/CHEMS instrument (on board of Cassini as well) and different simulation results. Our results show that MIMI/LEMMS indeed measures heavier ions as well. Also we discovered that wrapping of magnetic field lines, even if it caused local perturbations only about few percent of the background magnetic field, can cause measurable changes in the spatial and energy distribution of fluxes measured by MIMI/LEMMS. These results are important for correct interpretation of MIMI/LEMMS data, and offer capabilities for a precise in-flight instruments' cross-calibration. Besides that, our simulation approach can be employed in similar environments (Titan, Enceladus, jovian moons, etc.) for constraining the magnetic topology of their interaction region and for identifying the composition and charge-states of ions at high energies, where capabilities of the available or future instruments can be limited.

Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases

PubMed Central

Rázga, Filip; Koča, Jaroslav; Šponer, Jiří; Leontis, Neocles B.

2005-01-01

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent molecular dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in domain III, and for the K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle. PMID:15722438

PEGylated Liposomes as Carriers of Hydrophobic Porphyrins.

PubMed

Dzieciuch, Monika; Rissanen, Sami; Szydłowska, Natalia; Bunker, Alex; Kumorek, Marta; Jamróz, Dorota; Vattulainen, Ilpo; Nowakowska, Maria; Róg, Tomasz; Kepczynski, Mariusz

2015-06-04

Sterically stabilized liposomes (SSLs) (PEGylated liposomes) are applied as effective drug delivery vehicles. Understanding the interactions between hydrophobic compounds and PEGylated membranes is therefore important to determine the effectiveness of PEGylated liposomes for delivery of drugs or other bioactive substances. In this study, we have combined fluorescence quenching analysis (FQA) experiments and all-atom molecular dynamics (MD) simulations to study the effect of membrane PEGylation on the location and orientation of 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (p-THPP) that has been used in our study as a model hydrophobic compound. First, we consider the properties of p-THPP in the presence of different fluid phosphatidylcholine bilayers that we use as model systems for protein-free cell membranes. Next, we studied the interaction between PEGylated membranes and p-THPP. Our MD simulation results indicated that the arrangement of p-THPP within zwitterionic membranes is dependent on their free volume, and p-THPP solubilized in PEGylated liposomes is localized in two preferred positions: deep within the membrane (close to the center of the bilayer) and in the outer PEG corona (p-THPP molecules being wrapped with the polymer chains). Fluorescence quenching methods confirmed the results of atomistic MD simulations and showed two populations of p-THPP molecules as in MD simulations. Our results provide both an explanation for the experimental observation that PEGylation improves the drug-loading efficiency of membranes and also a more detailed molecular-level description of the interactions between porphyrins and lipid membranes.

High-resolution modeling of local air-sea interaction within the Marine Continent using COAMPS

NASA Astrophysics Data System (ADS)

Jensen, T. G.; Chen, S.; Flatau, M. K.; Smith, T.; Rydbeck, A.

2016-12-01

The Maritime Continent (MC) is a region of intense deep atmospheric convection that serves as an important source of forcing for the Hadley and Walker circulations. The convective activity in the MC region spans multiple scales from local mesoscales to regional scales, and impacts equatorial wave propagation, coupled air-sea interaction and intra seasonal oscillations. The complex distribution of islands, shallow seas with fairly small heat storage and deep seas with large heat capacity is challenging to model. Diurnal convection over land-sea is part of a land-sea breeze system on a small scale, and is highly influenced by large variations in orography over land and marginal seas. Daytime solar insolation, run-off from the Archipelago and nighttime rainfall tends to stabilize the water column, while mixing by tidal currents and locally forced winds promote vertical mixing. The runoff from land and rivers and high net precipitation result in fresh water lenses that enhance vertical stability in the water column and help maintain high SST. We use the fully coupled atmosphere-ocean-wave version of the Coupled Ocean-Atmosphere Mesoscale Prediction System (COAMPS) developed at NRL with resolution of a few kilometers to investigate the air-sea interaction associated with the land-sea breeze system in the MC under active and inactive phases of the Madden-Julian Oscillation. The high resolution enables simulation of strong SST gradients associated with local upwelling in deeper waters and strong salinity gradients near rivers and from heavy precipitation.

Current-induced damping of nanosized quantum moments in the presence of spin-orbit interaction

NASA Astrophysics Data System (ADS)

Mahfouzi, Farzad; Kioussis, Nicholas

2017-05-01

Motivated by the need to understand current-induced magnetization dynamics at the nanoscale, we have developed a formalism, within the framework of Keldysh Green function approach, to study the current-induced dynamics of a ferromagnetic (FM) nanoisland overlayer on a spin-orbit-coupling (SOC) Rashba plane. In contrast to the commonly employed classical micromagnetic LLG simulations the magnetic moments of the FM are treated quantum mechanically. We obtain the density matrix of the whole system consisting of conduction electrons entangled with the local magnetic moments and calculate the effective damping rate of the FM. We investigate two opposite limiting regimes of FM dynamics: (1) The precessional regime where the magnetic anisotropy energy (MAE) and precessional frequency are smaller than the exchange interactions and (2) the local spin-flip regime where the MAE and precessional frequency are comparable to the exchange interactions. In the former case, we show that due to the finite size of the FM domain, the "Gilbert damping" does not diverge in the ballistic electron transport regime, in sharp contrast to Kambersky's breathing Fermi surface theory for damping in metallic FMs. In the latter case, we show that above a critical bias the excited conduction electrons can switch the local spin moments resulting in demagnetization and reversal of the magnetization. Furthermore, our calculations show that the bias-induced antidamping efficiency in the local spin-flip regime is much higher than that in the rotational excitation regime.

A Responsive Client for Distributed Visualization

NASA Astrophysics Data System (ADS)

Bollig, E. F.; Jensen, P. A.; Erlebacher, G.; Yuen, D. A.; Momsen, A. R.

2006-12-01

As grids, web services and distributed computing continue to gain popularity in the scientific community, demand for virtual laboratories likewise increases. Today organizations such as the Virtual Laboratory for Earth and Planetary Sciences (VLab) are dedicated to developing web-based portals to perform various simulations remotely while abstracting away details of the underlying computation. Two of the biggest challenges in portal- based computing are fast visualization and smooth interrogation without over taxing clients resources. In response to this challenge, we have expanded on our previous data storage strategy and thick client visualization scheme [1] to develop a client-centric distributed application that utilizes remote visualization of large datasets and makes use of the local graphics processor for improved interactivity. Rather than waste precious client resources for visualization, a combination of 3D graphics and 2D server bitmaps are used to simulate the look and feel of local rendering. Java Web Start and Java Bindings for OpenGL enable install-on- demand functionality as well as low level access to client graphics for all platforms. Powerful visualization services based on VTK and auto-generated by the WATT compiler [2] are accessible through a standard web API. Data is permanently stored on compute nodes while separate visualization nodes fetch data requested by clients, caching it locally to prevent unnecessary transfers. We will demonstrate application capabilities in the context of simulated charge density visualization within the VLab portal. In addition, we will address generalizations of our application to interact with a wider number of WATT services and performance bottlenecks. [1] Ananthuni, R., Karki, B.B., Bollig, E.F., da Silva, C.R.S., Erlebacher, G., "A Web-Based Visualization and Reposition Scheme for Scientific Data," In Press, Proceedings of the 2006 International Conference on Modeling Simulation and Visualization Methods (MSV'06) (2006). [2] Jensen, P.A., Yuen, D.A., Erlebacher, G., Bollig, E.F., Kigelman, D.G., Shukh, E.A., Automated Generation of Web Services for Visualization Toolkits, Eos Trans. AGU, 86(52), Fall Meet. Suppl., Abstract IN42A-06, 2005.

A mathematical model and computational framework for three-dimensional chondrocyte cell growth in a porous tissue scaffold placed inside a bi-directional flow perfusion bioreactor.

PubMed

Shakhawath Hossain, Md; Bergstrom, D J; Chen, X B

2015-12-01

The in vitro chondrocyte cell culture for cartilage tissue regeneration in a perfusion bioreactor is a complex process. Mathematical modeling and computational simulation can provide important insights into the culture process, which would be helpful for selecting culture conditions to improve the quality of the developed tissue constructs. However, simulation of the cell culture process is a challenging task due to the complicated interaction between the cells and local fluid flow and nutrient transport inside the complex porous scaffolds. In this study, a mathematical model and computational framework has been developed to simulate the three-dimensional (3D) cell growth in a porous scaffold placed inside a bi-directional flow perfusion bioreactor. The model was developed by taking into account the two-way coupling between the cell growth and local flow field and associated glucose concentration, and then used to perform a resolved-scale simulation based on the lattice Boltzmann method (LBM). The simulation predicts the local shear stress, glucose concentration, and 3D cell growth inside the porous scaffold for a period of 30 days of cell culture. The predicted cell growth rate was in good overall agreement with the experimental results available in the literature. This study demonstrates that the bi-directional flow perfusion culture system can enhance the homogeneity of the cell growth inside the scaffold. The model and computational framework developed is capable of providing significant insight into the culture process, thus providing a powerful tool for the design and optimization of the cell culture process. © 2015 Wiley Periodicals, Inc.

A Semi-Structured MODFLOW-USG Model to Evaluate Local Water Sources to Wells for Decision Support.

PubMed

Feinstein, Daniel T; Fienen, Michael N; Reeves, Howard W; Langevin, Christian D

2016-07-01

In order to better represent the configuration of the stream network and simulate local groundwater-surface water interactions, a version of MODFLOW with refined spacing in the topmost layer was applied to a Lake Michigan Basin (LMB) regional groundwater-flow model developed by the U.S. Geological. Regional MODFLOW models commonly use coarse grids over large areas; this coarse spacing precludes model application to local management issues (e.g., surface-water depletion by wells) without recourse to labor-intensive inset models. Implementation of an unstructured formulation within the MODFLOW framework (MODFLOW-USG) allows application of regional models to address local problems. A "semi-structured" approach (uniform lateral spacing within layers, different lateral spacing among layers) was tested using the LMB regional model. The parent 20-layer model with uniform 5000-foot (1524-m) lateral spacing was converted to 4 layers with 500-foot (152-m) spacing in the top glacial (Quaternary) layer, where surface water features are located, overlying coarser resolution layers representing deeper deposits. This semi-structured version of the LMB model reproduces regional flow conditions, whereas the finer resolution in the top layer improves the accuracy of the simulated response of surface water to shallow wells. One application of the semi-structured LMB model is to provide statistical measures of the correlation between modeled inputs and the simulated amount of water that wells derive from local surface water. The relations identified in this paper serve as the basis for metamodels to predict (with uncertainty) surface-water depletion in response to shallow pumping within and potentially beyond the modeled area, see Fienen et al. (2015a). Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Non-Destructive Evaluation of Kissing Bonds using Local Defect Resonance (LDR) Spectroscopy: A Simulation Study

NASA Astrophysics Data System (ADS)

Delrue, S.; Tabatabaeipour, M.; Hettler, J.; Van Den Abeele, K.

With the growing demand from industry to optimize and further develop existing Non-Destructive Testing & Evaluation (NDT&E) techniques or new methods to detect and characterize incipient damage with high sensitivity and increased quality, ample efforts have been devoted to better understand the typical behavior of kissing bonds, such as delaminations and cracks. Recently, it has been shown experimentally that the nonlinear ultrasonic response of kissing bonds could be enhanced by using Local Defect Resonance (LDR) spectroscopy. LDR spectroscopy is an efficient NDT technique that takes advantage of the characteristic fre- quencies of the defect (defect resonances) in order to provide maximum acoustic wave-defect interaction. In fact, for nonlinear methodologies, the ultrasonic excitation of the sample should occur at either multiples or integer ratios of the characteristic defect resonance frequencies, in order to obtain the highest signal-to-noise response in the nonlinear LDR spectroscopy. In this paper, the potential of using LDR spectroscopy for the detection, localization and characterization of kissing bonds is illustrated using a 3D simulation code for elastic wave propagation in materials containing closed but dynamically active cracks or delaminations. Using the model, we are able to define an appropriate method, based on the Scaling Subtraction Method (SSM), to determine the local defect resonance frequencies of a delamination in a composite plate and to illustrate an increase in defect nonlinearity due to LDR. The simulation results will help us to obtain a better understanding of the concept of LDR and to assist in the further design and testing of LDR spectroscopy for the detection, localization and characterization of kissing bonds.

A semi-structured MODFLOW-USG model to evaluate local water sources to wells for decision support

USGS Publications Warehouse

Feinstein, Daniel T.; Fienen, Michael N.; Reeves, Howard W.; Langevin, Christian D.

2016-01-01

In order to better represent the configuration of the stream network and simulate local groundwater-surface water interactions, a version of MODFLOW with refined spacing in the topmost layer was applied to a Lake Michigan Basin (LMB) regional groundwater-flow model developed by the U.S. Geological. Regional MODFLOW models commonly use coarse grids over large areas; this coarse spacing precludes model application to local management issues (e.g., surface-water depletion by wells) without recourse to labor-intensive inset models. Implementation of an unstructured formulation within the MODFLOW framework (MODFLOW-USG) allows application of regional models to address local problems. A “semi-structured” approach (uniform lateral spacing within layers, different lateral spacing among layers) was tested using the LMB regional model. The parent 20-layer model with uniform 5000-foot (1524-m) lateral spacing was converted to 4 layers with 500-foot (152-m) spacing in the top glacial (Quaternary) layer, where surface water features are located, overlying coarser resolution layers representing deeper deposits. This semi-structured version of the LMB model reproduces regional flow conditions, whereas the finer resolution in the top layer improves the accuracy of the simulated response of surface water to shallow wells. One application of the semi-structured LMB model is to provide statistical measures of the correlation between modeled inputs and the simulated amount of water that wells derive from local surface water. The relations identified in this paper serve as the basis for metamodels to predict (with uncertainty) surface-water depletion in response to shallow pumping within and potentially beyond the modeled area, see Fienen et al. (2015a).

