Self-consistent field model for strong electrostatic correlations and inhomogeneous dielectric media.

PubMed

Ma, Manman; Xu, Zhenli

2014-12-28

Electrostatic correlations and variable permittivity of electrolytes are essential for exploring many chemical and physical properties of interfaces in aqueous solutions. We propose a continuum electrostatic model for the treatment of these effects in the framework of the self-consistent field theory. The model incorporates a space- or field-dependent dielectric permittivity and an excluded ion-size effect for the correlation energy. This results in a self-energy modified Poisson-Nernst-Planck or Poisson-Boltzmann equation together with state equations for the self energy and the dielectric function. We show that the ionic size is of significant importance in predicting a finite self energy for an ion in an inhomogeneous medium. Asymptotic approximation is proposed for the solution of a generalized Debye-Hückel equation, which has been shown to capture the ionic correlation and dielectric self energy. Through simulating ionic distribution surrounding a macroion, the modified self-consistent field model is shown to agree with particle-based Monte Carlo simulations. Numerical results for symmetric and asymmetric electrolytes demonstrate that the model is able to predict the charge inversion at high correlation regime in the presence of multivalent interfacial ions which is beyond the mean-field theory and also show strong effect to double layer structure due to the space- or field-dependent dielectric permittivity.

Energy Minimization of Molecular Features Observed on the (110) Face of Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Perozzo, Mary A.; Konnert, John H.; Li, Huayu; Nadarajah, Arunan; Pusey, Marc

1999-01-01

Molecular dynamics and energy minimization have been carried out using the program XPLOR to check the plausibility of a model lysozyme crystal surface. The molecular features of the (110) face of lysozyme were observed using atomic force microscopy (AFM). A model of the crystal surface was constructed using the PDB file 193L, and was used to simulate an AFM image. Molecule translations, van der Waals radii, and assumed AFM tip shape were adjusted to maximize the correlation coefficient between the experimental and simulated images. The highest degree of 0 correlation (0.92) was obtained with the molecules displaced over 6 A from their positions within the bulk of the crystal. The quality of this starting model, the extent of energy minimization, and the correlation coefficient between the final model and the experimental data will be discussed.

Dependence of structure factor and correlation energy on the width of electron wires

NASA Astrophysics Data System (ADS)

Ashokan, Vinod; Bala, Renu; Morawetz, Klaus; Pathak, Kare Narain

2018-02-01

The structure factor and correlation energy of a quantum wire of thickness b ≪ a B are studied in random phase approximation (RPA) and for the less investigated region r s < 1. Using the single-loop approximation, analytical expressions of the structure factor are obtained. The exact expressions for the exchange energy are also derived for a cylindrical and harmonic wire. The correlation energy in RPA is found to be represented by ɛ c ( b, r s ) = α( r s )/ b + β( r s ) ln( b) + η( r s ), for small b and high densities. For a pragmatic width of the wire, the correlation energy is in agreement with the quantum Monte Carlo simulation data.

A comparative study of inelastic scattering models at energy levels ranging from 0.5 keV to 10 keV

NASA Astrophysics Data System (ADS)

Hu, Chia-Yu; Lin, Chun-Hung

2017-03-01

Six models, including a single-scattering model, four hybrid models, and one dielectric function model, were evaluated using Monte Carlo simulations for aluminum and copper at incident beam energies ranging from 0.5 keV to 10 keV. The inelastic mean free path, mean energy loss per unit path length, and backscattering coefficients obtained by these models are compared and discussed to understand the merits of the various models. ANOVA (analysis of variance) statistical models were used to quantify the effects of inelastic cross section and energy loss models on the basis of the simulated results deviation from the experimental data for the inelastic mean free path, the mean energy loss per unit path length, and the backscattering coefficient, as well as their correlations. This work in this study is believed to be the first application of ANOVA models towards evaluating inelastic electron beam scattering models. This approach is an improvement over the traditional approach which involves only visual estimation of the difference between the experimental data and simulated results. The data suggests that the optimization of the effective electron number per atom, binding energy, and cut-off energy of an inelastic model for different materials at different beam energies is more important than the selection of inelastic models for Monte Carlo electron scattering simulation. During the simulations, parameters in the equations should be tuned according to different materials for different beam energies rather than merely employing default parameters for an arbitrary material. Energy loss models and cross-section formulas are not the main factors influencing energy loss. Comparison of the deviation of the simulated results from the experimental data shows a significant correlation (p < 0.05) between the backscattering coefficient and energy loss per unit path length. The inclusion of backscattering electrons generated by both primary and secondary electrons for backscattering coefficient simulation is recommended for elements with high atomic numbers. In hybrid models, introducing the inner shell ionization model improves the accuracy of simulated results.

An efficient computational approach to model statistical correlations in photon counting x-ray detectors

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

Faby, Sebastian; Maier, Joscha; Sawall, Stefan

2016-07-15

Purpose: To introduce and evaluate an increment matrix approach (IMA) describing the signal statistics of energy-selective photon counting detectors including spatial–spectral correlations between energy bins of neighboring detector pixels. The importance of the occurring correlations for image-based material decomposition is studied. Methods: An IMA describing the counter increase patterns in a photon counting detector is proposed. This IMA has the potential to decrease the number of required random numbers compared to Monte Carlo simulations by pursuing an approach based on convolutions. To validate and demonstrate the IMA, an approximate semirealistic detector model is provided, simulating a photon counting detector inmore » a simplified manner, e.g., by neglecting count rate-dependent effects. In this way, the spatial–spectral correlations on the detector level are obtained and fed into the IMA. The importance of these correlations in reconstructed energy bin images and the corresponding detector performance in image-based material decomposition is evaluated using a statistically optimal decomposition algorithm. Results: The results of IMA together with the semirealistic detector model were compared to other models and measurements using the spectral response and the energy bin sensitivity, finding a good agreement. Correlations between the different reconstructed energy bin images could be observed, and turned out to be of weak nature. These correlations were found to be not relevant in image-based material decomposition. An even simpler simulation procedure based on the energy bin sensitivity was tested instead and yielded similar results for the image-based material decomposition task, as long as the fact that one incident photon can increase multiple counters across neighboring detector pixels is taken into account. Conclusions: The IMA is computationally efficient as it required about 10{sup 2} random numbers per ray incident on a detector pixel instead of an estimated 10{sup 8} random numbers per ray as Monte Carlo approaches would need. The spatial–spectral correlations as described by IMA are not important for the studied image-based material decomposition task. Respecting the absolute photon counts and thus the multiple counter increases by a single x-ray photon, the same material decomposition performance could be obtained with a simpler detector description using the energy bin sensitivity.« less

Dissipation and particle energization in moderate to low beta turbulent plasma via PIC simulations

DOE PAGES

Makwana, Kirit; Li, Hui; Guo, Fan; ...

2017-05-30

Here, we simulate decaying turbulence in electron-positron pair plasmas using a fully-kinetic particle-in-cell (PIC) code. We run two simulations with moderate-to-low plasma β (the ratio of thermal pressure to magnetic pressure). The energy decay rate is found to be similar in both cases. The perpendicular wave-number spectrum of magnetic energy shows a slope betweenmore » $${k}_{\\perp }^{-1.3}$$ and $${k}_{\\perp }^{-1.1}$$, where the perpendicular (⊥) and parallel (∥) directions are defined with respect to the magnetic field. The particle kinetic energy distribution function shows the formation of a non-thermal feature in the case of lower plasma β, with a slope close to E-1. The correlation between thin turbulent current sheets and Ohmic heating by the dot product of electric field (E) and current density (J) is investigated. By heating the parallel E∥ centerdot J∥ term dominates the perpendicular E⊥ centerdot J⊥ term. Regions of strong E∥ centerdot J∥ are spatially well-correlated with regions of intense current sheets, which also appear correlated with regions of strong E∥ in the low β simulation, suggesting an important role of magnetic reconnection in the dissipation of low β plasma turbulence.« less

Dissipation and particle energization in moderate to low beta turbulent plasma via PIC simulations

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

Makwana, Kirit; Li, Hui; Guo, Fan

Here, we simulate decaying turbulence in electron-positron pair plasmas using a fully-kinetic particle-in-cell (PIC) code. We run two simulations with moderate-to-low plasma β (the ratio of thermal pressure to magnetic pressure). The energy decay rate is found to be similar in both cases. The perpendicular wave-number spectrum of magnetic energy shows a slope betweenmore » $${k}_{\\perp }^{-1.3}$$ and $${k}_{\\perp }^{-1.1}$$, where the perpendicular (⊥) and parallel (∥) directions are defined with respect to the magnetic field. The particle kinetic energy distribution function shows the formation of a non-thermal feature in the case of lower plasma β, with a slope close to E-1. The correlation between thin turbulent current sheets and Ohmic heating by the dot product of electric field (E) and current density (J) is investigated. By heating the parallel E∥ centerdot J∥ term dominates the perpendicular E⊥ centerdot J⊥ term. Regions of strong E∥ centerdot J∥ are spatially well-correlated with regions of intense current sheets, which also appear correlated with regions of strong E∥ in the low β simulation, suggesting an important role of magnetic reconnection in the dissipation of low β plasma turbulence.« less

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

PubMed

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

Correlational and thermodynamic properties of finite-temperature electron liquids in the hypernetted-chain approximation.

PubMed

Tanaka, Shigenori

2016-12-07

Correlational and thermodynamic properties of homogeneous electron liquids at finite temperatures are theoretically analyzed in terms of dielectric response formalism with the hypernetted-chain (HNC) approximation and its modified version. The static structure factor and the local-field correction to describe the strong Coulomb-coupling effects beyond the random-phase approximation are self-consistently calculated through solution to integral equations in the paramagnetic (spin unpolarized) and ferromagnetic (spin polarized) states. In the ground state with the normalized temperature θ=0, the present HNC scheme well reproduces the exchange-correlation energies obtained by quantum Monte Carlo (QMC) simulations over the whole fluid phase (the coupling constant r s ≤100), i.e., within 1% and 2% deviations from putative best QMC values in the paramagnetic and ferromagnetic states, respectively. As compared with earlier studies based on the Singwi-Tosi-Land-Sjölander and modified convolution approximations, some improvements on the correlation energies and the correlation functions including the compressibility sum rule are found in the intermediate to strong coupling regimes. When applied to the electron fluids at intermediate Fermi degeneracies (θ≈1), the static structure factors calculated in the HNC scheme show good agreements with the results obtained by the path integral Monte Carlo (PIMC) simulation, while a small negative region in the radial distribution function is observed near the origin, which may be associated with a slight overestimation for the exchange-correlation hole in the HNC approximation. The interaction energies are calculated for various combinations of density and temperature parameters ranging from strong to weak degeneracy and from weak to strong coupling, and the HNC values are then parametrized as functions of r s and θ. The HNC exchange-correlation free energies obtained through the coupling-constant integration show reasonable agreements with earlier results including the PIMC-based fitting over the whole fluid region at finite degeneracies in the paramagnetic state. In contrast, a systematic difference between the HNC and PIMC results is observed in the ferromagnetic state, which suggests a necessity of further studies on the exchange-correlation free energies from both aspects of analytical theory and simulation.

Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise.

PubMed

Liu, Chaoren; Beratan, David N; Zhang, Peng

2016-04-21

System-environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessible method, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds of sites, where the system-environment interactions are explicitly treated with numerical noise modeling of time-dependent site energies and couplings. The properties of the noise are tunable, providing us a flexible tool to investigate the detailed effects of correlated thermal fluctuations on CT mechanisms. The noise is parametrizable by molecular simulation and quantum calculation results of specific molecular systems, giving us better molecular resolution in simulating the system-environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are not readily incorporated using approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences (

Investigation of blast-induced traumatic brain injury.

PubMed

Taylor, Paul A; Ludwigsen, John S; Ford, Corey C

2014-01-01

Many troops deployed in Iraq and Afghanistan have sustained blast-related, closed-head injuries from being within non-lethal distance of detonated explosive devices. Little is known, however, about the mechanisms associated with blast exposure that give rise to traumatic brain injury (TBI). This study attempts to identify the precise conditions of focused stress wave energy within the brain, resulting from blast exposure, which will correlate with a threshold for persistent brain injury. This study developed and validated a set of modelling tools to simulate blast loading to the human head. Using these tools, the blast-induced, early-time intracranial wave motions that lead to focal brain damage were simulated. The simulations predict the deposition of three distinct wave energy components, two of which can be related to injury-inducing mechanisms, namely cavitation and shear. Furthermore, the results suggest that the spatial distributions of these damaging energy components are independent of blast direction. The predictions reported herein will simplify efforts to correlate simulation predictions with clinical measures of TBI and aid in the development of protective headwear.

Investigation of blast-induced traumatic brain injury

PubMed Central

Ludwigsen, John S.; Ford, Corey C.

2014-01-01

Objective Many troops deployed in Iraq and Afghanistan have sustained blast-related, closed-head injuries from being within non-lethal distance of detonated explosive devices. Little is known, however, about the mechanisms associated with blast exposure that give rise to traumatic brain injury (TBI). This study attempts to identify the precise conditions of focused stress wave energy within the brain, resulting from blast exposure, which will correlate with a threshold for persistent brain injury. Methods This study developed and validated a set of modelling tools to simulate blast loading to the human head. Using these tools, the blast-induced, early-time intracranial wave motions that lead to focal brain damage were simulated. Results The simulations predict the deposition of three distinct wave energy components, two of which can be related to injury-inducing mechanisms, namely cavitation and shear. Furthermore, the results suggest that the spatial distributions of these damaging energy components are independent of blast direction. Conclusions The predictions reported herein will simplify efforts to correlate simulation predictions with clinical measures of TBI and aid in the development of protective headwear. PMID:24766453

Real-valued composite filters for correlation-based optical pattern recognition

NASA Technical Reports Server (NTRS)

Rajan, P. K.; Balendra, Anushia

1992-01-01

Advances in the technology of optical devices such as spatial light modulators (SLMs) have influenced the research and growth of optical pattern recognition. In the research leading to this report, the design of real-valued composite filters that can be implemented using currently available SLMs for optical pattern recognition and classification was investigated. The design of real-valued minimum average correlation energy (RMACE) filter was investigated. Proper selection of the phase of the output response was shown to reduce the correlation energy. The performance of the filter was evaluated using computer simulations and compared with the complex filters. It was found that the performance degraded only slightly. Continuing the above investigation, the design of a real filter that minimizes the output correlation energy and the output variance due to noise was developed. Simulation studies showed that this filter had better tolerance to distortion and noise compared to that of the RMACE filter. Finally, the space domain design of RMACE filter was developed and implemented on the computer. It was found that the sharpness of the correlation peak was slightly reduced but the filter design was more computationally efficient than the complex filter.

Stopping dynamics of ions passing through correlated honeycomb clusters

NASA Astrophysics Data System (ADS)

Balzer, Karsten; Schlünzen, Niclas; Bonitz, Michael

2016-12-01

A combined nonequilibrium Green functions-Ehrenfest dynamics approach is developed that allows for a time-dependent study of the energy loss of a charged particle penetrating a strongly correlated system at zero and finite temperatures. Numerical results are presented for finite inhomogeneous two-dimensional Fermi-Hubbard models, where the many-electron dynamics in the target are treated fully quantum mechanically and the motion of the projectile is treated classically. The simulations are based on the solution of the two-time Dyson (Keldysh-Kadanoff-Baym) equations using the second-order Born, third-order, and T -matrix approximations of the self-energy. As application, we consider protons and helium nuclei with a kinetic energy between 1 and 500 keV/u passing through planar fragments of the two-dimensional honeycomb lattice and, in particular, examine the influence of electron-electron correlations on the energy exchange between projectile and electron system. We investigate the time dependence of the projectile's kinetic energy (stopping power), the electron density, the double occupancy, and the photoemission spectrum. Finally, we show that, for a suitable choice of the Hubbard model parameters, the results for the stopping power are in fair agreement with ab initio simulations for particle irradiation of single-layer graphene.

Neutron-neutron angular correlations in spontaneous fission of 252Cf and 240Pu

NASA Astrophysics Data System (ADS)

Verbeke, J. M.; Nakae, L. F.; Vogt, R.

2018-04-01

Background: Angular anisotropy has been observed between prompt neutrons emitted during the fission process. Such an anisotropy arises because the emitted neutrons are boosted along the direction of the parent fragment. Purpose: To measure the neutron-neutron angular correlations from the spontaneous fission of 252Cf and 240Pu oxide samples using a liquid scintillator array capable of pulse-shape discrimination. To compare these correlations to simulations combining the Monte Carlo radiation transport code MCNPX with the fission event generator FREYA. Method: Two different analysis methods were used to study the neutron-neutron correlations with varying energy thresholds. The first is based on setting a light output threshold while the second imposes a time-of-flight cutoff. The second method has the advantage of being truly detector independent. Results: The neutron-neutron correlation modeled by FREYA depends strongly on the sharing of the excitation energy between the two fragments. The measured asymmetry enabled us to adjust the FREYA parameter x in 240Pu, which controls the energy partition between the fragments and is so far inaccessible in other measurements. The 240Pu data in this analysis was the first available to quantify the energy partition for this isotope. The agreement between data and simulation is overall very good for 252Cf(sf ) and 240Pu(sf ) . Conclusions: The asymmetry in the measured neutron-neutron angular distributions can be predicted by FREYA. The shape of the correlation function depends on how the excitation energy is partitioned between the two fission fragments. Experimental data suggest that the lighter fragment is disproportionately excited.

Proton Linear Energy Transfer measurement using Emulsion Cloud Chamber

NASA Astrophysics Data System (ADS)

Shin, Jae-ik; Park, Seyjoon; Kim, Haksoo; Kim, Meyoung; Jeong, Chiyoung; Cho, Sungkoo; Lim, Young Kyung; Shin, Dongho; Lee, Se Byeong; Morishima, Kunihiro; Naganawa, Naotaka; Sato, Osamu; Kwak, Jungwon; Kim, Sung Hyun; Cho, Jung Sook; Ahn, Jung Keun; Kim, Ji Hyun; Yoon, Chun Sil; Incerti, Sebastien

2015-04-01

This study proposes to determine the correlation between the Volume Pulse Height (VPH) measured by nuclear emulsion and Linear Energy Transfer (LET) calculated by Monte Carlo simulation based on Geant4. The nuclear emulsion was irradiated at the National Cancer Center (NCC) with a therapeutic proton beam and was installed at 5.2 m distance from the beam nozzle structure with various thicknesses of water-equivalent material (PMMA) blocks to position with specific positions along the Bragg curve. After the beam exposure and development of the emulsion films, the films were scanned by S-UTS developed in Nagoya University. The proton tracks in the scanned films were reconstructed using the 'NETSCAN' method. Through this procedure, the VPH can be derived from each reconstructed proton track at each position along the Bragg curve. The VPH value indicates the magnitude of energy loss in proton track. By comparison with the simulation results obtained using Geant4, we found the correlation between the LET calculated by Monte Carlo simulation and the VPH measured by the nuclear emulsion.

Cluster correlation and fragment emission in 12C+12C at 95 MeV/nucleon

NASA Astrophysics Data System (ADS)

Tian, G.; Chen, Z.; Han, R.; Shi, F.; Luo, F.; Sun, Q.; Song, L.; Zhang, X.; Xiao, G. Q.; Wada, R.; Ono, A.

2018-03-01

The impact of cluster correlations has been studied in the intermediate mass fragment (IMF) emission in 12C+12C at 95 MeV/nucleon, using antisymmetrized molecular dynamics (AMD) model simulations. In AMD, the cluster correlation is introduced as a process to form light clusters with A ≤4 in the final states of a collision induced by the nucleon-nucleon residual interaction. Correlations between light clusters are also considered to form light nuclei with A ≤9 . This version of AMD, combined with GEMINI to calculate the decay of primary fragments, reproduces the experimental energy spectra of IMFs well overall with reasonable reproduction of light charged particles when we carefully analyze the excitation energies of primary fragments produced by AMD and their secondary decays. The results indicate that the cluster correlation plays a crucial role for producing fragments at relatively low excitation energies in the intermediate-energy heavy-ion collisions.

Ion Transport and Structural Properties of Polymeric Electrolytes and Ionic Liquids from Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Borodin, Oleg

2010-03-01

Molecular dynamics simulations are well suited for exploring electrolyte structure and ion transport mechanisms on the nanometer length scale and the nanosecond time scales. In this presentation we will describe how MD simulations assist in answering fundamental questions about the lithium transport mechanisms in polymeric electrolytes and ionic liquids. In particular, in the first part of the presentation the extent of ion aggregation, the structure of ion aggregates and the lithium cation diffusion in binary polymeric electrolytes will be compared with that of single-ion conducting polymers. In the second part of the talk, the lithium transport in polymeric electrolytes will be compared with that of three ionic liquids ( [emim][FSI] doped with LiFSI , [pyr13][FSI] doped with LiFSI, [emim][BF4] doped with LiBF4). The relation between ionic liquid self-diffusion, conductivity and thermodynamic properties will be discussed in details. A number of correlations between heat of vaporization Hvap, cation-anion binding energy (E+/-), molar volume (Vm), self-diffusion coefficient (D) and ionic conductivity for 29 ionic liquids have been investigated using MD simulations. A significant correlation between D and Hvap has been found, while best correlation was found for -log((D Vm)) vs. Hvap+0.28E+/-. A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids.

Magnetosphere-Ionosphere Coupling and Associated Ring Current Energization Processes

NASA Technical Reports Server (NTRS)

Liemohn, M. W.; Khazanov, G. V.

2004-01-01

Adiabatic processes in the ring current are examined. In particular, an analysis of the factors that parameterize the net adiabatic energy gain in the inner magnetosphere during magnetic storms is presented. A single storm was considered, that of April 17, 2002. Three simulations were conducted with similar boundary conditions but with different electric field descriptions. It is concluded that the best parameter for quantifying the net adiabatic energy gain in the inner magnetosphere during storms is the instantaneous value of the product of the maximum westward electric field at the outer simulation boundary with the nightside plasma sheet density. However, all of the instantaneous magnetospheric quantities considered in this study produced large correlation coefficients. Therefore, they all could be considered useful predictors of the net adiabatic energy gain of the ring current. Long integration times over the parameters lessen the significance of the correlation. Finally, some significant differences exist in the correlation coefficients depending on the electric field description.

Multiparticle collision simulations of two-dimensional one-component plasmas: Anomalous transport and dimensional crossovers

NASA Astrophysics Data System (ADS)

Di Cintio, Pierfrancesco; Livi, Roberto; Lepri, Stefano; Ciraolo, Guido

2017-04-01

By means of hybrid multiparticle collsion-particle-in-cell (MPC-PIC) simulations we study the dynamical scaling of energy and density correlations at equilibrium in moderately coupled two-dimensional (2D) and quasi-one-dimensional (1D) plasmas. We find that the predictions of nonlinear fluctuating hydrodynamics for the structure factors of density and energy fluctuations in 1D systems with three global conservation laws hold true also for 2D systems that are more extended along one of the two spatial dimensions. Moreover, from the analysis of the equilibrium energy correlators and density structure factors of both 1D and 2D neutral plasmas, we find that neglecting the contribution of the fluctuations of the vanishing self-consistent electrostatic fields overestimates the interval of frequencies over which the anomalous transport is observed. Such violations of the expected scaling in the currents correlation are found in different regimes, hindering the observation of the asymptotic scaling predicted by the theory.

Relation between heat of vaporization, ion transport, molar volume, and cation-anion binding energy for ionic liquids.

PubMed

Borodin, Oleg

2009-09-10

A number of correlations between heat of vaporization (H(vap)), cation-anion binding energy (E(+/-)), molar volume (V(m)), self-diffusion coefficient (D), and ionic conductivity for 29 ionic liquids have been investigated using molecular dynamics (MD) simulations that employed accurate and validated many-body polarizable force fields. A significant correlation between D and H(vap) has been found, while the best correlation was found for -log(DV(m)) vs H(vap) + 0.28E(+/-). A combination of enthalpy of vaporization and a fraction of the cation-anion binding energy was suggested as a measure of the effective cohesive energy for ionic liquids. A deviation of some ILs from the reported master curve is explained based upon ion packing and proposed diffusion pathways. No general correlations were found between the ion diffusion coefficient and molecular volume or the diffusion coefficient and cation/anion binding energy.

The pressure-dilatation correlation in compressible flows

NASA Technical Reports Server (NTRS)

Sarkar, S.

1992-01-01

Simulations of simple compressible flows have been performed to enable the direct estimation of the pressure-dilatation correlation. The generally accepted belief that this correlation may be important in high-speed flows has been verified by the simulations. The pressure-dilatation correlation is theoretically investigated by considering the equation for fluctuating pressure in an arbitrary compressible flow. This leads to the isolation of a component of the pressure-dilatation that exhibits temporal oscillations on a fast time scale. Direct numerical simulations of homogeneous shear turbulence and isotropic turbulence show that this fast component has a negligible contribution to the evolution of turbulent kinetic energy. Then, an analysis for the case of homogeneous turbulence is performed to obtain a formal solution for the nonoscillatory pressure-dilatation. Simplifications lead to a model that algebraically relates the pressure-dilatation to quantities traditionally obtained in incompressible turbulence closures. The model is validated by direct comparison with the simulations.

TU-CD-207-01: Characterization of Breast Tissue Composition Using Spectral Mammography

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

Ding, H; Cho, H; Kumar, N

Purpose: To investigate the feasibility of characterizing the chemical composition of breast tissue, in terms of water and lipid, by using spectral mammography in simulation and postmortem studies. Methods: Analytical simulations were performed to obtain low- and high-energy signals of breast tissue based on previously reported water, lipid, and protein contents. Dual-energy decomposition was used to characterize the simulated breast tissue into water and lipid basis materials and the measured water density was compared to the known value. In experimental studies, postmortem breasts were imaged with a spectral mammography system based on a scanning multi-slit Si strip photon-counting detector. Low-more » and high-energy images were acquired simultaneously from a single exposure by sorting the recorded photons into the corresponding energy bins. Dual-energy material decomposition of the low- and high-energy images yielded individual pixel measurements of breast tissue composition in terms of water and lipid thicknesses. After imaging, each postmortem breast was chemically decomposed into water, lipid and protein. The water density calculated from chemical analysis was used as the reference gold standard. Correlation of the water density measurements between spectral mammography and chemical analysis was analyzed using linear regression. Results: Both simulation and postmortem studies showed good linear correlation between the decomposed water thickness using spectral mammography and chemical analysis. The slope of the linear fitting function in the simulation and postmortem studies were 1.15 and 1.21, respectively. Conclusion: The results indicate that breast tissue composition, in terms of water and lipid, can be accurately measured using spectral mammography. Quantitative breast tissue composition can potentially be used to stratify patients according to their breast cancer risk.« less

Absolute Helmholtz free energy of highly anharmonic crystals: theory vs Monte Carlo.

PubMed

Yakub, Lydia; Yakub, Eugene

2012-04-14

We discuss the problem of the quantitative theoretical prediction of the absolute free energy for classical highly anharmonic solids. Helmholtz free energy of the Lennard-Jones (LJ) crystal is calculated accurately while accounting for both the anharmonicity of atomic vibrations and the pair and triple correlations in displacements of the atoms from their lattice sites. The comparison with most precise computer simulation data on sublimation and melting lines revealed that theoretical predictions are in excellent agreement with Monte Carlo simulation data in the whole range of temperatures and densities studied.

Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

PubMed

Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

2013-10-28

End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring protein-ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the nonpolar components of MM-GBSA and MM-PBSA, but not the electrostatic components, showed strong correlation to the ITC free energy; the computed entropies did not correlate with the ITC entropy.

Molecular Recognition in a Diverse Set of Protein-Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations

PubMed Central

Wang, Bo; Li, Liwei; Hurley, Thomas D.; Meroueh, Samy O.

2014-01-01

End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal•mol−1 highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10). But larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the non-polar and entropy components, rather than a better representation of the electrostatics. SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by pre-scoring protein-ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the non-polar components of MM-GBSA and MM-PBSA, but not the electrostatic components, showed strong correlation to the ITC free energy; the computed entropies did not correlate with the ITC entropy. PMID:24032517

Micro-Energy Rates for Damage Tolerance and Durability of Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Minnetyan, Levon

2006-01-01

In this paper, the adhesive bond strength of lap-jointed graphite/aluminum composites is examined by computational simulation. Computed micro-stress level energy release rates are used to identify the damage mechanisms associated with the corresponding acoustic emission (AE) signals. Computed damage regions are similarly correlated with ultrasonically scanned damage regions. Results show that computational simulation can be used with suitable NDE methods for credible in-service monitoring of composites.

Impact Testing and Simulation of a Crashworthy Composite Fuselage Section with Energy-Absorbing Seats and Dummies

NASA Technical Reports Server (NTRS)

Fasanella, Edwin L.; Jackson, Karen E.

2002-01-01

A 25-ft/s vertical drop test of a composite fuselage section was conducted with two energy-absorbing seats occupied by anthropomorphic dummies to evaluate the crashworthy features of the fuselage section and to determine its interaction with the seats and dummies. The 5-ft. diameter fuselage section consists of a stiff structural floor and an energy-absorbing subfloor constructed of Rohacel foam blocks. The experimental data from this test were analyzed and correlated with predictions from a crash simulation developed using the nonlinear, explicit transient dynamic computer code, MSC.Dytran. The anthropomorphic dummies were simulated using the Articulated Total Body (ATB) code, which is integrated into MSC.Dytran.

Impact Testing and Simulation of a Crashworthy Composite Fuselage Section with Energy-Absorbing Seats and Dummies

NASA Technical Reports Server (NTRS)

Fasanella, Edwin L.; Jackson, Karen E.

2002-01-01

A 25-ft/s vertical drop test of a composite fuselage section was conducted with two energy-absorbing seats occupied by anthropomorphic dummies to evaluate the crashworthy features of the fuselage section and to determine its interaction with the seats and dummies. The 5-ft diameter fuselage section consists of a stiff structural floor and an energy-absorbing subfloor constructed of Rohacel foam blocks. The experimental data from this test were analyzed and correlated with predictions from a crash simulation developed using the nonlinear, explicit transient dynamic computer code, MSC.Dytran. The anthropomorphic dummies were simulated using the Articulated Total Body (ATB) code, which is integrated into MSC.Dytran.

Kinetics of pattern formation in symmetric diblock copolymer melts

NASA Astrophysics Data System (ADS)

Ren, Yongzhi; Müller, Marcus

2018-05-01

In equilibrium, copolymers self-assemble into spatially modulated phases with long-range order. When the system is quenched far below the order-disorder transition temperature, however, such an idealized, defect-free structure is difficult to obtain in experiments and simulations, instead a fingerprint-like structure forms. The relaxation toward long-range order is very protracted because it involves numerous thermally activated processes, and the rugged free-energy landscape has been likened to that of glass-forming systems. Using large-scale particle-based simulations of high-aspect-ratio, quasi-two-dimensional systems with periodic boundary condition, we study the kinetics of structure formation in symmetric, lamella-forming diblock copolymers after a quench from the disordered state. We characterize the ordering process by the correlation length of the lamellar structure and its Euler characteristic and observe that the growth of the correlation length and the rate of change of the Euler characteristic significantly slow down in the range of incompatibilities, 15 ≤ χN ≤ 20, studied. The increase of the time scale of ordering is, however, gradual. The density fields of snapshots of the particle-based simulations are used as starting values for self-consistent field theory (SCFT) calculations. The latter converge to the local, metastable minimum of the free-energy basin. This combination of particle-based simulations and SCFT calculations allows us to relate an instantaneous configuration of the particle-based model to a corresponding metastable free-energy minimum of SCFT—the inherent morphology—and we typically observe that a change of a free-energy basin is associated with a change of the Euler characteristic of the particle-based morphology, i.e., changes of free-energy basins are correlated to changes of the domain topology. Subsequently, we employ the string method in conjunction with SCFT to study the minimum free-energy paths (MFEPs) of changes of the domain topology. Since the time scales of relaxing toward the inherent morphology within a free-energy basin and jumps between free-energy basins are not well separated, the MFEP may overestimate the barriers encountered in the course of ordering.

Monte Carlo simulations used to calculate the energy deposited in the coronary artery lumen as a function of iodine concentration and photon energy.

PubMed

Hocine, Nora; Meignan, Michel; Masset, Hélène

2018-04-01

To better understand the risks of cumulative medical X-ray investigations and the possible causal role of contrast agent on the coronary artery wall, the correlation between iodinated contrast media and the increase of energy deposited in the coronary artery lumen as a function of iodine concentration and photon energy is investigated. The calculations of energy deposition have been performed using Monte Carlo (MC) simulation codes, namely PENetration and Energy LOss of Positrons and Electrons (PENELOPE) and Monte Carlo N-Particle eXtended (MCNPX). Exposure of a cylinder phantom, artery and a metal stent (AISI 316L) to several X-ray photon beams were simulated. For the energies used in cardiac imaging the energy deposited in the coronary artery lumen increases with the quantity of iodine. Monte Carlo calculations indicate a strong dependence of the energy enhancement factor (EEF) on photon energy and iodine concentration. The maximum value of EEF is equal to 25; this factor is showed for 83 keV and for 400 mg Iodine/mL. No significant impact of the stent is observed on the absorbed dose in the artery for incident X-ray beams with mean energies of 44, 48, 52 and 55 keV. A strong correlation was shown between the increase in the concentration of iodine and the energy deposited in the coronary artery lumen for the energies used in cardiac imaging and over the energy range between 44 and 55 keV. The data provided by this study could be useful for creating new medical imaging protocols to obtain better diagnostic information with a lower level of radiation exposure.