A Nonlinear Interactions Approximation Model for Large-Eddy Simulation

NASA Astrophysics Data System (ADS)

Haliloglu, Mehmet U.; Akhavan, Rayhaneh

2003-11-01

A new approach to LES modelling is proposed based on direct approximation of the nonlinear terms \\overlineu_iuj in the filtered Navier-Stokes equations, instead of the subgrid-scale stress, τ_ij. The proposed model, which we call the Nonlinear Interactions Approximation (NIA) model, uses graded filters and deconvolution to parameterize the local interactions across the LES cutoff, and a Smagorinsky eddy viscosity term to parameterize the distant interactions. A dynamic procedure is used to determine the unknown eddy viscosity coefficient, rendering the model free of adjustable parameters. The proposed NIA model has been applied to LES of turbulent channel flows at Re_τ ≈ 210 and Re_τ ≈ 570. The results show good agreement with DNS not only for the mean and resolved second-order turbulence statistics but also for the full (resolved plus subgrid) Reynolds stress and turbulence intensities.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

2017-05-01

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

The evolution of the metallicity gradient and the star formation efficiency in disc galaxies

NASA Astrophysics Data System (ADS)

Sillero, Emanuel; Tissera, Patricia B.; Lambas, Diego G.; Michel-Dansac, Leo

2017-12-01

We study the oxygen abundance profiles of the gas-phase components in hydrodynamical simulations of pre-prepared disc galaxies including major mergers, close encounters and isolated configurations. We analyse the evolution of the slope of oxygen abundance profiles and the specific star formation rate (sSFR) along their evolution. We find that galaxy-galaxy interactions could generate either positive or negative gas-phase oxygen profiles, depending on the state of evolution. Along the interaction, galaxies are found to have metallicity gradients and sSFR consistent with observations, on average. Strong gas inflows produced during galaxy-galaxy interactions or as a result of strong local instabilities in gas-rich discs are able to produce both a quick dilution of the central gas-phase metallicity and a sudden increase of the sSFR. Our simulations show that, during these events, a correlation between the metallicity gradients and the sSFR can be set up if strong gas inflows are triggered in the central regions in short time-scales. Simulated galaxies without experiencing strong disturbances evolve smoothly without modifying the metallicity gradients. Gas-rich systems show large dispersion along the correlation. The dispersion in the observed relation could be interpreted as produced by the combination of galaxies with different gas-richness and/or experiencing different types of interactions. Hence, our findings suggest that the observed relation might be the smoking gun of galaxies forming in a hierarchical clustering scenario.

From inter-specific behavioural interactions to species distribution patterns along gradients of habitat heterogeneity.

PubMed

Laiolo, Paola

2013-01-01

The strength of the behavioural processes associated with competitor coexistence may vary when different physical environments, and their biotic communities, come into contact, although empirical evidence of how interference varies across gradients of environmental complexity is still scarce in vertebrates. Here, I analyse how behavioural interactions and habitat selection regulate the local distribution of steppeland larks (Alaudidae) in a gradient from simple to heterogeneous agricultural landscapes in Spain, using crested lark Galerida cristata and Thekla lark G. theklae as study models. Galerida larks significantly partitioned by habitat but frequently co-occurred in heterogeneous environments. Irrespective of habitat divergence, however, the local densities of the two larks were negatively correlated, and the mechanisms beyond this pattern were investigated by means of playback experiments. When simulating the intrusion of the congener by broadcasting the species territorial calls, both larks responded with an aggressive response as intense with respect to warning and approach behaviour as when responding to the intrusion of a conspecific. However, birds promptly responded to playbacks only when congener territories were nearby, a phenomenon that points to learning as the mechanisms through which individuals finely tune their aggressive responses to the local competition levels. Heterospecifics occurred in closer proximity in diverse agro-ecosystems, possibly because of more abundant or diverse resources, and here engage in antagonistic interactions. The drop of species diversity associated with agricultural homogenisation is therefore likely to also bring about the disappearance of the behavioural repertoires associated with species interactions.

The bZIP dimer localizes at DNA full-sites where each basic region can alternately translocate and bind to subsites at the half-site

PubMed Central

Chan, I-San; Al-Sarraj, Taufik; Shahravan, S. Hesam; Fedorova, Anna V.; Shin, Jumi A.

2012-01-01

Crystal structures of the GCN4 bZIP (basic region/leucine zipper) with the AP-1 or CRE site show how each GCN4 basic region binds to a 4-bp cognate half-site as a single DNA target; however, this may not always fully describe how bZIP proteins interact with their target sites. Previously, we showed that the GCN4 basic region interacts with all 5 bp in half-site TTGCG (termed 5H-LR), and that 5H-LR comprises two 4-bp subsites, TTGC and TGCG, which individually are also target sites of the basic region. In this work, we explored how the basic region interacts with 5H-LR when the bZIP dimer localizes to full-sites. Using AMBER molecular modeling, we simulated GCN4 bZIP complexes with full-sites containing 5H-LR to investigate in silico the interface between the basic region and 5H-LR. We also performed in vitro investigation of bZIP–DNA interactions at a number of full-sites that contain 5H-LR vs. either subsite: we analyzed results from DNase I footprinting and electrophoretic mobility shift assay (EMSA) and from EMSA titrations to quantify binding affinities. Our computational and experimental results together support a highly dynamic DNA-binding model: when a bZIP dimer localizes to its target full-site, the basic region can alternately recognize either subsite as a distinct target at 5H-LR and translocate between the subsites, potentially by sliding and hopping. This model provides added insights into how α-helical DNA-binding domains of transcription factors can localize to their gene regulatory sequences in vivo. PMID:22856882

The bZIP dimer localizes at DNA full-sites where each basic region can alternately translocate and bind to subsites at the half-site.

PubMed

Chan, I-San; Al-Sarraj, Taufik; Shahravan, S Hesam; Fedorova, Anna V; Shin, Jumi A

2012-08-21

Crystal structures of the GCN4 bZIP (basic region/leucine zipper) with the AP-1 or CRE site show how each GCN4 basic region binds to a 4 bp cognate half-site as a single DNA target; however, this may not always fully describe how bZIP proteins interact with their target sites. Previously, we showed that the GCN4 basic region interacts with all 5 bp in half-site TTGCG (termed 5H-LR) and that 5H-LR comprises two 4 bp subsites, TTGC and TGCG, which individually are also target sites of the basic region. In this work, we explore how the basic region interacts with 5H-LR when the bZIP dimer localizes to full-sites. Using AMBER molecular modeling, we simulated GCN4 bZIP complexes with full-sites containing 5H-LR to investigate in silico the interface between the basic region and 5H-LR. We also performed in vitro investigation of bZIP-DNA interactions at a number of full-sites that contain 5H-LR versus either subsite: we analyzed results from DNase I footprinting and electrophoretic mobility shift assay (EMSA) and from EMSA titrations to quantify binding affinities. Our computational and experimental results together support a highly dynamic DNA-binding model: when a bZIP dimer localizes to its target full-site, the basic region can alternately recognize either subsite as a distinct target at 5H-LR and translocate between the subsites, potentially by sliding and hopping. This model provides added insights into how α-helical DNA-binding domains of transcription factors can localize to their gene regulatory sequences in vivo.

CCN numerical simulations for the GoAmazon with the OLAM model

NASA Astrophysics Data System (ADS)

Ramos-da-Silva, R.; Haas, R.; Barbosa, H. M.; Machado, L.

2015-12-01

Manaus is a large city in the center of the Amazon rainforest. The GoAmazon field project is exploring the region through various data collection and modeling to investigate in impacts of the urban polluted plume on the surrounding pristine areas. In this study a numerical model was applied to simulate the atmospheric dynamics and the Cloud Condensation Nucleai (CCN) concentrations evolution. Simulations with and without the urban plume was performed to identify its dynamics and local impacts. The results show that the land surface characteristics has important hole on the CCN distribution and rainfall over the region. At the south of Manaus the atmospheric dynamics is dominated by the cloud streets that are aligned with the trade winds and the Amazon River. At the north of Manaus, the Negro River produces the advection of a more stable atmosphere causing a higher CCN concentration on the boundary layer. Assuming a local high CCN concentration at the Manaus boundary layer region, the simulations show that the land-atmosphere interaction sets important dynamics on the plume. The model shows that the CCN plume moves along with the flow towards southwest of Manaus following the cloud streets and the river direction having the highest concentrations over the most stable water surface regions.

Explicit ions/implicit water generalized Born model for nucleic acids

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

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model, and utilizes a non-standard approach to defining the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes – disconnected dielectric boundary around the solute-ion or ion-ion pairs. Fully analytical description of all energymore » components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force (PMF) for Na+-Cl− ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of DNA duplex; these differences in the counterion binding patters were shown earlier to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native Thymine bases are used to explore the physics behind CoHex-Thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-Thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range, and may be important to consider in the context of methylation effects on DNA condensation.« less

Explicit ions/implicit water generalized Born model for nucleic acids

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

2018-05-01

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

VEDA: a web-based virtual environment for dynamic atomic force microscopy.

PubMed

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

NASA Astrophysics Data System (ADS)

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Simulated Data for High Temperature Composite Design

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Abumeri, Galib H.

2006-01-01

The paper describes an effective formal method that can be used to simulate design properties for composites that is inclusive of all the effects that influence those properties. This effective simulation method is integrated computer codes that include composite micromechanics, composite macromechanics, laminate theory, structural analysis, and multi-factor interaction model. Demonstration of the method includes sample examples for static, thermal, and fracture reliability for a unidirectional metal matrix composite as well as rupture strength and fatigue strength for a high temperature super alloy. Typical results obtained for a unidirectional composite show that the thermal properties are more sensitive to internal local damage, the longitudinal properties degrade slowly with temperature, the transverse and shear properties degrade rapidly with temperature as do rupture strength and fatigue strength for super alloys.

PSI-Center Simulations of Validation Platform Experiments

NASA Astrophysics Data System (ADS)

Nelson, B. A.; Akcay, C.; Glasser, A. H.; Hansen, C. J.; Jarboe, T. R.; Marklin, G. J.; Milroy, R. D.; Morgan, K. D.; Norgaard, P. C.; Shumlak, U.; Victor, B. S.; Sovinec, C. R.; O'Bryan, J. B.; Held, E. D.; Ji, J.-Y.; Lukin, V. S.

2013-10-01

The Plasma Science and Innovation Center (PSI-Center - http://www.psicenter.org) supports collaborating validation platform experiments with extended MHD simulations. Collaborators include the Bellan Plasma Group (Caltech), CTH (Auburn U), FRX-L (Los Alamos National Laboratory), HIT-SI (U Wash - UW), LTX (PPPL), MAST (Culham), Pegasus (U Wisc-Madison), PHD/ELF (UW/MSNW), SSX (Swarthmore College), TCSU (UW), and ZaP/ZaP-HD (UW). Modifications have been made to the NIMROD, HiFi, and PSI-Tet codes to specifically model these experiments, including mesh generation/refinement, non-local closures, appropriate boundary conditions (external fields, insulating BCs, etc.), and kinetic and neutral particle interactions. The PSI-Center is exploring application of validation metrics between experimental data and simulations results. Biorthogonal decomposition is proving to be a powerful method to compare global temporal and spatial structures for validation. Results from these simulation and validation studies, as well as an overview of the PSI-Center status will be presented.

Biodiversity and ecosystem stability across scales in metacommunities

PubMed Central

Wang, Shaopeng; Loreau, Michel

2016-01-01

Although diversity-stability relationships have been extensively studied in local ecosystems, the global biodiversity crisis calls for an improved understanding of these relationships in a spatial context. Here we use a dynamical model of competitive metacommunities to study the relationships between species diversity and ecosystem variability across scales. We derive analytic relationships under a limiting case; these results are extended to more general cases with numerical simulations. Our model shows that, while alpha diversity decreases local ecosystem variability, beta diversity generally contributes to increasing spatial asynchrony among local ecosystems. Consequently, both alpha and beta diversity provide stabilizing effects for regional ecosystems, through local and spatial insurance effects, respectively. We further show that at the regional scale, the stabilizing effect of biodiversity increases as spatial environmental correlation increases. Our findings have important implications for understanding the interactive effects of global environmental changes (e.g. environmental homogenization) and biodiversity loss on ecosystem sustainability at large scales. PMID:26918536

A new physical model with multilayer architecture for facial expression animation using dynamic adaptive mesh.

PubMed

Zhang, Yu; Prakash, Edmond C; Sung, Eric

2004-01-01

This paper presents a new physically-based 3D facial model based on anatomical knowledge which provides high fidelity for facial expression animation while optimizing the computation. Our facial model has a multilayer biomechanical structure, incorporating a physically-based approximation to facial skin tissue, a set of anatomically-motivated facial muscle actuators, and underlying skull structure. In contrast to existing mass-spring-damper (MSD) facial models, our dynamic skin model uses the nonlinear springs to directly simulate the nonlinear visco-elastic behavior of soft tissue and a new kind of edge repulsion spring is developed to prevent collapse of the skin model. Different types of muscle models have been developed to simulate distribution of the muscle force applied on the skin due to muscle contraction. The presence of the skull advantageously constrain the skin movements, resulting in more accurate facial deformation and also guides the interactive placement of facial muscles. The governing dynamics are computed using a local semi-implicit ODE solver. In the dynamic simulation, an adaptive refinement automatically adapts the local resolution at which potential inaccuracies are detected depending on local deformation. The method, in effect, ensures the required speedup by concentrating computational time only where needed while ensuring realistic behavior within a predefined error threshold. This mechanism allows more pleasing animation results to be produced at a reduced computational cost.

Protostellar Disk Instabilities and the Formation of Substellar Companions

NASA Astrophysics Data System (ADS)

Pickett, Brian K.; Durisen, Richard H.; Cassen, Patrick; Mejia, Annie C.

2000-09-01

Recent numerical simulations of self-gravitating protostellar disks have suggested that gravitational instabilities can lead to the production of substellar companions. In these simulations, the disk is typically assumed to be locally isothermal; i.e., the initial, axisymmetric temperature in the disk remains everywhere unchanged. Such an idealized condition implies extremely efficient cooling for outwardly moving parcels of gas. While we have seen disk disruption in our own locally isothermal simulations of a small, massive protostellar disk, no long-lived companions formed as a result of the instabilities. Instead, thermal and tidal effects and the complex interactions of the disk material prevented permanent condensations from forming, despite the vigorous growth of spiral instabilities. In order to compare our results more directly with those of other authors, we here present three-dimensional evolutions of an older, larger, but less massive protostellar disk. We show that potentially long-lived condensations form only for the extreme of local isothermality, and then only when severe restrictions are placed on the natural tendency of the protostellar disk to expand in response to gravitational instabilities. A more realistic adiabatic evolution leads to vertical and radial expansion of the disk but no clump formation. We conclude that isothermal disk calculations cannot demonstrate companion formation by disk fragmentation but only suggest it at best. It will be necessary in future numerical work on this problem to treat the disk thermodynamics more realistically.

Re-Sonification of Objects, Events, and Environments

NASA Astrophysics Data System (ADS)

Fink, Alex M.

Digital sound synthesis allows the creation of a great variety of sounds. Focusing on interesting or ecologically valid sounds for music, simulation, aesthetics, or other purposes limits the otherwise vast digital audio palette. Tools for creating such sounds vary from arbitrary methods of altering recordings to precise simulations of vibrating objects. In this work, methods of sound synthesis by re-sonification are considered. Re-sonification, herein, refers to the general process of analyzing, possibly transforming, and resynthesizing or reusing recorded sounds in meaningful ways, to convey information. Applied to soundscapes, re-sonification is presented as a means of conveying activity within an environment. Applied to the sounds of objects, this work examines modeling the perception of objects as well as their physical properties and the ability to simulate interactive events with such objects. To create soundscapes to re-sonify geographic environments, a method of automated soundscape design is presented. Using recorded sounds that are classified based on acoustic, social, semantic, and geographic information, this method produces stochastically generated soundscapes to re-sonify selected geographic areas. Drawing on prior knowledge, local sounds and those deemed similar comprise a locale's soundscape. In the context of re-sonifying events, this work examines processes for modeling and estimating the excitations of sounding objects. These include plucking, striking, rubbing, and any interaction that imparts energy into a system, affecting the resultant sound. A method of estimating a linear system's input, constrained to a signal-subspace, is presented and applied toward improving the estimation of percussive excitations for re-sonification. To work toward robust recording-based modeling and re-sonification of objects, new implementations of banded waveguide (BWG) models are proposed for object modeling and sound synthesis. Previous implementations of BWGs use arbitrary model parameters and may produce a range of simulations that do not match digital waveguide or modal models of the same design. Subject to linear excitations, some models proposed here behave identically to other equivalently designed physical models. Under nonlinear interactions, such as bowing, many of the proposed implementations exhibit improvements in the attack characteristics of synthesized sounds.

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

Vener, M. V., E-mail: mikhail.vener@gmail.com; Odinokov, A. V.; Wehmeyer, C.

Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)–glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898–915 (2011)]. These structures are stabilized by the short {sup +}N–H⋯O{sup −} bonds.more » Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm{sup −1}. It is caused by the asymmetric stretching vibrations of the {sup +}N–H⋯O{sup −} fragment. Result of the present paper suggests that infrared spectroscopy in the 2000–2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.« less

Quantum Drude friction for time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Neuhauser, Daniel; Lopata, Kenneth

2008-10-01

Friction is a desired property in quantum dynamics as it allows for localization, prevents backscattering, and is essential in the description of multistage transfer. Practical approaches for friction generally involve memory functionals or interactions with system baths. Here, we start by requiring that a friction term will always reduce the energy of the system; we show that this is automatically true once the Hamiltonian is augmented by a term of the form ∫a(q ;n0)[∂j(q,t)/∂t]ṡJ(q)dq, which includes the current operator times the derivative of its expectation value with respect to time, times a local coefficient; the local coefficient will be fitted to experiment, to more sophisticated theories of electron-electron interaction and interaction with nuclear vibrations and the nuclear background, or alternately, will be artificially constructed to prevent backscattering of energy. We relate this term to previous results and to optimal control studies, and generalize it to further operators, i.e., any operator of the form ∫a(q ;n0)[∂c(q,t)/∂t]ṡC(q)dq (or a discrete sum) will yield friction. Simulations of a small jellium cluster, both in the linear and highly nonlinear excitation regime, demonstrate that the friction always reduces energy. The energy damping is essentially double exponential; the long-time decay is almost an order of magnitude slower than the rapid short-time decay. The friction term stabilizes the propagation (split-operator propagator here), therefore increasing the time-step needed for convergence, i.e., reducing the overall computational cost. The local friction also allows the simulation of a metal cluster in a uniform jellium as the energy loss in the excitation due to the underlying corrugation is accounted for by the friction. We also relate the friction to models of coupling to damped harmonic oscillators, which can be used for a more sophisticated description of the coupling, and to memory functionals. Our results open the way to very simple finite grid description of scattering and multistage conductance using time-dependent density functional theory away from the linear regime, just as absorbing potentials and self-energies are useful for noninteracting systems and leads.

Modeling of Outer Radiation Belt Electron Scattering due to Spatial and Spectral Properties of ULF Waves

NASA Astrophysics Data System (ADS)

Tornquist, Mattias

The research presented in this thesis covers wave-particle interactions for relativistic (0.5-10 MeV) electrons in Earth's outer radiation belt (r = 3-7 RE, or L-shells: L = 3-7) interacting with magnetospheric Pc-5 (ULF) waves. This dissertation focuses on ideal models for short and long term electron energy and radial position scattering caused by interactions with ULF waves. We use test particle simulations to investigate these wave-particle interactions with ideal wave and magnetic dipole fields. We demonstrate that the wave-particle phase can cause various patterns in phase space trajectories, i.e. local acceleration, and that for a global electron population, for all initial conditions accounted for, has a negligible net energy scattering. Working with GSM polar coordinates, the relevant wave field components are EL, Ephi and Bz, where we find that the maximum energy scattering is 3-10 times more effective for Ephi compared to EL in a magnetic dipole field with a realistic dayside compression amplitude. We also evaluate electron interactions with two coexisting waves for a set of small frequency separations and phases, where it is confirmed that multi-resonant transport is possible for overlapping resonances in phase space when the Chirikov criterion is met (stochasticity parameter K = 1). The electron energy scattering enhances with decreasing frequency separation, i.e. increasing K, and is also dependent on the phases of the waves. The global acceleration is non-zero, can be onset in about 1 hour and last for > 4 hours. The adiabatic wave-particle interaction discussed up to this point can be regarded as short-term scattering ( tau ˜ hours ). When the physical problem extends to longer time scales (tau ˜ days ) the process ceases to be adiabatic due to the introduction of stochastic element in the system and becomes a diffusive process. We show that any mode in a broadband spectrum can contribute to the total diffusion rate for a particular drift frequency within the spectral band via dynamic phases. Each mode contributes maximally at a phase reset frequency fr = 2.63fk, where fk is the mode frequency. We experiment with electron diffusion due to interaction with wave broadband spectra in MLT sectors and find the phase reset effect being strongest when there is no azimuthal wave vector (msec = 0) within the sector. DLL rapidly coheres to the local PSD as the wave number increases and, for example, at msec = 1.00+/-0.25 the effect of phase resets is only 10-30% as strong as for msec = 0. Since phase resets depend on particle drift frequencies when MLT sectors are involved, a consequence is that DLL must adjust as a function of L-shell as well. For example, from the local PSD as the sole contributor to diffusion Schulz and Lanzerotte (1979) has shown that DLL ˜ L6 , but we prove that the function becomes DLL ˜ L5 with some variations due to fd and MLT sector width. The final part of this dissertation evaluates a pre storm commencement event on November 7, 2004, when Earth's magnetopause was struck by a high-speed solar wind with a mostly northward component of interplanetary magnetic field. We obtained a global MHD field simulated by the OpenGGC model for the interval 17:00-18:40 in universal time from NASA's Community Coordinated Modeling Center. Global distribution plots of the electric and magnetic field PSD reveal strong ULF waves spanning the whole dayside sector. There are distinct electric field modes at approximately 0.9, 2.3 and 3.7-6.3 mHz within the dayside sector, which we then used in test-particle simulations and the variance calculations in order to evaluate the diffusion coefficients. To ensure diffusion by sufficient stochasticity, we run the event by repeating the interval 10 times in series for a total duration of 12 hours. For the wave electric fields, the predicted diffusion coefficient due to local PSD matches the outcome from simulated electron scattering at 0.9 and 2.3 mHz. The diffusion due to the wider frequency band at 3.7-6.3 mHz does not fit the PSD profile alone, and requires phase resets in non-resonant modes within the spectrum to yield an agreement between the calculations and the simulations. Furthermore, only msec = 1 provides the correct solution. We have thus demonstrated the importance in including both the MLT sector width and wave number as additional significant factors apart from the local PSD in determining the diffusion coefficient for a realistic wave field. (Abstract shortened by UMI.).

Mechanisms of interfacial reactivity in near surface and extreme environments

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

Chen, Ying; Balaska, Eric; Weare, John

The local water structure surrounding ions in aqueous solutions greatly affects their chemical properties such as reaction rates, ion association, and proton and electron transport. These properties result in the behavior of ions in natural aqueous environments. For example ore transport is facilitated by chloride ion pair formation and the reaction of ions in an interface is strongly dependent on the dehydration of the ion hydration shell. We are developing the use of high-­resolution XAFS observations and 1st principles based MD-­XAFS analysis (spectra simulated using 1st principle methods with no adjustable parameters, AIMD) to interpret the solution properties of stronglymore » interacting aqueous solutes under arbitrary pressure and temperature conditions. In the 1st principle MD-­XAFS method density functional theory (DFT) based MD simulations(Car and Parrinello, 1985) are used to generate a large ensemble of structural snap shots of the hydration region. These are then used to generate scattering intensities. I emphasize three points about this novel approach to analyzing XAFS data. 1st: As illustrated in Figure 1, the level of agreement between the calculated and observed intensities is considerably higher than has been obtained by any XAFS analysis to date (note 2nd shell region, R> 2 Å). 2nd: This result was obtained from a parameter free simulation with no fitting of the interaction potentials to any data. This supports the use of these methods for more difficult environments and more complex solutes (polyions). 3rd: New information about the shell structure (Figure 1) is now available because of this more detailed agreement. We note also that both multiple scattering and second shell features are well represented in the analysis. As far as we know this is the 1st analysis of second shell structure and multiple scattering. Excellent agreement has been obtained for most of the third row metal ions: Ca 2+, Zn 2+, Cu 2+, Ni 2+, Co 2+, Mn 2+, Fe 3+, Cr 3+. Calculations on these systems are demanding because of their open electronic shells, and high ionic charge. Principal Investigator: Professor John Weare (University of California, San Diego) The prediction of the interactions of geochemical fluids with minerals, nanoparticles, and colloids under extreme near surface conditions of temperature (T) and pressure (P) is a grand challenge research need in geosciences (U.S. DOE 2007, Basic Research Needs for Geosciences: Facilitating the 21st Energy Systems.). To evaluate the impact of these processes on energy production and management strategies it is necessary to have a high level of understanding of the interaction between complex natural fluids and mineral formations. This program emphasizes 1st principle parameter free simulations of complex chemical processes in solutions, in the mineral phase, and in the interfaces between these phases The development of new computational tools (with emphasis on oxide materials and reaction dynamics) tailored to treat wide range of conditions and time scales experienced in such geochemical applications is has been developed. Because of the sensitivity of the interaction in these systems to electronic structure and local bonding environments, and of the need to describe bond breaking/formation, our simulations are based on interactions calculated at the electronic structure level (ab-initio molecular dynamics, AIMD). The progress in the computational aspects of program may be summarized in terms of the following themes (objectives); Development of efficient parameter free dynamical simulation technology based on 1st principles force and energy calculations especially adapted for geochemical applications (e.g., mineral, interfaces and aqueous solutions) (continuing program); Calculation of the dynamics of water structure of in the surface-water interface of transition metal oxides and oxihydroxides; and Development of improved (beyond DFT+GGA) electronic structure calculations for minerals and the interface region that more accurately calculate electron correlation, spin density, and localization. The focus of the program is also on the iron oxide and oxihydroxide minerals and Fe 2+(aq)/Fe 3+(cr) oxidation in the mineral solution interface region. These methods included the development of model Hamilitonian methods that can be solved to near convergence for single site models (DMFT) and many-body perturbation methods (MP2, GW); Development of time decomposition methods to extend time scales of molecular dynamics (MD) simulations and support the use of high complexity electronic structure calculations (MP2, CCSD(T)) of forces for use in dynamical simulations where very high chemical accuracy is required (microsolvated reactions in absorbed surface layers); and The development of a new linear scaling finite element solver for eigenvalue problem that supports solution of quantum problems with unusual potential and boundary values. Application progress of the above new simulation technology to problems of geochemical interests includes; The prediction of metal oxide surface structure and the reduction/oxidation of Fe 3+(cr)/Fe 2+ (aq) in metal oxide (hematite, goethite)/solution interfaces. Result: water interacts strongly with the 001 Hematite surface; interaction of water with the 100 goethite is weak; The study of ion solvation and the composition of ion hydration shells under extreme conditions (focus on Fe 3+/2+, Al 3+ and Mg 2+ and their hydroxide speciation). Result: Ion association in water solutions can be calculated from 1st principle methods. Efficient sampling of the free energy requires more development; The continued development of new high resolution analysis of XAFS scattering of disordered systems (particularly Al, Mg) and of XANES calculations for aqueous ions. Result: EXAFS spectra can be calculated to high accuracy with DFT level dynamic simulations; The exploration of electron localization and electron transport in metal oxides (highly correlated materials). Result: Proper description of electron localization requires levels of calculation beyond DFT; and Localization of electrons in DFT type Hamiltonians was studied. Result: For very Dirac high exchange new solutions (New unphysical bifrucations) to the eigenvalue problem are found. The program was highly collaborative involving faculty and students in mathematics, physics and computer science departments as well as coworkers at the Pacific Northwest National Laboratories (PNNL). The students in this program had the opportunity to develop skills in the development of methods, the implementation of method on high performance parallel computers and the application of these methods to problem in geochemical science. Much of the software that was developed was incorporated in the NWchem software package maintained by PNNL.« less

Flame-Vortex Interactions in Microgravity to Improve Models of Turbulent Combustion

NASA Technical Reports Server (NTRS)

Driscoll, James F.

1999-01-01

A unique flame-vortex interaction experiment is being operated in microgravity in order to obtain fundamental data to assess the Theory of Flame Stretch which will be used to improve models of turbulent combustion. The experiment provides visual images of the physical process by which an individual eddy in a turbulent flow increases the flame surface area, changes the local flame propagation speed, and can extinguish the reaction. The high quality microgravity images provide benchmark data that are free from buoyancy effects. Results are used to assess Direct Numerical Simulations of Dr. K. Kailasanath at NRL, which were run for the same conditions.

Intramolecular interactions in polymethylenic chains with polar end groups: The spectroscopic signature

NASA Astrophysics Data System (ADS)

Milani, Alberto; Castiglioni, Chiara; Brambilla, Luigi; Zerbi, Giuseppe

2012-02-01

We present a computational study based on DFT simulations of the infrared spectra of several short alkyl chains carrying polar end groups. The work aims to provide guidelines for the detection of marker bands signalling the occurrence of specific intramolecular interactions between the polar head and CH2 groups at different distances. In particular, the CH stretching region is investigated and new features assigned to normal modes localized on the CH2 groups nearest to the electron-withdrawing atom are identified. The study has been extended also to the rationalization of the experimental IR features shown by a 1-Chloroeicosane (C20H41Cl) sample.