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.

On the road performance tests of electric test vehicle for correlation with road load simulator

NASA Technical Reports Server (NTRS)

Dustin, M. O.; Slavik, R. J.

1982-01-01

A dynamometer (road load simulator) is used to test and evaluate electric vehicle propulsion systems. To improve correlation between system tests on the road load simulator and on the road, similar performance tests are conducted using the same vehicle. The results of track tests on the electric propulsion system test vehicle are described. The tests include range at constant speeds and over SAE J227a driving cycles, maximum accelerations, maximum gradability, and tire rolling resistance determination. Road power requirements and energy consumption were also determined from coast down tests.

Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ngo, Son Tung; Nguyen, Minh Tung; Nguyen, Minh Tho

2017-05-01

The absolute binding free energy of an inhibitor to HIV-1 Protease (PR) was determined throughout evaluation of the non-bonded interaction energy difference between the two bound and unbound states of the inhibitor and surrounding molecules by the fast pulling of ligand (FPL) process using non-equilibrium molecular dynamics (NEMD) simulations. The calculated free energy difference terms help clarifying the nature of the binding. Theoretical binding affinities are in good correlation with experimental data, with R = 0.89. The paradigm used is able to rank two inhibitors having the maximum difference of ∼1.5 kcal/mol in absolute binding free energies.

Fully Resolved Simulations of Particle-Bed-Turbulence Interactions in Oscillatory Flows

NASA Astrophysics Data System (ADS)

Apte, S.; Ghodke, C.

2017-12-01

Particle-resolved direct numerical simulations (DNS) are performed to investigate the behavior of an oscillatory flow field over a bed of closely packed fixed spherical particles for a range of Reynolds numbers in transitional and rough turbulent flow regime. Presence of roughness leads to a substantial modification of the underlying boundary layer mechanism resulting in increased bed shear stress, reduction in the near-bed anisotropy, modification of the near-bed sweep and ejection motions along with marked changes in turbulent energy transport mechanisms. Characterization of such resulting flow field is performed by studying statistical descriptions of the near-bed turbulence for different roughness parameters. A double-averaging technique is employed to reveal spatial inhomogeneities at the roughness scale that provide alternate paths of energy transport in the turbulent kinetic energy (TKE) budget. Spatio-temporal characteristics of unsteady particle forces by studying their spatial distribution, temporal auto-correlations, frequency spectra, cross-correlations with near-bed turbulent flow variables and intermittency intermittency in the forces using the concept of impulse are investigated in detail. These first principle simulations provide substantial insights into the modeling of incipient motion of sediments.

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

PubMed

Ilott, Andrew J; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R

2013-10-10

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

The structure of molten CuCl: Reverse Monte Carlo modeling with high-energy X-ray diffraction data and molecular dynamics of a polarizable ion model

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

Alcaraz, Olga; Trullàs, Joaquim, E-mail: quim.trullas@upc.edu; Tahara, Shuta

2016-09-07

The results of the structural properties of molten copper chloride are reported from high-energy X-ray diffraction measurements, reverse Monte Carlo modeling method, and molecular dynamics simulations using a polarizable ion model. The simulated X-ray structure factor reproduces all trends observed experimentally, in particular the shoulder at around 1 Å{sup −1} related to intermediate range ordering, as well as the partial copper-copper correlations from the reverse Monte Carlo modeling, which cannot be reproduced by using a simple rigid ion model. It is shown that the shoulder comes from intermediate range copper-copper correlations caused by the polarized chlorides.

Statistical analysis of CSP plants by simulating extensive meteorological series

NASA Astrophysics Data System (ADS)

Pavón, Manuel; Fernández, Carlos M.; Silva, Manuel; Moreno, Sara; Guisado, María V.; Bernardos, Ana

2017-06-01

The feasibility analysis of any power plant project needs the estimation of the amount of energy it will be able to deliver to the grid during its lifetime. To achieve this, its feasibility study requires a precise knowledge of the solar resource over a long term period. In Concentrating Solar Power projects (CSP), financing institutions typically requires several statistical probability of exceedance scenarios of the expected electric energy output. Currently, the industry assumes a correlation between probabilities of exceedance of annual Direct Normal Irradiance (DNI) and energy yield. In this work, this assumption is tested by the simulation of the energy yield of CSP plants using as input a 34-year series of measured meteorological parameters and solar irradiance. The results of this work show that, even if some correspondence between the probabilities of exceedance of annual DNI values and energy yields is found, the intra-annual distribution of DNI may significantly affect this correlation. This result highlights the need of standardized procedures for the elaboration of representative DNI time series representative of a given probability of exceedance of annual DNI.

Introducing GEOPHIRES v2.0: Updated Geothermal Techno-Economic Simulation Tool: Preprint

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

Beckers, Koenraad J; McCabe, Kevin

This paper presents an updated version of the geothermal techno-economic simulation tool GEOPHIRES (GEOthermal Energy for Production of Heat and electricity (IR) Economically Simulated). GEOPHIRES combines reservoir, wellbore, surface plant and economic models to estimate the capital, and operation and maintenance costs, lifetime energy production, and overall levelized cost of energy of a geothermal plant. The available end-use options are electricity, direct-use heat and cogeneration. The main updates in the new version include conversion of the source code from FORTRAN to Python, the option to couple to an external reservoir simulator, updated cost correlations, and more flexibility in selecting themore » time step and number of injection and production wells. An overview of all the updates and two case-studies to illustrate the tool's new capabilities are provided in this paper.« less

Spectral functions at small energies and the electrical conductivity in hot quenched lattice QCD.

PubMed

Aarts, Gert; Allton, Chris; Foley, Justin; Hands, Simon; Kim, Seyong

2007-07-13

In lattice QCD, the maximum entropy method can be used to reconstruct spectral functions from Euclidean correlators obtained in numerical simulations. We show that at finite temperature the most commonly used algorithm, employing Bryan's method, is inherently unstable at small energies and gives a modification that avoids this. We demonstrate this approach using the vector current-current correlator obtained in quenched QCD at finite temperature. Our first results indicate a small electrical conductivity above the deconfinement transition.

On the application of accelerated molecular dynamics to liquid water simulations.

PubMed

de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew

2006-11-16

Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.

Four-electron model for singlet and triplet excitation energy transfers with inclusion of coherence memory, inelastic tunneling and nuclear quantum effects

NASA Astrophysics Data System (ADS)

Suzuki, Yosuke; Ebina, Kuniyoshi; Tanaka, Shigenori

2016-08-01

A computational scheme to describe the coherent dynamics of excitation energy transfer (EET) in molecular systems is proposed on the basis of generalized master equations with memory kernels. This formalism takes into account those physical effects in electron-bath coupling system such as the spin symmetry of excitons, the inelastic electron tunneling and the quantum features of nuclear motions, thus providing a theoretical framework to perform an ab initio description of EET through molecular simulations for evaluating the spectral density and the temporal correlation function of electronic coupling. Some test calculations have then been carried out to investigate the dependence of exciton population dynamics on coherence memory, inelastic tunneling correlation time, magnitude of electronic coupling, quantum correction to temporal correlation function, reorganization energy and energy gap.

Analysis of Composite Skin-Stiffener Debond Specimens Using Volume Elements and a Shell/3D Modeling Technique

NASA Technical Reports Server (NTRS)

Krueger, Ronald; Minguet, Pierre J.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The debonding of a skin/stringer specimen subjected to tension was studied using three-dimensional volume element modeling and computational fracture mechanics. Mixed mode strain energy release rates were calculated from finite element results using the virtual crack closure technique. The simulations revealed an increase in total energy release rate in the immediate vicinity of the free edges of the specimen. Correlation of the computed mixed-mode strain energy release rates along the delamination front contour with a two-dimensional mixed-mode interlaminar fracture criterion suggested that in spite of peak total energy release rates at the free edge the delamination would not advance at the edges first. The qualitative prediction of the shape of the delamination front was confirmed by X-ray photographs of a specimen taken during testing. The good correlation between prediction based on analysis and experiment demonstrated the efficiency of a mixed-mode failure analysis for the investigation of skin/stiffener separation due to delamination in the adherents. The application of a shell/3D modeling technique for the simulation of skin/stringer debond in a specimen subjected to three-point bending is also demonstrated. The global structure was modeled with shell elements. A local three-dimensional model, extending to about three specimen thicknesses on either side of the delamination front was used to capture the details of the damaged section. Computed total strain energy release rates and mixed-mode ratios obtained from shell/3D simulations were in good agreement with results obtained from full solid models. The good correlations of the results demonstrated the effectiveness of the shell/3D modeling technique for the investigation of skin/stiffener separation due to delamination in the adherents.

Assessing the dispersive and electrostatic components of the cohesive energy of ionic liquids using molecular dynamics simulations and molar refraction data.

PubMed

Shimizu, Karina; Tariq, Mohammad; Costa Gomes, Margarida F; Rebelo, Luís P N; Canongia Lopes, José N

2010-05-06

Molecular dynamics simulations were used to calculate the density and the cohesive molar internal energy of seventeen different ionic liquids in the liquid phase. The results were correlated with previously reported experimental density and molar refraction data. The link between the dispersive component of the total cohesive energy of the fluid and the corresponding molar refraction was established in an unequivocal way. The results have shown that the two components of the total cohesive energy (dispersive and electrostatic) exhibit strikingly different trends and ratios along different families of ionic liquids, a notion that may help explain their diverse behavior toward different molecular solutes and solvents.

Neutron-fragment and Neutron-neutron Correlations in Low-energy Fission

NASA Astrophysics Data System (ADS)

Lestone, J. P.

2016-01-01

A computational method has been developed to simulate neutron emission from thermal-neutron induced fission of 235U and from spontaneous fission of 252Cf. Measured pre-emission mass-yield curves, average total kinetic energies and their variances, both as functions of mass split, are used to obtain a representation of the distribution of fragment velocities. Measured average neutron multiplicities as a function of mass split and their dependence on total kinetic energy are used. Simulations can be made to reproduce measured factorial moments of neutron-multiplicity distributions with only minor empirical adjustments to some experimental inputs. The neutron-emission spectra in the rest-frame of the fragments are highly constrained by ENDF/B-VII.1 prompt-fission neutron-spectra evaluations. The n-f correlation measurements of Vorobyev et al. (2010) are consistent with predictions where all neutrons are assumed to be evaporated isotropically from the rest frame of fully accelerated fragments. Measured n-f and n-n correlations of others are a little weaker than the predictions presented here. These weaker correlations could be used to infer a weak scission-neutron source. However, the effect of neutron scattering on the experimental results must be studied in detail before moving away from a null hypothesis that all neutrons are evaporated from the fragments.

Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation.

PubMed

Guo, Zuojun; Li, Bo; Dzubiella, Joachim; Cheng, Li-Tien; McCammon, J Andrew; Che, Jianwei

2013-03-12

In this article, we systematically apply a novel implicit-solvent model, the variational implicit-solvent model (VISM) together with the Coulomb-Field Approximation (CFA), to calculate the hydration free energy of a large set of small organic molecules. Because these molecules have been studied in detail by molecular dynamics simulations and other implicit-solvent models, they provide a good benchmark for evaluating the performance of VISM-CFA. With all-atom Amber force field parameters, VISM-CFA is able to reproduce well not only the experimental and MD simulated total hydration free energy but also the polar and nonpolar contributions individually. The correlation between VISM-CFA and experiments is R 2 = 0.763 for the total hydration free energy, with a root-mean-square deviation (RMSD) of 1.83 kcal/mol, and the correlation to results from TIP3P explicit water MD simulations is R 2 = 0.839 with a RMSD = 1.36 kcal/mol. In addition, we demonstrate that VISM captures dewetting phenomena in the p53/MDM2 complex and hydrophobic characteristics in the system. This work demonstrates that the level-set VISM-CFA can be used to study the energetic behavior of realistic molecular systems with complicated geometries in solvation, protein-ligand binding, protein-protein association, and protein folding processes.

Introducing GEOPHIRES v2.0: Updated Geothermal Techno-Economic Simulation Tool

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

Beckers, Koenraad J; McCabe, Kevin

This paper presents an updated version of the geothermal techno-economic simulation tool GEOPHIRES (GEOthermal energy for Production of Heat and electricity ('IR') Economically Simulated). GEOPHIRES combines engineering models of the reservoir, wellbores, and surface plant facilities of a geothermal plant with an economic model to estimate the capital and operation and maintenance costs, lifetime energy production, and overall levelized cost of energy. The available end-use options are electricity, direct-use heat, and cogeneration. The main updates in the new version include conversion of the source code from FORTRAN to Python, the option to import temperature data (e.g., measured or from stand-alonemore » reservoir simulator), updated cost correlations, and more flexibility in selecting the time step and number of injection and production wells. In this paper, we provide an overview of all the updates and two case studies to illustrate the tool's new capabilities.« less

Coincident measurements of prompt fission γ rays and fission fragments at DANCE

NASA Astrophysics Data System (ADS)

Walker, C. L.; Baramsai, B.; Jandel, M.; Rusev, G.; Couture, A.; Mosby, S.; Ullmann, J.; Kawano, T.; Stetcu, I.; Talou, P.

2015-10-01

Modern statistical approaches to modeling fission involve the calculation of not only average quantities but also fully correlated distributions of all fission products. Applications such as those involving the detection of special nuclear materials also rely on fully correlated data of fission products. Experimental measurements of correlated data are thus critical to the validation of theory and the development of important applications. The goal of this experiment was to measure properties of prompt fission gamma-ray emission as a function of fission fragments' total kinetic energy in the spontaneous fission of 252Cf. The measurement was carried out at the Detector for Advanced Neutron Capture Experiments (DANCE), a 4 π γ-ray calorimeter. A prototype design consisting of two silicon detectors was installed in the center of DANCE, allowing simultaneous measurement of fission fragments and γ rays. Effort has been taken to simulate fragment kinetic energy losses as well as γ-ray attenuation in DANCE using such tools as GEANT4 and SRIM. Theoretical predictions generated by the code CGMF were also incorporated as input for these simulations. Results from the experiment and simulations will be presented, along with plans for future measurements.

Kinetics of self-interstitial migration in bcc and fcc transition metals

NASA Astrophysics Data System (ADS)

Bukkuru, S.; Bhardwaj, U.; Srinivasa Rao, K.; Rao, A. D. P.; Warrier, M.; Valsakumar, M. C.

2018-03-01

Radiation damage is a multi-scale phenomenon. A thorough understanding of diffusivities and the migration energies of defects is a pre-requisite to quantify the after-effects of irradiation. We investigate the thermally activated mobility of self-interstitial atom (SIA) in bcc transition metals Fe, Mo, Nb and fcc transition metals Ag, Cu, Ni, Pt using molecular dynamics (MD) simulations. The self-interstitial diffusion involves various mechanisms such as interstitialcy, dumbbell or crowdion mechanisms. Max-Space Clustering (MSC) method has been employed to identify the interstitial and its configuration over a wide range of temperature. The self-interstitial diffusion is Arrhenius like, however, there is a slight deviation at high temperatures. The migration energies, pre-exponential factors of diffusion and jump-correlation factors, obtained from these simulations can be used as inputs to Monte Carlo simulations of defect transport. The jump-correlation factor shows the degree of preference of rectilinear or rotational jumps. We obtain the average jump-correlation factor of 1.4 for bcc metals and 0.44 for fcc metals. It indicates that rectilinear jumps are preferred in bcc metals and rotational jumps are preferred in fcc metals.

Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase.

PubMed

De Beer, Stephanie B A; Glättli, Alice; Hutzler, Johannes; Vermeulen, Nico P E; Oostenbrink, Chris

2011-07-30

4-Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one-step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. Copyright © 2011 Wiley Periodicals, Inc.

Removing the barrier to the calculation of activation energies

DOE PAGES

Mesele, Oluwaseun O.; Thompson, Ward H.

2016-10-06

Approaches for directly calculating the activation energy for a chemical reaction from a simulation at a single temperature are explored with applications to both classical and quantum systems. The activation energy is obtained from a time correlation function that can be evaluated from the same molecular dynamics trajectories or quantum dynamics used to evaluate the rate constant itself and thus requires essentially no extra computational work.

Comparison of ALE and SPH Simulations of Vertical Drop Tests of a Composite Fuselage Section into Water

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Fuchs, Yvonne T.

2008-01-01

Simulation of multi-terrain impact has been identified as an important research area for improved prediction of rotorcraft crashworthiness within the NASA Subsonic Rotary Wing Aeronautics Program on Rotorcraft Crashworthiness. As part of this effort, two vertical drop tests were conducted of a 5-ft-diameter composite fuselage section into water. For the first test, the fuselage section was impacted in a baseline configuration without energy absorbers. For the second test, the fuselage section was retrofitted with a composite honeycomb energy absorber. Both tests were conducted at a nominal velocity of 25-ft/s. A detailed finite element model was developed to represent each test article and water impact was simulated using both Arbitrary Lagrangian Eulerian (ALE) and Smooth Particle Hydrodynamics (SPH) approaches in LS-DYNA, a nonlinear, explicit transient dynamic finite element code. Analytical predictions were correlated with experimental data for both test configurations. In addition, studies were performed to evaluate the influence of mesh density on test-analysis correlation.

Understanding the atomic-level Green-Kubo stress correlation function for a liquid through phonons in a model crystal

NASA Astrophysics Data System (ADS)

Levashov, V. A.

2014-11-01

In order to gain insight into the connection between the vibrational dynamics and the atomic-level Green-Kubo stress correlation function in liquids, we consider this connection in a model crystal instead. Of course, vibrational dynamics in liquids and crystals are quite different and it is not expected that the results obtained on a model crystal should be valid for liquids. However, these considerations provide a benchmark to which the results of the previous molecular dynamics simulations can be compared. Thus, assuming that vibrations are plane waves, we derive analytical expressions for the atomic-level stress correlation functions in the classical limit and analyze them. These results provide, in particular, a recipe for analysis of the atomic-level stress correlation functions in Fourier space and extraction of the wave-vector and frequency-dependent information. We also evaluate the energies of the atomic-level stresses. The energies obtained are significantly smaller than the energies previously determined in molecular dynamics simulations of several model liquids. This result suggests that the average energies of the atomic-level stresses in liquids and glasses are largely determined by the structural disorder. We discuss this result in the context of equipartition of the atomic-level stress energies. Analysis of the previously published data suggests that it is possible to speak about configurational and vibrational contributions to the average energies of the atomic-level stresses in a glass state. However, this separation in a liquid state is problematic. We also introduce and briefly consider the atomic-level transverse current correlation function. Finally, we address the broadening of the peaks in the pair distribution function with increase of distance. We find that the peaks' broadening (by ≈40 % ) occurs due to the transverse vibrational modes, while contribution from the longitudinal modes does not change with distance.

Towards prediction of correlated material properties using quantum Monte Carlo methods

NASA Astrophysics Data System (ADS)

Wagner, Lucas

Correlated electron systems offer a richness of physics far beyond noninteracting systems. If we would like to pursue the dream of designer correlated materials, or, even to set a more modest goal, to explain in detail the properties and effective physics of known materials, then accurate simulation methods are required. Using modern computational resources, quantum Monte Carlo (QMC) techniques offer a way to directly simulate electron correlations. I will show some recent results on a few extremely challenging materials including the metal-insulator transition of VO2, the ground state of the doped cuprates, and the pressure dependence of magnetic properties in FeSe. By using a relatively simple implementation of QMC, at least some properties of these materials can be described truly from first principles, without any adjustable parameters. Using the QMC platform, we have developed a way of systematically deriving effective lattice models from the simulation. This procedure is particularly attractive for correlated electron systems because the QMC methods treat the one-body and many-body components of the wave function and Hamiltonian on completely equal footing. I will show some examples of using this downfolding technique and the high accuracy of QMC to connect our intuitive ideas about interacting electron systems with high fidelity simulations. The work in this presentation was supported in part by NSF DMR 1206242, the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research, Scientific Discovery through Advanced Computing (SciDAC) program under Award Number FG02-12ER46875, and the Center for Emergent Superconductivity, Department of Energy Frontier Research Center under Grant No. DEAC0298CH1088. Computing resources were provided by a Blue Waters Illinois grant and INCITE PhotSuper and SuperMatSim allocations.

Complete event simulations of nuclear fission

NASA Astrophysics Data System (ADS)

Vogt, Ramona

2015-10-01

For many years, the state of the art for treating fission in radiation transport codes has involved sampling from average distributions. In these average fission models energy is not explicitly conserved and everything is uncorrelated because all particles are emitted independently. However, in a true fission event, the energies, momenta and multiplicities of the emitted particles are correlated. Such correlations are interesting for many modern applications. Event-by-event generation of complete fission events makes it possible to retain the kinematic information for all particles emitted: the fission products as well as prompt neutrons and photons. It is therefore possible to extract any desired correlation observables. Complete event simulations can be included in general Monte Carlo transport codes. We describe the general functionality of currently available fission event generators and compare results for several important observables. This work was performed under the auspices of the US DOE by LLNL, Contract DE-AC52-07NA27344. We acknowledge support of the Office of Defense Nuclear Nonproliferation Research and Development in DOE/NNSA.

Correlations between dynamics and atomic structures in Cu64.5Zr35.5 metallic glass

NASA Astrophysics Data System (ADS)

Wang, C. Z.; Zhang, Y.; Zhang, F.; Mendelev, M. I.; Kramer, M. J.; Ho, K. M.

2015-03-01

The atomic structure of Cu-Zr metallic glasses (MGs) has been widely accepted to be heterogeneous and dominated by icosahedral short range order (ISRO). However, the correlations between dynamics and atomic structures in Cu-Zr MGs remain an enigma. Using molecular dynamics (MD) simulations, we investigated the correlations between dynamics and atomic structures in Cu64.5Zr35.5 MG. The atomic structures are characterized using ISRO and the Bergman-type medium range order (BMRO). The simulation and analysis results show that the majority of the mobile atoms are not involved in ISRO or BMRO, indicating that the dynamical heterogeneity has a strong correlation to structural heterogeneity. Moreover, we found that the localized soft vibration modes below 1.0 THz are mostly concentrated on the mobile atoms. The diffusion was studied using the atomic trajectory collected in an extended time interval of 1.2 μs at 700 K in MD simulations. It was found that the long range diffusion in MGs is highly heterogeneous, which is confined to the liquid-like regions and strongly avoids the ISRO and the Bergman-type MRO. All These results clearly demonstrate strong correlations between dynamics (in terms of dynamical heterogeneity and diffusion) and atomic structures in Cu64.5Zr35.5 MGs. This work was supported by the U.S. Department of Energy, Basic Energy Sciences, Division of Materials Science and Engineering under the Contract No. DE-AC02-07CH11358.

Exploring Neural Network Models with Hierarchical Memories and Their Use in Modeling Biological Systems

NASA Astrophysics Data System (ADS)

Pusuluri, Sai Teja

Energy landscapes are often used as metaphors for phenomena in biology, social sciences and finance. Different methods have been implemented in the past for the construction of energy landscapes. Neural network models based on spin glass physics provide an excellent mathematical framework for the construction of energy landscapes. This framework uses a minimal number of parameters and constructs the landscape using data from the actual phenomena. In the past neural network models were used to mimic the storage and retrieval process of memories (patterns) in the brain. With advances in the field now, these models are being used in machine learning, deep learning and modeling of complex phenomena. Most of the past literature focuses on increasing the storage capacity and stability of stored patterns in the network but does not study these models from a modeling perspective or an energy landscape perspective. This dissertation focuses on neural network models both from a modeling perspective and from an energy landscape perspective. I firstly show how the cellular interconversion phenomenon can be modeled as a transition between attractor states on an epigenetic landscape constructed using neural network models. The model allows the identification of a reaction coordinate of cellular interconversion by analyzing experimental and simulation time course data. Monte Carlo simulations of the model show that the initial phase of cellular interconversion is a Poisson process and the later phase of cellular interconversion is a deterministic process. Secondly, I explore the static features of landscapes generated using neural network models, such as sizes of basins of attraction and densities of metastable states. The simulation results show that the static landscape features are strongly dependent on the correlation strength and correlation structure between patterns. Using different hierarchical structures of the correlation between patterns affects the landscape features. These results show how the static landscape features can be controlled by adjusting the correlations between patterns. Finally, I explore the dynamical features of landscapes generated using neural network models such as the stability of minima and the transition rates between minima. The results from this project show that the stability depends on the correlations between patterns. It is also found that the transition rates between minima strongly depend on the type of bias applied and the correlation between patterns. The results from this part of the dissertation can be useful in engineering an energy landscape without even having the complete information about the associated minima of the landscape.

Energy deposition of heavy ions in the regime of strong beam-plasma correlations.

PubMed

Gericke, D O; Schlanges, M

2003-03-01

The energy loss of highly charged ions in dense plasmas is investigated. The applied model includes strong beam-plasma correlation via a quantum T-matrix treatment of the cross sections. Dynamic screening effects are modeled by using a Debye-like potential with a velocity dependent screening length that guarantees the known low and high beam velocity limits. It is shown that this phenomenological model is in good agreement with simulation data up to very high beam-plasma coupling. An analysis of the stopping process shows considerably longer ranges and a less localized energy deposition if strong coupling is treated properly.

Data-Driven Correlation Analysis Between Observed 3D Fatigue-Crack Path and Computed Fields from High-Fidelity, Crystal-Plasticity, Finite-Element Simulations

NASA Astrophysics Data System (ADS)

Pierson, Kyle D.; Hochhalter, Jacob D.; Spear, Ashley D.

2018-05-01

Systematic correlation analysis was performed between simulated micromechanical fields in an uncracked polycrystal and the known path of an eventual fatigue-crack surface based on experimental observation. Concurrent multiscale finite-element simulation of cyclic loading was performed using a high-fidelity representation of grain structure obtained from near-field high-energy x-ray diffraction microscopy measurements. An algorithm was developed to parameterize and systematically correlate the three-dimensional (3D) micromechanical fields from simulation with the 3D fatigue-failure surface from experiment. For comparison, correlation coefficients were also computed between the micromechanical fields and hypothetical, alternative surfaces. The correlation of the fields with hypothetical surfaces was found to be consistently weaker than that with the known crack surface, suggesting that the micromechanical fields of the cyclically loaded, uncracked microstructure might provide some degree of predictiveness for microstructurally small fatigue-crack paths, although the extent of such predictiveness remains to be tested. In general, gradients of the field variables exhibit stronger correlations with crack path than the field variables themselves. Results from the data-driven approach implemented here can be leveraged in future model development for prediction of fatigue-failure surfaces (for example, to facilitate univariate feature selection required by convolution-based models).

Signatures of four-particle correlations associated with exciton-carrier interactions in coherent spectroscopy on bulk GaAs

NASA Astrophysics Data System (ADS)

Webber, D.; Wilmer, B. L.; Liu, X.; Dobrowolska, M.; Furdyna, J. K.; Bristow, A. D.; Hall, K. C.

2016-10-01

Transient four-wave mixing studies of bulk GaAs under conditions of broad bandwidth excitation of primarily interband transitions have enabled four-particle correlations tied to degenerate (exciton-exciton) and nondegenerate (exciton-carrier) interactions to be studied. Real two-dimensional Fourier-transform spectroscopy (2DFTS) spectra reveal a complex response at the heavy-hole exciton emission energy that varies with the absorption energy, ranging from dispersive on the diagonal through absorptive for low-energy interband transitions to dispersive with the opposite sign for interband transitions high above band gap. Simulations using a multilevel model augmented by many-body effects provide excellent agreement with the 2DFTS experiments and indicate that excitation-induced dephasing (EID) and excitation-induced shift (EIS) affect degenerate and nondegenerate interactions equivalently, with stronger exciton-carrier coupling relative to exciton-exciton coupling by approximately an order of magnitude. These simulations also indicate that EID effects are three times stronger than EIS in contributing to the coherent response of the semiconductor.

Spatial distribution of fluorescent light emitted from neon and nitrogen excited by low energy electron beams

NASA Astrophysics Data System (ADS)

Morozov, A.; Krücken, R.; Ulrich, A.; Wieser, J.

2006-11-01

Side-view intensity profiles of fluorescent light were measured for neon and nitrogen excited with 12keV electron beams at gas pressures from 250to1400hPa. The intensity profiles were compared with theoretical profiles calculated using the CASINO program which performs Monte Carlo simulations of electron scattering. It was assumed that the spatial distribution of fluorescent intensity is directly proportional to the spatial distribution of energy loss by primary electrons. The comparison shows good correlation of experimental data and the results of numeric simulations.

Application of artificial neural networks to identify equilibration in computer simulations

NASA Astrophysics Data System (ADS)

Leibowitz, Mitchell H.; Miller, Evan D.; Henry, Michael M.; Jankowski, Eric

2017-11-01

Determining which microstates generated by a thermodynamic simulation are representative of the ensemble for which sampling is desired is a ubiquitous, underspecified problem. Artificial neural networks are one type of machine learning algorithm that can provide a reproducible way to apply pattern recognition heuristics to underspecified problems. Here we use the open-source TensorFlow machine learning library and apply it to the problem of identifying which hypothetical observation sequences from a computer simulation are “equilibrated” and which are not. We generate training populations and test populations of observation sequences with embedded linear and exponential correlations. We train a two-neuron artificial network to distinguish the correlated and uncorrelated sequences. We find that this simple network is good enough for > 98% accuracy in identifying exponentially-decaying energy trajectories from molecular simulations.

Spatio-energetic cross talk in photon counting detectors: Detector model and correlated Poisson data generator.

PubMed

Taguchi, Katsuyuki; Polster, Christoph; Lee, Okkyun; Stierstorfer, Karl; Kappler, Steffen

2016-12-01

An x-ray photon interacts with photon counting detectors (PCDs) and generates an electron charge cloud or multiple clouds. The clouds (thus, the photon energy) may be split between two adjacent PCD pixels when the interaction occurs near pixel boundaries, producing a count at both of the pixels. This is called double-counting with charge sharing. (A photoelectric effect with K-shell fluorescence x-ray emission would result in double-counting as well). As a result, PCD data are spatially and energetically correlated, although the output of individual PCD pixels is Poisson distributed. Major problems include the lack of a detector noise model for the spatio-energetic cross talk and lack of a computationally efficient simulation tool for generating correlated Poisson data. A Monte Carlo (MC) simulation can accurately simulate these phenomena and produce noisy data; however, it is not computationally efficient. In this study, the authors developed a new detector model and implemented it in an efficient software simulator that uses a Poisson random number generator to produce correlated noisy integer counts. The detector model takes the following effects into account: (1) detection efficiency; (2) incomplete charge collection and ballistic effect; (3) interaction with PCDs via photoelectric effect (with or without K-shell fluorescence x-ray emission, which may escape from the PCDs or be reabsorbed); and (4) electronic noise. The correlation was modeled by using these two simplifying assumptions: energy conservation and mutual exclusiveness. The mutual exclusiveness is that no more than two pixels measure energy from one photon. The effect of model parameters has been studied and results were compared with MC simulations. The agreement, with respect to the spectrum, was evaluated using the reduced χ 2 statistics or a weighted sum of squared errors, χ red 2 (≥1), where χ red 2 =1 indicates a perfect fit. The model produced spectra with flat field irradiation that qualitatively agree with previous studies. The spectra generated with different model and geometry parameters allowed for understanding the effect of the parameters on the spectrum and the correlation of data. The agreement between the model and MC data was very strong. The mean spectra with 90 keV and 140 kVp agreed exceptionally well: χ red 2 values were 1.049 with 90 keV data and 1.007 with 140 kVp data. The degrees of cross talk (in terms of the relative increase from single pixel irradiation to flat field irradiation) were 22% with 90 keV and 19% with 140 kVp for MC simulations, while they were 21% and 17%, respectively, for the model. The covariance was in strong agreement qualitatively, although it was overestimated. The noisy data generation was very efficient, taking less than a CPU minute as opposed to CPU hours for MC simulators. The authors have developed a novel, computationally efficient PCD model that takes into account double-counting and resulting spatio-energetic correlation between PCD pixels. The MC simulation validated the accuracy.