Rocket Plume Scaling for Orion Wind Tunnel Testing

NASA Technical Reports Server (NTRS)

Brauckmann, Gregory J.; Greathouse, James S.; White, Molly E.

2011-01-01

A wind tunnel test program was undertaken to assess the jet interaction effects caused by the various solid rocket motors used on the Orion Launch Abort Vehicle (LAV). These interactions of the external flowfield and the various rocket plumes can cause localized aerodynamic disturbances yielding significant and highly non-linear control amplifications and attenuations. This paper discusses the scaling methodologies used to model the flight plumes in the wind tunnel using cold air as the simulant gas. Comparisons of predicted flight, predicted wind tunnel, and measured wind tunnel forces-and-moments and plume flowfields are made to assess the effectiveness of the selected scaling methodologies.

Exclusion processes: Short-range correlations induced by adhesion and contact interactions

NASA Astrophysics Data System (ADS)

Ascolani, Gianluca; Badoual, Mathilde; Deroulers, Christophe

2013-01-01

We analyze the out-of-equilibrium behavior of exclusion processes where agents interact with their nearest neighbors, and we study the short-range correlations which develop because of the exclusion and other contact interactions. The form of interactions we focus on, including adhesion and contact-preserving interactions, is especially relevant for migration processes of living cells. We show the local agent density and nearest-neighbor two-point correlations resulting from simulations on two-dimensional lattices in the transient regime where agents invade an initially empty space from a source and in the stationary regime between a source and a sink. We compare the results of simulations with the corresponding quantities derived from the master equation of the exclusion processes, and in both cases, we show that, during the invasion of space by agents, a wave of correlations travels with velocity v(t)˜t-1/2. The relative placement of this wave to the agent density front and the time dependence of its height may be used to discriminate between different forms of contact interactions or to quantitatively estimate the intensity of interactions. We discuss, in the stationary density profile between a full and an empty reservoir of agents, the presence of a discontinuity close to the empty reservoir. Then we develop a method for deriving approximate hydrodynamic limits of the processes. From the resulting systems of partial differential equations, we recover the self-similar behavior of the agent density and correlations during space invasion.

Study of the velocity gradient tensor in turbulent flow

NASA Technical Reports Server (NTRS)

Cheng, Wei-Ping; Cantwell, Brian

1996-01-01

The behavior of the velocity gradient tensor, A(ij)=delta u(i)/delta x(j), was studied using three turbulent flows obtained from direct numerical simulation The flows studies were: an inviscid calculation of the interaction between two vortex tubes, a homogeneous isotropic flow, and a temporally evolving planar wake. Self-similar behavior for each flow was obtained when A(ij) was normalized with the mean strain rate. The case of the interaction between two vortex tubes revealed a finite sized coherent structure with topological characteristics predictable by a restricted Euler model. This structure was found to evolve with the peak vorticity as the flow approached singularity. Invariants of A(ij) within this structure followed a straight line relationship of the form: gamma(sup 3)+gammaQ+R=0, where Q and R are the second and third invariants of A(ij), and the eigenvalue gamma is nearly constant over the volume of this structure. Data within this structure have local strain topology of unstable-node/saddle/saddle. The characteristics of the velocity gradient tensor and the anisotropic part of a related acceleration gradient tensor H(ij) were also studied for a homogeneous isotropic flow and a temporally evolving planar wake. It was found that the intermediate principal eigenvalue of the rate-of-strain tensor of H(ij) tended to be negative, with local strain topology of the type stable-node/saddle/saddle. There was also a preferential eigenvalue direction. The magnitude of H(ij) in the wake flow was found to be very small when data were conditioned at high local dissipation regions. This result was not observed in the relatively low Reynolds number simulation of homogeneous isotropic flow. A restricted Euler model of the evolution of A(ij) was found to reproduce many of the topological features identified in the simulations.

Effective grid-dependent dispersion coefficient for conservative and reactive transport simulations in heterogeneous porous media

NASA Astrophysics Data System (ADS)

Cortinez, J. M.; Valocchi, A. J.; Herrera, P. A.

2013-12-01

Because of the finite size of numerical grids, it is very difficult to correctly account for processes that occur at different spatial scales to accurately simulate the migration of conservative and reactive compounds dissolved in groundwater. In one hand, transport processes in heterogeneous porous media are controlled by local-scale dispersion associated to transport processes at the pore-scale. On the other hand, variations of velocity at the continuum- or Darcy-scale produce spreading of the contaminant plume, which is referred to as macro-dispersion. Furthermore, under some conditions both effects interact, so that spreading may enhance the action of local-scale dispersion resulting in higher mixing, dilution and reaction rates. Traditionally, transport processes at different spatial scales have been included in numerical simulations by using a single dispersion coefficient. This approach implicitly assumes that the separate effects of local-dispersion and macro-dispersion can be added and represented by a unique effective dispersion coefficient. Moreover, the selection of the effective dispersion coefficient for numerical simulations usually do not consider the filtering effect of the grid size over the small-scale flow features. We have developed a multi-scale Lagragian numerical method that allows using two different dispersion coefficients to represent local- and macro-scale dispersion. This technique considers fluid particles that carry solute mass and whose locations evolve according to a deterministic component given by the grid-scale velocity and a stochastic component that corresponds to a block-effective macro-dispersion coefficient. Mass transfer between particles due to local-scale dispersion is approximated by a meshless method. We use our model to test under which transport conditions the combined effect of local- and macro-dispersion are additive and can be represented by a single effective dispersion coefficient. We also demonstrate that for the situations where both processes are additive, an effective grid-dependent dispersion coefficient can be derived based on the concept of block-effective dispersion. We show that the proposed effective dispersion coefficient is able to reproduce dilution, mixing and reaction rates for a wide range of transport conditions similar to the ones found in many practical applications.

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

NASA Astrophysics Data System (ADS)

Williamson, R. L.; Capps, N. A.; Liu, W.; Rashid, Y. R.; Wirth, B. D.

2016-11-01

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial ( R- Z) or plane radial-circumferential ( R- θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. In comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

DOE PAGES

Williamson, R. L.; Capps, N. A.; Liu, W.; ...

2016-09-27

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial (R-Z) ormore » plane radial-circumferential (R-θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used in this paper to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. Finally, in comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.« less

Simulating the decentralized processes of the human immune system in a virtual anatomy model.

PubMed

Sarpe, Vladimir; Jacob, Christian

2013-01-01

Many physiological processes within the human body can be perceived and modeled as large systems of interacting particles or swarming agents. The complex processes of the human immune system prove to be challenging to capture and illustrate without proper reference to the spatial distribution of immune-related organs and systems. Our work focuses on physical aspects of immune system processes, which we implement through swarms of agents. This is our first prototype for integrating different immune processes into one comprehensive virtual physiology simulation. Using agent-based methodology and a 3-dimensional modeling and visualization environment (LINDSAY Composer), we present an agent-based simulation of the decentralized processes in the human immune system. The agents in our model - such as immune cells, viruses and cytokines - interact through simulated physics in two different, compartmentalized and decentralized 3-dimensional environments namely, (1) within the tissue and (2) inside a lymph node. While the two environments are separated and perform their computations asynchronously, an abstract form of communication is allowed in order to replicate the exchange, transportation and interaction of immune system agents between these sites. The distribution of simulated processes, that can communicate across multiple, local CPUs or through a network of machines, provides a starting point to build decentralized systems that replicate larger-scale processes within the human body, thus creating integrated simulations with other physiological systems, such as the circulatory, endocrine, or nervous system. Ultimately, this system integration across scales is our goal for the LINDSAY Virtual Human project. Our current immune system simulations extend our previous work on agent-based simulations by introducing advanced visualizations within the context of a virtual human anatomy model. We also demonstrate how to distribute a collection of connected simulations over a network of computers. As a future endeavour, we plan to use parameter tuning techniques on our model to further enhance its biological credibility. We consider these in silico experiments and their associated modeling and optimization techniques as essential components in further enhancing our capabilities of simulating a whole-body, decentralized immune system, to be used both for medical education and research as well as for virtual studies in immunoinformatics.

Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.

Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of 'atom typing' QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the 'size' of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and transferable models for the interactions between the quantum mechanical system and their solvated surroundings.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

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

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

FATSLiM: a fast and robust software to analyze MD simulations of membranes.

PubMed

Buchoux, Sébastien

2017-01-01

When studying biological membranes, Molecular Dynamics (MD) simulations reveal to be quite complementary to experimental techniques. Because the simulated systems keep increasing both in size and complexity, the analysis of MD trajectories need to be computationally efficient while being robust enough to perform analysis on membranes that may be curved or deformed due to their size and/or protein-lipid interactions. This work presents a new software named FATSLiM ('Fast Analysis Toolbox for Simulations of Lipid Membranes') that can extract physical properties from MD simulations of membranes (with or without interacting proteins). Because it relies on the calculation of local normals, FATSLiM does not depend of the bilayer morphology and thus can handle with the same accuracy vesicles for instance. Thanks to an efficiency-driven development, it is also fast and consumes a rather low amount of memory. FATSLiM (http://fatslim.github.io) is a stand-alone software written in Python. Source code is released under the GNU GPLv3 and is freely available at https://github.com/FATSLiM/fatslim A complete online documentation including instructions for platform-independent installation is available at http://pythonhosted.org/fatslim CONTACT: sebastien.buchoux@u-picardie.frSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

Matrix Completion Optimization for Localization in Wireless Sensor Networks for Intelligent IoT

PubMed Central

Nguyen, Thu L. N.; Shin, Yoan

2016-01-01

Localization in wireless sensor networks (WSNs) is one of the primary functions of the intelligent Internet of Things (IoT) that offers automatically discoverable services, while the localization accuracy is a key issue to evaluate the quality of those services. In this paper, we develop a framework to solve the Euclidean distance matrix completion problem, which is an important technical problem for distance-based localization in WSNs. The sensor network localization problem is described as a low-rank dimensional Euclidean distance completion problem with known nodes. The task is to find the sensor locations through recovery of missing entries of a squared distance matrix when the dimension of the data is small compared to the number of data points. We solve a relaxation optimization problem using a modification of Newton’s method, where the cost function depends on the squared distance matrix. The solution obtained in our scheme achieves a lower complexity and can perform better if we use it as an initial guess for an interactive local search of other higher precision localization scheme. Simulation results show the effectiveness of our approach. PMID:27213378

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

PubMed

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

2016-08-25

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

Three-Dimensional Numerical Simulation on Passively Excited Flows by Distributed Local Hot Sources Settled at the D" Layer Below Hotspots and/or Large-Scale Cool Masses at Subduction Zones Within the Static Layered Mantle

NASA Astrophysics Data System (ADS)

Eguchi, T.; Matsubara, K.; Ishida, M.

2001-12-01

To unveil dynamic process associated with three-dimensional unsteady mantle convection, we carried out numerical simulation on passively exerted flows by simplified local hot sources just above the CMB and large-scale cool masses beneath smoothed subduction zones. During the study, we used our individual code developed with the finite difference method. The basic three equations are for the continuity, the motion with the Boussinesq (incompressible) approximation, and the (thermal) energy conservation. The viscosity of our model is sensitive to temperature. To get time integration with high precision, we used the Newton method. In detail, the size and thermal energy of the hot or cool sources are not uniform along the latitude, because we could not select uniform local volumes assigned for the sources within the finite difference grids throughout the mantle. Our results, thus, accompany some latitude dependence. First, we treated the case of the hotspots, neglecting the contribution of the subduction zones. The local hot sources below the currently active hotspots were settled as dynamic driving forces included in the initial condition. Before starting the calculation, we assumed that the mantle was statically layered with zero velocity component. The thermal anomalies inserted instantaneously in the initial condition do excite dynamically passive flows. The type of the initial hot sources was not 'plume' but 'thermal.' The simulation results represent that local upwelling flows which were directly excited over the initial heat sources reached the upper mantle by approximately 30 My during the calculation. Each of the direct upwellings above the hotspots has its own dynamic potential to exert concentric down- and up-welling flows, alternately, at large distances. Simultaneously, the direct upwellings interact mutually within the spherical mantle. As an interesting feature, we numerically observed secondary upwellings somewhere in a wide region covering east Eurasia to the Bering Sea where no hot sources were initially input. It seems that the detailed location of the secondary upwellings depends partly on the numerical parameters such as the radial profile of mantle viscosity especially at the D" layer, etc., because the secondary flows are provoked by dynamic interaction among the distributed direct upwellings just above the CMB. Our results suggest that if we assume not only non-zero time delays during the input of the local hot sources but also parameters related with the difference of their historical surface flux rates, the pattern of the passively excited flows will be different from that obtained with the simultaneously settled hot sources stated above. Second, we simultaneously incorporated simplified thermal anomaly models associated with both the distributed local hotspots and the global subduction zones, as dynamic origins in the initial condition for the static layered mantle. In this case, the simulation result represents that the pattern of secondary radial flows, being different from those in the earlier case, is sensitive to the relative strength between the positive dynamic buoyancy integrated over all of the local hot sources below the hotspots and the total negative buoyancy beneath the subduction zones.

The influence of interspecific interactions on species range expansion rates

USGS Publications Warehouse

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D.; Schurr, Frank M.; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H.; Dullinger, Stefan; Edwards, Thomas C.; Hickler, Thomas; Higgins, Steven I.; Nabel, Julia E.M.S.; Pagel, Jörn; Normand, Signe

2014-01-01

Ongoing and predicted global change makes understanding and predicting species’ range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species.

The influence of interspecific interactions on species range expansion rates.

PubMed

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D; Schurr, Frank M; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H; Dullinger, Stefan; Edwards, Thomas C; Hickler, Thomas; Higgins, Steven I; Nabel, Julia E M S; Pagel, Jörn; Normand, Signe

2014-12-01

Ongoing and predicted global change makes understanding and predicting species' range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species.

The influence of interspecific interactions on species range expansion rates

PubMed Central

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D.; Schurr, Frank M.; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H.; Dullinger, Stefan; Edwards, Thomas C.; Hickler, Thomas; Higgins, Steven I.; Nabel, Julia E. M. S.; Pagel, Jörn; Normand, Signe

2014-01-01

Ongoing and predicted global change makes understanding and predicting species’ range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species. PMID:25722537

Role of Longwave Cloud-Radiation Feedback in the Simulation of the Madden-Julian Oscillation

NASA Technical Reports Server (NTRS)

Kim, Daehyun; Ahn, Min-Seop; Kang, In-Sik; Del Genio, Anthony D.