Experimental validation and model development for thermal transmittances of porous window screens and horizontal louvred blind systems

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

Hart, Robert; Goudey, Howdy; Curcija, D. Charlie

Virtually every home in the US has some form of shades, blinds, drapes, or other window attachment, but few have been designed for energy savings. In order to provide a common basis of comparison for thermal performance it is important to have validated simulation tools. This study outlines a review and validation of the ISO 15099 centre-of-glass thermal transmittance correlations for naturally ventilated cavities through measurement and detailed simulations. The focus is on the impacts of room-side ventilated cavities, such as those found with solar screens and horizontal louvred blinds. The thermal transmittance of these systems is measured experimentally, simulatedmore » using computational fluid dynamics analysis, and simulated utilizing simplified correlations from ISO 15099. Finally, correlation coefficients are proposed for the ISO 15099 algorithm that reduces the mean error between measured and simulated heat flux for typical solar screens from 16% to 3.5% and from 13% to 1% for horizontal blinds.« less

Experimental validation and model development for thermal transmittances of porous window screens and horizontal louvred blind systems

DOE PAGES

Hart, Robert; Goudey, Howdy; Curcija, D. Charlie

2017-05-16

Virtually every home in the US has some form of shades, blinds, drapes, or other window attachment, but few have been designed for energy savings. In order to provide a common basis of comparison for thermal performance it is important to have validated simulation tools. This study outlines a review and validation of the ISO 15099 centre-of-glass thermal transmittance correlations for naturally ventilated cavities through measurement and detailed simulations. The focus is on the impacts of room-side ventilated cavities, such as those found with solar screens and horizontal louvred blinds. The thermal transmittance of these systems is measured experimentally, simulatedmore » using computational fluid dynamics analysis, and simulated utilizing simplified correlations from ISO 15099. Finally, correlation coefficients are proposed for the ISO 15099 algorithm that reduces the mean error between measured and simulated heat flux for typical solar screens from 16% to 3.5% and from 13% to 1% for horizontal blinds.« less

Signatures of correlated excitonic dynamics in two-dimensional spectroscopy of the Fenna-Matthew-Olson photosynthetic complex

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

Caram, Justin R.; Lewis, Nicholas H. C.; Fidler, Andrew F.

2012-03-14

Long-lived excitonic coherence in photosynthetic proteins has become an exciting area of research because it may provide design principles for enhancing the efficiency of energy transfer in a broad range of materials. In this publication, we provide new evidence that long-lived excitonic coherence in the Fenna-Mathew-Olson pigment-protein (FMO) complex is consistent with the assumption of cross correlation in the site basis, indicating that each site shares bath fluctuations. We analyze the structure and character of the beating crosspeak between the two lowest energy excitons in two-dimensional (2D) electronic spectra of the FMO Complex. To isolate this dynamic signature, we usemore » the two-dimensional linear prediction Z-transform as a platform for filtering coherent beating signatures within 2D spectra. By separating signals into components in frequency and decay rate representations, we are able to improve resolution and isolate specific coherences. This strategy permits analysis of the shape, position, character, and phase of these features. Simulations of the crosspeak between excitons 1 and 2 in FMO under different regimes of cross correlation verify that statistically independent site fluctuations do not account for the elongation and persistence of the dynamic crosspeak. To reproduce the experimental results, we invoke near complete correlation in the fluctuations experienced by the sites associated with excitons 1 and 2. This model contradicts ab initio quantum mechanic/molecular mechanics simulations that observe no correlation between the energies of individual sites. This contradiction suggests that a new physical model for long-lived coherence may be necessary. The data presented here details experimental results that must be reproduced for a physical model of quantum coherence in photosynthetic energy transfer.« less

Monte Carlo parametric studies of neutron interrogation with the Associated Particle Technique for cargo container inspections

NASA Astrophysics Data System (ADS)

Deyglun, Clément; Carasco, Cédric; Pérot, Bertrand

2014-06-01

The detection of Special Nuclear Materials (SNM) by neutron interrogation is extensively studied by Monte Carlo simulation at the Nuclear Measurement Laboratory of CEA Cadarache (French Alternative Energies and Atomic Energy Commission). The active inspection system is based on the Associated Particle Technique (APT). Fissions induced by tagged neutrons (i.e. correlated to an alpha particle in the DT neutron generator) in SNM produce high multiplicity coincidences which are detected with fast plastic scintillators. At least three particles are detected in a short time window following the alpha detection, whereas nonnuclear materials mainly produce single events, or pairs due to (n,2n) and (n,n'γ) reactions. To study the performances of an industrial cargo container inspection system, Monte Carlo simulations are performed with the MCNP-PoliMi transport code, which records for each neutron history the relevant information: reaction types, position and time of interactions, energy deposits, secondary particles, etc. The output files are post-processed with a specific tool developed with ROOT data analysis software. Particles not correlated with an alpha particle (random background), counting statistics, and time-energy resolutions of the data acquisition system are taken into account in the numerical model. Various matrix compositions, suspicious items, SNM shielding and positions inside the container, are simulated to assess the performances and limitations of an industrial system.

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

PubMed Central

Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

2016-01-01

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Lu, Yan; Salsbury, Freddie R.

2015-01-01

ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.

Experimental validation for thermal transmittances of window shading systems with perimeter gaps

DOE PAGES

Hart, Robert; Goudey, Howdy; Curcija, D. Charlie

2018-02-22

Virtually all residential and commercial windows in the U.S. have some form of window attachment, but few have been designed for energy savings. ISO 15099 presents a simulation framework to determine thermal performance of window attachments, but the model has not been validated for these products. This paper outlines a review and validation of the ISO 15099 centre-of-glass heat transfer correlations for perimeter gaps (top, bottom, and side) in naturally ventilated cavities through measurement and simulation. The thermal transmittance impact due to dimensional variations of these gaps is measured experimentally, simulated using computational fluid dynamics, and simulated utilizing simplified correlationsmore » from ISO 15099. Results show that the ISO 15099 correlations produce a mean error between measured and simulated heat flux of 2.5 ± 7%. These tolerances are similar to those obtained from sealed cavity comparisons and are deemed acceptable within the ISO 15099 framework.« less

Path integral molecular dynamic simulation of flexible molecular systems in their ground state: Application to the water dimer

NASA Astrophysics Data System (ADS)

Schmidt, Matthew; Roy, Pierre-Nicholas

2018-03-01

We extend the Langevin equation Path Integral Ground State (LePIGS), a ground state quantum molecular dynamics method, to simulate flexible molecular systems and calculate both energetic and structural properties. We test the approach with the H2O and D2O monomers and dimers. We systematically optimize all simulation parameters and use a unity trial wavefunction. We report ground state energies, dissociation energies, and structural properties using three different water models, two of which are empirically based, q-TIP4P/F and q-SPC/Fw, and one which is ab initio, MB-pol. We demonstrate that our energies calculated from LePIGS can be merged seamlessly with low temperature path integral molecular dynamics calculations and note the similarities between the two methods. We also benchmark our energies against previous diffusion Monte Carlo calculations using the same potentials and compare to experimental results. We further demonstrate that accurate vibrational energies of the H2O and D2O monomer can be calculated from imaginary time correlation functions generated from the LePIGS simulations using solely the unity trial wavefunction.

Stable Eigenmodes and Energy Dynamics in a Model of LAPD Turbulence

NASA Astrophysics Data System (ADS)

Friedman, Brett; Carter, T. A.; Umansky, M. V.

2011-10-01

A three field Braginskii fluid model that semi-quantitatively predicts turbulent statistics in the Large Plasma Device (LAPD) at UCLA is analyzed. A 3D simulation of turbulence in LAPD using the BOUT++ fluid code is shown to reproduce experimental turbulent properties such as the frequency spectrum and correlation length with semi-qualitative and semi-quantitative accuracy. In an attempt to explain turbulent saturation in the simulation, equations for the energy dynamics are derived and applied to the results. The degree to which stable linear drift wave eigenmodes draw energy from the system and the affect that zonal flows have on transferring energy to stable eigenmode branches is explored. It is also shown that zonal flows drive Kelvin-Helmholtz flute modes, which come to dominate the energy dynamics in the quasi steady state regime.

The Numerical Analysis of a Turbulent Compressible Jet. Degree awarded by Ohio State Univ., 2000

NASA Technical Reports Server (NTRS)

DeBonis, James R.

2001-01-01

A numerical method to simulate high Reynolds number jet flows was formulated and applied to gain a better understanding of the flow physics. Large-eddy simulation was chosen as the most promising approach to model the turbulent structures due to its compromise between accuracy and computational expense. The filtered Navier-Stokes equations were developed including a total energy form of the energy equation. Subgrid scale models for the momentum and energy equations were adapted from compressible forms of Smagorinsky's original model. The effect of using disparate temporal and spatial accuracy in a numerical scheme was discovered through one-dimensional model problems and a new uniformly fourth-order accurate numerical method was developed. Results from two- and three-dimensional validation exercises show that the code accurately reproduces both viscous and inviscid flows. Numerous axisymmetric jet simulations were performed to investigate the effect of grid resolution, numerical scheme, exit boundary conditions and subgrid scale modeling on the solution and the results were used to guide the three-dimensional calculations. Three-dimensional calculations of a Mach 1.4 jet showed that this LES simulation accurately captures the physics of the turbulent flow. The agreement with experimental data was relatively good and is much better than results in the current literature. Turbulent intensities indicate that the turbulent structures at this level of modeling are not isotropic and this information could lend itself to the development of improved subgrid scale models for LES and turbulence models for RANS simulations. A two point correlation technique was used to quantify the turbulent structures. Two point space correlations were used to obtain a measure of the integral length scale, which proved to be approximately 1/2 D(sub j). Two point space-time correlations were used to obtain the convection velocity for the turbulent structures. This velocity ranged from 0.57 to 0.71 U(sub j).

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Joint image reconstruction method with correlative multi-channel prior for x-ray spectral computed tomography

NASA Astrophysics Data System (ADS)

Kazantsev, Daniil; Jørgensen, Jakob S.; Andersen, Martin S.; Lionheart, William R. B.; Lee, Peter D.; Withers, Philip J.

2018-06-01

Rapid developments in photon-counting and energy-discriminating detectors have the potential to provide an additional spectral dimension to conventional x-ray grayscale imaging. Reconstructed spectroscopic tomographic data can be used to distinguish individual materials by characteristic absorption peaks. The acquired energy-binned data, however, suffer from low signal-to-noise ratio, acquisition artifacts, and frequently angular undersampled conditions. New regularized iterative reconstruction methods have the potential to produce higher quality images and since energy channels are mutually correlated it can be advantageous to exploit this additional knowledge. In this paper, we propose a novel method which jointly reconstructs all energy channels while imposing a strong structural correlation. The core of the proposed algorithm is to employ a variational framework of parallel level sets to encourage joint smoothing directions. In particular, the method selects reference channels from which to propagate structure in an adaptive and stochastic way while preferring channels with a high data signal-to-noise ratio. The method is compared with current state-of-the-art multi-channel reconstruction techniques including channel-wise total variation and correlative total nuclear variation regularization. Realistic simulation experiments demonstrate the performance improvements achievable by using correlative regularization methods.

Test of Hadronic Interaction Models with the KASCADE Hadron Calorimeter

NASA Astrophysics Data System (ADS)

Milke, J.; KASCADE Collaboration

The interpretation of extensive air shower (EAS) measurements often requires the comparison with EAS simulations based on high-energy hadronic interaction models. These interaction models have to extrapolate into kinematical regions and energy ranges beyond the limit of present accelerators. Therefore, it is necessary to test whether these models are able to describe the EAS development in a consistent way. By measuring simultaneously the hadronic, electromagnetic, and muonic part of an EAS the experiment KASCADE offers best facilities for checking the models. For the EAS simulations the program CORSIKA with several hadronic event generators implemented is used. Different hadronic observables, e.g. hadron number, energy spectrum, lateral distribution, are investigated, as well as their correlations with the electromagnetic and muonic shower size. By comparing measurements and simulations the consistency of the description of the EAS development is checked. First results with the new interaction model NEXUS and the version II.5 of the model DPMJET, recently included in CORSIKA, are presented and compared with QGSJET simulations.

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2011-01-01

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c

NASA Astrophysics Data System (ADS)

Karino, Yasuhito; Matubayasi, Nobuyuki

2011-01-01

The relationship between the protein conformation and the hydration effect is investigated for the equilibrium fluctuation of cytochrome c. To elucidate the hydration effect with explicit solvent, the solvation free energy of the protein immersed in water was calculated using the molecular dynamics simulation coupled with the method of energy representation. The variations of the protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation. The roles of the attractive and repulsive components in the protein-water interaction are further examined for the solvation free energy. The attractive component represented as the average sum of protein-water interaction energy is dominated by the electrostatic effect and is correlated to the solvation free energy through the linear-response-type relationship. No correlation with the (total) solvation free energy is seen, on the other hand, for the repulsive component expressed as the excluded-volume effect.

Enantiospecific adsorption of propranolol enantiomers on naturally chiral copper surface: A molecular dynamics simulation investigation

NASA Astrophysics Data System (ADS)

Sedghamiz, Tahereh; Bahrami, Maryam; Ghatee, Mohammad Hadi

2017-04-01

Adsorption of propranolol enantiomers on naturally chiral copper (Cu(3,1,17)S) and achiral copper (Cu(100)) surfaces were studied by molecular dynamics simulation to unravel the features of adsorbate-adsorbent enantioselectivity. Adsorption of S- and R-propranolol on Cu(3,1,17)S terraces (with 100 plane) leads mainly to endo- and exo-conformers, respectively. Simulated pair correlation function (g(r)) and mean square displacement (MSD) were analyzed to identify adsorption sites of enantiomers on Cu(3,1,17)S substrate surface, and their simulated binding energies were used to access the adsorption strength. According to (g(r)), R-propranolol adsorbs via naphtyl group while S-propranolol mainly adsorbs through chain group. R-enantiomer binds more tightly to the chiral substrate surface than S-enantiomer as indicated by a higher simulated binding energy by 2.74 kJ mol-1 per molecule. The difference in binding energies of propranolol enantiomers on naturally chiral Cu(3,1,17)S is almost six times larger than on the achiral Cu(100) surface, which substantiates the appreciably strong specific enantioselective adsorption on the former surface.

Oxygen reduction on a Pt(111) catalyst in HT-PEM fuel cells by density functional theory

NASA Astrophysics Data System (ADS)

Sun, Hong; Li, Jie; Almheiri, Saif; Xiao, Jianyu

2017-08-01

The oxygen reduction reaction plays an important role in the performance of high-temperature proton exchange membrane (HT-PEM) fuel cells. In this study, a molecular dynamics model, which is based on the density functional theory and couples the system's energy, the exchange-correlation energy functional, the charge density distribution function, and the simplified Kohn-Sham equation, was developed to simulate the oxygen reduction reaction on a Pt(111) surface. Additionally, an electrochemical reaction system on the basis of a four-electron reaction mechanism was also developed for this simulation. The reaction path of the oxygen reduction reaction, the product structure of each reaction step and the system's energy were simulated. It is found that the first step reaction of the first hydrogen ion with the oxygen molecule is the controlling step of the overall reaction. Increasing the operating temperature speeds up the first step reaction rate and slightly decreases its reaction energy barrier. Our results provide insight into the working principles of HT-PEM fuel cells.

Cross-matching: a modified cross-correlation underlying threshold energy model and match-based depth perception

PubMed Central

Doi, Takahiro; Fujita, Ichiro

2014-01-01

Three-dimensional visual perception requires correct matching of images projected to the left and right eyes. The matching process is faced with an ambiguity: part of one eye's image can be matched to multiple parts of the other eye's image. This stereo correspondence problem is complicated for random-dot stereograms (RDSs), because dots with an identical appearance produce numerous potential matches. Despite such complexity, human subjects can perceive a coherent depth structure. A coherent solution to the correspondence problem does not exist for anticorrelated RDSs (aRDSs), in which luminance contrast is reversed in one eye. Neurons in the visual cortex reduce disparity selectivity for aRDSs progressively along the visual processing hierarchy. A disparity-energy model followed by threshold nonlinearity (threshold energy model) can account for this reduction, providing a possible mechanism for the neural matching process. However, the essential computation underlying the threshold energy model is not clear. Here, we propose that a nonlinear modification of cross-correlation, which we term “cross-matching,” represents the essence of the threshold energy model. We placed half-wave rectification within the cross-correlation of the left-eye and right-eye images. The disparity tuning derived from cross-matching was attenuated for aRDSs. We simulated a psychometric curve as a function of graded anticorrelation (graded mixture of aRDS and normal RDS); this simulated curve reproduced the match-based psychometric function observed in human near/far discrimination. The dot density was 25% for both simulation and observation. We predicted that as the dot density increased, the performance for aRDSs should decrease below chance (i.e., reversed depth), and the level of anticorrelation that nullifies depth perception should also decrease. We suggest that cross-matching serves as a simple computation underlying the match-based disparity signals in stereoscopic depth perception. PMID:25360107

Simulations of material mixing in laser-driven reshock experiments

NASA Astrophysics Data System (ADS)

Haines, Brian M.; Grinstein, Fernando F.; Welser-Sherrill, Leslie; Fincke, James R.

2013-02-01

We perform simulations of a laser-driven reshock experiment [Welser-Sherrill et al., High Energy Density Phys. (unpublished)] in the strong-shock high energy-density regime to better understand material mixing driven by the Richtmyer-Meshkov instability. Validation of the simulations is based on direct comparison of simulation and radiographic data. Simulations are also compared with published direct numerical simulation and the theory of homogeneous isotropic turbulence. Despite the fact that the flow is neither homogeneous, isotropic nor fully turbulent, there are local regions in which the flow demonstrates characteristics of homogeneous isotropic turbulence. We identify and isolate these regions by the presence of high levels of turbulent kinetic energy (TKE) and vorticity. After reshock, our analysis shows characteristics consistent with those of incompressible isotropic turbulence. Self-similarity and effective Reynolds number assessments suggest that the results are reasonably converged at the finest resolution. Our results show that in shock-driven transitional flows, turbulent features such as self-similarity and isotropy only fully develop once de-correlation, characteristic vorticity distributions, and integrated TKE, have decayed significantly. Finally, we use three-dimensional simulation results to test the performance of two-dimensional Reynolds-averaged Navier-Stokes simulations. In this context, we also test a presumed probability density function turbulent mixing model extensively used in combustion applications.

Laser fractional photothermolysis of the skin: numerical simulation of microthermal zones.

PubMed

Marqa, Mohamad Feras; Mordon, Serge

2014-04-01

Laser Fractional Photothermolysis (FP) is one of the innovative techniques for skin remodeling and resurfacing. During treatment, the control of the Microscopic Thermal Zones' (MTZs) dimensions versus pulse energy requires detailed knowledge of the various parameters governing the heat transfer process. In this study, a mathematical model is devised to simulate the effect of pulse energy variations on the dimensions of MTZs. Two series of simulations for ablative (10.6 μm CO2) and non-ablative (1.550 μm Er:Glass) lasers systems were performed. In each series, simulations were carried for the following pulses energies: 5, 10, 15, 20, 25, 30, 35, and 40 mJ. Results of simulations are validated by histological analysis images of MTZs sections reported in works by Hantash et al. and Bedi et al. MTZs dimensions were compared between histology and those achieved using our simulation model using fusion data technique for both ablative FP and non-ablative FP treatment methods. Depths and widths from simulations are usually deeper (21 ± 2%) and wider (12 ± 2%) when compared with histological analysis data. When accounting for the shrinkage effect of excision of cutaneous tissues, a good correlation can be established between the simulation and the histological analysis results.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals.

PubMed

Wilson, S R; Mendelev, M I

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

NASA Astrophysics Data System (ADS)

Wilson, S. R.; Mendelev, M. I.

2016-04-01

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

Workshop on data acquisition and trigger system simulations for high energy physics

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

NONE

1992-12-31

This report discusses the following topics: DAQSIM: A data acquisition system simulation tool; Front end and DCC Simulations for the SDC Straw Tube System; Simulation of Non-Blocklng Data Acquisition Architectures; Simulation Studies of the SDC Data Collection Chip; Correlation Studies of the Data Collection Circuit & The Design of a Queue for this Circuit; Fast Data Compression & Transmission from a Silicon Strip Wafer; Simulation of SCI Protocols in Modsim; Visual Design with vVHDL; Stochastic Simulation of Asynchronous Buffers; SDC Trigger Simulations; Trigger Rates, DAQ & Online Processing at the SSC; Planned Enhancements to MODSEM II & SIMOBJECT -- anmore » Overview -- R.; DAGAR -- A synthesis system; Proposed Silicon Compiler for Physics Applications; Timed -- LOTOS in a PROLOG Environment: an Algebraic language for Simulation; Modeling and Simulation of an Event Builder for High Energy Physics Data Acquisition Systems; A Verilog Simulation for the CDF DAQ; Simulation to Design with Verilog; The DZero Data Acquisition System: Model and Measurements; DZero Trigger Level 1.5 Modeling; Strategies Optimizing Data Load in the DZero Triggers; Simulation of the DZero Level 2 Data Acquisition System; A Fast Method for Calculating DZero Level 1 Jet Trigger Properties and Physics Input to DAQ Studies.« less

Frequency-resolved Monte Carlo.

PubMed

López Carreño, Juan Camilo; Del Valle, Elena; Laussy, Fabrice P

2018-05-03

We adapt the Quantum Monte Carlo method to the cascaded formalism of quantum optics, allowing us to simulate the emission of photons of known energy. Statistical processing of the photon clicks thus collected agrees with the theory of frequency-resolved photon correlations, extending the range of applications based on correlations of photons of prescribed energy, in particular those of a photon-counting character. We apply the technique to autocorrelations of photon streams from a two-level system under coherent and incoherent pumping, including the Mollow triplet regime where we demonstrate the direct manifestation of leapfrog processes in producing an increased rate of two-photon emission events.

Systematic investigations of low energy Ar ion beam sputtering of Si and Ag

NASA Astrophysics Data System (ADS)

Feder, R.; Frost, F.; Neumann, H.; Bundesmann, C.; Rauschenbach, B.

2013-12-01

Ion beam sputter deposition (IBD) delivers some intrinsic features influencing the growing film properties, because ion properties and geometrical process conditions generate different energy and spatial distributions of the sputtered and scattered particles. Even though IBD has been used for decades, the full capabilities are not investigated systematically and specifically used yet. Therefore, a systematic and comprehensive analysis of the correlation between the properties of the ion beam, the generated secondary particles and backscattered ions and the deposited films needs to be done.A vacuum deposition chamber has been set up which allows ion beam sputtering of different targets under variation of geometrical parameters (ion incidence angle, position of substrates and analytics in respect to the target) and of ion beam parameters (ion species, ion energy) to perform a systematic and comprehensive analysis of the correlation between the properties of the ion beam, the properties of the sputtered and scattered particles, and the properties of the deposited films. A set of samples was prepared and characterized with respect to selected film properties, such as thickness and surface topography. The experiments indicate a systematic influence of the deposition parameters on the film properties as hypothesized before. Because of this influence, the energy distribution of secondary particles was measured using an energy-selective mass spectrometer. Among others, experiments revealed a high-energetic maximum for backscattered primary ions, which shifts with increasing emission angle to higher energies. Experimental data are compared with Monte Carlo simulations done with the well-known Transport and Range of Ions in Matter, Sputtering version (TRIM.SP) code [J.P. Biersack, W. Eckstein, Appl. Phys. A: Mater. Sci. Process. 34 (1984) 73]. The thicknesses of the films are in good agreement with those calculated from simulated particle fluxes. For the positions of the high-energetic maxima in the energy distribution of the backscattered primary ions, a deviation between simulated and measured data was found, most likely originating in a higher energy loss under experimental conditions than considered in the simulation.

Determination of the strong coupling constant α _{s} from transverse energy-energy correlations in multijet events at √{s} = 8 TeV using the ATLAS detector

NASA Astrophysics Data System (ADS)