2015-01-01

The role of the cloud-radiation interaction in the simulation of the Madden-Julian oscillation (MJO) is investigated. A special focus is on the enhancement of column-integrated diabatic heating due to the greenhouse effects of clouds and moisture in the region of anomalous convection. The degree of this enhancement, the greenhouse enhancement factor (GEF), is measured at different precipitation anomaly regimes as the negative ratio of anomalous outgoing longwave radiation to anomalous precipitation. Observations show that the GEF varies significantly with precipitation anomaly and with the MJO cycle. The greenhouse enhancement is greater in weak precipitation anomaly regimes and its effectiveness decreases monotonically with increasing precipitation anomaly. The GEF also amplifies locally when convection is strengthened in association with the MJO, especially in the weak precipitation anomaly regime (less than 5 mm day(exp -1)). A robust statistical relationship is found among CMIP5 climate model simulations between the GEF and the MJO simulation fidelity. Models that simulate a stronger MJO also simulate a greater GEF, especially in the weak precipitation anomaly regime (less than 5 mm day(exp -1)). Models with a greater GEF in the strong precipitation anomaly regime (greater than 30 mm day(-1)) represent a slightly slower MJO propagation speed. Many models that lack the MJO underestimate the GEF in general and in particular in the weak precipitation anomaly regime. The results herein highlight that the cloud-radiation interaction is a crucial process for climate models to correctly represent the MJO.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

Development of an Intelligent Digital Watershed to understand water-human interaction for a sustainable Agroeconomy in Midwest USA

NASA Astrophysics Data System (ADS)

Mishra, S. K.; Rapolu, U.; Ding, D.; Muste, M.; Bennett, D.; Schnoor, J. L.

2011-12-01

Human activity is intricately linked to the quality and quantity of water resources. Although many studies have examined water-human interaction, the complexity of such coupled systems is not well understood largely because of gaps in our knowledge of water-cycle processes which are heavily influenced by socio-economic drivers. Considerable research has been performed to develop an understanding of the impact of local land use decisions on field and catchment processes at an annual basis. Still less is known about the impact of economic and environmental outcomes on decision-making processes at the local and national level. Traditional geographic information management systems lack the ability to support the modeling and analysis of complex spatial processes. New frameworks are needed to track, query, and analyze the massive amounts of data generated by ensembles of simulations produced by multiple models that couple socioeconomic and natural system processes. On this context, we propose to develop an Intelligent Digital Watershed (IDW) which fuses emerging concepts of Digital Watershed (DW). DW is a comprehensive characterization of the eco hydrologic systems based on the best available digital data generated by measurements and simulations models. Prototype IDW in the form of a cyber infrastructure based engineered system will facilitate novel insights into human/environment interactions through multi-disciplinary research focused on watershed-related processes at multiple spatio-temporal scales. In ongoing effort, the prototype IDW is applied to Clear Creek watershed, an agricultural dominating catchment in Iowa, to understand water-human processes relevant to management decisions by farmers regarding agro ecosystems. This paper would also lay out the database design that stores metadata about simulation scenarios, scenario inputs and outputs, and connections among these elements- essentially the database. The paper describes the cyber infrastructure and workflows developed for connecting the IDW modeling tools: ABM, Data-Driven Modeling, and SWAT.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones. PMID:26619280

Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans

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

Lopez, Cesar A.; Unkefer, Clifford J.; Swanson, Basil I.

Mycolactone is the exotoxin produced by Mycobacterium ulcerans and is the virulence factor behind the neglected tropical disease Buruli ulcer. The toxin has a broad spectrum of biological effects within the host organism, stemming from its interaction with at least two molecular targets and the inhibition of protein uptake into the endoplasmic reticulum. Although it has been shown that the toxin can passively permeate into host cells, it is clearly lipophilic. Association with lipid carriers would have substantial implications for the toxin’s distribution within a host organism, delivery to cellular targets, diagnostic susceptibility, and mechanisms of pathogenicity. Yet the toxin’smore » interactions with, and distribution in, lipids are unknown. Herein we have used coarse-grained molecular dynamics simulations, guided by all-atom simulations, to study the interaction of mycolactone with pure and mixed lipid membranes. Using established techniques, we calculated the toxin’s preferential localization, membrane translocation, and impact on membrane physical and dynamical properties. The computed water-octanol partition coefficient indicates that mycolactone prefers to be in an organic phase rather than in an aqueous environment. Our results show that in a solvated membrane environment the exotoxin mainly localizes in the water-membrane interface, with a preference for the glycerol moiety of lipids, consistent with the reported studies that found it in lipid extracts of the cell. The calculated association constant to the model membrane is similar to the reported association constant for Wiskott-Aldrich syndrome protein. Mycolactone is shown to modify the physical properties of membranes, lowering the transition temperature, compressibility modulus, and critical line tension at which pores can be stabilized. It also shows a tendency to behave as a linactant, a molecule that localizes at the boundary between different fluid lipid domains in membranes and promotes inter-mixing of domains. This property has implications for the toxin’s cellular access, T-cell immunosuppression, and therapeutic potential.« less

Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans

DOE PAGES

Lopez, Cesar A.; Unkefer, Clifford J.; Swanson, Basil I.; ...

2018-02-05

Mycolactone is the exotoxin produced by Mycobacterium ulcerans and is the virulence factor behind the neglected tropical disease Buruli ulcer. The toxin has a broad spectrum of biological effects within the host organism, stemming from its interaction with at least two molecular targets and the inhibition of protein uptake into the endoplasmic reticulum. Although it has been shown that the toxin can passively permeate into host cells, it is clearly lipophilic. Association with lipid carriers would have substantial implications for the toxin’s distribution within a host organism, delivery to cellular targets, diagnostic susceptibility, and mechanisms of pathogenicity. Yet the toxin’smore » interactions with, and distribution in, lipids are unknown. Herein we have used coarse-grained molecular dynamics simulations, guided by all-atom simulations, to study the interaction of mycolactone with pure and mixed lipid membranes. Using established techniques, we calculated the toxin’s preferential localization, membrane translocation, and impact on membrane physical and dynamical properties. The computed water-octanol partition coefficient indicates that mycolactone prefers to be in an organic phase rather than in an aqueous environment. Our results show that in a solvated membrane environment the exotoxin mainly localizes in the water-membrane interface, with a preference for the glycerol moiety of lipids, consistent with the reported studies that found it in lipid extracts of the cell. The calculated association constant to the model membrane is similar to the reported association constant for Wiskott-Aldrich syndrome protein. Mycolactone is shown to modify the physical properties of membranes, lowering the transition temperature, compressibility modulus, and critical line tension at which pores can be stabilized. It also shows a tendency to behave as a linactant, a molecule that localizes at the boundary between different fluid lipid domains in membranes and promotes inter-mixing of domains. This property has implications for the toxin’s cellular access, T-cell immunosuppression, and therapeutic potential.« less

Flexible Charged Macromolecules on Mixed Fluid Lipid Membranes: Theory and Monte Carlo Simulations

PubMed Central

Tzlil, Shelly; Ben-Shaul, Avinoam

2005-01-01

Fluid membranes containing charged lipids enhance binding of oppositely charged proteins by mobilizing these lipids into the interaction zone, overcoming the concomitant entropic losses due to lipid segregation and lower conformational freedom upon macromolecule adsorption. We study this energetic-entropic interplay using Monte Carlo simulations and theory. Our model system consists of a flexible cationic polyelectrolyte, interacting, via Debye-Hückel and short-ranged repulsive potentials, with membranes containing neutral lipids, 1% tetravalent, and 10% (or 1%) monovalent anionic lipids. Adsorption onto a fluid membrane is invariably stronger than to an equally charged frozen or uniform membrane. Although monovalent lipids may suffice for binding rigid macromolecules, polyvalent counter-lipids (e.g., phosphatidylinositol 4,5 bisphosphate), whose entropy loss upon localization is negligible, are crucial for binding flexible macromolecules, which lose conformational entropy upon adsorption. Extending Rosenbluth's Monte Carlo scheme we directly simulate polymer adsorption on fluid membranes. Yet, we argue that similar information could be derived from a biased superposition of quenched membrane simulations. Using a simple cell model we account for surface concentration effects, and show that the average adsorption probabilities on annealed and quenched membranes coincide at vanishing surface concentrations. We discuss the relevance of our model to the electrostatic-switch mechanism of, e.g., the myristoylated alanine-rich C kinase substrate protein. PMID:16126828

In-situ electrochemical study of interaction of tribology and corrosion in artificial hip prosthesis simulators.

PubMed

Yan, Yu; Dowson, Duncan; Neville, Anne

2013-02-01

The second generation Metal-on-Metal (MoM) hip replacements have been considered as an alternative to commonly used Polyethylene-on-Metal (PoM) joint prostheses due to polyethylene wear debris induced osteolysis. However, the role of corrosion and the biofilm formed under tribological contact are still not fully understood. Enhanced metal ion concentrations have been reported widely from hair, blood and urine samples of patients who received metal hip replacements and in isolated cases when abnormally high levels have caused adverse local tissue reactions. An understanding of the origin of metal ions is really important in order to design alloys for reduced ion release. Reciprocating pin-on-plate wear tester is a standard instrument to assess the interaction of corrosion and wear. However, more realistic hip simulator can provide a better understanding of tribocorrosion process for hip implants. It is very important to instrument the conventional hip simulator to enable electrochemical measurements. In this study, simple reciprocating pin-on-plate wear tests and hip simulator tests were compared. It was found that metal ions originated from two sources: (a) a depassivation of the contacting surfaces due to tribology (rubbing) and (b) corrosion of nano-sized wear particles generated from the contacting surfaces. Copyright © 2012 Elsevier Ltd. All rights reserved.

Brownian dynamics simulations of simplified cytochrome c molecules in the presence of a charged surface

NASA Astrophysics Data System (ADS)

Gorba, C.; Geyer, T.; Helms, V.

2004-07-01

Simulations were performed for up to 150 simplified spherical horse heart cytochrome c molecules in the presence of a charged surface, which serves as an approximate model for a lipid membrane. Screened electrostatic and short-ranged attractive as well as repulsive van der Waals forces for interparticle and particle-membrane interactions are utilized in the simulations. At a distance from the membrane, where particle-membrane interactions are negligible, the simulation is coupled to a noninteraction continuum analogous to a heat bath [Geyer et al., J. Chem. Phys. 120, 4573 (2004)]. From the particles' density profiles perpendicular to the planar surface binding isotherms are derived and compared to experimental results [Heimburg et al. (1999)]. Using a negatively charged structureless membrane surface a saturation effect was found for relatively large particle concentrations. Since biological membranes often contain membrane proteins, we also studied the influence of additional charges on our model membrane mimicking bacterial reaction centers. We find that the onset of the saturation occurs for much lower concentrations and is sensitive to the detailed implementation. Therefore we suggest that local distortion of membrane planarity (undulation), or lipid demixing, or the presence of charged integral membrane proteins create preferential binding sites on the membrane. Only then do we observe saturation at physiological concentrations.

The role of water molecules in stereoselectivity of glucose/galactose-binding protein

NASA Astrophysics Data System (ADS)

Kim, Minsup; Cho, Art E.

2016-11-01

Using molecular dynamics (MD) simulation methods, we attempted to explain the experimental results on ligand specificity of glucose/galactose-binding protein (GGBP) to β-D-glucose and β-D-galactose. For the simulation, a three-dimensional structure of GGBP was prepared, and homology modeling was performed to generate variant structures of GGBP with mutations at Asp14. Then, docking was carried out to find a reasonable β-D-glucose and β-D-galactose binding conformations with GGBP. Subsequent molecular dynamics simulations of β-D-glucose-GGBP and β-D-galactose-GGBP complexes and estimation of the orientation and stability of water molecules at the binding site revealed how water molecules influence ligand specificity. In our simulation, water molecules mediated interactions of β-D-glucose or β-D-galactose with residue 14 of GGBP. In this mechanism, the Phe16Ala mutant leaves both sugar molecules free to move, and the specific role of water molecules were eliminated, while the wild type, Asp14Asn mutant, and Asp14Glu mutant make hydrogen bond interactions with β-D-glucose more favorable. Our results demonstrate that bound water molecules at the binding site of GGBP are related to localized conformational change, contributing to ligand specificity of GGBP for β-D-glucose over β-D-galactose.

Incorporating Hot Topics in Ocean Sciences to Outreach Activities in Marine and Environmental Science Education

NASA Astrophysics Data System (ADS)

Bergondo, D. L.; Mrakovcich, K. L.; Vlietstra, L.; Tebeau, P.; Verlinden, C.; Allen, L. A.; James, R.

2016-02-01

The US Coast Guard Academy, an undergraduate military Academy, in New London CT, provides STEM education programs to the local community that engage the public on hot topics in ocean sciences. Outreach efforts include classroom, lab, and field-based activities at the Academy as well as at local schools. In one course, we partner with a STEM high school collecting fish and environmental data on board a research vessel and subsequently students present the results of their project. In another course, cadets develop and present interactive demonstrations of marine science to local school groups. In addition, the Academy develops In another course, cadets develop and present interactive demonstrations of marine science to local school groups. In addition, the Academy develops and/or participates in outreach programs including Science Partnership for Innovation in Learning (SPIL), Women in Science, Physics of the Sea, and the Ocean Exploration Trust Honors Research Program. As part of the programs, instructors and cadets create interactive and collaborative activities that focus on hot topics in ocean sciences such as oil spill clean-up, ocean exploration, tsunamis, marine biodiversity, and conservation of aquatic habitats. Innovative science demonstrations such as real-time interactions with the Exploration Vessel (E/V) Nautilus, rotating tank simulations of ocean circulation, wave tank demonstrations, and determining what materials work best to contain and clean-up oil, are used to enhance ocean literacy. Children's books, posters and videos are some creative ways students summarize their understanding of ocean sciences and marine conservation. Despite time limitations of students and faculty, and challenges associated with securing funding to keep these programs sustainable, the impact of the programs is overwhelmingly positive. We have built stronger relationships with local community, enhanced ocean literacy, facilitated communication and mentorship between young students and scientists, and encouraged interest of underrepresented minorities in STEM education.

Enhanced vibronic interaction caused by local lattice symmetry lowering in the (Fe, Mg)As2 ternary system

NASA Astrophysics Data System (ADS)

Pishtshev, A.; Rubin, P.

2018-04-01

By means of periodic density functional theory (DFT) electronic structure calculations, we investigate iron-site doping effects in a structural model of bulk FeAs2. Simulations performed within the projector augmented-wave method-Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) functional scheme reveal that the impacts of the two stoichiometric substitutions Fe → Mg and Fe → Ni are radically different with respect to the structural and electronic behavior of the dopants. In particular, unlike the Ni dopant, the Mg dopant incorporated in FeAs2 occupies a noncentral equilibrium position characterized by an off-center displacement from the reference higher-symmetry position. Analysis of the respective electron and vibrational factors allows us to explain this result in terms of the local pseudo Jahn-Teller effect (pJTE). On the basis of DFT calculations, we deduce which electron orbitals and lattice vibrational modes are appropriate for promoting the local instability at the origin of the pJTE. Quantitative evaluations of the pJTE parameters performed within the polyatomic formalism of an effective tight-binding model show that it is just the enhanced vibronic interaction in the Mg-[FeAs6] cluster that is responsible for the local lattice symmetry breaking.