Aaboud, M.; Aad, G.; Abbott, B.; Abdallah, J.; Abdinov, O.; Abeloos, B.; Abidi, S. H.; AbouZeid, O. S.; Abraham, N. L.; Abramowicz, H.; Abreu, H.; Abreu, R.; Abulaiti, Y.; Acharya, B. S.; Adachi, S.; Adamczyk, L.; Adelman, J.; Adersberger, M.; Adye, T.; Affolder, A. A.; Agatonovic-Jovin, T.; Agheorghiesei, C.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akatsuka, S.; Akerstedt, H.; Åkesson, T. P. A.; Akilli, E.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albicocco, P.; Alconada Verzini, M. J.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Ali, B.; Aliev, M.; Alimonti, G.; Alison, J.; Alkire, S. P.; Allbrooke, B. M. M.; Allen, B. W.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Alshehri, A. A.; Alstaty, M. I.; Alvarez Gonzalez, B.; Álvarez Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amaral Coutinho, Y.; Amelung, C.; Amidei, D.; Amor Dos Santos, S. P.; Amorim, A.; Amoroso, S.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Angerami, A.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antel, C.; Antonelli, M.; Antonov, A.; Antrim, D. J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Araujo Ferraz, V.; Arce, A. T. H.; Ardell, R. E.; Arduh, F. A.; Arguin, J.-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Armitage, L. J.; Arnaez, O.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Artz, S.; Asai, S.; Asbah, N.; Ashkenazi, A.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Avolio, G.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baas, A. E.; Baca, M. J.; Bachacou, H.; Bachas, K.; Backes, M.; Backhaus, M.; Bagnaia, P.; Bahrasemani, H.; Baines, J. T.; Bajic, M.; Baker, O. K.; Baldin, E. M.; Balek, P.; Balli, F.; Balunas, W. K.; Banas, E.; Banerjee, Sw.; Bannoura, A. A. E.; Barak, L.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisits, M.-S.; Barkeloo, J. T.; Barklow, T.; Barlow, N.; Barnes, S. L.; Barnett, B. M.; Barnett, R. M.; Barnovska-Blenessy, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barranco Navarro, L.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Basalaev, A.; Bassalat, A.; Bates, R. L.; Batista, S. J.; Batley, J. R.; Battaglia, M.; Bauce, M.; Bauer, F.; Bawa, H. S.; Beacham, J. B.; Beattie, M. D.; Beau, T.; Beauchemin, P. H.; Bechtle, P.; Beck, H. P.; Becker, K.; Becker, M.; Beckingham, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bedognetti, M.; Bee, C. P.; Beermann, T. A.; Begalli, M.; Begel, M.; Behr, J. K.; Bell, A. S.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belotskiy, K.; Beltramello, O.; Belyaev, N. L.; Benary, O.; Benchekroun, D.; Bender, M.; Bendtz, K.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez, J.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Bentvelsen, S.; Beresford, L.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Beringer, J.; Berlendis, S.; Bernard, N. R.; Bernardi, G.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertoli, G.; Bertolucci, F.; Bertram, I. A.; Bertsche, C.; Bertsche, D.; Besjes, G. J.; Bessidskaia Bylund, O.; Bessner, M.; Besson, N.; Betancourt, C.; Bethani, A.; Bethke, S.; Bevan, A. J.; Beyer, J.; Bianchi, R. M.; Biebel, O.; Biedermann, D.; Bielski, R.; Biesuz, N. V.; Biglietti, M.; Bilbao De Mendizabal, J.; Billoud, T. R. V.; Bilokon, H.; Bindi, M.; Bingul, A.; Bini, C.; Biondi, S.; Bisanz, T.; Bittrich, C.; Bjergaard, D. M.; Black, C. W.; Black, J. E.; Black, K. M.; Blair, R. E.; Blazek, T.; Bloch, I.; Blocker, C.; Blue, A.; Blum, W.; Blumenschein, U.; Blunier, S.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Bock, C.; Boehler, M.; Boerner, D.; Bogavac, D.; Bogdanchikov, A. G.; Bohm, C.; Boisvert, V.; Bokan, P.; Bold, T.; Boldyrev, A. S.; Bolz, A. E.; Bomben, M.; Bona, M.; Boonekamp, M.; Borisov, A.; Borissov, G.; Bortfeldt, J.; Bortoletto, D.; Bortolotto, V.; Boscherini, D.; Bosman, M.; Bossio Sola, J. D.; Boudreau, J.; Bouffard, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Boutle, S. K.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bracinik, J.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Breaden Madden, W. D.; Brendlinger, K.; Brennan, A. J.; Brenner, L.; Brenner, R.; Bressler, S.; Briglin, D. L.; Bristow, T. M.; Britton, D.; Britzger, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brosamer, J.; Brost, E.; Broughton, J. H.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruni, A.; Bruni, G.; Bruni, L. S.; Brunt, BH; Bruschi, M.; Bruscino, N.; Bryant, P.; Bryngemark, L.; Buanes, T.; Buat, Q.; Buchholz, P.; Buckley, A. G.; Budagov, I. A.; Buehrer, F.; Bugge, M. K.; Bulekov, O.; Bullock, D.; Burch, T. J.; Burdin, S.; Burgard, C. D.; Burger, A. M.; Burghgrave, B.; Burka, K.; Burke, S.; Burmeister, I.; Burr, J. T. P.; Busato, E.; Büscher, D.; Büscher, V.; Bussey, P.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Butti, P.; Buttinger, W.; Buzatu, A.; Buzykaev, A. R.; Cabrera Urbán, S.; Caforio, D.; Cairo, V. M.; Cakir, O.; Calace, N.; Calafiura, P.; Calandri, A.; Calderini, G.; Calfayan, P.; Callea, G.; Caloba, L. P.; Calvente Lopez, S.; Calvet, D.; Calvet, S.; Calvet, T. P.; Camacho Toro, R.; Camarda, S.; Camarri, P.; Cameron, D.; Caminal Armadans, R.; Camincher, C.; Campana, S.; Campanelli, M.; Camplani, A.; Campoverde, A.; Canale, V.; Cano Bret, M.; Cantero, J.; Cao, T.; Capeans Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capua, M.; Carbone, R. M.; Cardarelli, R.; Cardillo, F.; Carli, I.; Carli, T.; Carlino, G.; Carlson, B. T.; Carminati, L.; Carney, R. M. D.; Caron, S.; Carquin, E.; Carrá, S.; Carrillo-Montoya, G. D.; Carvalho, J.; Casadei, D.; Casado, M. P.; Casolino, M.; Casper, D. W.; Castelijn, R.; Castillo Gimenez, V.; Castro, N. F.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Caudron, J.; Cavaliere, V.; Cavallaro, E.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Celebi, E.; Ceradini, F.; Cerda Alberich, L.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cervelli, A.; Cetin, S. A.; Chafaq, A.; Chakraborty, D.; Chan, S. K.; Chan, W. S.; Chan, Y. L.; Chang, P.; Chapman, J. D.; Charlton, D. G.; Chau, C. C.; Chavez Barajas, C. A.; Che, S.; Cheatham, S.; Chegwidden, A.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, H.; Chen, S.; Chen, S.; Chen, X.; Chen, Y.; Cheng, H. C.; Cheng, H. J.; Cheplakov, A.; Cheremushkina, E.; Cherkaoui El Moursli, R.; Chernyatin, V.; Cheu, E.; Cheung, K.; Chevalier, L.; Chiarella, V.; Chiarelli, G.; Chiodini, G.; Chisholm, A. S.; Chitan, A.; Chiu, Y. H.; Chizhov, M. V.; Choi, K.; Chomont, A. R.; Chouridou, S.; Christodoulou, V.; Chromek-Burckhart, D.; Chu, M. C.; Chudoba, J.; Chuinard, A. J.; Chwastowski, J. J.; Chytka, L.; Ciftci, A. K.; Cinca, D.; Cindro, V.; Cioara, I. A.; Ciocca, C.; Ciocio, A.; Cirotto, F.; Citron, Z. H.; Citterio, M.; Ciubancan, M.; Clark, A.; Clark, B. L.; Clark, M. R.; Clark, P. J.; Clarke, R. N.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Colasurdo, L.; Cole, B.; Colijn, A. P.; Collot, J.; Colombo, T.; Conde Muiño, P.; Coniavitis, E.; Connell, S. H.; Connelly, I. A.; Constantinescu, S.; Conti, G.; Conventi, F.; Cooke, M.; Cooper-Sarkar, A. M.; Cormier, F.; Cormier, K. J. R.; Corradi, M.; Corriveau, F.; Cortes-Gonzalez, A.; Cortiana, G.; Costa, G.; Costa, M. J.; Costanzo, D.; Cottin, G.; Cowan, G.; Cox, B. E.; Cranmer, K.; Crawley, S. J.; Creager, R. A.; Cree, G.; Crépé-Renaudin, S.; Crescioli, F.; Cribbs, W. A.; Cristinziani, M.; Croft, V.; Crosetti, G.; Cueto, A.; Cuhadar Donszelmann, T.; Cukierman, A. R.; Cummings, J.; Curatolo, M.; Cúth, J.; Czirr, H.; Czodrowski, P.; D'amen, G.; D'Auria, S.; D'eramo, L.; D'Onofrio, M.; Da Cunha Sargedas De Sousa, M. J.; Da Via, C.; Dabrowski, W.; Dado, T.; Dai, T.; Dale, O.; Dallaire, F.; Dallapiccola, C.; Dam, M.; Dandoy, J. R.; Daneri, M. F.; Dang, N. P.; Daniells, A. C.; Dann, N. S.; Danninger, M.; Dano Hoffmann, M.; Dao, V.; Darbo, G.; Darmora, S.; Dassoulas, J.; Dattagupta, A.; Daubney, T.; Davey, W.; David, C.; Davidek, T.; Davies, M.; Davis, D. R.; Davison, P.; Dawe, E.; Dawson, I.; De, K.; de Asmundis, R.; De Benedetti, A.; De Castro, S.; De Cecco, S.; De Groot, N.; de Jong, P.; De la Torre, H.; De Lorenzi, F.; De Maria, A.; De Pedis, D.; De Salvo, A.; De Sanctis, U.; De Santo, A.; De Vasconcelos Corga, K.; De Vivie De Regie, J. B.; Dearnaley, W. J.; Debbe, R.; Debenedetti, C.; Dedovich, D. V.; Dehghanian, N.; Deigaard, I.; Del Gaudio, M.; Del Peso, J.; Del Prete, T.; Delgove, D.; Deliot, F.; Delitzsch, C. M.; Dell'Acqua, A.; Dell'Asta, L.; Dell'Orso, M.; Della Pietra, M.; della Volpe, D.; Delmastro, M.; Delporte, C.; Delsart, P. A.; DeMarco, D. A.; Demers, S.; Demichev, M.; Demilly, A.; Denisov, S. P.; Denysiuk, D.; Derendarz, D.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Deterre, C.; Dette, K.; Devesa, M. R.; Deviveiros, P. O.; Dewhurst, A.; Dhaliwal, S.; Di Bello, F. A.; Di Ciaccio, A.; Di Ciaccio, L.; Di Clemente, W. K.; Di Donato, C.; Di Girolamo, A.; Di Girolamo, B.; Di Micco, B.; Di Nardo, R.; Di Petrillo, K. F.; Di Simone, A.; Di Sipio, R.; Di Valentino, D.; Diaconu, C.; Diamond, M.; Dias, F. A.; Diaz, M. A.; Diehl, E. B.; Dietrich, J.; Díez Cornell, S.; Dimitrievska, A.; Dingfelder, J.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djobava, T.; Djuvsland, J. I.; do Vale, M. A. B.; Dobos, D.; Dobre, M.; Doglioni, C.; Dolejsi, J.; Dolezal, Z.; Donadelli, M.; Donati, S.; Dondero, P.; Donini, J.; Dopke, J.; Doria, A.; Dova, M. T.; Doyle, A. T.; Drechsler, E.; Dris, M.; Du, Y.; Duarte-Campderros, J.; Dubreuil, A.; Duchovni, E.; Duckeck, G.; Ducourthial, A.; Ducu, O. A.; Duda, D.; Dudarev, A.; Dudder, A. Chr.; Duffield, E. M.; Duflot, L.; Dührssen, M.; Dumancic, M.; Dumitriu, A. E.; Duncan, A. K.; Dunford, M.; Duran Yildiz, H.; Düren, M.; Durglishvili, A.; Duschinger, D.; Dutta, B.; Dyndal, M.; Dziedzic, B. S.; Eckardt, C.; Ecker, K. M.; Edgar, R. C.; Eifert, T.; Eigen, G.; Einsweiler, K.; Ekelof, T.; El Kacimi, M.; El Kosseifi, R.; Ellajosyula, V.; Ellert, M.; Elles, S.; Ellinghaus, F.; Elliot, A. A.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Emeliyanov, D.; Enari, Y.; Endner, O. C.; Ennis, J. S.; Erdmann, J.; Ereditato, A.; Ernis, G.; Ernst, M.; Errede, S.; Escalier, M.; Escobar, C.; Esposito, B.; Estrada Pastor, O.; Etienvre, A. I.; Etzion, E.; Evans, H.; Ezhilov, A.; Ezzi, M.; Fabbri, F.; Fabbri, L.; Fabiani, V.; Facini, G.; Fakhrutdinov, R. M.; Falciano, S.; Falla, R. J.; Faltova, J.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farina, C.; Farina, E. M.; Farooque, T.; Farrell, S.; Farrington, S. M.; Farthouat, P.; Fassi, F.; Fassnacht, P.; Fassouliotis, D.; Faucci Giannelli, M.; Favareto, A.; Fawcett, W. J.; Fayard, L.; Fedin, O. L.; Fedorko, W.; Feigl, S.; Feligioni, L.; Feng, C.; Feng, E. J.; Feng, H.; Fenton, M. J.; Fenyuk, A. B.; Feremenga, L.; Fernandez Martinez, P.; Fernandez Perez, S.; Ferrando, J.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferreira de Lima, D. E.; Ferrer, A.; Ferrere, D.; Ferretti, C.; Fiedler, F.; Filipčič, A.; Filipuzzi, M.; Filthaut, F.; Fincke-Keeler, M.; Finelli, K. D.; Fiolhais, M. C. N.; Fiorini, L.; Fischer, A.; Fischer, C.; Fischer, J.; Fisher, W. C.; Flaschel, N.; Fleck, I.; Fleischmann, P.; Fletcher, R. R. M.; Flick, T.; Flierl, B. M.; Flores Castillo, L. R.; Flowerdew, M. J.; Forcolin, G. T.; Formica, A.; Förster, F. A.; Forti, A.; Foster, A. G.; Fournier, D.; Fox, H.; Fracchia, S.; Francavilla, P.; Franchini, M.; Franchino, S.; Francis, D.; Franconi, L.; Franklin, M.; Frate, M.; Fraternali, M.; Freeborn, D.; Fressard-Batraneanu, S. M.; Freund, B.; Froidevaux, D.; Frost, J. A.; Fukunaga, C.; Fusayasu, T.; Fuster, J.; Gabaldon, C.; Gabizon, O.; Gabrielli, A.; Gabrielli, A.; Gach, G. P.; Gadatsch, S.; Gadomski, S.; Gagliardi, G.; Gagnon, L. 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C.; Ohman, H.; Oide, H.; Okawa, H.; Okumura, Y.; Okuyama, T.; Olariu, A.; Oleiro Seabra, L. F.; Olivares Pino, S. A.; Oliveira Damazio, D.; Olszewski, A.; Olszowska, J.; Onofre, A.; Onogi, K.; Onyisi, P. U. E.; Oreglia, M. J.; Oren, Y.; Orestano, D.; Orlando, N.; Orr, R. S.; Osculati, B.; Ospanov, R.; Otero y Garzon, G.; Otono, H.; Ouchrif, M.; Ould-Saada, F.; Ouraou, A.; Oussoren, K. P.; Ouyang, Q.; Owen, M.; Owen, R. E.; Ozcan, V. E.; Ozturk, N.; Pachal, K.; Pacheco Pages, A.; Pacheco Rodriguez, L.; Padilla Aranda, C.; Pagan Griso, S.; Paganini, M.; Paige, F.; Palacino, G.; Palazzo, S.; Palestini, S.; Palka, M.; Pallin, D.; St. Panagiotopoulou, E.; Panagoulias, I.; Pandini, C. E.; Panduro Vazquez, J. G.; Pani, P.; Panitkin, S.; Pantea, D.; Paolozzi, L.; Papadopoulou, Th. D.; Papageorgiou, K.; Paramonov, A.; Paredes Hernandez, D.; Parker, A. J.; Parker, M. A.; Parker, K. A.; Parodi, F.; Parsons, J. A.; Parzefall, U.; Pascuzzi, V. R.; Pasner, J. M.; Pasqualucci, E.; Passaggio, S.; Pastore, Fr.; Pataraia, S.; Pater, J. R.; Pauly, T.; Pearson, B.; Pedraza Lopez, S.; Pedro, R.; Peleganchuk, S. V.; Penc, O.; Peng, C.; Peng, H.; Penwell, J.; Peralva, B. S.; Perego, M. M.; Perepelitsa, D. V.; Peri, F.; Perini, L.; Pernegger, H.; Perrella, S.; Peschke, R.; Peshekhonov, V. D.; Peters, K.; Peters, R. F. Y.; Petersen, B. A.; Petersen, T. C.; Petit, E.; Petridis, A.; Petridou, C.; Petroff, P.; Petrolo, E.; Petrov, M.; Petrucci, F.; Pettersson, N. E.; Peyaud, A.; Pezoa, R.; Phillips, F. H.; Phillips, P. W.; Piacquadio, G.; Pianori, E.; Picazio, A.; Piccaro, E.; Pickering, M. A.; Piegaia, R.; Pilcher, J. E.; Pilkington, A. D.; Pin, A. W. J.; Pinamonti, M.; Pinfold, J. L.; Pirumov, H.; Pitt, M.; Plazak, L.; Pleier, M.-A.; Pleskot, V.; Plotnikova, E.; Pluth, D.; Podberezko, P.; Poettgen, R.; Poggi, R.; Poggioli, L.; Pohl, D.; Polesello, G.; Poley, A.; Policicchio, A.; Polifka, R.; Polini, A.; Pollard, C. S.; Polychronakos, V.; Pommès, K.; Ponomarenko, D.; Pontecorvo, L.; Pope, B. G.; Popeneciu, G. A.; Poppleton, A.; Pospisil, S.; Potamianos, K.; Potrap, I. N.; Potter, C. J.; Poulard, G.; Poulsen, T.; Poveda, J.; Pozo Astigarraga, M. E.; Pralavorio, P.; Pranko, A.; Prell, S.; Price, D.; Price, L. E.; Primavera, M.; Prince, S.; Proklova, N.; Prokofiev, K.; Prokoshin, F.; Protopopescu, S.; Proudfoot, J.; Przybycien, M.; Puri, A.; Puzo, P.; Qian, J.; Qin, G.; Qin, Y.; Quadt, A.; Queitsch-Maitland, M.; Quilty, D.; Raddum, S.; Radeka, V.; Radescu, V.; Radhakrishnan, S. K.; Radloff, P.; Rados, P.; Ragusa, F.; Rahal, G.; Raine, J. A.; Rajagopalan, S.; Rangel-Smith, C.; Rashid, T.; Raspopov, S.; Ratti, M. G.; Rauch, D. M.; Rauscher, F.; Rave, S.; Ravinovich, I.; Rawling, J. H.; Raymond, M.; Read, A. L.; Readioff, N. P.; Reale, M.; Rebuzzi, D. M.; Redelbach, A.; Redlinger, G.; Reece, R.; Reed, R. G.; Reeves, K.; Rehnisch, L.; Reichert, J.; Reiss, A.; Rembser, C.; Ren, H.; Rescigno, M.; Resconi, S.; Resseguie, E. D.; Rettie, S.; Reynolds, E.; Rezanova, O. L.; Reznicek, P.; Rezvani, R.; Richter, R.; Richter, S.; Richter-Was, E.; Ricken, O.; Ridel, M.; Rieck, P.; Riegel, C. J.; Rieger, J.; Rifki, O.; Rijssenbeek, M.; Rimoldi, A.; Rimoldi, M.; Rinaldi, L.; Ripellino, G.; Ristić, B.; Ritsch, E.; Riu, I.; Rizatdinova, F.; Rizvi, E.; Rizzi, C.; Roberts, R. T.; Robertson, S. H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, J. E. M.; Robson, A.; Rocco, E.; Roda, C.; Rodina, Y.; Rodriguez Bosca, S.; Rodriguez Perez, A.; Rodriguez Rodriguez, D.; Roe, S.; Rogan, C. S.; Røhne, O.; Roloff, J.; Romaniouk, A.; Romano, M.; Romano Saez, S. M.; Romero Adam, E.; Rompotis, N.; Ronzani, M.; Roos, L.; Rosati, S.; Rosbach, K.; Rose, P.; Rosien, N.-A.; Rossi, E.; Rossi, L. P.; Rosten, J. H. N.; Rosten, R.; Rotaru, M.; Roth, I.; Rothberg, J.; Rousseau, D.; Rozanov, A.; Rozen, Y.; Ruan, X.; Rubbo, F.; Rühr, F.; Ruiz-Martinez, A.; Rurikova, Z.; Rusakovich, N. A.; Russell, H. L.; Rutherfoord, J. P.; Ruthmann, N.; Ryabov, Y. F.; Rybar, M.; Rybkin, G.; Ryu, S.; Ryzhov, A.; Rzehorz, G. F.; Saavedra, A. F.; Sabato, G.; Sacerdoti, S.; Sadrozinski, H. F.-W.; Sadykov, R.; Safai Tehrani, F.; Saha, P.; Sahinsoy, M.; Saimpert, M.; Saito, M.; Saito, T.; Sakamoto, H.; Sakurai, Y.; Salamanna, G.; Salazar Loyola, J. E.; Salek, D.; Sales De Bruin, P. H.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sammel, D.; Sampsonidis, D.; Sampsonidou, D.; Sánchez, J.; Sanchez Martinez, V.; Sanchez Pineda, A.; Sandaker, H.; Sandbach, R. L.; Sander, C. O.; Sandhoff, M.; Sandoval, C.; Sankey, D. P. C.; Sannino, M.; Sano, Y.; Sansoni, A.; Santoni, C.; Santonico, R.; Santos, H.; Santoyo Castillo, I.; Sapronov, A.; Saraiva, J. G.; Sarrazin, B.; Sasaki, O.; Sato, K.; Sauvan, E.; Savage, G.; Savard, P.; Savic, N.; Sawyer, C.; Sawyer, L.; Saxon, J.; Sbarra, C.; Sbrizzi, A.; Scanlon, T.; Scannicchio, D. A.; Scarcella, M.; Scarfone, V.; Schaarschmidt, J.; Schacht, P.; Schachtner, B. M.; Schaefer, D.; Schaefer, L.; Schaefer, R.; Schaeffer, J.; Schaepe, S.; Schaetzel, S.; Schäfer, U.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Scharf, V.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Schiavi, C.; Schier, S.; Schildgen, L. K.; Schillo, C.; Schioppa, M.; Schlenker, S.; Schmidt-Sommerfeld, K. R.; Schmieden, K.; Schmitt, C.; Schmitt, S.; Schmitz, S.; Schnoor, U.; Schoeffel, L.; Schoening, A.; Schoenrock, B. D.; Schopf, E.; Schott, M.; Schouwenberg, J. F. P.; Schovancova, J.; Schramm, S.; Schuh, N.; Schulte, A.; Schultens, M. J.; Schultz-Coulon, H.-C.; Schulz, H.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwartzman, A.; Schwarz, T. A.; Schweiger, H.; Schwemling, Ph.; Schwienhorst, R.; Schwindling, J.; Sciandra, A.; Sciolla, G.; Scornajenghi, M.; Scuri, F.; Scutti, F.; Searcy, J.; Seema, P.; Seidel, S. C.; Seiden, A.; Seixas, J. M.; Sekhniaidze, G.; Sekhon, K.; Sekula, S. J.; Semprini-Cesari, N.; Senkin, S.; Serfon, C.; Serin, L.; Serkin, L.; Sessa, M.; Seuster, R.; Severini, H.; Sfiligoj, T.; Sforza, F.; Sfyrla, A.; Shabalina, E.; Shaikh, N. W.; Shan, L. Y.; Shang, R.; Shank, J. T.; Shapiro, M.; Shatalov, P. B.; Shaw, K.; Shaw, S. M.; Shcherbakova, A.; Shehu, C. Y.; Shen, Y.; Sherafati, N.; Sherwood, P.; Shi, L.; Shimizu, S.; Shimmin, C. O.; Shimojima, M.; Shipsey, I. P. J.; Shirabe, S.; Shiyakova, M.; Shlomi, J.; Shmeleva, A.; Shoaleh Saadi, D.; Shochet, M. J.; Shojaii, S.; Shope, D. R.; Shrestha, S.; Shulga, E.; Shupe, M. A.; Sicho, P.; Sickles, A. M.; Sidebo, P. E.; Sideras Haddad, E.; Sidiropoulou, O.; Sidoti, A.; Siegert, F.; Sijacki, Dj.; Silva, J.; Silverstein, S. B.; Simak, V.; Simic, Lj.; Simion, S.; Simioni, E.; Simmons, B.; Simon, M.; Sinervo, P.; Sinev, N. B.; Sioli, M.; Siragusa, G.; Siral, I.; Sivoklokov, S. Yu.; Sjölin, J.; Skinner, M. B.; Skubic, P.; Slater, M.; Slavicek, T.; Slawinska, M.; Sliwa, K.; Slovak, R.; Smakhtin, V.; Smart, B. H.; Smiesko, J.; Smirnov, N.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, J. W.; Smith, M. N. K.; Smith, R. W.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snyder, I. M.; Snyder, S.; Sobie, R.; Socher, F.; Soffer, A.; Soh, D. A.; Sokhrannyi, G.; Solans Sanchez, C. A.; Solar, M.; Soldatov, E. Yu.; Soldevila, U.; Solodkov, A. A.; Soloshenko, A.; Solovyanov, O. V.; Solovyev, V.; Sommer, P.; Son, H.; Sopczak, A.; Sosa, D.; Sotiropoulou, C. L.; Soualah, R.; Soukharev, A. M.; South, D.; Sowden, B. C.; Spagnolo, S.; Spalla, M.; Spangenberg, M.; Spanò, F.; Sperlich, D.; Spettel, F.; Spieker, T. M.; Spighi, R.; Spigo, G.; Spiller, L. A.; Spousta, M.; St. Denis, R. D.; Stabile, A.; Stamen, R.; Stamm, S.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stanitzki, M. M.; Stapf, B. S.; Stapnes, S.; Starchenko, E. A.; Stark, G. H.; Stark, J.; Stark, S. H.; Staroba, P.; Starovoitov, P.; Stärz, S.; Staszewski, R.; Steinberg, P.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stewart, G. A.; Stockton, M. C.; Stoebe, M.; Stoicea, G.; Stolte, P.; Stonjek, S.; Stradling, A. R.; Straessner, A.; Stramaglia, M. E.; Strandberg, J.; Strandberg, S.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Strubig, A.; Stucci, S. A.; Stugu, B.; Styles, N. A.; Su, D.; Su, J.; Suchek, S.; Sugaya, Y.; Suk, M.; Sulin, V. V.; Sultan, DMS; Sultansoy, S.; Sumida, T.; Sun, S.; Sun, X.; Suruliz, K.; Suster, C. J. E.; Sutton, M. R.; Suzuki, S.; Svatos, M.; Swiatlowski, M.; Swift, S. P.; Sykora, I.; Sykora, T.; Ta, D.; Tackmann, K.; Taenzer, J.; Taffard, A.; Tafirout, R.; Taiblum, N.; Takai, H.; Takashima, R.; Takasugi, E. H.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tanaka, J.; Tanaka, M.; Tanaka, R.; Tanaka, S.; Tanioka, R.; Tannenwald, B. B.; Tapia Araya, S.; Tapprogge, S.; Tarem, S.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavares Delgado, A.; Tayalati, Y.; Taylor, A. C.; Taylor, G. N.; Taylor, P. T. E.; Taylor, W.; Teixeira-Dias, P.; Temple, D.; Ten Kate, H.; Teng, P. K.; Teoh, J. J.; Tepel, F.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Theveneaux-Pelzer, T.; Thomas, J. P.; Thomas-Wilsker, J.; Thompson, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Tibbetts, M. J.; Ticse Torres, R. E.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tipton, P.; Tisserant, S.; Todome, K.; Todorova-Nova, S.; Todt, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tolley, E.; Tomlinson, L.; Tomoto, M.; Tompkins, L.; Toms, K.; Tong, B.; Tornambe, P.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Treado, C. J.; Trefzger, T.; Tresoldi, F.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trocmé, B.; Trofymov, A.; Troncon, C.; Trottier-McDonald, M.; Trovatelli, M.; Truong, L.; Trzebinski, M.; Trzupek, A.; Tsang, K. W.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsipolitis, G.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsui, K. M.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tu, Y.; Tudorache, A.; Tudorache, V.; Tulbure, T. T.; Tuna, A. N.; Tupputi, S. A.; Turchikhin, S.; Turgeman, D.; Turk Cakir, I.; Turra, R.; Tuts, P. M.; Ucchielli, G.; Ueda, I.; Ughetto, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Unverdorben, C.; Urban, J.; Urquijo, P.; Urrejola, P.; Usai, G.; Usui, J.; Vacavant, L.; Vacek, V.; Vachon, B.; Vaidya, A.; Valderanis, C.; Valdes Santurio, E.; Valentinetti, S.; Valero, A.; Valéry, L.; Valkar, S.; Vallier, A.; Valls Ferrer, J. A.; Van Den Wollenberg, W.; van der Graaf, H.; van Gemmeren, P.; Van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vaniachine, A.; Vankov, P.; Vardanyan, G.; Vari, R.; Varnes, E. W.; Varni, C.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasquez, J. G.; Vasquez, G. A.; Vazeille, F.; Vazquez Schroeder, T.; Veatch, J.; Veeraraghavan, V.; Veloce, L. M.; Veloso, F.; Veneziano, S.; Ventura, A.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, A. T.; Vermeulen, J. C.; Vetterli, M. C.; Viaux Maira, N.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigani, L.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vishwakarma, A.; Vittori, C.; Vivarelli, I.; Vlachos, S.; Vogel, M.; Vokac, P.; Volpi, G.; von der Schmitt, H.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Voss, R.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Wagner, W.; Wagner-Kuhr, J.; Wahlberg, H.; Wahrmund, S.; Wakabayashi, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wallangen, V.; Wang, C.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, Q.; Wang, R.; Wang, S. M.; Wang, T.; Wang, W.; Wang, W.; Wang, Z.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, A. F.; Webb, S.; Weber, M. S.; Weber, S. W.; Weber, S. A.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weirich, M.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M. D.; Werner, P.; Wessels, M.; Whalen, K.; Whallon, N. L.; Wharton, A. M.; White, A. S.; White, A.; White, M. J.; White, R.; Whiteson, D.; Whitmore, B. W.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilk, F.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wingerter-Seez, I.; Winkels, E.; Winklmeier, F.; Winston, O. J.; Winter, B. T.; Wittgen, M.; Wobisch, M.; Wolf, T. M. H.; Wolff, R.; Wolter, M. W.; Wolters, H.; Wong, V. W. S.; Worm, S. D.; Wosiek, B. K.; Wotschack, J.; Wozniak, K. W.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xi, Z.; Xia, L.; Xu, D.; Xu, L.; Xu, T.; Yabsley, B.; Yacoob, S.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, S.; Yamanaka, T.; Yamatani, M.; Yamauchi, K.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yap, Y. C.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yigitbasi, E.; Yildirim, E.; Yorita, K.; Yoshihara, K.; Young, C.; Young, C. J. S.; Yu, J.; Yu, J.; Yuen, S. P. Y.; Yusuff, I.; Zabinski, B.; Zacharis, G.; Zaidan, R.; Zaitsev, A. M.; Zakharchuk, N.; Zalieckas, J.; Zaman, A.; Zambito, S.; Zanzi, D.; Zeitnitz, C.; Zemaityte, G.; Zemla, A.; Zeng, J. C.; Zeng, Q.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, F.; Zhang, G.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, L.; Zhang, M.; Zhang, P.; Zhang, R.; Zhang, R.; Zhang, X.; Zhang, Y.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, M.; Zhou, M.; Zhou, N.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhukov, K.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, C.; Zimmermann, S.; Zinonos, Z.; Zinser, M.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zou, R.; zur Nedden, M.; Zwalinski, L.

2017-12-01

Measurements of transverse energy-energy correlations and their associated asymmetries in multi-jet events using the ATLAS detector at the LHC are presented. The data used correspond to √{s} = 8 TeV proton-proton collisions with an integrated luminosity of 20.2 fb^{-1}. The results are presented in bins of the scalar sum of the transverse momenta of the two leading jets, unfolded to the particle level and compared to the predictions from Monte Carlo simulations. A comparison with next-to-leading-order perturbative QCD is also performed, showing excellent agreement within the uncertainties. From this comparison, the value of the strong coupling constant is extracted for different energy regimes, thus testing the running of α s(μ ) predicted in QCD up to scales over 1 TeV. A global fit to the transverse energy-energy correlation distributions yields α s(m_Z) = 0.1162 ± 0.0011 (exp.) ^{+0.0084}_{-0.0070} (theo.) , while a global fit to the asymmetry distributions yields a value of α s(m_Z) = 0.1196 ± 0.0013 (exp.) ^{+0.0075}_{-0.0045} (theo.).

Integrating peatlands into the coupled Canadian Land Surface Scheme (CLASS) v3.6 and the Canadian Terrestrial Ecosystem Model (CTEM) v2.0

NASA Astrophysics Data System (ADS)

Wu, Yuanqiao; Verseghy, Diana L.; Melton, Joe R.

2016-08-01

Peatlands, which contain large carbon stocks that must be accounted for in the global carbon budget, are poorly represented in many earth system models. We integrated peatlands into the coupled Canadian Land Surface Scheme (CLASS) and the Canadian Terrestrial Ecosystem Model (CTEM), which together simulate the fluxes of water, energy, and CO2 at the land surface-atmosphere boundary in the family of Canadian Earth system models (CanESMs). New components and algorithms were added to represent the unique features of peatlands, such as their characteristic ground floor vegetation (mosses), the slow decomposition of carbon in the water-logged soils and the interaction between the water, energy, and carbon cycles. This paper presents the modifications introduced into the CLASS-CTEM modelling framework together with site-level evaluations of the model performance for simulated water, energy and carbon fluxes at eight different peatland sites. The simulated daily gross primary production (GPP) and ecosystem respiration are well correlated with observations, with values of the Pearson correlation coefficient higher than 0.8 and 0.75 respectively. The simulated mean annual net ecosystem production at the eight test sites is 87 g C m-2 yr-1, which is 22 g C m-2 yr-1 higher than the observed annual mean. The general peatland model compares well with other site-level and regional-level models for peatlands, and is able to represent bogs and fens under a range of climatic and geographical conditions.

Integrating peatlands into the coupled Canadian Land Surface Scheme (CLASS) v3.6 and the Canadian Terrestrial Ecosystem Model (CTEM) v2.0

NASA Astrophysics Data System (ADS)

Wu, Y.; Verseghy, D. L.; Melton, J. R.

2015-11-01

Peatlands, which contain large carbon stocks that must be accounted for in the global carbon budget, are poorly represented in many earth system models. We integrated peatlands into the coupled Canadian Land Surface Scheme (CLASS) and the Canadian Terrestrial Ecosystem Model (CTEM), which together simulate the fluxes of water, energy and CO2 at the land surface-atmosphere boundary in the family of Canadian Earth System Models (CanESMs). New components and algorithms were added to represent the unique features of peatlands, such as their characteristic ground floor vegetation (mosses), the slow decomposition of carbon in the water-logged soils and the interaction between the water, energy and carbon cycles. This paper presents the modifications introduced into the CLASS-CTEM modelling framework together with site-level evaluations of the model performance for simulated water, energy and carbon fluxes at eight different peatland sites. The simulated daily gross primary production and ecosystem respiration are well correlated with observations, with values of the Pearson correlation coefficient higher than 0.8 and 0.75 respectively. The simulated mean annual net ecosystem production at the eight test sites is 87 g C m-2 yr-1, which is 22 g C m-2 yr-1 higher than the observed annual mean. The general peatland model compares well with other site-level and regional-level models for peatlands, and is able to represent bogs and fens under a range of climatic and geographical conditions.

Numerical simulation for a vortex street near the poleward boundary of the nighttime auroral oval

NASA Astrophysics Data System (ADS)

Yamamoto, T.

2012-02-01

The formation of a vortex street is numerically studied as an aftermath of a transient (≈1 min) depression of the energy density of injected particles. It is basically assumed that the kinetic energies of auroral particles are substantially provided by nonadiabatic acceleration in the tail current sheet. One of the causes of such energy density depression is an outward (away from the Earth) movement of the neutral line because in such situation, a particle passes the acceleration zone for a shorter time interval while it is inwardly transported in the current sheet. The numerical simulation shows that a long chain of many (≥5) vortices can be formed in the nighttime high-latitude auroral oval as a result of the hybrid Kelvin-Helmholtz/Rayleigh-Taylor (KH/RT) instability. The main characteristics of long vortex chains in the simulation such as the short lifetime (≲2 min) and the correlation between wavelength, λ, and arc system width, A, compare well with those of the periodic auroral distortions observed primarily in the high-latitude auroral oval. Specifically, either λ-A relationship from simulation or observation shows a positive correlation between λ and A but with considerable dispersion in λ. Since auroral vortices arising from the hybrid KH/RT instability are not accompanied by significant rotational motions, the magnetic shear instability caused by undulations in the field-aligned current (FAC) sheet could turn the vortices into spirals which wind or unwind in response to increase or decrease of FACs, respectively.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection

NASA Astrophysics Data System (ADS)

Cox, Courtney E.; Phifer, Jeremy R.; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T.; O'Loughlin, Elizabeth J.; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T.; Paluch, Andrew S.

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.

PubMed

Cox, Courtney E; Phifer, Jeremy R; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T; O'Loughlin, Elizabeth J; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T; Paluch, Andrew S

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

Standardized performance tests of collectors of solar thermal energy: Prototype moderately concentrating grooved collectors

NASA Technical Reports Server (NTRS)

1976-01-01

Prototypes of moderately concentrating grooved collectors were tested with a solar simulator for varying inlet temperature, flux level, and incident angle. Collector performance is correlated in terms of inlet temperature and flux level.

Development of new methodologies for evaluating the energy performance of new commercial buildings

NASA Astrophysics Data System (ADS)

Song, Suwon

The concept of Measurement and Verification (M&V) of a new building continues to become more important because efficient design alone is often not sufficient to deliver an efficient building. Simulation models that are calibrated to measured data can be used to evaluate the energy performance of new buildings if they are compared to energy baselines such as similar buildings, energy codes, and design standards. Unfortunately, there is a lack of detailed M&V methods and analysis methods to measure energy savings from new buildings that would have hypothetical energy baselines. Therefore, this study developed and demonstrated several new methodologies for evaluating the energy performance of new commercial buildings using a case-study building in Austin, Texas. First, three new M&V methods were developed to enhance the previous generic M&V framework for new buildings, including: (1) The development of a method to synthesize weather-normalized cooling energy use from a correlation of Motor Control Center (MCC) electricity use when chilled water use is unavailable, (2) The development of an improved method to analyze measured solar transmittance against incidence angle for sample glazing using different solar sensor types, including Eppley PSP and Li-Cor sensors, and (3) The development of an improved method to analyze chiller efficiency and operation at part-load conditions. Second, three new calibration methods were developed and analyzed, including: (1) A new percentile analysis added to the previous signature method for use with a DOE-2 calibration, (2) A new analysis to account for undocumented exhaust air in DOE-2 calibration, and (3) An analysis of the impact of synthesized direct normal solar radiation using the Erbs correlation on DOE-2 simulation. Third, an analysis of the actual energy savings compared to three different energy baselines was performed, including: (1) Energy Use Index (EUI) comparisons with sub-metered data, (2) New comparisons against Standards 90.1-1989 and 90.1-2001, and (3) A new evaluation of the performance of selected Energy Conservation Design Measures (ECDMs). Finally, potential energy savings were also simulated from selected improvements, including: minimum supply air flow, undocumented exhaust air, and daylighting.

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

PubMed

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

2014-02-01

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

Propeller torque load and propeller shaft torque response correlation during ice-propeller interaction

NASA Astrophysics Data System (ADS)

Polić, Dražen; Ehlers, Sören; Æsøy, Vilmar

2017-03-01

Ships use propulsion machinery systems to create directional thrust. Sailing in ice-covered waters involves the breaking of ice pieces and their submergence as the ship hull advances. Sometimes, submerged ice pieces interact with the propeller and cause irregular fluctuations of the torque load. As a result, the propeller and engine dynamics become imbalanced, and energy propagates through the propulsion machinery system until equilibrium is reached. In such imbalanced situations, the measured propeller shaft torque response is not equal to the propeller torque. Therefore, in this work, the overall system response is simulated under the ice-related torque load using the Bond graph model. The energy difference between the propeller and propeller shaft is estimated and related to their corresponding mechanical energy. Additionally, the mechanical energy is distributed among modes. Based on the distribution, kinetic and potential energy are important for the correlation between propeller torque and propeller shaft response.

Signals of dynamical and statistical process from IMF-IMF correlation function

NASA Astrophysics Data System (ADS)

Pagano, E. V.; Acosta, L.; Auditore, L.; Baran, V.; Cap, T.; Cardella, G.; Colonna, M.; De Luca, S.; De Filippo, E.; Dell'Aquila, D.; Francalanza, L.; Gnoffo, B.; Lanzalone, G.; Lombardo, I.; Maiolino, C.; Martorana, N. S.; Norella, S.; Pagano, A.; Papa, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Rosato, E.; Russotto, P.; Siwek-Wilczyńska, K.; Trifiro, A.; Trimarchi, M.; Verde, G.; Vigilante, M.; Wilczyńsky, J.

2017-11-01

In this paper we briefly discuss about a novel application of the IMF-IMF correlation function to the physical case of binary massive projectile-like (PLF) splitting for dynamical and statistical breakup/fission in heavy ion collisions at Fermi energy. Theoretical simulations are also shown for comparisons with the data. These preliminary results have been obtained for the reverse kinematics reaction 124Sn + 64Ni at 35 AMeV that was studied using the forward part of CHIMERA detector. In that reaction a strong competition between a dynamical and a statistical components and its evolution with the charge asymmetry of the binary break up was already shown. In this work we show that the IMF-IMF correlation function can be used to pin down the timescale of the fragments production in binary fission-like phenomena. We also made simulations with the CoMDII model in order to compare to the experimental IMF-IMF correlation function. In future we plan to extend these studies to different reaction mechanisms and nuclear systems and to compare with different theoretical transport simulations.

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

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.

Hydration property of globular proteins: An analysis of solvation free energy by energy representation method

NASA Astrophysics Data System (ADS)

Saito, Hiroaki; Matubayasi, Nobuyuki; Nishikawa, Kiyoshi; Nagao, Hidemi

2010-09-01

Molecular dynamics simulations and solvation free energy calculations of five globular proteins (BPTI, RNase A, Lysozyme, β-lactoglobulin A, and α-chymotrypsinogen A) have been carried out to elucidate the hydration properties. Solvation free energies of the proteins with explicit solvent were estimated by energy representation (ER) method. The calculated solvation free energies were correlated with the solvent accessible surface area of hydrophilic portion, being consistent with the hydrophilic property of the proteins. These results showed that the ER method should be a powerful tool for estimating the hydration property of proteins, showing a progress of the free energy calculation with explicit solvent.