Deciphering microbial interactions and detecting keystone species with co-occurrence networks.

PubMed

Berry, David; Widder, Stefanie

2014-01-01

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study.

PubMed

Martínez, Leandro; Malliavin, Thérèse E; Blondel, Arnaud

2011-05-01

The anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two-Mg(2+) binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg(2+) ions. This provides an explanation for the inhibitory effect of high Mg(2+) concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two-step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mechanism, product protonation facilitates dissociation.

Interaction between local and regional pollution during Escompte 2001: impact on surface ozone concentrations (IOP2a and 2b)

NASA Astrophysics Data System (ADS)

Cousin, F.; Tulet, P.; Rosset, R.

2005-03-01

Escompte, a European programme which took place in the Marseille region in June-July 2001, has been designed as an exhaustive database to be used for the development and validation of air pollution models. The air quality Mesoscale NonHydrostatic Chemistry model (Meso-NH-C) is used to simulate 2 days of an Intensive Observation Period (IOP) documented during the Escompte campaign, June 23 and 24, 2001. We first study the synoptic and local meteorological situation on June 23 and 24, using surface and aircraft measurements. Then, we focus on the pollution episode of June 24. This study emphasizes the deep impact of synoptic and local dynamics on observed ozone concentrations. It is shown that ozone levels are due both to regional and local factors, with highlights of the importance of ozone layering. More generally this confirms, even in an otherwise predominant local sea-breeze regime, the need to consider larger scale regional pollutant transport.

Classical density functional theory and Monte Carlo simulation study of electric double layer in the vicinity of a cylindrical electrode

NASA Astrophysics Data System (ADS)

Zhou, Shiqi; Lamperski, Stanisław; Sokołowska, Marta

2017-07-01

We have performed extensive Monte-Carlo simulations and classical density functional theory (DFT) calculations of the electrical double layer (EDL) near a cylindrical electrode in a primitive model (PM) modified by incorporating interionic dispersion interactions. It is concluded that (i) in general, an unsophisticated use of the mean field (MF) approximation for the interionic dispersion interactions does not distinctly worsen the classical DFT performance, even if the salt ions considered are highly asymmetrical in size (3:1) and charge (5:1), the bulk molar concentration considered is high up to a total bulk ion packing fraction of 0.314, and the surface charge density of up to 0.5 C m-2. (ii) More specifically, considering the possible noises in the simulation, the local volume charge density profiles are the most accurately predicted by the classical DFT in all situations, and the co- and counter-ion singlet distributions are also rather accurately predicted; whereas the mean electrostatic potential profile is relatively less accurately predicted due to an integral amplification of minor inaccuracy of the singlet distributions. (iii) It is found that the layered structure of the co-ion distribution is abnormally possible only if the surface charge density is high enough (for example 0.5 C m-2) moreover, the co-ion valence abnormally influences the peak height of the first counter-ion layer, which decreases with the former. (iv) Even if both the simulation and DFT indicate an insignificant contribution of the interionic dispersion interaction to the above three ‘local’ quantities, it is clearly shown by the classical DFT that the interionic dispersion interaction does significantly influence a ‘global’ quantity like the cylinder surface-aqueous electrolyte interfacial tension, and this may imply the role of the interionic dispersion interaction in explaining the specific Hofmeister effects. We elucidate all of the above observations based on the arguments from the liquid state theory and at the molecular scale.

Particle-based membrane model for mesoscopic simulation of cellular dynamics

NASA Astrophysics Data System (ADS)

Sadeghi, Mohsen; Weikl, Thomas R.; Noé, Frank

2018-01-01

We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.

Interface collisions

NASA Astrophysics Data System (ADS)

Aarão Reis, F. D. A.; Pierre-Louis, O.

2018-04-01

We provide a theoretical framework to analyze the properties of frontal collisions of two growing interfaces considering different short-range interactions between them. Due to their roughness, the collision events spread in time and form rough domain boundaries, which defines collision interfaces in time and space. We show that statistical properties of such interfaces depend on the kinetics of the growing interfaces before collision, but are independent of the details of their interaction and of their fluctuations during the collision. Those properties exhibit dynamic scaling with exponents related to the growth kinetics, but their distributions may be nonuniversal. Our results are supported by simulations of lattice models with irreversible dynamics and local interactions. Relations to first passage processes are discussed and a possible application to grain-boundary formation in two-dimensional materials is suggested.

Theoretical study of band gap in CuAlO2: Pressure dependence and self-interaction correction

NASA Astrophysics Data System (ADS)

Nakanishi, Akitaka; Katayama-Yoshida, Hiroshi

2012-08-01

By using first-principles calculations, we studied the energy gaps of delafossite CuAlO2: (1) pressure dependence and (2) self-interaction correction (SIC). Our simulation shows that CuAlO2 transforms from a delafossite structure to a leaning delafossite structure at 60 GPa. The energy gap of CuAlO2 increases through the structural transition due to the enhanced covalency of Cu 3d and O 2p states. We implemented a self-interaction correction (SIC) into first-principles calculation code to go beyond local density approximation and applied it to CuAlO2. The energy gap calculated within the SIC is close to experimental data while one calculated without the SIC is about 1 eV smaller than the experimental data.

Pigeon interaction mode switch-based UAV distributed flocking control under obstacle environments.

PubMed

Qiu, Huaxin; Duan, Haibin

2017-11-01

Unmanned aerial vehicle (UAV) flocking control is a serious and challenging problem due to local interactions and changing environments. In this paper, a pigeon flocking model and a pigeon coordinated obstacle-avoiding model are proposed based on a behavior that pigeon flocks will switch between hierarchical and egalitarian interaction mode at different flight phases. Owning to the similarity between bird flocks and UAV swarms in essence, a distributed flocking control algorithm based on the proposed pigeon flocking and coordinated obstacle-avoiding models is designed to coordinate a heterogeneous UAV swarm to fly though obstacle environments with few informed individuals. The comparative simulation results are elaborated to show the feasibility, validity and superiority of our proposed algorithm. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Fluoropolymer Dynamics: Effects of Perfluoromethyl Branches

NASA Astrophysics Data System (ADS)

Eby, R. K.; Holt, D. B.; Farmer, B. L.; Adams, D. D.

1997-03-01

Previous simulations of polytetrafluoroethylene (PTFE) in the solid state showed that the interaction and movement of helix reversals plays an important role in the dynamic behavior of this important polymer. Copolymers of TFE and hexafluoropropylene (HFP), which can be viewed as PTFE with perfluoromethyl (PFM) group branch defects, is also widely used. Molecular mechanics and dynamics calculations have been performed with PTFE chain clusters containing PFM branches to investigate the effect of these defects on the local crystalline environment (and vice versa) and on the motions and interactions of helix reversals. Initial results indicate that helix reversals are attracted to sites of PFM branches in a chain. Such an interaction will impede the motions of helix reversals and have an impact on macroscopic mechanical properties such as resistance to plastic deformation under shear.

Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling.

PubMed

Elías-Wolff, Federico; Lindén, Martin; Lyubartsev, Alexander P; Brandt, Erik G

2018-03-13

Membrane curvature sensing, where the binding free energies of membrane-associated molecules depend on the local membrane curvature, is a key factor to modulate and maintain the shape and organization of cell membranes. However, the microscopic mechanisms are not well understood, partly due to absence of efficient simulation methods. Here, we describe a method to compute the curvature dependence of the binding free energy of a membrane-associated probe molecule that interacts with a buckled membrane, which has been created by lateral compression of a flat bilayer patch. This buckling approach samples a wide range of curvatures in a single simulation, and anisotropic effects can be extracted from the orientation statistics. We develop an efficient and robust algorithm to extract the motion of the probe along the buckled membrane surface, and evaluate its numerical properties by extensive sampling of three coarse-grained model systems: local lipid density in a curved environment for single-component bilayers, curvature preferences of individual lipids in two-component membranes, and curvature sensing by a homotrimeric transmembrane protein. The method can be used to complement experimental data from curvature partition assays and provides additional insight into mesoscopic theories and molecular mechanisms for curvature sensing.

Discrete crack growth analysis methodology for through cracks in pressurized fuselage structures

NASA Technical Reports Server (NTRS)

Potyondy, David O.; Wawrzynek, Paul A.; Ingraffea, Anthony R.

1994-01-01

A methodology for simulating the growth of long through cracks in the skin of pressurized aircraft fuselage structures is described. Crack trajectories are allowed to be arbitrary and are computed as part of the simulation. The interaction between the mechanical loads acting on the superstructure and the local structural response near the crack tips is accounted for by employing a hierarchical modeling strategy. The structural response for each cracked configuration is obtained using a geometrically nonlinear shell finite element analysis procedure. Four stress intensity factors, two for membrane behavior and two for bending using Kirchhoff plate theory, are computed using an extension of the modified crack closure integral method. Crack trajectories are determined by applying the maximum tangential stress criterion. Crack growth results in localized mesh deletion, and the deletion regions are remeshed automatically using a newly developed all-quadrilateral meshing algorithm. The effectiveness of the methodology and its applicability to performing practical analyses of realistic structures is demonstrated by simulating curvilinear crack growth in a fuselage panel that is representative of a typical narrow-body aircraft. The predicted crack trajectory and fatigue life compare well with measurements of these same quantities from a full-scale pressurized panel test.

Permeation across hydrated DPPC lipid bilayers: simulation of the titrable amphiphilic drug valproic acid.

PubMed

Ulander, Johan; Haymet, A D J

2003-12-01

Valproic acid is a short branched fatty acid used as an anticonvulsant drug whose therapeutic action has been proposed to arise from membrane-disordering properties. Static and kinetic properties of valproic acid interacting with fully hydrated dipalmitoyl phosphatidylcholine lipid bilayers are studied using molecular-dynamics simulations. We calculate spatially resolved free energy profiles and local diffusion coefficients using the distance between the bilayer and valproic acid respective centers-of-mass along the bilayer normal as reaction coordinate. To investigate the pH dependence, we calculate profiles for the neutral valproic acid as well as its water-soluble anionic conjugate base valproate. The local diffusion constants for valproate/valproic acid along the bilayer normal are found to be approximately 10(-6) to 10(-5) cm2 s(-1). Assuming protonation of valproic acid upon association with--or insertion into--the lipid bilayer, we calculate the permeation coefficient to be approximately 2.0 10(-3) cm s(-1), consistent with recent experimental estimates of fast fatty acid transport. The ability of the lipid bilayer to sustain local defects such as water intrusions stresses the importance of going beyond mean field and taking into account correlation effects in theoretical descriptions of bilayer translocation processes.

Thermo-elastic wave model of the photothermal and photoacoustic signal

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

Meja, P.; Steiger, B.; Delsanto, P.P.

1996-12-31

By means of the thermo-elastic wave equation the dynamical propagation of mechanical stress and temperature can be described and applied to model the photothermal and photoacoustic signal. Analytical solutions exist only in particular cases. Using massively parallel computers it is possible to simulate the photothermal and photoacoustic signal in a most sufficient way. In this paper the method of local interaction simulation approach (LISA) is presented and selected examples of its application are given. The advantages of this method, which is particularly suitable for parallel processing, consist in reduced computation time and simple description of the photoacoustic signal in opticalmore » materials. The present contribution introduces the authors model, the formalism and some results in the 1 D case for homogeneous nonattenuative materials. The photoacoustic wave can be understood as a wave with locally limited displacement. This displacement corresponds to a temperature variation. Both variables are usually measured in photoacoustics and photothermal measurements. Therefore the temperature and displacement dependence on optical, elastic and thermal constants is analysed.« less

Simulation of laser propagation through a three-layer human skin model in the spectral range from 1000 to 1900 nm.

PubMed

Nasouri, Babak; Murphy, Thomas E; Berberoglu, Halil

2014-01-01

For understanding the mechanisms of low-level laser/light therapy (LLLT), accurate knowledge of light interaction with tissue is necessary. We present a three-dimensional, multilayer reduced-variance Monte Carlo simulation tool for studying light penetration and absorption in human skin. Local profiles of light penetration and volumetric absorption were calculated for uniform as well as Gaussian profile beams with different spreads over the spectral range from 1000 to 1900 nm. The results showed that lasers within this wavelength range could be used to effectively and safely deliver energy to specific skin layers as well as achieve large penetration depths for treating deep tissues, without causing skin damage. In addition, by changing the beam profile from uniform to Gaussian, the local volumetric dosage could increase as much as three times for otherwise similar lasers. We expect that this tool along with the results presented will aid researchers in selecting wavelength and laser power in LLLT.

Multiscale Modeling of Primary Cilium Deformations Under Local Forces and Shear Flows

NASA Astrophysics Data System (ADS)

Peng, Zhangli; Feng, Zhe; Resnick, Andrew; Young, Yuan-Nan

2017-11-01

We study the detailed deformations of a primary cilium under local forces and shear flows by developing a multiscale model based on the state-of-the-art understanding of its molecular structure. Most eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in chemosensation, thermosensation, and mechanosensation, but the detailed mechanism for mechanosensation is not well understood. We apply the dissipative particle dynamics (DPD) to model an entire well with a primary cilium and consider its different components, including the basal body, microtubule doublets, actin cortex, and lipid bilayer. We calibrate the mechanical properties of individual components and their interactions from experimental measurements and molecular dynamics simulations. We validate the simulations by comparing the deformation profile of the cilium and the rotation of the basal body with optical trapping experiments. After validations, we investigate the deformation of the primary cilium under shear flows. Furthermore, we calculate the membrane tensions and cytoskeleton stresses, and use them to predict the activation of mechanosensitive channels.

First ERO2.0 modeling of Be erosion and non-local transport in JET ITER-like wall

NASA Astrophysics Data System (ADS)

Romazanov, J.; Borodin, D.; Kirschner, A.; Brezinsek, S.; Silburn, S.; Huber, A.; Huber, V.; Bufferand, H.; Firdaouss, M.; Brömmel, D.; Steinbusch, B.; Gibbon, P.; Lasa, A.; Borodkina, I.; Eksaeva, A.; Linsmeier, Ch; Contributors, JET

2017-12-01

ERO is a Monte-Carlo code for modeling plasma-wall interaction and 3D plasma impurity transport for applications in fusion research. The code has undergone a significant upgrade (ERO2.0) which allows increasing the simulation volume in order to cover the entire plasma edge of a fusion device, allowing a more self-consistent treatment of impurity transport and comparison with a larger number and variety of experimental diagnostics. In this contribution, the physics-relevant technical innovations of the new code version are described and discussed. The new capabilities of the code are demonstrated by modeling of beryllium (Be) erosion of the main wall during JET limiter discharges. Results for erosion patterns along the limiter surfaces and global Be transport including incident particle distributions are presented. A novel synthetic diagnostic, which mimics experimental wide-angle 2D camera images, is presented and used for validating various aspects of the code, including erosion, magnetic shadowing, non-local impurity transport, and light emission simulation.

Analysis and modeling of localized heat generation by tumor-targeted nanoparticles (Monte Carlo methods)

NASA Astrophysics Data System (ADS)

Sanattalab, Ehsan; SalmanOgli, Ahmad; Piskin, Erhan

2016-04-01

We investigated the tumor-targeted nanoparticles that influence heat generation. We suppose that all nanoparticles are fully functionalized and can find the target using active targeting methods. Unlike the commonly used methods, such as chemotherapy and radiotherapy, the treatment procedure proposed in this study is purely noninvasive, which is considered to be a significant merit. It is found that the localized heat generation due to targeted nanoparticles is significantly higher than other areas. By engineering the optical properties of nanoparticles, including scattering, absorption coefficients, and asymmetry factor (cosine scattering angle), the heat generated in the tumor's area reaches to such critical state that can burn the targeted tumor. The amount of heat generated by inserting smart agents, due to the surface Plasmon resonance, will be remarkably high. The light-matter interactions and trajectory of incident photon upon targeted tissues are simulated by MIE theory and Monte Carlo method, respectively. Monte Carlo method is a statistical one by which we can accurately probe the photon trajectories into a simulation area.

Theoretical approach to the ground state of spherically confined Yukawa plasmas

NASA Astrophysics Data System (ADS)

Henning, Christian; Bonitz, Michael; Piel, Alexander; Ludwig, Patrick; Baumgartner, Henning

2007-11-01

Recently spherical 3D dust crystals (aka Yukawa balls) were discovered [1], which allow direct observation of strong correlation phenomena and the structure of which is well explained by computer simulations of charged Yukawa interacting particles within an external parabolic confinement [2]. Here we present an analytical approach to the ground state of these systems using the minimization of the system's energy. Applying the non-local mean-field approximation we show that screening has a dramatic effect on the density profile, which can be derived explicitly [3]. In addition the local density approximation allows for the inclusion of correlations, which further improves the results in the regime of large screening [4]. Comparisons with MD simulations of Yukawa balls show excellent agreement.[1] O. Arp et al. Phys. Rev. Lett. 93, 165004 (2004)[2] M. Bonitz et al., Phys. Rev. Lett. 96, 075001 (2006)[3] C. Henning et al., Phys. Rev. E 74, 056403 (2006)[4] C. Henning at al., Phys. Rev. E (2007)

Simulation of laser propagation through a three-layer human skin model in the spectral range from 1000 to 1900 nm

NASA Astrophysics Data System (ADS)

Nasouri, Babak; Murphy, Thomas E.; Berberoglu, Halil

2014-07-01

For understanding the mechanisms of low-level laser/light therapy (LLLT), accurate knowledge of light interaction with tissue is necessary. We present a three-dimensional, multilayer reduced-variance Monte Carlo simulation tool for studying light penetration and absorption in human skin. Local profiles of light penetration and volumetric absorption were calculated for uniform as well as Gaussian profile beams with different spreads over the spectral range from 1000 to 1900 nm. The results showed that lasers within this wavelength range could be used to effectively and safely deliver energy to specific skin layers as well as achieve large penetration depths for treating deep tissues, without causing skin damage. In addition, by changing the beam profile from uniform to Gaussian, the local volumetric dosage could increase as much as three times for otherwise similar lasers. We expect that this tool along with the results presented will aid researchers in selecting wavelength and laser power in LLLT.

Modeling of time dependent localized flow shear stress and its impact on cellular growth within additive manufactured titanium implants

PubMed Central

Zhang, Ziyu; Yuan, Lang; Lee, Peter D; Jones, Eric; Jones, Julian R

2014-01-01

Bone augmentation implants are porous to allow cellular growth, bone formation and fixation. However, the design of the pores is currently based on simple empirical rules, such as minimum pore and interconnects sizes. We present a three-dimensional (3D) transient model of cellular growth based on the Navier–Stokes equations that simulates the body fluid flow and stimulation of bone precursor cellular growth, attachment, and proliferation as a function of local flow shear stress. The model's effectiveness is demonstrated for two additive manufactured (AM) titanium scaffold architectures. The results demonstrate that there is a complex interaction of flow rate and strut architecture, resulting in partially randomized structures having a preferential impact on stimulating cell migration in 3D porous structures for higher flow rates. This novel result demonstrates the potential new insights that can be gained via the modeling tool developed, and how the model can be used to perform what-if simulations to design AM structures to specific functional requirements. PMID:24664988

Civil Tiltrotor Feasibility Study for the New York and Washington Terminal Areas

NASA Technical Reports Server (NTRS)

Stouffer, Virginia; Johnson, Jesse; Gribko, Joana; Yackovetsky, Robert (Technical Monitor)

2001-01-01

NASA tasked LMI to assess the potential contributions of a yet-undeveloped Civil Tiltrotor aircraft (CTR) in improving capacity in the National Airspace System in all weather conditions. The CTRs studied have assumed operating parameters beyond current CTR capabilities. LMI analyzed CTRs three ways: in fast-time terminal area modeling simulations of New York and Washington to determine delay and throughput impacts; in the Integrated Noise Model, to determine local environmental impact; and with an economic model, to determine the price viability of a CTR. The fast-time models encompassed a 250 nmi range and included traffic interactions from local airports. Both the fast-time simulation and the noise model assessed impacts from traffic levels projected for 1999, 2007, and 2017. Results: CTRs can reduce terminal area delays due to concrete congestion in all time frames. The maximum effect, the ratio of CTRs to jets and turboprop aircraft at a subject airport should be optimized. The economic model considered US traffic only and forecasted CTR sales beginning in 2010.

Molecular Theory and the Effects of Solute Attractive Forces on Hydrophobic Interactions.

PubMed

Chaudhari, Mangesh I; Rempe, Susan B; Asthagiri, D; Tan, L; Pratt, L R

2016-03-03

The role of solute attractive forces on hydrophobic interactions is studied by coordinated development of theory and simulation results for Ar atoms in water. We present a concise derivation of the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions, a derivation that clarifies the close relation of LMF theory to the EXP approximation applied to this problem long ago. The simulation results show that change from purely repulsive atomic solute interactions to include realistic attractive interactions diminishes the strength of hydrophobic bonds. For the Ar-Ar rdfs considered pointwise, the numerical results for the effects of solute attractive forces on hydrophobic interactions are opposite in sign and larger in magnitude than predicted by LMF theory. That comparison is discussed from the point of view of quasichemical theory, and it is suggested that the first reason for this difference is the incomplete evaluation within LMF theory of the hydration energy of the Ar pair. With a recent suggestion for the system-size extrapolation of the required correlation function integrals, the Ar-Ar rdfs permit evaluation of osmotic second virial coefficients B2. Those B2's also show that incorporation of attractive interactions leads to more positive (repulsive) values. With attractive interactions in play, B2 can change from positive to negative values with increasing temperatures. This is consistent with the puzzling suggestions of decades ago that B2 ≈ 0 for intermediate cases of temperature or solute size. In all cases here, B2 becomes more attractive with increasing temperature.

Molecular theory and the effects of solute attractive forces on hydrophobic interactions

DOE PAGES

Chaudhari, Mangesh I.; Rempe, Susan B.; Asthagiri, D.; ...

2015-12-22

The role of solute attractive forces on hydrophobic interactions is studied by coordinated development of theory and simulation results for Ar atoms in water. In this paper, we present a concise derivation of the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions, a derivation that clarifies the close relation of LMF theory to the EXP approximation applied to this problem long ago. The simulation results show that change from purely repulsive atomic solute interactions to include realistic attractive interactions diminishes the strength of hydrophobic bonds. For the Ar–Ar rdfs considered pointwise, the numericalmore » results for the effects of solute attractive forces on hydrophobic interactions are opposite in sign and larger in magnitude than predicted by LMF theory. That comparison is discussed from the point of view of quasichemical theory, and it is suggested that the first reason for this difference is the incomplete evaluation within LMF theory of the hydration energy of the Ar pair. With a recent suggestion for the system-size extrapolation of the required correlation function integrals, the Ar–Ar rdfs permit evaluation of osmotic second virial coefficients B 2. Those B 2’s also show that incorporation of attractive interactions leads to more positive (repulsive) values. With attractive interactions in play, B 2 can change from positive to negative values with increasing temperatures. Furthermore, this is consistent with the puzzling suggestions of decades ago that B 2 ≈ 0 for intermediate cases of temperature or solute size. In all cases here, B 2 becomes more attractive with increasing temperature.« less

Internal curvature signal and noise in low- and high-level vision

PubMed Central

Grabowecky, Marcia; Kim, Yee Joon; Suzuki, Satoru

2011-01-01

How does internal processing contribute to visual pattern perception? By modeling visual search performance, we estimated internal signal and noise relevant to perception of curvature, a basic feature important for encoding of three-dimensional surfaces and objects. We used isolated, sparse, crowded, and face contexts to determine how internal curvature signal and noise depended on image crowding, lateral feature interactions, and level of pattern processing. Observers reported the curvature of a briefly flashed segment, which was presented alone (without lateral interaction) or among multiple straight segments (with lateral interaction). Each segment was presented with no context (engaging low-to-intermediate-level curvature processing), embedded within a face context as the mouth (engaging high-level face processing), or embedded within an inverted-scrambled-face context as a control for crowding. Using a simple, biologically plausible model of curvature perception, we estimated internal curvature signal and noise as the mean and standard deviation, respectively, of the Gaussian-distributed population activity of local curvature-tuned channels that best simulated behavioral curvature responses. Internal noise was increased by crowding but not by face context (irrespective of lateral interactions), suggesting prevention of noise accumulation in high-level pattern processing. In contrast, internal curvature signal was unaffected by crowding but modulated by lateral interactions. Lateral interactions (with straight segments) increased curvature signal when no contextual elements were added, but equivalent interactions reduced curvature signal when each segment was presented within a face. These opposing effects of lateral interactions are consistent with the phenomena of local-feature contrast in low-level processing and global-feature averaging in high-level processing. PMID:21209356

A numerical study of mixing in stationary, nonpremixed, turbulent reacting flows

NASA Astrophysics Data System (ADS)

Overholt, Matthew Ryan

1998-10-01

In this work a detailed numerical study is made of a statistically-stationary, non-premixed, turbulent reacting model flow known as Periodic Reaction Zones. The mixture fraction-progress variable approach is used, with a mean gradient in the mixture fraction and a model, single-step, reversible, finite-rate thermochemistry, yielding both stationary and local extinction behavior. The passive scalar is studied first, using a statistical forcing scheme to achieve stationarity of the velocity field. Multiple independent direct numerical simulations (DNS) are performed for a wide range of Reynolds numbers with a number of results including a bilinear model for scalar mixing jointly conditioned on the scalar and x2-component of velocity, Gaussian scalar probability density function tails which were anticipated to be exponential, and the quantification of the dissipation of scalar flux. A new deterministic forcing scheme for DNS is then developed which yields reduced fluctuations in many quantities and a more natural evolution of the velocity fields. This forcing method is used for the final portion of this work. DNS results for Periodic Reaction Zones are compared with the Conditional Moment Closure (CMC) model, the Quasi-Equilibrium Distributed Reaction (QEDR) model, and full probability density function (PDF) simulations using the Euclidean Minimum Spanning Tree (EMST) and the Interaction by Exchange with the Mean (IEM) mixing models. It is shown that CMC and QEDR results based on the local scalar dissipation match DNS wherever local extinction is not present. However, due to the large spatial variations of scalar dissipation, and hence local Damkohler number, local extinction is present even when the global Damkohler number is twenty-five times the critical value for extinction. Finally, in the PDF simulations the EMST mixing model closely reproduces CMC and DNS results when local extinction is not present, whereas the IEM model results in large error.

Modelling Coral Reef Futures to Inform Management: Can Reducing Local-Scale Stressors Conserve Reefs under Climate Change?

PubMed Central

Gurney, Georgina G.; Melbourne-Thomas, Jessica; Geronimo, Rollan C.; Aliño, Perry M.; Johnson, Craig R.

2013-01-01

Climate change has emerged as a principal threat to coral reefs, and is expected to exacerbate coral reef degradation caused by more localised stressors. Management of local stressors is widely advocated to bolster coral reef resilience, but the extent to which management of local stressors might affect future trajectories of reef state remains unclear. This is in part because of limited understanding of the cumulative impact of multiple stressors. Models are ideal tools to aid understanding of future reef state under alternative management and climatic scenarios, but to date few have been sufficiently developed to be useful as decision support tools for local management of coral reefs subject to multiple stressors. We used a simulation model of coral reefs to investigate the extent to which the management of local stressors (namely poor water quality and fishing) might influence future reef state under varying climatic scenarios relating to coral bleaching. We parameterised the model for Bolinao, the Philippines, and explored how simulation modelling can be used to provide decision support for local management. We found that management of water quality, and to a lesser extent fishing, can have a significant impact on future reef state, including coral recovery following bleaching-induced mortality. The stressors we examined interacted antagonistically to affect reef state, highlighting the importance of considering the combined impact of multiple stressors rather than considering them individually. Further, by providing explicit guidance for management of Bolinao's reef system, such as which course of management action will most likely to be effective over what time scales and at which sites, we demonstrated the utility of simulation models for supporting management. Aside from providing explicit guidance for management of Bolinao's reef system, our study offers insights which could inform reef management more broadly, as well as general understanding of reef systems. PMID:24260347

Modelling coral reef futures to inform management: can reducing local-scale stressors conserve reefs under climate change?