The solvation of ions in acetonitrile and acetone. II. Monte Carlo simulations using polarizable solvent models

NASA Astrophysics Data System (ADS)

Fischer, R.; Richardi, J.; Fries, P. H.; Krienke, H.

2002-11-01

Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site-site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion-solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain (HNC) approximation of the molecular Ornstein-Zernike (MOZ) theory [J. Richardi, P. H. Fries, and H. Krienke, J. Chem. Phys. 108, 4079 (1998)]. The MOZ(HNC) formalism gives an overall qualitatively correct picture of the solvation and its various unexpected findings are corroborated. For the larger ions, its predictions become quantitative. The MOZ approach allows to calculate solvent-solvent and ion-solvent potentials of mean force, which shed light on the 3D labile molecular and ionic architectures in the solution. These potentials of mean force convey a unique information which is necessary to fully interpret the angle-averaged structural functions computed from the simulations. Finally, simulations of solutions at finite concentrations show that the solvent-solvent and ion-solvent spatial correlations at infinite dilution are marginally altered by the introduction of fair amounts of ions.

Theoretical prediction and direct observation of the 9R structure in Ag

NASA Astrophysics Data System (ADS)

Ernst, F.; Finnis, M. W.; Hofmann, D.; Muschik, T.; Schönberger, U.; Wolf, U.; Methfessel, M.

1992-07-01

Molecular-dynamics simulations of the Σ3<110>(211) twin boundary in Ag predict a thin (1 nm) boundary phase of the 9R (α-Sm) structure. High-resolution electron microscopy shows the presence of the predicted structure. We also calculate the energy ab initio for several hypothetical structures of Cu and Ag. Low energies of the 9R structure and other polytypes, low experimental stacking-fault energies, and the hcp-fcc energy difference are correlated and explained in terms of an effective nearest-neighbor Ising interaction.

Understanding GPU Power. A Survey of Profiling, Modeling, and Simulation Methods

DOE PAGES

Bridges, Robert A.; Imam, Neena; Mintz, Tiffany M.

2016-09-01

Modern graphics processing units (GPUs) have complex architectures that admit exceptional performance and energy efficiency for high throughput applications.Though GPUs consume large amounts of power, their use for high throughput applications facilitate state-of-the-art energy efficiency and performance. Consequently, continued development relies on understanding their power consumption. Our work is a survey of GPU power modeling and profiling methods with increased detail on noteworthy efforts. Moreover, as direct measurement of GPU power is necessary for model evaluation and parameter initiation, internal and external power sensors are discussed. Hardware counters, which are low-level tallies of hardware events, share strong correlation to powermore » use and performance. Statistical correlation between power and performance counters has yielded worthwhile GPU power models, yet the complexity inherent to GPU architectures presents new hurdles for power modeling. Developments and challenges of counter-based GPU power modeling is discussed. Often building on the counter-based models, research efforts for GPU power simulation, which make power predictions from input code and hardware knowledge, provide opportunities for optimization in programming or architectural design. Noteworthy strides in power simulations for GPUs are included along with their performance or functional simulator counterparts when appropriate. Lastly, possible directions for future research are discussed.« less

Understanding GPU Power. A Survey of Profiling, Modeling, and Simulation Methods

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

Bridges, Robert A.; Imam, Neena; Mintz, Tiffany M.

Modern graphics processing units (GPUs) have complex architectures that admit exceptional performance and energy efficiency for high throughput applications.Though GPUs consume large amounts of power, their use for high throughput applications facilitate state-of-the-art energy efficiency and performance. Consequently, continued development relies on understanding their power consumption. Our work is a survey of GPU power modeling and profiling methods with increased detail on noteworthy efforts. Moreover, as direct measurement of GPU power is necessary for model evaluation and parameter initiation, internal and external power sensors are discussed. Hardware counters, which are low-level tallies of hardware events, share strong correlation to powermore » use and performance. Statistical correlation between power and performance counters has yielded worthwhile GPU power models, yet the complexity inherent to GPU architectures presents new hurdles for power modeling. Developments and challenges of counter-based GPU power modeling is discussed. Often building on the counter-based models, research efforts for GPU power simulation, which make power predictions from input code and hardware knowledge, provide opportunities for optimization in programming or architectural design. Noteworthy strides in power simulations for GPUs are included along with their performance or functional simulator counterparts when appropriate. Lastly, possible directions for future research are discussed.« less

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.

PubMed

Ogata, Koji; Hatakeyama, Makoto; Nakamura, Shinichiro

2018-02-15

The octanol-water partition coefficient (log P ow ) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the log P ow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆ G water values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of log P ow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted log P ow values.

Correlation as a Determinant of Configurational Entropy in Supramolecular and Protein Systems

PubMed Central

2015-01-01

For biomolecules in solution, changes in configurational entropy are thought to contribute substantially to the free energies of processes like binding and conformational change. In principle, the configurational entropy can be strongly affected by pairwise and higher-order correlations among conformational degrees of freedom. However, the literature offers mixed perspectives regarding the contributions that changes in correlations make to changes in configurational entropy for such processes. Here we take advantage of powerful techniques for simulation and entropy analysis to carry out rigorous in silico studies of correlation in binding and conformational changes. In particular, we apply information-theoretic expansions of the configurational entropy to well-sampled molecular dynamics simulations of a model host–guest system and the protein bovine pancreatic trypsin inhibitor. The results bear on the interpretation of NMR data, as they indicate that changes in correlation are important determinants of entropy changes for biologically relevant processes and that changes in correlation may either balance or reinforce changes in first-order entropy. The results also highlight the importance of main-chain torsions as contributors to changes in protein configurational entropy. As simulation techniques grow in power, the mathematical techniques used here will offer new opportunities to answer challenging questions about complex molecular systems. PMID:24702693

Toward simulating complex systems with quantum effects

NASA Astrophysics Data System (ADS)

Kenion-Hanrath, Rachel Lynn

Quantum effects like tunneling, coherence, and zero point energy often play a significant role in phenomena on the scales of atoms and molecules. However, the exact quantum treatment of a system scales exponentially with dimensionality, making it impractical for characterizing reaction rates and mechanisms in complex systems. An ongoing effort in the field of theoretical chemistry and physics is extending scalable, classical trajectory-based simulation methods capable of capturing quantum effects to describe dynamic processes in many-body systems; in the work presented here we explore two such techniques. First, we detail an explicit electron, path integral (PI)-based simulation protocol for predicting the rate of electron transfer in condensed-phase transition metal complex systems. Using a PI representation of the transferring electron and a classical representation of the transition metal complex and solvent atoms, we compute the outer sphere free energy barrier and dynamical recrossing factor of the electron transfer rate while accounting for quantum tunneling and zero point energy effects. We are able to achieve this employing only a single set of force field parameters to describe the system rather than parameterizing along the reaction coordinate. Following our success in describing a simple model system, we discuss our next steps in extending our protocol to technologically relevant materials systems. The latter half focuses on the Mixed Quantum-Classical Initial Value Representation (MQC-IVR) of real-time correlation functions, a semiclassical method which has demonstrated its ability to "tune'' between quantum- and classical-limit correlation functions while maintaining dynamic consistency. Specifically, this is achieved through a parameter that determines the quantumness of individual degrees of freedom. Here, we derive a semiclassical correction term for the MQC-IVR to systematically characterize the error introduced by different choices of simulation parameters, and demonstrate the ability of this approach to optimize MQC-IVR simulations.

Improved estimation of ligand macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods

NASA Astrophysics Data System (ADS)

Khandelwal, Akash; Balaz, Stefan

2007-01-01

Structure-based predictions of binding affinities of ligands binding to proteins by coordination bonds with transition metals, covalent bonds, and bonds involving charge re-distributions are hindered by the absence of proper force fields. This shortcoming affects all methods which use force-field-based molecular simulation data on complex formation for affinity predictions. One of the most frequently used methods in this category is the Linear Response (LR) approach of Åquist, correlating binding affinities with van der Waals and electrostatic energies, as extended by Jorgensen's inclusion of solvent-accessible surface areas. All these terms represent the differences, upon binding, in the ensemble averages of pertinent quantities, obtained from molecular dynamics (MD) or Monte Carlo simulations of the complex and of single components. Here we report a modification of the LR approach by: (1) the replacement of the two energy terms through the single-point QM/MM energy of the time-averaged complex structure from an MD simulation; and (2) a rigorous consideration of multiple modes (mm) of binding. The first extension alleviates the force-field related problems, while the second extension deals with the ligands exhibiting large-scale motions in the course of an MD simulation. The second modification results in the correlation equation that is nonlinear in optimized coefficients, but does not lead to an increase in the number of optimized coefficients. The application of the resulting mm QM/MM LR approach to the inhibition of zinc-dependent gelatinase B (matrix metalloproteinase 9) by 28 hydroxamate ligands indicates a significant improvement of descriptive and predictive abilities.

Interaction-component analysis of the hydration and urea effects on cytochrome c

NASA Astrophysics Data System (ADS)

Yamamori, Yu; Ishizuka, Ryosuke; Karino, Yasuhito; Sakuraba, Shun; Matubayasi, Nobuyuki

2016-02-01

Energetics was analyzed for cytochrome c in pure-water solvent and in a urea-water mixed solvent to elucidate the solvation effect in the structural variation of the protein. The solvation free energy was computed through all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were examined over sets of protein structures against the electrostatic and van der Waals components in the average interaction energy of the protein with the solvent and the excluded-volume component in the solvation free energy. It was observed in pure-water solvent that the solvation free energy varies in parallel to the electrostatic component with minor roles played by the van der Waals and excluded-volume components. The effect of urea on protein structure was then investigated in terms of the free-energy change upon transfer of the protein solute from pure-water solvent to the urea-water mixed solvent. The decomposition of the transfer free energy into the contributions from urea and water showed that the urea contribution is partially canceled by the water contribution and governs the total free energy of transfer. When correlated against the change in the solute-solvent interaction energy upon transfer and the corresponding changes in the electrostatic, van der Waals, and excluded-volume components, the transfer free energy exhibited strong correlations with the total change in the solute-solvent energy and its van der Waals component. The solute-solvent energy was decomposed into the contributions from the protein backbone and side chain, furthermore, and neither of the contributions was seen to be decisive in the correlation to the transfer free energy.

Analysis of vibrational-translational energy transfer using the direct simulation Monte Carlo method

NASA Technical Reports Server (NTRS)

Boyd, Iain D.

1991-01-01

A new model is proposed for energy transfer between the vibrational and translational modes for use in the direct simulation Monte Carlo method (DSMC). The model modifies the Landau-Teller theory for a harmonic oscillator and the rate transition is related to an experimental correlation for the vibrational relaxation time. Assessment of the model is made with respect to three different computations: relaxation in a heat bath, a one-dimensional shock wave, and hypersonic flow over a two-dimensional wedge. These studies verify that the model achieves detailed balance, and excellent agreement with experimental data is obtained in the shock wave calculation. The wedge flow computation reveals that the usual phenomenological method for simulating vibrational nonequilibrium in the DSMC technique predicts much higher vibrational temperatures in the wake region.

Influence of sample preparation on the transformation of low-density to high-density amorphous ice: An explanation based on the potential energy landscape

NASA Astrophysics Data System (ADS)

Giovambattista, Nicolas; Starr, Francis W.; Poole, Peter H.

2017-07-01

Experiments and computer simulations of the transformations of amorphous ices display different behaviors depending on sample preparation methods and on the rates of change of temperature and pressure to which samples are subjected. In addition to these factors, simulation results also depend strongly on the chosen water model. Using computer simulations of the ST2 water model, we study how the sharpness of the compression-induced transition from low-density amorphous ice (LDA) to high-density amorphous ice (HDA) is influenced by the preparation of LDA. By studying LDA samples prepared using widely different procedures, we find that the sharpness of the LDA-to-HDA transformation is correlated with the depth of the initial LDA sample in the potential energy landscape (PEL), as characterized by the inherent structure energy. Our results show that the complex phenomenology of the amorphous ices reported in experiments and computer simulations can be understood and predicted in a unified way from knowledge of the PEL of the system.

General surgery training and robotics: Are residents improving their skills?

PubMed

Finnerty, Brendan M; Afaneh, Cheguevara; Aronova, Anna; Fahey, Thomas J; Zarnegar, Rasa

2016-02-01

While robotic-assisted operations have become more prevalent, many general surgery residencies do not have a formal robotic training curriculum. We sought to ascertain how well current general surgery training permits acquisition of robotic skills by comparing robotic simulation performance across various training levels. Thirty-six participants were categorized by level of surgical training: eight medical students (MS), ten junior residents (JR), ten mid-level residents (MLR), and eight senior residents (SR). Participants performed three simulation tasks on the da Vinci (®) Skills Simulator (MatchBoard, EnergyDissection, SutureSponge). Each task's scores (0-100) and cumulative scores (0-300) were compared between groups. There were no differences in sex, hand dominance, video gaming history, or prior robotic experience between groups; however, SR was the oldest (p < 0.001). The median overall scores did not differ: 188 (84-201) for MS, 183 (91-234) for JR, 197 (153-218) for MLR, and 205 (169-229) for SR (p = 0.14). The median SutureSponge score was highest for SR (61, range 39-81) compared to MS (43, range 26-61), JR (43, range 11-72), and MLR (55, range 36-68) (p = 0.039). However, there were no significant differences in MatchBoard (p = 0.27) or EnergyDissection (p = 0.99) scores between groups. There was a positive correlation between SutureSponge score and number of laparoscopic cases logged (p = 0.005, r(2) = 0.21), but this correlation did not exist for the MatchBoard or EnergyDissection tasks. Lastly, there was no correlation between total lifetime hours of video gaming and overall score (p = 0.89, R(2) = 0.0006). Robotic skillsets acquired during general surgery residency show minimal improvement during the course of training, although laparoscopic experience is correlated with advanced robotic task performance. Changes in residency curricula or pursuit of fellowship training may be warranted for surgeons seeking proficiency.

Event-shape-engineering study of charge separation in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Wen, Fufang; Bryon, Jacob; Wen, Liwen; Wang, Gang

2018-01-01

Recent measurements of charge-dependent azimuthal correlations in high-energy heavy-ion collisions have indicated charge-separation signals perpendicular to the reaction plane, and have been related to the chiral magnetic effect (CME). However, the correlation signal is contaminated with the background caused by the collective motion (flow) of the collision system, and an effective approach is needed to remove the flow background from the correlation. We present a method study with simplified Monte Carlo simulations and a multi-phase transport model, and develop a scheme to reveal the true CME signal via event-shape engineering with the flow vector of the particles of interest. Supported by a grant (DE-FG02-88ER40424) from U.S. Department of Energy, Office of Nuclear Physics

Engineering molecular machines

NASA Astrophysics Data System (ADS)

Erman, Burak

2016-04-01

Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system. Correlations are consequences of the molecular architecture of the protein. The idea that synthetic molecular machines may be constructed by designing the proper molecular architecture is challenging. In their paper, Sarkar et al (2016 New J. Phys. 18 043006) propose a synthetic molecular motor based on the coarse grained elastic network model of proteins and show by numerical simulations that motor function is realized, ranging from deterministic to thermal, depending on temperature. This work opens up a new range of possibilities of molecular architecture based engine design.

Treatment of Nuclear Data Covariance Information in Sample Generation

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

Swiler, Laura Painton; Adams, Brian M.; Wieselquist, William

This report summarizes a NEAMS (Nuclear Energy Advanced Modeling and Simulation) project focused on developing a sampling capability that can handle the challenges of generating samples from nuclear cross-section data. The covariance information between energy groups tends to be very ill-conditioned and thus poses a problem using traditional methods for generated correlated samples. This report outlines a method that addresses the sample generation from cross-section matrices.

DES Y1 Results: Validating Cosmological Parameter Estimation Using Simulated Dark Energy Surveys

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

MacCrann, N.; et al.

We use mock galaxy survey simulations designed to resemble the Dark Energy Survey Year 1 (DES Y1) data to validate and inform cosmological parameter estimation. When similar analysis tools are applied to both simulations and real survey data, they provide powerful validation tests of the DES Y1 cosmological analyses presented in companion papers. We use two suites of galaxy simulations produced using different methods, which therefore provide independent tests of our cosmological parameter inference. The cosmological analysis we aim to validate is presented in DES Collaboration et al. (2017) and uses angular two-point correlation functions of galaxy number counts and weak lensing shear, as well as their cross-correlation, in multiple redshift bins. While our constraints depend on the specific set of simulated realisations available, for both suites of simulations we find that the input cosmology is consistent with the combined constraints from multiple simulated DES Y1 realizations in themore » $$\\Omega_m-\\sigma_8$$ plane. For one of the suites, we are able to show with high confidence that any biases in the inferred $$S_8=\\sigma_8(\\Omega_m/0.3)^{0.5}$$ and $$\\Omega_m$$ are smaller than the DES Y1 $$1-\\sigma$$ uncertainties. For the other suite, for which we have fewer realizations, we are unable to be this conclusive; we infer a roughly 70% probability that systematic biases in the recovered $$\\Omega_m$$ and $$S_8$$ are sub-dominant to the DES Y1 uncertainty. As cosmological analyses of this kind become increasingly more precise, validation of parameter inference using survey simulations will be essential to demonstrate robustness.« less

Dark Energy Survey Year 1 results: the impact of galaxy neighbours on weak lensing cosmology with IM3SHAPE

NASA Astrophysics Data System (ADS)

Samuroff, S.; Bridle, S. L.; Zuntz, J.; Troxel, M. A.; Gruen, D.; Rollins, R. P.; Bernstein, G. M.; Eifler, T. F.; Huff, E. M.; Kacprzak, T.; Krause, E.; MacCrann, N.; Abdalla, F. B.; Allam, S.; Annis, J.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Crocce, M.; D'Andrea, C. B.; da Costa, L. N.; Davis, C.; Desai, S.; Doel, P.; Fausti Neto, A.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Gruendl, R. A.; Gschwend, J.; Gutierrez, G.; Honscheid, K.; James, D. J.; Jarvis, M.; Jeltema, T.; Kirk, D.; Kuehn, K.; Kuhlmann, S.; Li, T. S.; Lima, M.; Maia, M. A. G.; March, M.; Marshall, J. L.; Martini, P.; Melchior, P.; Menanteau, F.; Miquel, R.; Nord, B.; Ogando, R. L. C.; Plazas, A. A.; Roodman, A.; Sanchez, E.; Scarpine, V.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, M.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Tarle, G.; Thomas, D.; Tucker, D. L.; DES Collaboration

2018-04-01

We use a suite of simulated images based on Year 1 of the Dark Energy Survey to explore the impact of galaxy neighbours on shape measurement and shear cosmology. The HOOPOE image simulations include realistic blending, galaxy positions, and spatial variations in depth and point spread function properties. Using the IM3SHAPE maximum-likelihood shape measurement code, we identify four mechanisms by which neighbours can have a non-negligible influence on shear estimation. These effects, if ignored, would contribute a net multiplicative bias of m ˜ 0.03-0.09 in the Year One of the Dark Energy Survey (DES Y1) IM3SHAPE catalogue, though the precise impact will be dependent on both the measurement code and the selection cuts applied. This can be reduced to percentage level or less by removing objects with close neighbours, at a cost to the effective number density of galaxies neff of 30 per cent. We use the cosmological inference pipeline of DES Y1 to explore the cosmological implications of neighbour bias and show that omitting blending from the calibration simulation for DES Y1 would bias the inferred clustering amplitude S8 ≡ σ8(Ωm/0.3)0.5 by 2σ towards low values. Finally, we use the HOOPOE simulations to test the effect of neighbour-induced spatial correlations in the multiplicative bias. We find the impact on the recovered S8 of ignoring such correlations to be subdominant to statistical error at the current level of precision.

Simulating crop phenology in the Community Land Model and its impact on energy and carbon fluxes

NASA Astrophysics Data System (ADS)

Chen, Ming; Griffis, Tim J.; Baker, John; Wood, Jeffrey D.; Xiao, Ke

2015-02-01

A reasonable representation of crop phenology and biophysical processes in land surface models is necessary to accurately simulate energy, water, and carbon budgets at the field, regional, and global scales. However, the evaluation of crop models that can be coupled to Earth system models is relatively rare. Here we evaluated two such models (CLM4-Crop and CLM3.5-CornSoy), both implemented within the Community Land Model (CLM) framework, at two AmeriFlux corn-soybean sites to assess their ability to simulate phenology, energy, and carbon fluxes. Our results indicated that the accuracy of net ecosystem exchange and gross primary production simulations was intimately connected to the phenology simulations. The CLM4-Crop model consistently overestimated early growing season leaf area index, causing an overestimation of gross primary production, to such an extent that the model simulated a carbon sink instead of the measured carbon source for corn. The CLM3.5-CornSoy-simulated leaf area index (LAI), energy, and carbon fluxes showed stronger correlations with observations compared to CLM4-Crop. Net radiation was biased high in both models and was especially pronounced for soybeans. This was primarily caused by the positive LAI bias, which led to a positive net long-wave radiation bias. CLM4-Crop underestimated soil water content during midgrowing season in all soil layers at the two sites, which caused unrealistic water stress, especially for soybean. Future work regarding the mechanisms that drive early growing season phenology and soil water dynamics is needed to better represent crops including their net radiation balance, energy partitioning, and carbon cycle processes.

Numerical and Experimental Studies on Crash Characteristics of Closed Form Thin—Walled Steel Sections

NASA Astrophysics Data System (ADS)

Veerasamy, M.; Srinivasan, K.; Prakash, Raghu V.

2010-10-01

The crash behavior of Cold Rolled Mild Steel (CRMS) closed form thin section was studied by conducting compressive tests at loading velocities of 5 mm/min and 1000 mm/min. The numerical simulations were conducted for the same experimental conditions to understand the deformation shape, peak forces and energy absorption capacity of sections at different impact velocities. The simulation results correlated well with the experimental results.

Photodissociation Dynamics of Phenol: Multistate Trajectory Simulations including Tunneling

DOE PAGES

Xu, Xuefei; Zheng, Jingjing; Yang, Ke R.; ...

2014-10-27

We report multistate trajectory simulations, including coherence, decoherence, and multidimensional tunneling, of phenol photodissociation dynamics. The calculations are based on full-dimensional anchor-points reactive potential surfaces and state couplings fit to electronic structure calculations including dynamical correlation with an augmented correlation-consistent polarized valence double-ζ basis set. The calculations successfully reproduce the experimentally observed bimodal character of the total kinetic energy release spectra and confirm the interpretation of the most recent experiments that the photodissociation process is dominated by tunneling. Analysis of the trajectories uncovers an unexpected dissociation pathway for one quantum excitation of the O–H stretching mode of the S 1more » state, namely, tunneling in a coherent mixture of states starting in a smaller R OH (~0.9–1.0 Å) region than has previously been invoked. The simulations also show that most trajectories do not pass close to the S 1–S 2 conical intersection (they have a minimum gap greater than 0.6 eV), they provide statistics on the out-of-plane angles at the locations of the minimum energy adiabatic gap, and they reveal information about which vibrational modes are most highly activated in the products.« less

Heterogeneity in ultrathin films simulated by Monte Carlo method

NASA Astrophysics Data System (ADS)

Sun, Jiebing; Hannon, James B.; Kellogg, Gary L.; Pohl, Karsten

2007-03-01

The 3D composition profile of ultra-thin Pd films on Cu(001) has been experimentally determined using low energy electron microscopy (LEEM).^[1] Quantitative measurements of the alloy concentration profile near steps show that the Pd distribution in the 3^rd layer is heterogeneous due to step overgrowth during Pd deposition. Interestingly, the Pd distribution in the 2^nd layer is also heterogeneous, and appears to be correlated with the distribution in the 1^st layer. We describe Monte Carlo simulations that show that correlation is due to Cu-Pd attraction, and that the 2^nd layer Pd is, in fact, laterally equilibrated. By comparing measured and simulated concentration profiles, we can estimate this attraction within a simple bond counting model. [1] J. B. Hannon, J. Sun, K. Pohl, G. L. Kellogg, Phys. Rev. Lett. 96, 246103 (2006)

Panchromatic spectral energy distributions of simulated galaxies: results at redshift z = 0

NASA Astrophysics Data System (ADS)

Goz, David; Monaco, Pierluigi; Granato, Gian Luigi; Murante, Giuseppe; Domínguez-Tenreiro, Rosa; Obreja, Aura; Annunziatella, Marianna; Tescari, Edoardo

2017-08-01

We present predictions of spectral energy distributions (SEDs), from the UV to the FIR, of simulated galaxies at z = 0. These were obtained by post-processing the results of an N-body+hydro simulation of a cosmological box of side 25 Mpc, which uses the Multi-Phase Particle Integrator (MUPPI) for star formation and stellar feedback, with the grasil-3d radiative transfer code that includes reprocessing of UV light by dust. Physical properties of our sample of ˜500 galaxies resemble observed ones, though with some tension at small and large stellar masses. Comparing predicted SEDs of simulated galaxies with different samples of local galaxies, we find that these resemble observed ones, when normalized at 3.6 μm. A comparison with the Herschel Reference Survey shows that the average SEDs of galaxies, divided in bins of star formation rate (SFR), are reproduced in shape and absolute normalization to within a factor of ˜2, while average SEDs of galaxies divided in bins of stellar mass show tensions that are an effect of the difference of simulated and observed galaxies in the stellar mass-SFR plane. We use our sample to investigate the correlation of IR luminosity in Spitzer and Herschel bands with several galaxy properties. SFR is the quantity that best correlates with IR light up to 160 μm, while at longer wavelengths better correlations are found with molecular mass and, at 500 μm, with dust mass. However, using the position of the FIR peak as a proxy for cold dust temperature, we assess that heating of cold dust is mostly determined by SFR, with stellar mass giving only a minor contribution. We finally show how our sample of simulated galaxies can be used as a guide to understand the physical properties and selection biases of observed samples.

The Effect of Correlated Energetic Disorder on Charge Transport in Organic Semiconductors

NASA Astrophysics Data System (ADS)

Allen, Jonathan; Röding, Sebastian; Cherqui, Charles; Dunlap, David

2012-10-01

In their 1995 paper describing a Monte Carlo simulation for dissociation of an electron-hole pair in the presence of Gaussian energetic disorder, Albrect and Bäassler reported a surprising result. They found that increasing the width σ of the energetic disorder increases the quantum yield φ. They attributed this behavior to the tendency for energy fluctuations to compete against the Coulombic pair attraction, driving the electron-hole pair apart at short distances where, without disorder, recombination would be almost certain. We have expanded upon this notion, and introduced spatial correlation into the energetic disorder. By correlating the energetic disorder, we have demonstrated even larger quantum yields in simulation, attributable to the tendency of correlation to drive the charges further apart spatially than merely random disorder. Our results generally support the findings of Greenham et al. in that a larger correlation radius gives a larger quantum yield. In addition to larger quantum yield, we believe that correlated disorder could be used to create pathways for charge transport within a material, allowing the charge carrier behavior to be tuned.

Profiling the interaction mechanism of quinoline/quinazoline derivatives as MCHR1 antagonists: an in silico method.

PubMed

Wu, Mingwei; Li, Yan; Fu, Xinmei; Wang, Jinghui; Zhang, Shuwei; Yang, Ling

2014-09-01

Melanin concentrating hormone receptor 1 (MCHR1), a crucial regulator of energy homeostasis involved in the control of feeding and energy metabolism, is a promising target for treatment of obesity. In the present work, the up-to-date largest set of 181 quinoline/quinazoline derivatives as MCHR1 antagonists was subjected to both ligand- and receptor-based three-dimensional quantitative structure-activity (3D-QSAR) analysis applying comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The optimal predictable CoMSIA model exhibited significant validity with the cross-validated correlation coefficient (Q²) = 0.509, non-cross-validated correlation coefficient (R²(ncv)) = 0.841 and the predicted correlation coefficient (R²(pred)) = 0.745. In addition, docking studies and molecular dynamics (MD) simulations were carried out for further elucidation of the binding modes of MCHR1 antagonists. MD simulations in both water and lipid bilayer systems were performed. We hope that the obtained models and information may help to provide an insight into the interaction mechanism of MCHR1 antagonists and facilitate the design and optimization of novel antagonists as anti-obesity agents.

Thermodynamics of Ising spins on the triangular kagome lattice: Exact analytical method and Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Loh, Y. L.; Yao, D. X.; Carlson, E. W.

2008-04-01

A new class of two-dimensional magnetic materials Cu9X2(cpa)6ṡxH2O ( cpa=2 -carboxypentonic acid; X=F,Cl,Br ) was recently fabricated in which Cu sites form a triangular kagome lattice (TKL). As the simplest model of geometric frustration in such a system, we study the thermodynamics of Ising spins on the TKL using exact analytic method as well as Monte Carlo simulations. We present the free energy, internal energy, specific heat, entropy, sublattice magnetizations, and susceptibility. We describe the rich phase diagram of the model as a function of coupling constants, temperature, and applied magnetic field. For frustrated interactions in the absence of applied field, the ground state is a spin liquid phase with residual entropy per spin s0/kB=(1)/(9)ln72≈0.4752… . In weak applied field, the system maps to the dimer model on a honeycomb lattice, with residual entropy 0.0359 per spin and quasi-long-range order with power-law spin-spin correlations that should be detectable by neutron scattering. The power-law correlations become exponential at finite temperatures, but the correlation length may still be long.

Quantitative study of fluctuation effects by fast lattice Monte Carlo simulations: Compression of grafted homopolymers

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

Zhang, Pengfei; Wang, Qiang, E-mail: q.wang@colostate.edu

2014-01-28

Using fast lattice Monte Carlo (FLMC) simulations [Q. Wang, Soft Matter 5, 4564 (2009)] and the corresponding lattice self-consistent field (LSCF) calculations, we studied a model system of grafted homopolymers, in both the brush and mushroom regimes, in an explicit solvent compressed by an impenetrable surface. Direct comparisons between FLMC and LSCF results, both of which are based on the same Hamiltonian (thus without any parameter-fitting between them), unambiguously and quantitatively reveal the fluctuations/correlations neglected by the latter. We studied both the structure (including the canonical-ensemble averages of the height and the mean-square end-to-end distances of grafted polymers) and thermodynamicsmore » (including the ensemble-averaged reduced energy density and the related internal energy per chain, the differences in the Helmholtz free energy and entropy per chain from the uncompressed state, and the pressure due to compression) of the system. In particular, we generalized the method for calculating pressure in lattice Monte Carlo simulations proposed by Dickman [J. Chem. Phys. 87, 2246 (1987)], and combined it with the Wang-Landau–Optimized Ensemble sampling [S. Trebst, D. A. Huse, and M. Troyer, Phys. Rev. E 70, 046701 (2004)] to efficiently and accurately calculate the free energy difference and the pressure due to compression. While we mainly examined the effects of the degree of compression, the distance between the nearest-neighbor grafting points, the reduced number of chains grafted at each grafting point, and the system fluctuations/correlations in an athermal solvent, the θ-solvent is also considered in some cases.« less

Exponential yield sensitivity to long-wavelength asymmetries in three-dimensional simulations of inertial confinement fusion capsule implosions

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

Haines, Brian M., E-mail: bmhaines@lanl.gov

2015-08-15

In this paper, we perform a series of high-resolution 3D simulations of an OMEGA-type inertial confinement fusion (ICF) capsule implosion with varying levels of initial long-wavelength asymmetries in order to establish the physical energy loss mechanism for observed yield degradation due to long-wavelength asymmetries in symcap (gas-filled capsule) implosions. These simulations demonstrate that, as the magnitude of the initial asymmetries is increased, shell kinetic energy is increasingly retained in the shell instead of being converted to fuel internal energy. This is caused by the displacement of fuel mass away from and shell material into the center of the implosion duemore » to complex vortical flows seeded by the long-wavelength asymmetries. These flows are not fully turbulent, but demonstrate mode coupling through non-linear instability development during shell stagnation and late-time shock interactions with the shell interface. We quantify this effect by defining a separation lengthscale between the fuel mass and internal energy and show that this is correlated with yield degradation. The yield degradation shows an exponential sensitivity to the RMS magnitude of the long-wavelength asymmetries. This strong dependence may explain the lack of repeatability frequently observed in OMEGA ICF experiments. In contrast to previously reported mechanisms for yield degradation due to turbulent instability growth, yield degradation is not correlated with mixing between shell and fuel material. Indeed, an integrated measure of mixing decreases with increasing initial asymmetry magnitude due to delayed shock interactions caused by growth of the long-wavelength asymmetries without a corresponding delay in disassembly.« less

Energy Dissipation and Dynamics in Large Guide Field Turbulence Driven Reconnection at the Magnetopause

NASA Astrophysics Data System (ADS)

TenBarge, J. M.; Shay, M. A.; Sharma, P.; Juno, J.; Haggerty, C. C.; Drake, J. F.; Bhattacharjee, A.; Hakim, A.

2017-12-01

Turbulence and magnetic reconnection are the primary mechanisms responsible for the conversion of stored magnetic energy into particle energy in many space and astrophysical plasmas. The magnetospheric multiscale mission (MMS) has given us unprecedented access to high cadence particle and field data of turbulence and magnetic reconnection at earth's magnetopause. The observations include large guide field reconnection events generated within the turbulent magnetopause. Motivated by these observations, we present a study of large guide reconnection using the fully kinetic Eulerian Vlasov-Maxwell component of the Gkeyll simulation framework, and we also employ and compare with gyrokinetics to explore the asymptotically large guide field limit. In addition to studying the configuration space dynamics, we leverage the recently developed field-particle correlations to diagnose the dominant sources of dissipation and compare the results of the field-particle correlation to other energy dissipation measures.

Exciton Transport Simulations in Phenyl Cored Thiophene Dendrimers

NASA Astrophysics Data System (ADS)

Kim, Kwiseon; Erkan Kose, Muhammet; Graf, Peter; Kopidakis, Nikos; Rumbles, Garry; Shaheen, Sean E.

2009-03-01

Phenyl cored 3-arm and 4-arm thiophene dendrimers are promising materials for use in photovoltaic devices. It is important to understand the energy transfer mechanisms in these molecules to guide the synthesis of novel dendrimers with improved efficiency. A method is developed to estimate the exciton diffusion lengths for the dendrimers and similar chromophores in amorphous films. The approach exploits Fermi's Golden Rule to estimate the energy transfer rates for an ensemble of bimolecular complexes in random orientations. Using Poisson's equation to evaluate Coulomb integrals led to efficient calculation of excitonic couplings between the transition densities. Monte-Carlo simulations revealed the dynamics of energy transport in the dendrimers. Experimental exciton diffusion lengths of the dendrimers range 10 ˜ 20 nm, increasing with the size of the dendrimer. Simulated diffusion lengths correlate well with experiments. The chemical structure of the chromophore, the shape of the transition densities and the exciton lifetime are found to be the most important factors that determine the exciton diffusion length in amorphous films.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

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

Wilson, S. R.; Mendelev, M. I., E-mail: mendelev@ameslab.gov

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, wemore » found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).« less

Jet-induced medium excitation in γ-hadron correlation at RHIC

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

Chen, Wei; Cao, Shanshan; Luo, Tan

Both jet transport and jet-induced medium excitation are investigated simultaneously within the coupled Linear Boltzmann Transport and hydro (CoLBT-hydro) model. In this coupled approach, energy-momentum deposition from propagating jet shower partons in the elastic and radiation processes is taken as a source term in hydrodynamics and the hydro background for LBT simulation is updated for next time step. We use CoLBT-hydro model to simulate γ-jet events of Au+Au collisions at RHIC. Hadron spectra from both the hadronization of jet shower partons and jet-induced medium excitation are calculated and compared to experimental data. Parton energy loss of jet shower partons leadsmore » to the suppression of hadron yields at large z T = p h T/p γ T while medium excitations leads to enhancement of hadron yields at small z T. Meanwhile, a significant broadening of low p T hadron yields and the depletion of soft hadrons in the γ direction are observed in the calculation of γ-hadron angular correlation.« less

Jet-induced medium excitation in γ-hadron correlation at RHIC

DOE PAGES

Chen, Wei; Cao, Shanshan; Luo, Tan; ...

2017-09-25

Both jet transport and jet-induced medium excitation are investigated simultaneously within the coupled Linear Boltzmann Transport and hydro (CoLBT-hydro) model. In this coupled approach, energy-momentum deposition from propagating jet shower partons in the elastic and radiation processes is taken as a source term in hydrodynamics and the hydro background for LBT simulation is updated for next time step. We use CoLBT-hydro model to simulate γ-jet events of Au+Au collisions at RHIC. Hadron spectra from both the hadronization of jet shower partons and jet-induced medium excitation are calculated and compared to experimental data. Parton energy loss of jet shower partons leadsmore » to the suppression of hadron yields at large z T = p h T/p γ T while medium excitations leads to enhancement of hadron yields at small z T. Meanwhile, a significant broadening of low p T hadron yields and the depletion of soft hadrons in the γ direction are observed in the calculation of γ-hadron angular correlation.« less

Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model.

PubMed

Wang, Wei Bu; Liang, Yu; Zhang, Jing; Wu, Yi Dong; Du, Jian Jun; Li, Qi Ming; Zhu, Jian Zhuo; Su, Ji Guo

2018-06-22

Intra-molecular energy transport between distant functional sites plays important roles in allosterically regulating the biochemical activity of proteins. How to identify the specific intra-molecular signaling pathway from protein tertiary structure remains a challenging problem. In the present work, a non-equilibrium dynamics method based on the elastic network model (ENM) was proposed to simulate the energy propagation process and identify the specific signaling pathways within proteins. In this method, a given residue was perturbed and the propagation of energy was simulated by non-equilibrium dynamics in the normal modes space of ENM. After that, the simulation results were transformed from the normal modes space to the Cartesian coordinate space to identify the intra-protein energy transduction pathways. The proposed method was applied to myosin and the third PDZ domain (PDZ3) of PSD-95 as case studies. For myosin, two signaling pathways were identified, which mediate the energy transductions form the nucleotide binding site to the 50 kDa cleft and the converter subdomain, respectively. For PDZ3, one specific signaling pathway was identified, through which the intra-protein energy was transduced from ligand binding site to the distant opposite side of the protein. It is also found that comparing with the commonly used cross-correlation analysis method, the proposed method can identify the anisotropic energy transduction pathways more effectively.

Ab initio simulation of structure and surface energy of low-index surfaces of stoichiometric α-Fe2O3

NASA Astrophysics Data System (ADS)

Stirner, Thomas; Scholz, David; Sun, Jizhong

2018-05-01

The structure and surface energy of a series of low-index surfaces of stoichiometric α-Fe2O3 (hematite) are investigated using the periodic Hartree-Fock approach with an a posteriori correction of the correlation energy. The simulations show that, amongst the modeled facets, (01 1 bar2) and (0001) are the most stable surfaces of hematite, which is consistent with the fact that the latter are the dominant growth faces exposed on natural α-Fe2O3. The Fe-terminated (0001) surface is shown to exhibit a large relaxation of the surface atoms. It is argued that this arises mainly due to the fact that the surface cations are located opposite empty cation sites in the filled-filled-unfilled cation sequence along the c-axis. In contrast, the (01 1 bar2) plane cuts the crystal through a plane of empty cation sites, thus giving rise to relatively small relaxations and surface energies. The small relaxations and concomitant exposure of five-coordinate cation sites may be important for the catalytic activity of hematite. The simulations also show that the relative stability of the investigated surfaces changes after a full lattice relaxation with the (0001) and (11 2 bar6) facets relaxing disproportionately large. Wherever possible, the simulations are compared with previous simulation data and experimental results. A Wulff-Gibbs construction is also presented.

Monte Carlo simulations of dipolar and quadrupolar linear Kihara fluids. A test of thermodynamic perturbation theory

NASA Astrophysics Data System (ADS)

Garzon, B.

Several simulations of dipolar and quadrupolar linear Kihara fluids using the Monte Carlo method in the canonical ensemble have been performed. Pressure and internal energy have been directly determined from simulations and Helmholtz free energy using thermodynamic integration. Simulations were carried out for fluids of fixed elongation at two different densities and several values of temperature and dipolar or quadrupolar moment for each density. Results are compared with the perturbation theory developed by Boublik for this same type of fluid and good agreement between simulated and theoretical values was obtained especially for quadrupole fluids. Simulations are also used to obtain the liquid structure giving the first few coefficients of the expansion of pair correlation functions in terms of spherical harmonics. Estimations of the triple point temperature to critical temperature ratio are given for some dipole and quadrupole linear fluids. The stability range of the liquid phase of these substances is shortly discussed and an analysis about the opposite roles of the dipole moment and the molecular elongation on this stability is also given.

A Spalart-Allmaras local correlation-based transition model for Thermo-fuid dynamics

NASA Astrophysics Data System (ADS)

D'Alessandro, V.; Garbuglia, F.; Montelpare, S.; Zoppi, A.

2017-11-01

The study of innovative energy systems often involves complex fluid flows problems and the Computational Fluid-Dynamics (CFD) is one of the main tools of analysis. It is important to put in evidence that in several energy systems the flow field experiences the laminar-to-turbulent transition. Direct Numerical Simulations (DNS) or Large Eddy Simulation (LES) are able to predict the flow transition but they are still inapplicable to the study of real problems due to the significant computational resources requirements. Differently standard Reynolds Averaged Navier Stokes (RANS) approaches are not always reliable since they assume a fully turbulent regime. In order to overcome this drawback in the recent years some locally formulated transition RANS models have been developed. In this work, we present a local correlation-based transition approach adding two equations that control the laminar-toturbulent transition process -γ and \\[\\overset{}{\\mathop{{{\\operatorname{Re}}θ, \\text{t}}}} \\] - to the well-known Spalart-Allmaras (SA) turbulence model. The new model was implemented within OpenFOAM code. The energy equation is also implemented in order to evaluate the model performance in thermal-fluid dynamics applications. In all the considered cases a very good agreement between numerical and experimental data was observed.

Energy conversion in polyelectrolyte hydrogels

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica; Erbas, Aykut; Olvera de la Cruz Team

Energy conversion and storage have been an active field of research in nanotechnology parallel to recent interests towards renewable energy. Polyelectrolyte (PE) hydrogels have attracted considerable attention in this field due to their mechanical flexibility and stimuli-responsive properties. Ideally, when a hydrogel is deformed, applied mechanical work can be converted into electrostatic, elastic and steric-interaction energies. In this talk, we discuss the results of our extensive molecular dynamics simulations of PE hydrogels. We demonstrate that, on deformation, hydrogels adjust their deformed state predominantly by altering electrostatic interactions between their charged groups rather than excluded-volume and bond energies. This is due to the hydrogel's inherent tendency to preserve electro-neutrality in its interior, in combination with correlations imposed by backbone charges. Our findings are valid for a wide range of compression ratios and ionic strengths. The electrostatic-energy alterations that we observe in our MD simulations may induce pH or redox-potential changes inside the hydrogels. The resulting energetic difference can be harvested, for instance, analogously to a Carnot engine, or facilitated for sensor applications. Center for Bio-inspired Energy Science (CBES).

Effect of helicity on the correlation time of large scales in turbulent flows

NASA Astrophysics Data System (ADS)

Cameron, Alexandre; Alexakis, Alexandros; Brachet, Marc-Étienne

2017-11-01

Solutions of the forced Navier-Stokes equation have been conjectured to thermalize at scales larger than the forcing scale, similar to an absolute equilibrium obtained for the spectrally truncated Euler equation. Using direct numeric simulations of Taylor-Green flows and general-periodic helical flows, we present results on the probability density function, energy spectrum, autocorrelation function, and correlation time that compare the two systems. In the case of highly helical flows, we derive an analytic expression describing the correlation time for the absolute equilibrium of helical flows that is different from the E-1 /2k-1 scaling law of weakly helical flows. This model predicts a new helicity-based scaling law for the correlation time as τ (k ) ˜H-1 /2k-1 /2 . This scaling law is verified in simulations of the truncated Euler equation. In simulations of the Navier-Stokes equations the large-scale modes of forced Taylor-Green symmetric flows (with zero total helicity and large separation of scales) follow the same properties as absolute equilibrium including a τ (k ) ˜E-1 /2k-1 scaling for the correlation time. General-periodic helical flows also show similarities between the two systems; however, the largest scales of the forced flows deviate from the absolute equilibrium solutions.

Molecular dynamics simulation of the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide.

PubMed

Siqueira, Leonardo J A; Ribeiro, Mauro C C

2007-10-11

Thermodynamics, structure, and dynamics of an ionic liquid based on a quaternary ammonium salt with ether side chain, namely, N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide, MOENM2E TFSI, are investigated by molecular dynamics (MD) simulations. Average density and configurational energy of simulated MOENM2E TFSI are interpreted with models that take into account empirical ionic volumes. A throughout comparison of the equilibrium structure of MOENM2E TFSI with previous results for the more common ionic liquids based on imidazolium cations is provided. Several time correlation functions are used to reveal the microscopic dynamics of MOENM2E TFSI. Structural relaxation is discussed by the calculation of simultaneous space-time correlation functions. Temperature effects on transport coefficients (diffusion, conductivity, and viscosity) are investigated. The ratio between the actual conductivity and the estimate from ionic diffusion by the Nernst-Einstein equation indicates that correlated motion of neighboring ions in MOENM2E TFSI is similar to imidazolium ionic liquids. In line with experiment, Walden plot of conductivity and viscosity indicates that simulated MOENM2E TFSI should be classified as a poor ionic liquid.

An equation-of-state-meter of quantum chromodynamics transition from deep learning.

PubMed

Pang, Long-Gang; Zhou, Kai; Su, Nan; Petersen, Hannah; Stöcker, Horst; Wang, Xin-Nian

2018-01-15

A primordial state of matter consisting of free quarks and gluons that existed in the early universe a few microseconds after the Big Bang is also expected to form in high-energy heavy-ion collisions. Determining the equation of state (EoS) of such a primordial matter is the ultimate goal of high-energy heavy-ion experiments. Here we use supervised learning with a deep convolutional neural network to identify the EoS employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering the nature of the phase transition in quantum chromodynamics. Such EoS-meter is model-independent and insensitive to other simulation inputs including the initial conditions for hydrodynamic simulations.

Multiscale Simulations of Protein Landscapes: Using Coarse Grained Models as Reference Potentials to Full Explicit Models

PubMed Central

Messer, Benjamin M.; Roca, Maite; Chu, Zhen T.; Vicatos, Spyridon; Kilshtain, Alexandra Vardi; Warshel, Arieh

2009-01-01

Evaluating the free energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al, Theor Chem Acc (1999) 103:77-80) uses the CG model as a reference potential for free energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. This application includes: evaluation of changes of folding energy upon mutations, calculations of transition states binding free energies (which are crucial for rational enzyme design), evaluation of catalytic landscape and simulation of the time dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed. PMID:20052756

Multi-scale properties of large eddy simulations: correlations between resolved-scale velocity-field increments and subgrid-scale quantities

NASA Astrophysics Data System (ADS)

Linkmann, Moritz; Buzzicotti, Michele; Biferale, Luca

2018-06-01

We provide analytical and numerical results concerning multi-scale correlations between the resolved velocity field and the subgrid-scale (SGS) stress-tensor in large eddy simulations (LES). Following previous studies for Navier-Stokes equations, we derive the exact hierarchy of LES equations governing the spatio-temporal evolution of velocity structure functions of any order. The aim is to assess the influence of the subgrid model on the inertial range intermittency. We provide a series of predictions, within the multifractal theory, for the scaling of correlation involving the SGS stress and we compare them against numerical results from high-resolution Smagorinsky LES and from a-priori filtered data generated from direct numerical simulations (DNS). We find that LES data generally agree very well with filtered DNS results and with the multifractal prediction for all leading terms in the balance equations. Discrepancies are measured for some of the sub-leading terms involving cross-correlation between resolved velocity increments and the SGS tensor or the SGS energy transfer, suggesting that there must be room to improve the SGS modelisation to further extend the inertial range properties for any fixed LES resolution.

Plasma instabilities in the terrestrial magnetosphere - A review of recent theoretical research

NASA Technical Reports Server (NTRS)

Gary, S. Peter

1987-01-01

This paper reviews recent theoretical research on plasma instabilities in the terrestrial magnetosphere. This paper is organized with respect to particle free energies: electron-ion currents, electron beams, ion beams, electron anisotropies and ion anisotropies are successively considered. For each free energy, the associated instability properties are summarized, and their applications to magnetospheric physics are briefly described. Theory and simulations which have established close correlations with observations are emphasized.

MJO simulation in CMIP5 climate models: MJO skill metrics and process-oriented diagnosis

NASA Astrophysics Data System (ADS)

Ahn, Min-Seop; Kim, Daehyun; Sperber, Kenneth R.; Kang, In-Sik; Maloney, Eric; Waliser, Duane; Hendon, Harry

2017-12-01

The Madden-Julian Oscillation (MJO) simulation diagnostics developed by MJO Working Group and the process-oriented MJO simulation diagnostics developed by MJO Task Force are applied to 37 Coupled Model Intercomparison Project phase 5 (CMIP5) models in order to assess model skill in representing amplitude, period, and coherent eastward propagation of the MJO, and to establish a link between MJO simulation skill and parameterized physical processes. Process-oriented diagnostics include the Relative Humidity Composite based on Precipitation (RHCP), Normalized Gross Moist Stability (NGMS), and the Greenhouse Enhancement Factor (GEF). Numerous scalar metrics are developed to quantify the results. Most CMIP5 models underestimate MJO amplitude, especially when outgoing longwave radiation (OLR) is used in the evaluation, and exhibit too fast phase speed while lacking coherence between eastward propagation of precipitation/convection and the wind field. The RHCP-metric, indicative of the sensitivity of simulated convection to low-level environmental moisture, and the NGMS-metric, indicative of the efficiency of a convective atmosphere for exporting moist static energy out of the column, show robust correlations with a large number of MJO skill metrics. The GEF-metric, indicative of the strength of the column-integrated longwave radiative heating due to cloud-radiation interaction, is also correlated with the MJO skill metrics, but shows relatively lower correlations compared to the RHCP- and NGMS-metrics. Our results suggest that modifications to processes associated with moisture-convection coupling and the gross moist stability might be the most fruitful for improving simulations of the MJO. Though the GEF-metric exhibits lower correlations with the MJO skill metrics, the longwave radiation feedback is highly relevant for simulating the weak precipitation anomaly regime that may be important for the establishment of shallow convection and the transition to deep convection.

MJO simulation in CMIP5 climate models: MJO skill metrics and process-oriented diagnosis

DOE PAGES

Ahn, Min-Seop; Kim, Daehyun; Sperber, Kenneth R.; ...

2017-03-23

The Madden-Julian Oscillation (MJO) simulation diagnostics developed by MJO Working Group and the process-oriented MJO simulation diagnostics developed by MJO Task Force are applied to 37 Coupled Model Intercomparison Project phase 5 (CMIP5) models in order to assess model skill in representing amplitude, period, and coherent eastward propagation of the MJO, and to establish a link between MJO simulation skill and parameterized physical processes. Process-oriented diagnostics include the Relative Humidity Composite based on Precipitation (RHCP), Normalized Gross Moist Stability (NGMS), and the Greenhouse Enhancement Factor (GEF). Numerous scalar metrics are developed to quantify the results. Most CMIP5 models underestimate MJOmore » amplitude, especially when outgoing longwave radiation (OLR) is used in the evaluation, and exhibit too fast phase speed while lacking coherence between eastward propagation of precipitation/convection and the wind field. The RHCP-metric, indicative of the sensitivity of simulated convection to low-level environmental moisture, and the NGMS-metric, indicative of the efficiency of a convective atmosphere for exporting moist static energy out of the column, show robust correlations with a large number of MJO skill metrics. The GEF-metric, indicative of the strength of the column-integrated longwave radiative heating due to cloud-radiation interaction, is also correlated with the MJO skill metrics, but shows relatively lower correlations compared to the RHCP- and NGMS-metrics. Our results suggest that modifications to processes associated with moisture-convection coupling and the gross moist stability might be the most fruitful for improving simulations of the MJO. Though the GEF-metric exhibits lower correlations with the MJO skill metrics, the longwave radiation feedback is highly relevant for simulating the weak precipitation anomaly regime that may be important for the establishment of shallow convection and the transition to deep convection.« less

MJO simulation in CMIP5 climate models: MJO skill metrics and process-oriented diagnosis

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

Ahn, Min-Seop; Kim, Daehyun; Sperber, Kenneth R.

The Madden-Julian Oscillation (MJO) simulation diagnostics developed by MJO Working Group and the process-oriented MJO simulation diagnostics developed by MJO Task Force are applied to 37 Coupled Model Intercomparison Project phase 5 (CMIP5) models in order to assess model skill in representing amplitude, period, and coherent eastward propagation of the MJO, and to establish a link between MJO simulation skill and parameterized physical processes. Process-oriented diagnostics include the Relative Humidity Composite based on Precipitation (RHCP), Normalized Gross Moist Stability (NGMS), and the Greenhouse Enhancement Factor (GEF). Numerous scalar metrics are developed to quantify the results. Most CMIP5 models underestimate MJOmore » amplitude, especially when outgoing longwave radiation (OLR) is used in the evaluation, and exhibit too fast phase speed while lacking coherence between eastward propagation of precipitation/convection and the wind field. The RHCP-metric, indicative of the sensitivity of simulated convection to low-level environmental moisture, and the NGMS-metric, indicative of the efficiency of a convective atmosphere for exporting moist static energy out of the column, show robust correlations with a large number of MJO skill metrics. The GEF-metric, indicative of the strength of the column-integrated longwave radiative heating due to cloud-radiation interaction, is also correlated with the MJO skill metrics, but shows relatively lower correlations compared to the RHCP- and NGMS-metrics. Our results suggest that modifications to processes associated with moisture-convection coupling and the gross moist stability might be the most fruitful for improving simulations of the MJO. Though the GEF-metric exhibits lower correlations with the MJO skill metrics, the longwave radiation feedback is highly relevant for simulating the weak precipitation anomaly regime that may be important for the establishment of shallow convection and the transition to deep convection.« less

Forward-backward multiplicity correlation in high-energy nucleus-nucleus interactions at a few AGeV/c

NASA Astrophysics Data System (ADS)

Bhattacharyya, Swarnapratim; Haiduc, Maria; Neagu, Alina Tania; Firu, Elena

2014-07-01

We have presented a systematic study of two-particle rapidity correlations in terms of investigating the dynamical fluctuation observable \\sigma _c^2 in the forward-backward pseudo-rapidity windows by analyzing the experimental data of {}_{}^{16} O{--}AgBr interactions at 4.5 AGeV/c, {}_{}^{22} Ne{--}AgBr interactions at 4.1 AGeV/c, {}_{}^{28} Si{--}AgBr and {}_{}^{32} S{--}AgBr interactions at 4.5 AGeV/c. The experimental results have been compared with the results obtained from the analysis of event sample simulated (MC-RAND) by generating random numbers and also with the analysis of events generated by the UrQMD and AMPT model. Our study confirms the presence of strong short-range correlations among the produced particles in the forward and the backward pseudo-rapidity region. The analysis of the simple Monte Carlo-simulated (MC-RAND) events signifies that the observed correlations are not due to mere statistics only; explanation of such correlations can be attributed to the presence of dynamical fluctuations during the production of charged pions. Comparisons of the experimental results with the results obtained from analyzing the UrQMD data sample indicate that the UrQMD model cannot reproduce the experimental findings. The AMPT model also cannot explain the experimental results satisfactorily. Comparisons of our experimental results with the results obtained from the analysis of higher energy emulsion data and with the results of the RHIC data have also been presented.

Towards a 3d Spatial Urban Energy Modelling Approach

NASA Astrophysics Data System (ADS)

Bahu, J.-M.; Koch, A.; Kremers, E.; Murshed, S. M.

2013-09-01

Today's needs to reduce the environmental impact of energy use impose dramatic changes for energy infrastructure and existing demand patterns (e.g. buildings) corresponding to their specific context. In addition, future energy systems are expected to integrate a considerable share of fluctuating power sources and equally a high share of distributed generation of electricity. Energy system models capable of describing such future systems and allowing the simulation of the impact of these developments thus require a spatial representation in order to reflect the local context and the boundary conditions. This paper describes two recent research approaches developed at EIFER in the fields of (a) geo-localised simulation of heat energy demand in cities based on 3D morphological data and (b) spatially explicit Agent-Based Models (ABM) for the simulation of smart grids. 3D city models were used to assess solar potential and heat energy demand of residential buildings which enable cities to target the building refurbishment potentials. Distributed energy systems require innovative modelling techniques where individual components are represented and can interact. With this approach, several smart grid demonstrators were simulated, where heterogeneous models are spatially represented. Coupling 3D geodata with energy system ABMs holds different advantages for both approaches. On one hand, energy system models can be enhanced with high resolution data from 3D city models and their semantic relations. Furthermore, they allow for spatial analysis and visualisation of the results, with emphasis on spatially and structurally correlations among the different layers (e.g. infrastructure, buildings, administrative zones) to provide an integrated approach. On the other hand, 3D models can benefit from more detailed system description of energy infrastructure, representing dynamic phenomena and high resolution models for energy use at component level. The proposed modelling strategies conceptually and practically integrate urban spatial and energy planning approaches. The combined modelling approach that will be developed based on the described sectorial models holds the potential to represent hybrid energy systems coupling distributed generation of electricity with thermal conversion systems.

Long range stress correlations in the inherent structures of liquids at rest

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

Chowdhury, Sadrul; Abraham, Sneha; Hudson, Toby

2016-03-28

Simulation studies of the atomic shear stress in the local potential energy minima (inherent structures) are reported for binary liquid mixtures in 2D and 3D. These inherent structure stresses are fundamental to slow stress relaxation and high viscosity in supercooled liquids. We find that the atomic shear stress in the inherent structures (IS’s) of both liquids at rest exhibits slowly decaying anisotropic correlations. We show that the stress correlations contribute significantly to the variance of the total shear stress of the IS configurations and consider the origins of the anisotropy and spatial extent of the stress correlations.

Monte Carlo Study of the abBA Experiment: Detector Response and Physics Analysis.

PubMed

Frlež, E

2005-01-01

The abBA collaboration proposes to conduct a comprehensive program of precise measurements of neutron β-decay coefficients a (the correlation between the neutrino momentum and the decay electron momentum), b (the electron energy spectral distortion term), A (the correlation between the neutron spin and the decay electron momentum), and B (the correlation between the neutron spin and the decay neutrino momentum) at a cold neutron beam facility. We have used a GEANT4-based code to simulate the propagation of decay electrons and protons in the electromagnetic spectrometer and study the energy and timing response of a pair of Silicon detectors. We used these results to examine systematic effects and find the uncertainties with which the physics parameters a, b, A, and B can be extracted from an over-determined experimental data set.

The bioinformatics of nucleotide sequence coding for proteins requiring metal coenzymes and proteins embedded with metals

NASA Astrophysics Data System (ADS)

Tremberger, G.; Dehipawala, Sunil; Cheung, E.; Holden, T.; Sullivan, R.; Nguyen, A.; Lieberman, D.; Cheung, T.

2015-09-01

All metallo-proteins need post-translation metal incorporation. In fact, the isotope ratio of Fe, Cu, and Zn in physiology and oncology have emerged as an important tool. The nickel containing F430 is the prosthetic group of the enzyme methyl coenzyme M reductase which catalyzes the release of methane in the final step of methano-genesis, a prime energy metabolism candidate for life exploration space mission in the solar system. The 3.5 Gyr early life sulfite reductase as a life switch energy metabolism had Fe-Mo clusters. The nitrogenase for nitrogen fixation 3 billion years ago had Mo. The early life arsenite oxidase needed for anoxygenic photosynthesis energy metabolism 2.8 billion years ago had Mo and Fe. The selection pressure in metal incorporation inside a protein would be quantifiable in terms of the related nucleotide sequence complexity with fractal dimension and entropy values. Simulation model showed that the studied metal-required energy metabolism sequences had at least ten times more selection pressure relatively in comparison to the horizontal transferred sequences in Mealybug, guided by the outcome histogram of the correlation R-sq values. The metal energy metabolism sequence group was compared to the circadian clock KaiC sequence group using magnesium atomic level bond shifting mechanism in the protein, and the simulation model would suggest a much higher selection pressure for the energy life switch sequence group. The possibility of using Kepler 444 as an example of ancient life in Galaxy with the associated exoplanets has been proposed and is further discussed in this report. Examples of arsenic metal bonding shift probed by Synchrotron-based X-ray spectroscopy data and Zn controlled FOXP2 regulated pathways in human and chimp brain studied tissue samples are studied in relationship to the sequence bioinformatics. The analysis results suggest that relatively large metal bonding shift amount is associated with low probability correlation R-sq outcome in the bioinformatics simulation.

Neutron kinetics in moderators and SNM detection through epithermal-neutron-induced fissions

NASA Astrophysics Data System (ADS)

Gozani, Tsahi; King, Michael J.

2016-01-01

Extension of the well-established Differential Die Away Analysis (DDAA) into a faster time domain, where more penetrating epithermal neutrons induce fissions, is proposed and demonstrated via simulations and experiments. In the proposed method the fissions stimulated by thermal, epithermal and even higher-energy neutrons are measured after injection of a narrow pulse of high-energy 14 MeV (d,T) or 2.5 MeV (d,D) source neutrons, appropriately moderated. The ability to measure these fissions stems from the inherent correlation of neutron energy and time ("E-T" correlation) during the process of slowing down of high-energy source neutrons in common moderating materials such as hydrogenous compounds (e.g., polyethylene), heavy water, beryllium and graphite. The kinetic behavior following injection of a delta-function-shaped pulse (in time) of 14 MeV neutrons into such moderators is studied employing MCNPX simulations and, when applicable, some simple "one-group" models. These calculations served as a guide for the design of a source moderator which was used in experiments. Qualitative relationships between slowing-down time after the pulse and the prevailing neutron energy are discussed. A laboratory system consisting of a 14 MeV neutron generator, a polyethylene-reflected Be moderator, a liquid scintillator with pulse-shape discrimination (PSD) and a two-parameter E-T data acquisition system was set up to measure prompt neutron and delayed gamma-ray fission signatures in a 19.5% enriched LEU sample. The measured time behavior of thermal and epithermal neutron fission signals agreed well with the detailed simulations. The laboratory system can readily be redesigned and deployed as a mobile inspection system for SNM in, e.g., cars and vans. A strong pulsed neutron generator with narrow pulse (<75 ns) at a reasonably high pulse frequency could make the high-energy neutron induced fission modality a realizable SNM detection technique.

Energetic Profile of the Basketball Exercise Simulation Test in Junior Elite Players.

PubMed

Latzel, Richard; Hoos, Olaf; Stier, Sebastian; Kaufmann, Sebastian; Fresz, Volker; Reim, Dominik; Beneke, Ralph

2017-11-28

To analyze the energetic profile of the basketball exercise simulation test (BEST). 10 male elite junior basketball players (age: 15.5±0.6yrs, height: 180±9cm, body mass: 66.1±11.2kg) performed a modified BEST (20 circuits consisting of jumping, sprinting, jogging, shuffling, and short breaks) simulating professional basketball game play. Circuit time, sprint time, sprint decrement, oxygen uptake (VO2), heart rate (HR), and blood lactate concentration (BLC) were obtained. Metabolic energy and metabolic power above rest (W tot , P tot ) as well as energy share in terms of aerobic (W aer ), glycolytic (W blc ), and high energy phosphates (W PCr ) were calculated from VO2 during exercise, net lactate production, and the fast component of post-exercise VO2 kinetics, respectively. W aer , W blc , and W PCr reflect 89±2%, 5±1%, and 6±1% of total energy needed, respectively. Assuming an aerobic replenishment of PCr energy stores during short breaks, the adjusted energy share yielded W aer : 66±4%, W blc : 5±1%, and W PCr : 29±1%. W aer and W PCr were negatively correlated (-0.72, -0.59) with sprint time, which was not the case for W blc . Consistent with general findings on energy system interaction during repeated high intensity exercise bouts, the intermittent profile of the BEST relies primarily on aerobic energy combined with repetitive supplementation by anaerobic utilization of high energy phosphates.

CORE-COLLAPSE SUPERNOVA EQUATIONS OF STATE BASED ON NEUTRON STAR OBSERVATIONS

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

Steiner, A. W.; Hempel, M.; Fischer, T.

2013-09-01

Many of the currently available equations of state for core-collapse supernova simulations give large neutron star radii and do not provide large enough neutron star masses, both of which are inconsistent with some recent neutron star observations. In addition, one of the critical uncertainties in the nucleon-nucleon interaction, the nuclear symmetry energy, is not fully explored by the currently available equations of state. In this article, we construct two new equations of state which match recent neutron star observations and provide more flexibility in studying the dependence on nuclear matter properties. The equations of state are also provided in tabularmore » form, covering a wide range in density, temperature, and asymmetry, suitable for astrophysical simulations. These new equations of state are implemented into our spherically symmetric core-collapse supernova model, which is based on general relativistic radiation hydrodynamics with three-flavor Boltzmann neutrino transport. The results are compared with commonly used equations of state in supernova simulations of 11.2 and 40 M{sub Sun} progenitors. We consider only equations of state which are fitted to nuclear binding energies and other experimental and observational constraints. We find that central densities at bounce are weakly correlated with L and that there is a moderate influence of the symmetry energy on the evolution of the electron fraction. The new models also obey the previously observed correlation between the time to black hole formation and the maximum mass of an s = 4 neutron star.« less

Wave-Particle Interactions Involving Correlated Electron Bursts and Whistler Chorus in Earth's Radiation Belts

NASA Astrophysics Data System (ADS)

Echterling, N.; Schriver, D.; Roeder, J. L.; Fennell, J. F.