PubMed

Gurney, Georgina G; Melbourne-Thomas, Jessica; Geronimo, Rollan C; Aliño, Perry M; Johnson, Craig R

2013-01-01

Climate change has emerged as a principal threat to coral reefs, and is expected to exacerbate coral reef degradation caused by more localised stressors. Management of local stressors is widely advocated to bolster coral reef resilience, but the extent to which management of local stressors might affect future trajectories of reef state remains unclear. This is in part because of limited understanding of the cumulative impact of multiple stressors. Models are ideal tools to aid understanding of future reef state under alternative management and climatic scenarios, but to date few have been sufficiently developed to be useful as decision support tools for local management of coral reefs subject to multiple stressors. We used a simulation model of coral reefs to investigate the extent to which the management of local stressors (namely poor water quality and fishing) might influence future reef state under varying climatic scenarios relating to coral bleaching. We parameterised the model for Bolinao, the Philippines, and explored how simulation modelling can be used to provide decision support for local management. We found that management of water quality, and to a lesser extent fishing, can have a significant impact on future reef state, including coral recovery following bleaching-induced mortality. The stressors we examined interacted antagonistically to affect reef state, highlighting the importance of considering the combined impact of multiple stressors rather than considering them individually. Further, by providing explicit guidance for management of Bolinao's reef system, such as which course of management action will most likely to be effective over what time scales and at which sites, we demonstrated the utility of simulation models for supporting management. Aside from providing explicit guidance for management of Bolinao's reef system, our study offers insights which could inform reef management more broadly, as well as general understanding of reef systems.

Defect classification in sparsity-based structural health monitoring

NASA Astrophysics Data System (ADS)

Golato, Andrew; Ahmad, Fauzia; Santhanam, Sridhar; Amin, Moeness G.

2017-05-01

Guided waves have gained popularity in structural health monitoring (SHM) due to their ability to inspect large areas with little attenuation, while providing rich interactions with defects. For thin-walled structures, the propagating waves are Lamb waves, which are a complex but well understood type of guided waves. Recent works have cast the defect localization problem of Lamb wave based SHM within the sparse reconstruction framework. These methods make use of a linear model relating the measurements with the scene reflectivity under the assumption of point-like defects. However, most structural defects are not perfect points but tend to assume specific forms, such as surface cracks or internal cracks. Knowledge of the "type" of defects is useful in the assessment phase of SHM. In this paper, we present a dual purpose sparsity-based imaging scheme which, in addition to accurately localizing defects, properly classifies the defects present simultaneously. The proposed approach takes advantage of the bias exhibited by certain types of defects toward a specific Lamb wave mode. For example, some defects strongly interact with the anti-symmetric modes, while others strongly interact with the symmetric modes. We build model based dictionaries for the fundamental symmetric and anti-symmetric wave modes, which are then utilized in unison to properly localize and classify the defects present. Simulated data of surface and internal defects in a thin Aluminum plate are used to validate the proposed scheme.

Study of a tri-trophic prey-dependent food chain model of interacting populations.

PubMed

Haque, Mainul; Ali, Nijamuddin; Chakravarty, Santabrata

2013-11-01

The current paper accounts for the influence of intra-specific competition among predators in a prey dependent tri-trophic food chain model of interacting populations. We offer a detailed mathematical analysis of the proposed food chain model to illustrate some of the significant results that has arisen from the interplay of deterministic ecological phenomena and processes. Biologically feasible equilibria of the system are observed and the behaviours of the system around each of them are described. In particular, persistence, stability (local and global) and bifurcation (saddle-node, transcritical, Hopf-Andronov) analysis of this model are obtained. Relevant results from previous well known food chain models are compared with the current findings. Global stability analysis is also carried out by constructing appropriate Lyapunov functions. Numerical simulations show that the present system is capable enough to produce chaotic dynamics when the rate of self-interaction is very low. On the other hand such chaotic behaviour disappears for a certain value of the rate of self interaction. In addition, numerical simulations with experimented parameters values confirm the analytical results and shows that intra-specific competitions bears a potential role in controlling the chaotic dynamics of the system; and thus the role of self interactions in food chain model is illustrated first time. Finally, a discussion of the ecological applications of the analytical and numerical findings concludes the paper. Copyright © 2013 Elsevier Inc. All rights reserved.

JET TRAILS AND MACH CONES: THE INTERACTION OF MICROQUASARS WITH THE INTERSTELLAR MEDIUM

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

Yoon, D.; Morsony, B.; Heinz, S.

2011-11-20

A subset of microquasars exhibits high peculiar velocity with respect to the local standard of rest due to the kicks they receive when being born in supernovae. The interaction between the radio plasma released by microquasar jets from such high-velocity binaries with the interstellar medium must lead to the production of trails and bow shocks similar to what is observed in narrow-angle tailed radio galaxies and pulsar wind nebulae. We present a set of numerical simulations of this interaction that illuminate the long-term dynamical evolution and the observational properties of these microquasar bow-shock nebulae and trails. We find that thismore » interaction always produces a structure that consists of a bow shock, a trailing neck, and an expanding bubble. Using our simulations to model emission, we predict that the shock surrounding the bubble and the neck should be visible in H{sub {alpha}} emission, the interior of the bubble should be visible in synchrotron radio emission, and only the bow shock is likely to be detectable in X-ray emission. We construct an analytic model for the evolution of the neck and bubble shape and compare this model with observations of the X-ray binary SAX J1712.6-3739.« less

Variability of community interaction networks in marine reserves and adjacent exploited areas

USGS Publications Warehouse

Montano-Moctezuma, G.; Li, H.W.; Rossignol, P.A.

2008-01-01

Regional and small-scale local oceanographic conditions can lead to high variability in community structure even among similar habitats. Communities with identical species composition can depict distinct networks due to different levels of disturbance as well as physical and biological processes. In this study we reconstruct community networks in four different areas off the Oregon Coast by matching simulated communities with observed dynamics. We compared reserves with harvested areas. Simulations suggested that different community networks, but with the same species composition, can represent each study site. Differences were found in predator-prey interactions as well as non-predatory interactions between community members. In addition, each site can be represented as a set of models, creating alternative stages among sites. The set of alternative models that characterize each study area depicts a sequence of functional responses where each specific model or interaction structure creates different species composition patterns. Different management practices, either in the past or of the present, may lead to alternative communities. Our findings suggest that management strategies should be analyzed at a community level that considers the possible consequences of shifting from one community scenario to another. This analysis provides a novel conceptual framework to assess the consequences of different management options for ecological communities. ?? 2008 Elsevier B.V. All rights reserved.

Model of annual plants dynamics with facilitation and competition.

PubMed

Droz, Michel; Pękalski, Andrzej

2013-10-21

An individual-based model describing the dynamics of one type of annual plants is presented. We use Monte Carlo simulations where each plant has its own history and the interactions among plants are between nearest neighbours. The character of the interaction (positive or negative) depends on local conditions. The plants compete for two external resources-water and light. The amount of water and/or light a plant receives depends on the external factor but also on local arrangement. Survival, growth and seed production of plants are determined by how well their demands for the resources are met. The survival and seeds production tests have a probabilistic character, which makes the dynamics more realistic than by using a deterministic approach. There is a non-linear coupling between the external supplies. Water evaporates from the soil at a rate depending on constant evaporation rate, local conditions and the amount of light. We examine the dynamics of the plant population along two environmental gradients, allowing also for surplus of water and/or light. We show that the largest number of plants is when the demands for both resources are equal to the supplies. We estimate also the role of evaporation and we find that it depends on the situation. It could be negative, but sometimes it has a positive character. We show that the link between the type of interaction (positive or negative) and external conditions has a complex character. In general in favourable environment plants have a stronger tendency for competitive interactions, leading to mostly isolated plants. When the conditions are getting more difficult, cooperation becomes the dominant type of interactions and the plants grow in clusters. The type of plants-sun-loving or shade tolerating, plays also an important role. © 2013 Elsevier Ltd. All rights reserved.

Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes.

PubMed

Sonntag, Yonathan; Musgaard, Maria; Olesen, Claus; Schiøtt, Birgit; Møller, Jesper Vuust; Nissen, Poul; Thøgersen, Lea

2011-01-01

The structural elucidation of membrane proteins continues to gather pace, but we know little about their molecular interactions with the lipid environment or how they interact with the surrounding bilayer. Here, with the aid of low-resolution X-ray crystallography, we present direct structural information on membrane interfaces as delineated by lipid phosphate groups surrounding the sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) in its phosphorylated and dephosphorylated Ca(2+)-free forms. The protein-lipid interactions are further analysed using molecular dynamics simulations. We find that SERCA adapts to membranes of different hydrophobic thicknesses by inducing local deformations in the lipid bilayers and by undergoing small rearrangements of the amino-acid side chains and helix tilts. These mutually adaptive interactions allow smooth transitions through large conformational changes associated with the transport cycle of SERCA, a strategy that may be of general nature for many membrane proteins.

Analytical interatomic potential for modeling nonequilibrium processes in the W-C-H system

NASA Astrophysics Data System (ADS)

Juslin, N.; Erhart, P.; Träskelin, P.; Nord, J.; Henriksson, K. O. E.; Nordlund, K.; Salonen, E.; Albe, K.

2005-12-01

A reactive interatomic potential based on an analytical bond-order scheme is developed for the ternary system W-C-H. The model combines Brenner's hydrocarbon potential with parameter sets for W-W, W-C, and W-H interactions and is adjusted to materials properties of reference structures with different local atomic coordinations including tungsten carbide, W-H molecules, as well as H dissolved in bulk W. The potential has been tested in various scenarios, such as surface, defect, and melting properties, none of which were considered in the fitting. The intended area of application is simulations of hydrogen and hydrocarbon interactions with tungsten, which have a crucial role in fusion reactor plasma-wall interactions. Furthermore, this study shows that the angular-dependent bond-order scheme can be extended to second nearest-neighbor interactions, which are relevant in body-centered-cubic metals. Moreover, it provides a possibly general route for modeling metal carbides.

Jet formation at the interaction of localized waves on the free surface of dielectric liquid in a tangential electric field

NASA Astrophysics Data System (ADS)

Kochurin, E. A.; Zubarev, N. M.

2018-01-01

Nonlinear dynamics of the free surface of finite depth non-conducting fluid with high dielectric constant subjected to a strong horizontal electric field is considered. Using the conformal transformation of the region occupied by the fluid into a strip, the process of interaction of counter-propagating waves is numerically simulated. The nonlinear solitary waves on the surface can separately propagate along or against the direction of electric field without distortion. At the same time, the shape of the oppositely traveling waves can be distorted as the result of their interaction. In the problem under study, the nonlinearity leads to increasing the wave amplitudes and the duration of their interaction. This effect is inversely proportional to the fluid depth. In the shallow water limit, the tendency to the formation of a vertical liquid jet is observed.

Colloidal Asphaltene Deposition and Aggregation in Capillary Flow: Experiments and Mesoscopic Simulation

NASA Astrophysics Data System (ADS)

Boek, Edo S.; Ladva, Hemant K.; Crawshaw, John P.; Padding, Johan T.

2008-07-01

The aggregation and deposition of colloidal asphaltene in reservoir rock is a significant problem in the oil industry. To obtain a fundamental understanding of this phenomenon, we have studied the deposition and aggregation of colloidal asphaltene in capillary flow by experiment and simulation. For the simulation, we have used the stochastic rotation dynamics (SRD) method, in which the solvent hydrodynamic emerges from the collisions between the solvent particles, while the Brownian motion emerges naturally from the interactions between the colloidal asphaltene particles and the solvent. The asphaltene colloids interact through a screened Coulomb potential. We vary the well depth ɛ∝ and the flow rate v to obtain Peflow≫1 (hydrodynamic interactions dominate) and Re≪1 (Stokes flow). In the simulations, we impose a pressure drop over the capillary length and measure the corresponding solvent flow rate. We observe that the transient solvent flow rate decreases when the asphaltene particles become more "sticky". For a well depth ɛ∝ = 2kBT, a monolayer deposits on the capillary wall. With an increasing well depth, the capillary becomes totally blocked. The clogging is transient for ɛ∝ = 5kBT, but appears to be permanent for ɛ∝ = 10-20 kBT. We compare our simulation results with flow experiments in glass capillaries, where we use extracted asphaltenes in toluene, reprecipitated with n-heptane. In the experiments, the dynamics of asphaltene precipitation and deposition were monitored in a slot capillary using optical microscopy under flow conditions similar to those used in the simulation. Maintaining a constant flow rate of 5 μL min-1, we found that the pressure drop across the capillary first increased slowly, followed by a sharp increase, corresponding to a complete local blockage of the capillary. Doubling the flow rate to 10 μL min-1, we observe that the initial deposition occurs faster but the deposits are subsequently entrained by the flow. We calculate the change in the dimensionless permeability as a function of time for both experiment and simulation. By matching the experimental and simulation results, we obtain information about (1) the interaction potential well depth for the particular asphaltenes used in the experiments and (2) the flow conditions associated with the asphaltene deposition process.

Meeting the memory challenges of brain-scale network simulation.

PubMed

Kunkel, Susanne; Potjans, Tobias C; Eppler, Jochen M; Plesser, Hans Ekkehard; Morrison, Abigail; Diesmann, Markus

2011-01-01

The development of high-performance simulation software is crucial for studying the brain connectome. Using connectome data to generate neurocomputational models requires software capable of coping with models on a variety of scales: from the microscale, investigating plasticity, and dynamics of circuits in local networks, to the macroscale, investigating the interactions between distinct brain regions. Prior to any serious dynamical investigation, the first task of network simulations is to check the consistency of data integrated in the connectome and constrain ranges for yet unknown parameters. Thanks to distributed computing techniques, it is possible today to routinely simulate local cortical networks of around 10(5) neurons with up to 10(9) synapses on clusters and multi-processor shared-memory machines. However, brain-scale networks are orders of magnitude larger than such local networks, in terms of numbers of neurons and synapses as well as in terms of computational load. Such networks have been investigated in individual studies, but the underlying simulation technologies have neither been described in sufficient detail to be reproducible nor made publicly available. Here, we discover that as the network model sizes approach the regime of meso- and macroscale simulations, memory consumption on individual compute nodes becomes a critical bottleneck. This is especially relevant on modern supercomputers such as the Blue Gene/P architecture where the available working memory per CPU core is rather limited. We develop a simple linear model to analyze the memory consumption of the constituent components of neuronal simulators as a function of network size and the number of cores used. This approach has multiple benefits. The model enables identification of key contributing components to memory saturation and prediction of the effects of potential improvements to code before any implementation takes place. As a consequence, development cycles can be shorter and less expensive. Applying the model to our freely available Neural Simulation Tool (NEST), we identify the software components dominant at different scales, and develop general strategies for reducing the memory consumption, in particular by using data structures that exploit the sparseness of the local representation of the network. We show that these adaptations enable our simulation software to scale up to the order of 10,000 processors and beyond. As memory consumption issues are likely to be relevant for any software dealing with complex connectome data on such architectures, our approach and our findings should be useful for researchers developing novel neuroinformatics solutions to the challenges posed by the connectome project.