2017-12-01

During the recovery phase of substorm plasma injections, the Van Allen Probes commonly observe events of quasi-periodic energetic electron bursts correlating with simultaneously detected upper-band, whistler-mode chorus emissions. These electron bursts exhibit narrow ranges of pitch angles (75-80° and 100-105°) and energies (20-40 keV). Electron cyclotron harmonic (ECH) emissions are also commonly detected, but typically do not display correlation with the electron bursts. To examine sources of free energy and the generation of these wave emissions, an observed electron velocity distribution on January 13, 2013 is used as the starting condition for a particle in cell (PIC) simulation. Effects of temperature anisotropy (perpendicular temperature greater than parallel temperature), the presence of a loss cone and a cold electron population on the generation of whistler and ECH waves are examined to understand wave generation and nonlinear interactions with the particle population. These nonlinear interactions produce energy diffusion along with strong pitch angle scattering into the loss cone on the order of milliseconds, which is faster than a typical bounce period of seconds. To examine the quasi-periodic nature of the electron bursts, a loss-cone recycling technique is implemented to model the effects of the periodic emptying of the loss cone and electron injection on the growth of whistler and ECH waves. The results of the simulations are compared to the Van Allen Probe observations to determine electron acceleration, heating and transport in Earth's radiation belts due to wave-particle interactions.

NIMROD Simulations of Spheromak Formation, Magnetic Reconnection and Energy Confinement in SSPX

NASA Astrophysics Data System (ADS)

Hooper, E. B.; Sovinec, C. R.

2005-10-01

The SSPX spheromak is formed and driven by a coaxial electrostatic gun that injects current and magnetic flux. Magnetic fluctuations are associated with the conversion of toroidal to poloidal magnetic flux during formation. After formation, fluctuations that break axisymmetry degrade magnetic surfaces, and are anti-correlated with the core temperature and energy confinement time. We report NIMROD simulations extending earlier work^1 supporting the SSPX experiment through predictions of performance and providing insight. The simulations are in fairly good agreement with features observed in SSPX and underscore the importance of current profile control in mitigating magnetic fluctuation amplitudes and improving confinement. The simulations yield insight into magnetic reconnection and the relationship of fluctuations to field line stochasticity. We have added external circuit equations for the new 32 module capacitor bank in SSPX that will add flexibility in shaping the injector current pulses and substantially increase the injected currents and the magnetic energy. New NIMROD simulations of SSPX lead to higher temperature plasmas than in previous simulations. *Work supported by U.S. DOE, under Contr. No. W-7405-ENG-48 at U. Cal. LLNL and under grant FG02-01ER54661 at U. Wisc Madison. ^1C. R. Sovinec, B. I. Cohen, et al., Phys. Rev. Lett. 94, 035003 (2005); B. I. Cohen, E. B. Hooper, et al., Phys. Plasmas 12, 056106 (2005).

Simulating the dynamics of the mechanochemical cycle of myosin-V

PubMed Central

Mukherjee, Shayantani; Alhadeff, Raphael; Warshel, Arieh

2017-01-01

The detailed dynamics of the cycle of myosin-V are explored by simulation approaches, examining the nature of the energy-driven motion. Our study started with Langevin dynamics (LD) simulations on a very coarse landscape with a single rate-limiting barrier and reproduced the stall force and the hand-over-hand dynamics. We then considered a more realistic landscape and used time-dependent Monte Carlo (MC) simulations that allowed trajectories long enough to reproduce the force/velocity characteristic sigmoidal correlation, while also reproducing the hand-over-hand motion. Overall, our study indicated that the notion of a downhill lever-up to lever-down process (popularly known as the powerstroke mechanism) is the result of the energetics of the complete myosin-V cycle and is not the source of directional motion or force generation on its own. The present work further emphasizes the need to use well-defined energy landscapes in studying molecular motors in general and myosin in particular. PMID:28193897

Significance of aerosol radiative effect in energy balance control on global precipitation change

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

Suzuki, Kentaroh; Stephens, Graeme L.; Golaz, Jean-Christophe

Historical changes of global precipitation in the 20th century simulated by a climate model are investigated. The results simulated with alternate configurations of cloud microphysics are analyzed in the context of energy balance controls on global precipitation, where the latent heat changes associated with the precipitation change is nearly balanced with changes to atmospheric radiative cooling. The atmospheric radiative cooling is dominated by its clear-sky component, which is found to correlate with changes to both column water vapor and aerosol optical depth (AOD). The water vapor-dependent component of the clear-sky radiative cooling is then found to scale with global temperaturemore » change through the Clausius–Clapeyron relationship. This component results in a tendency of global precipitation increase with increasing temperature at a rate of approximately 2%K -1. Another component of the clear-sky radiative cooling, which is well correlated with changes to AOD, is also found to vary in magnitude among different scenarios with alternate configurations of cloud microphysics that controls the precipitation efficiency, a major factor influencing the aerosol scavenging process that can lead to different aerosol loadings. These results propose how different characteristics of cloud microphysics can cause different aerosol loadings that in turn perturb global energy balance to significantly change global precipitation. This implies a possible coupling of aerosol–cloud interaction with aerosol–radiation interaction in the context of global energy balance.« less

Significance of aerosol radiative effect in energy balance control on global precipitation change

DOE PAGES

Suzuki, Kentaroh; Stephens, Graeme L.; Golaz, Jean-Christophe

2017-10-17

Historical changes of global precipitation in the 20th century simulated by a climate model are investigated. The results simulated with alternate configurations of cloud microphysics are analyzed in the context of energy balance controls on global precipitation, where the latent heat changes associated with the precipitation change is nearly balanced with changes to atmospheric radiative cooling. The atmospheric radiative cooling is dominated by its clear-sky component, which is found to correlate with changes to both column water vapor and aerosol optical depth (AOD). The water vapor-dependent component of the clear-sky radiative cooling is then found to scale with global temperaturemore » change through the Clausius–Clapeyron relationship. This component results in a tendency of global precipitation increase with increasing temperature at a rate of approximately 2%K -1. Another component of the clear-sky radiative cooling, which is well correlated with changes to AOD, is also found to vary in magnitude among different scenarios with alternate configurations of cloud microphysics that controls the precipitation efficiency, a major factor influencing the aerosol scavenging process that can lead to different aerosol loadings. These results propose how different characteristics of cloud microphysics can cause different aerosol loadings that in turn perturb global energy balance to significantly change global precipitation. This implies a possible coupling of aerosol–cloud interaction with aerosol–radiation interaction in the context of global energy balance.« less

Contrastive Analysis of Meteorological Element Effect Simulated by parameterization schemes Land Surface Process of Noah and CLM4 over the Yellow River Source Region

NASA Astrophysics Data System (ADS)

Zhang, Y.; Wen, X.

2017-12-01

The Yellow River source region is situated in the northeast Tibetan Plateau, which is considered as a global climate change hot-spot and one of the most sensitive areas in terms of response to global warming in view of its fragile ecosystem. This region plays an irreplaceable role for downstream water supply of The Yellow River because of its unique topography and variable climate. The water energy cycle processes of the Yellow River source Region from July to September in 2015 were simulated by using the WRF mesoscale numerical model. The two groups respectively used Noah and CLM4 parameterization schemes of land surface process. Based on the observation data of GLDAS data set, ground automatic weather station and Zoige plateau wetland ecosystem research station, the simulated values of near surface meteorological elements and surface energy parameters of two different schemes were compared. The results showed that the daily variations about meteorological factors in Zoige station in September were simulated quite well by the model. The correlation coefficient between the simulated temperature and humidity of the CLM scheme were 0.88 and 0.83, the RMSE were 1.94 ° and 9.97%, and the deviation Bias were 0.04 ° and 3.30%, which was closer to the observation data than the Noah scheme. The correlation coefficients of net radiation, surface heat flux, upward short wave and upward longwave radiation were respectively 0.86, 0.81, 0.84 and 0.88, which corresponded better than the observation data. The sensible heat flux and latent heat flux distribution of the Noah scheme corresponded quite well to GLDAS. the distribution and magnitude of 2m relative humidity and soil moisture were closer to surface observation data because the CLM scheme described the photosynthesis and evapotranspiration of land surface vegetation more rationally. The simulating abilities of precipitation and downward longwave radiation need to be improved. This study provides a theoretical basis for the numerical simulation of water energy cycle in the source region over the Yellow River basin.

Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.

PubMed

Wang, Qiantao; Edupuganti, Ramakrishna; Tavares, Clint D J; Dalby, Kevin N; Ren, Pengyu

2015-01-01

A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r (2) coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r (2) of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

Correlated Production and Analog Transport of Fission Neutrons and Photons using Fission Models FREYA, FIFRELIN and the Monte Carlo Code TRIPOLI-4® .

NASA Astrophysics Data System (ADS)

Verbeke, Jérôme M.; Petit, Odile; Chebboubi, Abdelhazize; Litaize, Olivier

2018-01-01

Fission modeling in general-purpose Monte Carlo transport codes often relies on average nuclear data provided by international evaluation libraries. As such, only average fission multiplicities are available and correlations between fission neutrons and photons are missing. Whereas uncorrelated fission physics is usually sufficient for standard reactor core and radiation shielding calculations, correlated fission secondaries are required for specialized nuclear instrumentation and detector modeling. For coincidence counting detector optimization for instance, precise simulation of fission neutrons and photons that remain correlated in time from birth to detection is essential. New developments were recently integrated into the Monte Carlo transport code TRIPOLI-4 to model fission physics more precisely, the purpose being to access event-by-event fission events from two different fission models: FREYA and FIFRELIN. TRIPOLI-4 simulations can now be performed, either by connecting via an API to the LLNL fission library including FREYA, or by reading external fission event data files produced by FIFRELIN beforehand. These new capabilities enable us to easily compare results from Monte Carlo transport calculations using the two fission models in a nuclear instrumentation application. In the first part of this paper, broad underlying principles of the two fission models are recalled. We then present experimental measurements of neutron angular correlations for 252Cf(sf) and 240Pu(sf). The correlations were measured for several neutron kinetic energy thresholds. In the latter part of the paper, simulation results are compared to experimental data. Spontaneous fissions in 252Cf and 240Pu are modeled by FREYA or FIFRELIN. Emitted neutrons and photons are subsequently transported to an array of scintillators by TRIPOLI-4 in analog mode to preserve their correlations. Angular correlations between fission neutrons obtained independently from these TRIPOLI-4 simulations, using either FREYA or FIFRELIN, are compared to experimental results. For 240Pu(sf), the measured correlations were used to tune the model parameters.

Use of refinery computer model to predict fuel production

NASA Technical Reports Server (NTRS)

Flores, F. J.

1979-01-01

Several factors (crudes, refinery operation and specifications) that affect yields and properties of broad specification jet fuel were parameterized using the refinery simulation model which can simulate different types of refineries were used to make the calculations. Results obtained from the program are used to correlate yield as a function of final boiling point, hydrogen content and freezing point for jet fuels produced in two refinery configurations, each one processing a different crude mix. Refinery performances are also compared in terms of energy consumption.

Scalable tuning of building models to hourly data

DOE PAGES

Garrett, Aaron; New, Joshua Ryan

2015-03-31

Energy models of existing buildings are unreliable unless calibrated so they correlate well with actual energy usage. Manual tuning requires a skilled professional, is prohibitively expensive for small projects, imperfect, non-repeatable, non-transferable, and not scalable to the dozens of sensor channels that smart meters, smart appliances, and cheap/ubiquitous sensors are beginning to make available today. A scalable, automated methodology is needed to quickly and intelligently calibrate building energy models to all available data, increase the usefulness of those models, and facilitate speed-and-scale penetration of simulation-based capabilities into the marketplace for actualized energy savings. The "Autotune'' project is a novel, model-agnosticmore » methodology which leverages supercomputing, large simulation ensembles, and big data mining with multiple machine learning algorithms to allow automatic calibration of simulations that match measured experimental data in a way that is deployable on commodity hardware. This paper shares several methodologies employed to reduce the combinatorial complexity to a computationally tractable search problem for hundreds of input parameters. Furthermore, accuracy metrics are provided which quantify model error to measured data for either monthly or hourly electrical usage from a highly-instrumented, emulated-occupancy research home.« less

Understanding the Effect of Grain Boundary Character on Dynamic Recrystallization in Stainless Steel 316L

NASA Astrophysics Data System (ADS)

Beck, Megan; Morse, Michael; Corolewski, Caleb; Fritchman, Koyuki; Stifter, Chris; Poole, Callum; Hurley, Michael; Frary, Megan

2017-08-01

Dynamic recrystallization (DRX) occurs during high-temperature deformation in metals and alloys with low to medium stacking fault energies. Previous simulations and experimental research have shown the effect of temperature and grain size on DRX behavior, but not the effect of the grain boundary character distribution. To investigate the effects of the distribution of grain boundary types, experimental testing was performed on stainless steel 316L specimens with different initial special boundary fractions (SBF). This work was completed in conjunction with computer simulations that used a modified Monte Carlo method which allowed for the addition of anisotropic grain boundary energies using orientation data from electron backscatter diffraction (EBSD). The correlation of the experimental and simulation work allows for a better understanding of how the input parameters in the simulations correspond to what occurs experimentally. Results from both simulations and experiments showed that a higher fraction of so-called "special" boundaries ( e.g., Σ3 twin boundaries) delayed the onset of recrystallization to larger strains and that it is energetically favorable for nuclei to form on triple junctions without these so-called "special" boundaries.

Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues

NASA Astrophysics Data System (ADS)

Fiorentini, Raffaele; Kremer, Kurt; Potestio, Raffaello; Fogarty, Aoife C.

2017-06-01

The calculation of free energy differences is a crucial step in the characterization and understanding of the physical properties of biological molecules. In the development of efficient methods to compute these quantities, a promising strategy is that of employing a dual-resolution representation of the solvent, specifically using an accurate model in the proximity of a molecule of interest and a simplified description elsewhere. One such concurrent multi-resolution simulation method is the Adaptive Resolution Scheme (AdResS), in which particles smoothly change their resolution on-the-fly as they move between different subregions. Before using this approach in the context of free energy calculations, however, it is necessary to make sure that the dual-resolution treatment of the solvent does not cause undesired effects on the computed quantities. Here, we show how AdResS can be used to calculate solvation free energies of small polar solutes using Thermodynamic Integration (TI). We discuss how the potential-energy-based TI approach combines with the force-based AdResS methodology, in which no global Hamiltonian is defined. The AdResS free energy values agree with those calculated from fully atomistic simulations to within a fraction of kBT. This is true even for small atomistic regions whose size is on the order of the correlation length, or when the properties of the coarse-grained region are extremely different from those of the atomistic region. These accurate free energy calculations are possible because AdResS allows the sampling of solvation shell configurations which are equivalent to those of fully atomistic simulations. The results of the present work thus demonstrate the viability of the use of adaptive resolution simulation methods to perform free energy calculations and pave the way for large-scale applications where a substantial computational gain can be attained.

Black hole feedback in a multiphase interstellar medium

NASA Astrophysics Data System (ADS)

Bourne, Martin A.; Nayakshin, Sergei; Hobbs, Alexander

2014-07-01

Ultrafast outflows (UFOs) from supermassive black holes (SMBHs) are thought to regulate the growth of SMBHs and host galaxies, resulting in a number of observational correlations. We present high-resolution numerical simulations of the impact of a thermalized UFO on the ambient gas in the inner part of the host galaxy. Our results depend strongly on whether the gas is homogeneous or clumpy. In the former case all of the ambient gas is driven outward rapidly as expected based on commonly used energy budget arguments, while in the latter the flows of mass and energy de-couple. Carrying most of the energy, the shocked UFO escapes from the bulge via paths of least resistance, taking with it only the low-density phase of the host. Most of the mass is however in the high-density phase, and is affected by the UFO much less strongly, and may even continue to flow inwards. We suggest that the UFO energy leakage through the pores in the multiphase interstellar medium (ISM) may explain why observed SMBHs are so massive despite their overwhelmingly large energy production rates. The multiphase ISM effects reported here are probably under-resolved in cosmological simulations but may be included in prescriptions for active galactic nuclei feedback in future simulations and in semi-analytical models.

Entropy, energy, and entanglement of localized states in bent triatomic molecules

NASA Astrophysics Data System (ADS)

Yuan, Qiang; Hou, Xi-Wen

2017-05-01

The dynamics of quantum entropy, energy, and entanglement is studied for various initial states in an important spectroscopic Hamiltonian of bent triatomic molecules H2O, D2O, and H2S. The total quantum correlation is quantified in terms of the mutual information and the entanglement by the concurrence borrowed from the theory of quantum information. The Pauli entropy and the intramolecular energy usually used in the theory of molecules are calculated to establish a possible relationship between both theories. Sections of two quantities among these four quantities are introduced to visualize such relationship. Analytic and numerical simulations demonstrate that if an initial state is taken to be the stretch- or the bend-vibrationally localized state, the mutual information, the Pauli entropy, and the concurrence are dominant-positively correlated while they are dominantly anti-correlated with the interacting energy among three anharmonic vibrational modes. In particular, such correlation is more distinct for the localized state with high excitations in the bending mode. The nice quasi-periodicity of those quantities in D2O molecule reveals that this molecule prepared in the localized state in the stretching or the bending mode can be more appreciated for molecular quantum computation. However, the dynamical correlations of those quantities behave irregularly for the dislocalized states. Moreover, the hierarchy of the mutual information and the Pauli entropy is explicitly proved. Quantum entropy and energy in every vibrational mode are investigated. Thereby, the relation between bipartite and tripartite entanglements is discussed as well. Those are useful for the understanding of quantum correlations in high-dimensional states in polyatomic molecules from quantum information and intramolecular dynamics.

An equation-of-state-meter of quantum chromodynamics transition from deep learning

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

Pang, Long-Gang; Zhou, Kai; Su, Nan

A primordial state of matter consisting of free quarks and gluons that existed in the early universe a few microseconds after the Big Bang is also expected to form in high-energy heavy-ion collisions. Determining the equation of state (EoS) of such a primordial matter is the ultimate goal of high-energy heavy-ion experiments. Here we use supervised learning with a deep convolutional neural network to identify the EoS employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering themore » nature of the phase transition in quantum chromodynamics. Finally, such EoS-meter is model-independent and insensitive to other simulation inputs including the initial conditions for hydrodynamic simulations.« less

An equation-of-state-meter of quantum chromodynamics transition from deep learning

DOE PAGES

Pang, Long-Gang; Zhou, Kai; Su, Nan; ...

2018-01-15

A primordial state of matter consisting of free quarks and gluons that existed in the early universe a few microseconds after the Big Bang is also expected to form in high-energy heavy-ion collisions. Determining the equation of state (EoS) of such a primordial matter is the ultimate goal of high-energy heavy-ion experiments. Here we use supervised learning with a deep convolutional neural network to identify the EoS employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering themore » nature of the phase transition in quantum chromodynamics. Finally, such EoS-meter is model-independent and insensitive to other simulation inputs including the initial conditions for hydrodynamic simulations.« less

Modeling the pressure-dilatation correlation

NASA Technical Reports Server (NTRS)

Sarkar, S.

1991-01-01

It is generally accepted that pressure dilatation, which is an additional compressibility term in turbulence transport equations, may be important for high speed flows. Recent direct simulations of homogeneous shear turbulence have given concrete evidence that the pressure dilatation is important insofar that it contributes to the reduced growth of turbulent kinetic energy due to compressibility effects. The problem of modeling pressure dilatation is addressed. A component of the pressure dilatation is isolated which exhibits temporal oscillations and, using direct numerical simulations of homogeneous shear turbulence and isotropic turbulence, show that it has a negligible contribution to the evolution of turbulent kinetic energy. Then, an analysis for the case of homogeneous turbulence is performed to obtain a model for the nonoscillatory pressure dilatation. This model algebraically relates the pressure dilatation to quantities traditionally obtained in incompressible turbulence closures. The model is validated by direct comparison with the pressure dilatation data obtained from the simulations.

A two-tiered correlation of dark matter with missing transverse energy: reconstructing the lightest supersymmetric particle mass at the LHC

NASA Astrophysics Data System (ADS)

Li, Tianjun; Maxin, James A.; Nanopoulos, Dimitri V.; Walker, Joel W.

2012-02-01

We suggest that non-trivial correlations between the dark matter particle mass and collider based probes of missing transverse energy H_{text{T}}^{text{miss}} may facilitate a two tiered approach to the initial discovery of supersymmetry and the subsequent reconstruction of the lightest supersymmetric particle (LSP) mass at the LHC. These correlations are demonstrated via extensive Monte Carlo simulation of seventeen benchmark models, each sampled at five distinct LHC center-of-mass beam energies, spanning the parameter space of No-Scale mathcal{F} -SU(5). This construction is defined in turn by the union of the mathcal{F} -lipped SU(5) Grand Unified Theory, two pairs of hypothetical TeV scale vector-like supersymmetric multiplets with origins in mathcal{F} -theory, and the dynamically established boundary conditions of No-Scale Supergravity. In addition, we consider a control sample comprised of a standard minimal Supergravity benchmark point. Led by a striking similarity between the H_{text{T}}^{text{miss}} distribution and the familiar power spectrum of a black body radiator at various temperatures, we implement a broad empirical fit of our simulation against a Poisson distribution ansätz. We advance the resulting fit as a theoretical blueprint for deducing the mass of the LSP, utilizing only the missing transverse energy in a statistical sampling of ≥ 9 jet events. Cumulative uncertainties central to the method subsist at a satisfactory 12-15% level. The fact that supersymmetric particle spectrum of No-Scale mathcal{F} -SU(5) has thrived the withering onslaught of early LHC data that is steadily decimating the Constrained Minimal Supersymmetric Standard Model and minimal Supergravity parameter spaces is a prime motivation for augmenting more conventional LSP search methodologies with the presently proposed alternative.

An investigation of the energy balance of solar active regions using the ACRIM irradiance data

NASA Technical Reports Server (NTRS)

Petro, L. D.

1986-01-01

The detection of a significant correlation between the solar irradiance, corrected for flux deficit due to sunspots, and both the 205 nm flux and a photometric facular index were examined. A detailed analysis supports facular emission as the more likely source of correlation with the corrected radiance, rather then the error in sunspot correction. A computer program which simulates two dimensional convection in a compressible, stratified medium was investigated. Subroutines to calculate ionization and other thermodynamic variables were also completed.

Kinetic theory-based numerical modeling and analysis of bi-disperse segregated mixture fluidized bed

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

Konan, N. A.; Huckaby, E. D.

We discuss a series of continuum Euler-Euler simulations of an initially mixed bi-disperse fluidized bed which segregates under certain operating conditions. The simulations use the multi-phase kinetic theory-based description of the momentum and energy exchanges between the phases by Simonin’s Group [see e.g. Gourdel, Simonin and Brunier (1999). Proceedings of 6th International Conference on Circulating Fluidized Beds, Germany, pp. 205-210]. The discussion and analysis of the results focus on the fluid-particle momentum exchange (i.e. drag). Simulations using mono- and poly-disperse fluid-particle drag correlations are analyzed for the Geldart D-type size bi-disperse gas-solid experiments performed by Goldschmidt et al. [Powder Tech.,more » pp. 135-159 (2003)]. The poly-disperse gas-particle drag correlations account for the local particle size distribution by using an effective mixture diameter when calculating the Reynolds number and then correcting the resulting force coefficient. Simulation results show very good predictions of the segregation index for bidisperse beds with the mono-disperse drag correlations contrary to the poly-disperse drag correlations for which the segregation rate is systematically under-predicted. The statistical analysis of the results shows a clear separation in the distribution of the gas-particle mean relaxation times of the small and large particles with simulations using the mono-disperse drag. In contrast, the poly-disperse drag simulations have a significant overlap and also a smaller difference in the mean particle relaxation times. This results in the small and large particles in the bed to respond to the gas similarly without enough relative time lag. The results suggest that the difference in the particle response time induce flow dynamics favorable to a force imbalance which results in the segregation.« less

Kinetic theory-based numerical modeling and analysis of bi-disperse segregated mixture fluidized bed

DOE PAGES

Konan, N. A.; Huckaby, E. D.

2017-06-21

We discuss a series of continuum Euler-Euler simulations of an initially mixed bi-disperse fluidized bed which segregates under certain operating conditions. The simulations use the multi-phase kinetic theory-based description of the momentum and energy exchanges between the phases by Simonin’s Group [see e.g. Gourdel, Simonin and Brunier (1999). Proceedings of 6th International Conference on Circulating Fluidized Beds, Germany, pp. 205-210]. The discussion and analysis of the results focus on the fluid-particle momentum exchange (i.e. drag). Simulations using mono- and poly-disperse fluid-particle drag correlations are analyzed for the Geldart D-type size bi-disperse gas-solid experiments performed by Goldschmidt et al. [Powder Tech.,more » pp. 135-159 (2003)]. The poly-disperse gas-particle drag correlations account for the local particle size distribution by using an effective mixture diameter when calculating the Reynolds number and then correcting the resulting force coefficient. Simulation results show very good predictions of the segregation index for bidisperse beds with the mono-disperse drag correlations contrary to the poly-disperse drag correlations for which the segregation rate is systematically under-predicted. The statistical analysis of the results shows a clear separation in the distribution of the gas-particle mean relaxation times of the small and large particles with simulations using the mono-disperse drag. In contrast, the poly-disperse drag simulations have a significant overlap and also a smaller difference in the mean particle relaxation times. This results in the small and large particles in the bed to respond to the gas similarly without enough relative time lag. The results suggest that the difference in the particle response time induce flow dynamics favorable to a force imbalance which results in the segregation.« less

Contributions of Kinetic Energy and Viscous Dissipation to Airway Resistance in Pulmonary Inspiratory and Expiratory Airflows in Successive Symmetric Airway Models With Various Bifurcation Angles.

PubMed

Choi, Sanghun; Choi, Jiwoong; Lin, Ching-Long

2018-01-01

The aim of this study was to investigate and quantify contributions of kinetic energy and viscous dissipation to airway resistance during inspiration and expiration at various flow rates in airway models of different bifurcation angles. We employed symmetric airway models up to the 20th generation with the following five different bifurcation angles at a tracheal flow rate of 20 L/min: 15 deg, 25 deg, 35 deg, 45 deg, and 55 deg. Thus, a total of ten computational fluid dynamics (CFD) simulations for both inspiration and expiration were conducted. Furthermore, we performed additional four simulations with tracheal flow rate values of 10 and 40 L/min for a bifurcation angle of 35 deg to study the effect of flow rate on inspiration and expiration. Using an energy balance equation, we quantified contributions of the pressure drop associated with kinetic energy and viscous dissipation. Kinetic energy was found to be a key variable that explained the differences in airway resistance on inspiration and expiration. The total pressure drop and airway resistance were larger during expiration than inspiration, whereas wall shear stress and viscous dissipation were larger during inspiration than expiration. The dimensional analysis demonstrated that the coefficients of kinetic energy and viscous dissipation were strongly correlated with generation number. In addition, the viscous dissipation coefficient was significantly correlated with bifurcation angle and tracheal flow rate. We performed multiple linear regressions to determine the coefficients of kinetic energy and viscous dissipation, which could be utilized to better estimate the pressure drop in broader ranges of successive bifurcation structures.

Validation of micro-mechanical FFT-based simulations using High Energy Diffraction Microscopy on Ti-7Al

DOE PAGES

Tari, Vahid; Lebensohn, Ricardo A.; Pokharel, Reeju; ...

2018-08-01

Here, a validation is reported for micromechanical simulation using a reimplementation of an elasto-viscoplastic FFT-based (EVPFFT) formulation, i.e., the Micromechanical Analysis of Stress-strain Inhomogeneities with fast Fourier transform (MASSIF) code, against experimental data obtained from synchrotron x-ray diffraction. The experimental data was collected during in-situ deformation of a titanium alloy specimen by High Energy Diffraction Microscopy (HEDM), which provided the average elastic strain tensor and orientation of each grain in a polycrystalline sample. MASSIF was used to calculate the local micromechanical fields in a Ti-7Al polycrystalline sample at different load levels. The initially attempted simulation showed that, although the effectivemore » response was calibrated to reproduce the experiment, MASSIF was not able to reproduce the micromechanical fields at the scale of individual grains. The differences between calculated and measured averages at the grain scale were related to initial residual strains resulting from the prior processing of the material, which had not been incorporated in the original calculation. Accordingly, a new simulation was instantiated using information on the measured residual strains to define a set of eigenstrains, calculated via an Eshelby approximation. This initialization significantly improved the correlation between calculated and simulated fields for all strain and stress components, for measurements performed within the elastic regime. For the measurements at the highest load, which was past plastic yield, the correlations deteriorated because of plastic deformation at the grain level and the lack of an accurate enough constitutive description in this deformation regime.« less

Validation of micro-mechanical FFT-based simulations using High Energy Diffraction Microscopy on Ti-7Al

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

Tari, Vahid; Lebensohn, Ricardo A.; Pokharel, Reeju

Here, a validation is reported for micromechanical simulation using a reimplementation of an elasto-viscoplastic FFT-based (EVPFFT) formulation, i.e., the Micromechanical Analysis of Stress-strain Inhomogeneities with fast Fourier transform (MASSIF) code, against experimental data obtained from synchrotron x-ray diffraction. The experimental data was collected during in-situ deformation of a titanium alloy specimen by High Energy Diffraction Microscopy (HEDM), which provided the average elastic strain tensor and orientation of each grain in a polycrystalline sample. MASSIF was used to calculate the local micromechanical fields in a Ti-7Al polycrystalline sample at different load levels. The initially attempted simulation showed that, although the effectivemore » response was calibrated to reproduce the experiment, MASSIF was not able to reproduce the micromechanical fields at the scale of individual grains. The differences between calculated and measured averages at the grain scale were related to initial residual strains resulting from the prior processing of the material, which had not been incorporated in the original calculation. Accordingly, a new simulation was instantiated using information on the measured residual strains to define a set of eigenstrains, calculated via an Eshelby approximation. This initialization significantly improved the correlation between calculated and simulated fields for all strain and stress components, for measurements performed within the elastic regime. For the measurements at the highest load, which was past plastic yield, the correlations deteriorated because of plastic deformation at the grain level and the lack of an accurate enough constitutive description in this deformation regime.« less

Solute rotational dynamics at the water liquid/vapor interface.

PubMed

Benjamin, Ilan

2007-11-28

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.

Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

2011-01-01

The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

Regional-specific Stochastic Simulation of Spatially-distributed Ground-motion Time Histories using Wavelet Packet Analysis

NASA Astrophysics Data System (ADS)

Huang, D.; Wang, G.

2014-12-01

Stochastic simulation of spatially distributed ground-motion time histories is important for performance-based earthquake design of geographically distributed systems. In this study, we develop a novel technique to stochastically simulate regionalized ground-motion time histories using wavelet packet analysis. First, a transient acceleration time history is characterized by wavelet-packet parameters proposed by Yamamoto and Baker (2013). The wavelet-packet parameters fully characterize ground-motion time histories in terms of energy content, time- frequency-domain characteristics and time-frequency nonstationarity. This study further investigates the spatial cross-correlations of wavelet-packet parameters based on geostatistical analysis of 1500 regionalized ground motion data from eight well-recorded earthquakes in California, Mexico, Japan and Taiwan. The linear model of coregionalization (LMC) is used to develop a permissible spatial cross-correlation model for each parameter group. The geostatistical analysis of ground-motion data from different regions reveals significant dependence of the LMC structure on regional site conditions, which can be characterized by the correlation range of Vs30 in each region. In general, the spatial correlation and cross-correlation of wavelet-packet parameters are stronger if the site condition is more homogeneous. Using the regional-specific spatial cross-correlation model and cokriging technique, wavelet packet parameters at unmeasured locations can be best estimated, and regionalized ground-motion time histories can be synthesized. Case studies and blind tests demonstrated that the simulated ground motions generally agree well with the actual recorded data, if the influence of regional-site conditions is considered. The developed method has great potential to be used in computational-based seismic analysis and loss estimation in a regional scale.

Development of a Gas Dynamic and Thermodynamic Simulation Model of the Lontra Blade Compressor™

NASA Astrophysics Data System (ADS)

Karlovsky, Jerome

2015-08-01

The Lontra Blade Compressor™ is a patented double acting, internally compressing, positive displacement rotary compressor of innovative design. The Blade Compressor is in production for waste-water treatment, and will soon be launched for a range of applications at higher pressure ratios. In order to aid the design and development process, a thermodynamic and gas dynamic simulation program has been written in house. The software has been successfully used to optimise geometries and running conditions of current designs, and is also being used to evaluate future designs for different applications and markets. The simulation code has three main elements. A positive displacement chamber model, a leakage model and a gas dynamic model to simulate gas flow through ports and to track pressure waves in the inlet and outlet pipes. All three of these models are interlinked in order to track mass and energy flows within the system. A correlation study has been carried out to verify the software. The main correlation markers used were mass flow, chamber pressure, pressure wave tracking in the outlet pipe, and volumetric efficiency. It will be shown that excellent correlation has been achieved between measured and simulated data. Mass flow predictions were to within 2% of measured data, and the timings and magnitudes of all major gas dynamic effects were well replicated. The simulation will be further developed in the near future to help with the optimisation of exhaust and inlet silencers.

In-plane crashworthiness of bio-inspired hierarchical honeycombs

DOE PAGES

Yin, Hanfeng; Huang, Xiaofei; Scarpa, Fabrizio; ...

2018-03-13

Biological tissues like bone, wood, and sponge possess hierarchical cellular topologies, which are lightweight and feature an excellent energy absorption capability. Here we present a system of bio-inspired hierarchical honeycomb structures based on hexagonal, Kagome, and triangular tessellations. The hierarchical designs and a reference regular honeycomb configuration are subjected to simulated in-plane impact using the nonlinear finite element code LS-DYNA. The numerical simulation results show that the triangular hierarchical honeycomb provides the best performance compared to the other two hierarchical honeycombs, and features more than twice the energy absorbed by the regular honeycomb under similar loading conditions. We also proposemore » a parametric study correlating the microstructure parameters (hierarchical length ratio r and the number of sub cells N) to the energy absorption capacity of these hierarchical honeycombs. The triangular hierarchical honeycomb with N = 2 and r = 1/8 shows the highest energy absorption capacity among all the investigated cases, and this configuration could be employed as a benchmark for the design of future safety protective systems.« less

In-plane crashworthiness of bio-inspired hierarchical honeycombs

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

Yin, Hanfeng; Huang, Xiaofei; Scarpa, Fabrizio

Biological tissues like bone, wood, and sponge possess hierarchical cellular topologies, which are lightweight and feature an excellent energy absorption capability. Here we present a system of bio-inspired hierarchical honeycomb structures based on hexagonal, Kagome, and triangular tessellations. The hierarchical designs and a reference regular honeycomb configuration are subjected to simulated in-plane impact using the nonlinear finite element code LS-DYNA. The numerical simulation results show that the triangular hierarchical honeycomb provides the best performance compared to the other two hierarchical honeycombs, and features more than twice the energy absorbed by the regular honeycomb under similar loading conditions. We also proposemore » a parametric study correlating the microstructure parameters (hierarchical length ratio r and the number of sub cells N) to the energy absorption capacity of these hierarchical honeycombs. The triangular hierarchical honeycomb with N = 2 and r = 1/8 shows the highest energy absorption capacity among all the investigated cases, and this configuration could be employed as a benchmark for the design of future safety protective systems.« less

Quantum Monte Carlo calculations of van der Waals interactions between aromatic benzene rings

NASA Astrophysics Data System (ADS)

Azadi, Sam; Kühne, T. D.

2018-05-01

The magnitude of finite-size effects and Coulomb interactions in quantum Monte Carlo simulations of van der Waals interactions between weakly bonded benzene molecules are investigated. To that extent, two trial wave functions of the Slater-Jastrow and Backflow-Slater-Jastrow types are employed to calculate the energy-volume equation of state. We assess the impact of the backflow coordinate transformation on the nonlocal correlation energy. We found that the effect of finite-size errors in quantum Monte Carlo calculations on energy differences is particularly large and may even be more important than the employed trial wave function. In addition to the cohesive energy, the singlet excitonic energy gap and the energy gap renormalization of crystalline benzene at different densities are computed.

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores

PubMed Central

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; Valdez, James A.; Smith, Roger; Wang, Yongqiang; Sickafus, Kurt E.

2015-01-01

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinel that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. These results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives. PMID:26510750

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores

DOE PAGES

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; ...

2015-10-29

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinelmore » that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. Furthermore, these results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives.« less

Microsecond protein dynamics observed at the single-molecule level

NASA Astrophysics Data System (ADS)

Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

2015-07-01

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

Microsecond protein dynamics observed at the single-molecule level

PubMed Central

Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

2015-01-01

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

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores.

PubMed

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; Valdez, James A; Smith, Roger; Wang, Yongqiang; Sickafus, Kurt E

2015-10-29

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinel that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. These results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives.

Fundus oculi pigmentation studies simulating the fs-LASIK process Fundus oculi pigmentation studies simulating the fs-LASIK process

NASA Astrophysics Data System (ADS)

Sander, M.; Minet, O.; Zabarylo, U.; Müller, M.; Tetz, M. R.

2012-06-01

The femtosecond-laser in situ keratomileusis (fs-LASIK) technique has successfully entered the refractive surgery market to correct ametropia by cutting transparent corneal tissue with ultra-short laser pulses based on photodisruption. The laser pulses in the near infrared range (NIR) generate a laser-induced breakdown (LIOB) in the cornea. By propagating through the eye, a certain amount of the pulse is deposited in the cornea and the remaining energy interacts with the strong absorbing tissue behind. Due to the absorption by the retinal pigment epithelium and the transfer of the thermal energy to surrounding tissue, the transmitted energy can induce damage to the retina. The aim of this project was to find out the threshold influences concerning the tissue and the correlation between the results of the macroscopical appraisal and the fundus oculi pigmentation by simulating the fs-LASIK procedure with two various laser systems in the continuous wave (CW) and fs-regime. Therefore ex-vivo determinations were carried out macroscopically and histopathologically on porcine tissue.

Equilibrium and Dynamics Properties of Poly(oxyethylene) Melts and Related Poly(alkylethers) from Simulations and Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

1994-01-01

Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.

A generalized correlation of experimental flat-plate collector performance. [solar collectors, performance tests, energy policy

NASA Technical Reports Server (NTRS)

Simon, F. F.; Miller, D. R.

1975-01-01

A generalized collector performance correlation was derived and shown by experimental verification to be of the proper form to account for the majority of the variable conditions encountered both in outdoor and in indoor collector tests. This correlation permits a determination of collector parameters which are essentially nonvarying under conditions which do vary randomly (outdoors) or conditions which vary in a controlled manner (indoors - simulator). It was shown that correlation of the experimental performance of collectors allows the following: (1) comparisons of different collector designs; (2) collector performance prediction under conditions that differ from the conditions of the test program; and (3) monitoring performance degradation effects.

Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures.

PubMed

Mak, Chi H

2015-11-25

While single-stranded (ss) segments of DNAs and RNAs are ubiquitous in biology, details about their structures have only recently begun to emerge. To study ssDNA and RNAs, we have developed a new Monte Carlo (MC) simulation using a free energy model for nucleic acids that has the atomisitic accuracy to capture fine molecular details of the sugar-phosphate backbone. Formulated on the basis of a first-principle calculation of the conformational entropy of the nucleic acid chain, this free energy model correctly reproduced both the long and short length-scale structural properties of ssDNA and RNAs in a rigorous comparison against recent data from fluorescence resonance energy transfer, small-angle X-ray scattering, force spectroscopy and fluorescence correlation transport measurements on sequences up to ∼100 nucleotides long. With this new MC algorithm, we conducted a comprehensive investigation of the entropy landscape of small RNA stem-loop structures. From a simulated ensemble of ∼10(6) equilibrium conformations, the entropy for the initiation of different size RNA hairpin loops was computed and compared against thermodynamic measurements. Starting from seeded hairpin loops, constrained MC simulations were then used to estimate the entropic costs associated with propagation of the stem. The numerical results provide new direct molecular insights into thermodynaimc measurement from macroscopic calorimetry and melting experiments.

aCORN Beta Spectrometer and Electrostatic Mirror

NASA Astrophysics Data System (ADS)

Hassan, Md; aCORN Collaboration

2013-10-01

aCORN uses a high efficiency backscatter suppressed beta spectrometer to measure the electron-antineutrino correlation in neutron beta decay. We measure the correlation by counting protons and beta electrons in coincidence with precisely determined electron energy. There are 19 photomultiplier tubes arranged in a hexagonal array coupled to a single phosphor doped polystyrene scintillator. The magnetic field is shaped so that electrons that backscatter without depositing their full energy strike a tulip-shaped array of scintillator paddles and these events are vetoed. The detailed construction, performance and calibration of this beta spectrometer will be presented. I will also present the simulation, construction, and features of our novel electrostatic mirror. This work was supported by the National Science Foundation and the NIST Center for Neutron Research.

Analysis of digital communication signals and extraction of parameters

NASA Astrophysics Data System (ADS)

Al-Jowder, Anwar

1994-12-01

The signal classification performance of four types of electronics support measure (ESM) communications detection systems is compared from the standpoint of the unintended receiver (interceptor). Typical digital communication signals considered include binary phase shift keying (BPSK), quadrature phase shift keying (QPSK), frequency shift keying (FSK), and on-off keying (OOK). The analysis emphasizes the use of available signal processing software. Detection methods compared include broadband energy detection, FFT-based narrowband energy detection, and two correlation methods which employ the fast Fourier transform (FFT). The correlation methods utilize modified time-frequency distributions, where one of these is based on the Wigner-Ville distribution (WVD). Gaussian white noise is added to the signal to simulate various signal-to-noise ratios (SNR's).

Micromagnetism in a planar system with a random magnetic anisotropy and two-dimensional magnetic correlations

NASA Astrophysics Data System (ADS)

Komogortsev, S. V.; Fel'k, V. A.; Iskhakov, R. S.; Shadrina, G. V.

2017-08-01

The hysteresis loops and the micromagnetic structure of a ferromagnetic nanolayer with a randomly oriented local easy magnetization axis and two-dimensional magnetization correlations are studied using a micromagnetic simulation. The properties and the micromagnetic structure of the nanolayer are determined by the competition between the anisotropy and exchange energies and by the dipole-dipole interaction energy. The magnetic microstructure can be described as an ensemble of stochastic magnetic domains and topological magnetization defects. Dipole-dipole interaction suppresses the formation of topological magnetization defects. The topological defects in the magnetic microstructure can cause a sharper change in the coercive force with the crystallite size than that predicted by the random magnetic anisotropy model.

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

Jassal, Anjali Rao; Vadawale, Santosh V.; Mithun, N. P. S.

Low-frequency quasi-periodic oscillations (QPOs) are commonly observed during the hard states of black hole binaries. Several studies have established various observational/empirical correlations between spectral parameters and QPO properties, indicating a close link between the two. However, the exact mechanism of generation of QPOs is not yet well understood. In this paper, we present our attempts to comprehend the connection between the spectral components and the low-frequency QPO (LFQPO) observed in GRS 1915+105 using the data from NuSTAR. Detailed spectral modeling as well as the presence of the LFQPO and its energy dependence during this observation have been reported by Millermore » et al. and Zhang et al., respectively. We investigate the compatibility of the spectral model and the energy dependence of the QPO by simulating light curves in various energy bands for small variation of the spectral parameters. The basic concept here is to establish the connection, if any, between the QPO and the variation of either a spectral component or a specific parameter, which in turn can shed some light on the origin of the QPO. We begin with the best-fit spectral model of Miller et al. and simulate the light curve by varying the spectral parameters at frequencies close to the observed QPO frequency in order to generate the simulated QPO. Furthermore we simulate similar light curves in various energy bands in order to reproduce the observed energy dependence of the rms amplitude of the QPO. We find that the observed trend of increasing rms amplitude with energy can be reproduced qualitatively if the spectral index is assumed to be varying with the phases of the QPO. Variation of any other spectral parameter does not reproduce the observed energy dependence.« less

Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models?

PubMed Central

Baker, Nathan A.; McCammon, J. Andrew

2008-01-01

The solvent reaction field potential of an uncharged protein immersed in Simple Point Charge/Extended (SPC/E) explicit solvent was computed over a series of molecular dynamics trajectories, intotal 1560 ns of simulation time. A finite, positive potential of 13 to 24 kbTec−1 (where T = 300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 Å from the solute surface, on average 0.008 ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit-solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99. PMID:17949217

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

NASA Astrophysics Data System (ADS)

Cerutti, David S.; Baker, Nathan A.; McCammon, J. Andrew

2007-10-01

The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560ns of simulation time. A finite, positive potential of 13-24 kbTec-1 (where T =300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0Å from the solute surface, on average 0.008ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.

Phase change thermal storage for a solar total energy system

NASA Technical Reports Server (NTRS)

Rice, R. E.; Cohen, B. M.

1978-01-01

An analytical and experimental program is being conducted on a one-tenth scale model of a high-temperature (584 K) phase-change thermal energy storage system for installation in a solar total energy test facility at Albuquerque, New Mexico, U.S.A. The thermal storage medium is anhydrous sodium hydroxide with 8% sodium nitrate. The program will produce data on the dynamic response of the system to repeated cycles of charging and discharging simulating those of the test facility. Data will be correlated with a mathematical model which will then be used in the design of the full-scale system.

Standardized performance tests of collectors of solar thermal energy: A selectively coated, steel collector with one transparent cover

NASA Technical Reports Server (NTRS)

1976-01-01

Basic test results are presented of a flat-plate solar collector whose performance was determined in solar simulator. The collector was tested over ranges of inlet temperatures, fluxes and coolant flow rates. Collector efficiency was correlated in terms of inlet temperature and flux level.

Experimental and Theoretical Study of Molecular Response of Amine Bases in Organic Solvents

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

Kathmann, Shawn M.; Cho, Herman M.; Chang, Tsun-Mei

2014-05-08

Reorientational correlation times of various amine bases (viz., pyridine, 2,6-lutidene, 2,2,6,6-tetramethylpiperidine) and organic solvents (dichloromethane, toluene) were determined by solution-state NMR relaxation time measurements and compared with predictions from molecular dynamics (MD) simulations. The bases and solvents are reagents in complex reactions involving Frustrated Lewis Pairs (FLP), which display remarkable catalytic activity in metal-free H2 scission. The comparison of measured and simulated correlation times is a key test of the ability of recent MD and quantum electronic structure calculations to elucidate the mechanism of FLP activity. Correla- tion times were found to be in the range 1.4-3.4 ps (NMR) andmore » 1.23-5.28 ps (MD) for the amines, and 0.9-2.3 ps (NMR) and 0.2-1.7 ps (MD) for the solvent molecules. This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacic Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

Weak lensing magnification in the Dark Energy Survey Science Verification data

NASA Astrophysics Data System (ADS)

Garcia-Fernandez, M.; Sanchez, E.; Sevilla-Noarbe, I.; Suchyta, E.; Huff, E. M.; Gaztanaga, E.; Aleksić, J.; Ponce, R.; Castander, F. J.; Hoyle, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bernstein, G. M.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Eifler, T. F.; Evrard, A. E.; Fernandez, E.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Giannantonio, T.; Gruen, D.; Gruendl, R. A.; Gschwend, J.; Gutierrez, G.; James, D. J.; Jarvis, M.; Kirk, D.; Krause, E.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Lima, M.; MacCrann, N.; Maia, M. A. G.; March, M.; Marshall, J. L.; Melchior, P.; Miquel, R.; Mohr, J. J.; Plazas, A. A.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Scarpine, V.; Schubnell, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Tarle, G.; Thomas, D.; Walker, A. R.; Wester, W.; DES Collaboration

2018-05-01

In this paper, the effect of weak lensing magnification on galaxy number counts is studied by cross-correlating the positions of two galaxy samples, separated by redshift, using the Dark Energy Survey Science Verification data set. This analysis is carried out for galaxies that are selected only by its photometric redshift. An extensive analysis of the systematic effects, using new methods based on simulations is performed, including a Monte Carlo sampling of the selection function of the survey.

MCNP HPGe detector benchmark with previously validated Cyltran model.

PubMed

Hau, I D; Russ, W R; Bronson, F

2009-05-01

An exact copy of the detector model generated for Cyltran was reproduced as an MCNP input file and the detection efficiency was calculated similarly with the methodology used in previous experimental measurements and simulation of a 280 cm(3) HPGe detector. Below 1000 keV the MCNP data correlated to the Cyltran results within 0.5% while above this energy the difference between MCNP and Cyltran increased to about 6% at 4800 keV, depending on the electron cut-off energy.

Budget of Turbulent Kinetic Energy in a Shock Wave Boundary-Layer Interaction

NASA Technical Reports Server (NTRS)

Vyas, Manan; Waindim, Mbu; Gaitonde, Datta

2016-01-01

Implicit large-eddy simulation (ILES) of a shock wave boundary-layer interaction (SBLI) was performed. Quantities present in the exact equation of the turbulent kinetic energy (TKE) transport were accumulated. These quantities will be used to calculate the components of TKE-like production, dissipation, transport, and dilatation. Correlations of these terms will be presented to study the growth and interaction between various terms. A comparison with its RANS (Reynolds-Averaged Navier-Stokes) counterpart will also be presented.

Energy Dissipation and Phase-Space Dynamics in Eulerian Vlasov-Maxwell Turbulence

NASA Astrophysics Data System (ADS)

Tenbarge, Jason; Juno, James; Hakim, Ammar

2017-10-01

Turbulence in a magnetized plasma is a primary mechanism responsible for transforming energy at large injection scales into small-scale motions, which are ultimately dissipated as heat in systems such as the solar corona, wind, and other astrophysical objects. At large scales, the turbulence is well described by fluid models of the plasma; however, understanding the processes responsible for heating a weakly collisional plasma such as the solar wind requires a kinetic description. We present a fully kinetic Eulerian Vlasov-Maxwell study of turbulence using the Gkeyll simulation framework, including studies of the cascade of energy in phase space and formation and dissipation of coherent structures. We also leverage the recently developed field-particle correlations to diagnose the dominant sources of dissipation and compare the results of the field-particle correlation to other dissipation measures. NSF SHINE AGS-1622306 and DOE DE-AC02-09CH11466.

Dynamics of a molecular glass former: Energy landscapes for diffusion in ortho-terphenyl

NASA Astrophysics Data System (ADS)

Niblett, S. P.; de Souza, V. K.; Stevenson, J. D.; Wales, D. J.

2016-07-01

Relaxation times and transport processes of many glass-forming supercooled liquids exhibit a super-Arrhenius temperature dependence. We examine this phenomenon by computer simulation of the Lewis-Wahnström model for ortho-terphenyl. We propose a microscopic definition for a single-molecule cage-breaking transition and show that, when correlation behaviour is taken into account, these rearrangements are sufficient to reproduce the correct translational diffusion constants over an intermediate temperature range in the supercooled regime. We show that super-Arrhenius behaviour can be attributed to increasing negative correlation in particle movement at lower temperatures and relate this to the cage-breaking description. Finally, we sample the potential energy landscape of the model and show that it displays hierarchical ordering. Substructures in the landscape, which may correspond to metabasins, have boundaries defined by cage-breaking transitions. The cage-breaking formulation provides a direct link between the potential energy landscape and macroscopic diffusion behaviour.

Ab initio molecular dynamics simulations of low energy recoil events in MgO

NASA Astrophysics Data System (ADS)

Petersen, B. A.; Liu, B.; Weber, W. J.; Zhang, Y.

2017-04-01

Low-energy recoil events in MgO are studied using ab intio molecular dynamics simulations to reveal the dynamic displacement processes and final defect configurations. Threshold displacement energies, Ed, are obtained for Mg and O along three low-index crystallographic directions, [100], [110], and [111]. The minimum values for Ed are found along the [110] direction consisting of the same element, either Mg or O atoms. Minimum threshold values of 29.5 eV for Mg and 25.5 eV for O, respectively, are suggested from the calculations. For other directions, the threshold energies are considerably higher, 65.5 and 150.0 eV for O along [111] and [100], and 122.5 eV for Mg along both [111] and [100] directions, respectively. These results show that the recoil events in MgO are partial-charge transfer assisted processes where the charge transfer plays an important role. There is a similar trend found in other oxide materials, where the threshold displacement energy correlates linearly with the peak partial-charge transfer, suggesting this behavior might be universal in ceramic oxides.

Energy transfer, pressure tensor, and heating of kinetic plasma

NASA Astrophysics Data System (ADS)

Yang, Yan; Matthaeus, William H.; Parashar, Tulasi N.; Haggerty, Colby C.; Roytershteyn, Vadim; Daughton, William; Wan, Minping; Shi, Yipeng; Chen, Shiyi

2017-07-01

Kinetic plasma turbulence cascade spans multiple scales ranging from macroscopic fluid flow to sub-electron scales. Mechanisms that dissipate large scale energy, terminate the inertial range cascade, and convert kinetic energy into heat are hotly debated. Here, we revisit these puzzles using fully kinetic simulation. By performing scale-dependent spatial filtering on the Vlasov equation, we extract information at prescribed scales and introduce several energy transfer functions. This approach allows highly inhomogeneous energy cascade to be quantified as it proceeds down to kinetic scales. The pressure work, - ( P . ∇ ) . u , can trigger a channel of the energy conversion between fluid flow and random motions, which contains a collision-free generalization of the viscous dissipation in collisional fluid. Both the energy transfer and the pressure work are strongly correlated with velocity gradients.

Correlated prompt fission data in transport simulations

DOE PAGES

Talou, P.; Vogt, R.; Randrup, J.; ...

2018-01-24

Detailed information on the fission process can be inferred from the observation, modeling and theoretical understanding of prompt fission neutron and γ-ray observables. Beyond simple average quantities, the study of distributions and correlations in prompt data, e.g., multiplicity-dependent neutron and γ-ray spectra, angular distributions of the emitted particles, n -n, n - γ, and γ - γ correlations, can place stringent constraints on fission models and parameters that would otherwise be free to be tuned separately to represent individual fission observables. The FREYA and CGMF codes have been developed to follow the sequential emissions of prompt neutrons and γ raysmore » from the initial excited fission fragments produced right after scission. Both codes implement Monte Carlo techniques to sample initial fission fragment configurations in mass, charge and kinetic energy and sample probabilities of neutron and γ emission at each stage of the decay. This approach naturally leads to using simple but powerful statistical techniques to infer distributions and correlations among many observables and model parameters. The comparison of model calculations with experimental data provides a rich arena for testing various nuclear physics models such as those related to the nuclear structure and level densities of neutron-rich nuclei, the γ-ray strength functions of dipole and quadrupole transitions, the mechanism for dividing the excitation energy between the two nascent fragments near scission, and the mechanisms behind the production of angular momentum in the fragments, etc. Beyond the obvious interest from a fundamental physics point of view, such studies are also important for addressing data needs in various nuclear applications. The inclusion of the FREYA and CGMF codes into the MCNP6.2 and MCNPX - PoliMi transport codes, for instance, provides a new and powerful tool to simulate correlated fission events in neutron transport calculations important in nonproliferation, safeguards, nuclear energy, and defense programs. Here, this review provides an overview of the topic, starting from theoretical considerations of the fission process, with a focus on correlated signatures. It then explores the status of experimental correlated fission data and current efforts to address some of the known shortcomings. Numerical simulations employing the FREYA and CGMF codes are compared to experimental data for a wide range of correlated fission quantities. The inclusion of those codes into the MCNP6.2 and MCNPX - PoliMi transport codes is described and discussed in the context of relevant applications. The accuracy of the model predictions and their sensitivity to model assumptions and input parameters are discussed. Lastly, a series of important experimental and theoretical questions that remain unanswered are presented, suggesting a renewed effort to address these shortcomings.« less

Correlated prompt fission data in transport simulations

NASA Astrophysics Data System (ADS)

Talou, P.; Vogt, R.; Randrup, J.; Rising, M. E.; Pozzi, S. A.; Verbeke, J.; Andrews, M. T.; Clarke, S. D.; Jaffke, P.; Jandel, M.; Kawano, T.; Marcath, M. J.; Meierbachtol, K.; Nakae, L.; Rusev, G.; Sood, A.; Stetcu, I.; Walker, C.

2018-01-01

Detailed information on the fission process can be inferred from the observation, modeling and theoretical understanding of prompt fission neutron and γ-ray observables. Beyond simple average quantities, the study of distributions and correlations in prompt data, e.g., multiplicity-dependent neutron and γ-ray spectra, angular distributions of the emitted particles, n - n, n - γ, and γ - γ correlations, can place stringent constraints on fission models and parameters that would otherwise be free to be tuned separately to represent individual fission observables. The FREYA and CGMF codes have been developed to follow the sequential emissions of prompt neutrons and γ rays from the initial excited fission fragments produced right after scission. Both codes implement Monte Carlo techniques to sample initial fission fragment configurations in mass, charge and kinetic energy and sample probabilities of neutron and γ emission at each stage of the decay. This approach naturally leads to using simple but powerful statistical techniques to infer distributions and correlations among many observables and model parameters. The comparison of model calculations with experimental data provides a rich arena for testing various nuclear physics models such as those related to the nuclear structure and level densities of neutron-rich nuclei, the γ-ray strength functions of dipole and quadrupole transitions, the mechanism for dividing the excitation energy between the two nascent fragments near scission, and the mechanisms behind the production of angular momentum in the fragments, etc. Beyond the obvious interest from a fundamental physics point of view, such studies are also important for addressing data needs in various nuclear applications. The inclusion of the FREYA and CGMF codes into the MCNP6.2 and MCNPX - PoliMi transport codes, for instance, provides a new and powerful tool to simulate correlated fission events in neutron transport calculations important in nonproliferation, safeguards, nuclear energy, and defense programs. This review provides an overview of the topic, starting from theoretical considerations of the fission process, with a focus on correlated signatures. It then explores the status of experimental correlated fission data and current efforts to address some of the known shortcomings. Numerical simulations employing the FREYA and CGMF codes are compared to experimental data for a wide range of correlated fission quantities. The inclusion of those codes into the MCNP6.2 and MCNPX - PoliMi transport codes is described and discussed in the context of relevant applications. The accuracy of the model predictions and their sensitivity to model assumptions and input parameters are discussed. Finally, a series of important experimental and theoretical questions that remain unanswered are presented, suggesting a renewed effort to address these shortcomings.

Correlated prompt fission data in transport simulations

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

Talou, P.; Vogt, R.; Randrup, J.

Detailed information on the fission process can be inferred from the observation, modeling and theoretical understanding of prompt fission neutron and γ-ray observables. Beyond simple average quantities, the study of distributions and correlations in prompt data, e.g., multiplicity-dependent neutron and γ-ray spectra, angular distributions of the emitted particles, n -n, n - γ, and γ - γ correlations, can place stringent constraints on fission models and parameters that would otherwise be free to be tuned separately to represent individual fission observables. The FREYA and CGMF codes have been developed to follow the sequential emissions of prompt neutrons and γ raysmore » from the initial excited fission fragments produced right after scission. Both codes implement Monte Carlo techniques to sample initial fission fragment configurations in mass, charge and kinetic energy and sample probabilities of neutron and γ emission at each stage of the decay. This approach naturally leads to using simple but powerful statistical techniques to infer distributions and correlations among many observables and model parameters. The comparison of model calculations with experimental data provides a rich arena for testing various nuclear physics models such as those related to the nuclear structure and level densities of neutron-rich nuclei, the γ-ray strength functions of dipole and quadrupole transitions, the mechanism for dividing the excitation energy between the two nascent fragments near scission, and the mechanisms behind the production of angular momentum in the fragments, etc. Beyond the obvious interest from a fundamental physics point of view, such studies are also important for addressing data needs in various nuclear applications. The inclusion of the FREYA and CGMF codes into the MCNP6.2 and MCNPX - PoliMi transport codes, for instance, provides a new and powerful tool to simulate correlated fission events in neutron transport calculations important in nonproliferation, safeguards, nuclear energy, and defense programs. Here, this review provides an overview of the topic, starting from theoretical considerations of the fission process, with a focus on correlated signatures. It then explores the status of experimental correlated fission data and current efforts to address some of the known shortcomings. Numerical simulations employing the FREYA and CGMF codes are compared to experimental data for a wide range of correlated fission quantities. The inclusion of those codes into the MCNP6.2 and MCNPX - PoliMi transport codes is described and discussed in the context of relevant applications. The accuracy of the model predictions and their sensitivity to model assumptions and input parameters are discussed. Lastly, a series of important experimental and theoretical questions that remain unanswered are presented, suggesting a renewed effort to address these shortcomings.« less

A density functional theory study of the correlation between analyte basicity, ZnPc adsorption strength, and sensor response.

PubMed

Tran, N L; Bohrer, F I; Trogler, W C; Kummel, A C

2009-05-28

Density functional theory (DFT) simulations were used to determine the binding strength of 12 electron-donating analytes to the zinc metal center of a zinc phthalocyanine molecule (ZnPc monomer). The analyte binding strengths were compared to the analytes' enthalpies of complex formation with boron trifluoride (BF(3)), which is a direct measure of their electron donating ability or Lewis basicity. With the exception of the most basic analyte investigated, the ZnPc binding energies were found to correlate linearly with analyte basicities. Based on natural population analysis calculations, analyte complexation to the Zn metal of the ZnPc monomer resulted in limited charge transfer from the analyte to the ZnPc molecule, which increased with analyte-ZnPc binding energy. The experimental analyte sensitivities from chemiresistor ZnPc sensor data were proportional to an exponential of the binding energies from DFT calculations consistent with sensitivity being proportional to analyte coverage and binding strength. The good correlation observed suggests DFT is a reliable method for the prediction of chemiresistor metallophthalocyanine binding strengths and response sensitivities.

Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.

PubMed Central

Soares, C M; Martel, P J; Mendes, J; Carrondo, M A

1998-01-01

The tetraheme cytochrome c3 from Desulfovibrio vulgaris Hildenborough is studied using molecular dynamics simulation studies in explicit solvent. The high heme content of the protein, which has its core almost entirely made up of c-type heme, presents specific problems in the simulation. Instability in the structure is observed in long simulations above 1 ns, something that does not occur in a monoheme cytochrome, suggesting problems in heme parametrization. Given these stability problems, a partially restrained model, which avoids destruction of the structure, was created with the objective of performing free energy calculations of heme reduction, studies that require long simulations. With this model, the free energy of reduction of each individual heme was calculated. A correction in the long-range electrostatic interactions of charge groups belonging to the redox centers had to be made in order to make the system physically meaningful. Correlation is obtained between the calculated free energies and the experimental data for three of four hemes. However, the relative scale of the calculated energies is different from the scale of the experimental free energies. Reasons for this are discussed. In addition to the free energy calculations, this model allows the study of conformational changes upon reduction. Even if the precise details of the structural changes that take place in this system upon individual heme reduction are probably out of the reach of this study, it appears that these structural changes are small, similarly to what is observed for other redox proteins. This does not mean that their effect is minor, and one example is the conformational change observed in propionate D from heme I when heme II becomes reduced. A motion of this kind could be the basis of the experimentally observed cooperativity effects between heme reduction, namely positive cooperativity. PMID:9545034

The Sensitivity of WRF Daily Summertime Simulations over West Africa to Alternative Parameterizations. Part 1: African Wave Circulation

NASA Technical Reports Server (NTRS)

Noble, Erik; Druyan, Leonard M.; Fulakeza, Matthew

2014-01-01

The performance of the NCAR Weather Research and Forecasting Model (WRF) as a West African regional-atmospheric model is evaluated. The study tests the sensitivity of WRF-simulated vorticity maxima associated with African easterly waves to 64 combinations of alternative parameterizations in a series of simulations in September. In all, 104 simulations of 12-day duration during 11 consecutive years are examined. The 64 combinations combine WRF parameterizations of cumulus convection, radiation transfer, surface hydrology, and PBL physics. Simulated daily and mean circulation results are validated against NASA's Modern-Era Retrospective Analysis for Research and Applications (MERRA) and NCEP/Department of Energy Global Reanalysis 2. Precipitation is considered in a second part of this two-part paper. A wide range of 700-hPa vorticity validation scores demonstrates the influence of alternative parameterizations. The best WRF performers achieve correlations against reanalysis of 0.40-0.60 and realistic amplitudes of spatiotemporal variability for the 2006 focus year while a parallel-benchmark simulation by the NASA Regional Model-3 (RM3) achieves higher correlations, but less realistic spatiotemporal variability. The largest favorable impact on WRF-vorticity validation is achieved by selecting the Grell-Devenyi cumulus convection scheme, resulting in higher correlations against reanalysis than simulations using the Kain-Fritch convection. Other parameterizations have less-obvious impact, although WRF configurations incorporating one surface model and PBL scheme consistently performed poorly. A comparison of reanalysis circulation against two NASA radiosonde stations confirms that both reanalyses represent observations well enough to validate the WRF results. Validation statistics for optimized WRF configurations simulating the parallel period during 10 additional years are less favorable than for 2006.

Dynamical downscaling of wind fields for wind power applications

NASA Astrophysics Data System (ADS)

Mengelkamp, H.-T.; Huneke, S.; Geyer, J.

2010-09-01

Dynamical downscaling of wind fields for wind power applications H.-T. Mengelkamp*,**, S. Huneke**, J, Geyer** *GKSS Research Center Geesthacht GmbH **anemos Gesellschaft für Umweltmeteorologie mbH Investments in wind power require information on the long-term mean wind potential and its temporal variations on daily to annual and decadal time scales. This information is rarely available at specific wind farm sites. Short-term on-site measurements usually are only performed over a 12 months period. These data have to be set into the long-term perspective through correlation to long-term consistent wind data sets. Preliminary wind information is often asked for to select favourable wind sites over regional and country wide scales. Lack of high-quality wind measurements at weather stations was the motivation to start high resolution wind field simulations The simulations are basically a refinement of global scale reanalysis data by means of high resolution simulations with an atmospheric mesoscale model using high-resolution terrain and land-use data. The 3-dimensional representation of the atmospheric state available every six hours at 2.5 degree resolution over the globe, known as NCAR/NCEP reanalysis data, forms the boundary conditions for continuous simulations with the non-hydrostatic atmospheric mesoscale model MM5. MM5 is nested in itself down to a horizontal resolution of 5 x 5 km². The simulation is performed for different European countries and covers the period 2000 to present and is continuously updated. Model variables are stored every 10 minutes for various heights. We have analysed the wind field primarily. The wind data set is consistent in space and time and provides information on the regional distribution of the long-term mean wind potential, the temporal variability of the wind potential, the vertical variation of the wind potential, and the temperature, and pressure distribution (air density). In the context of wind power these data are used • as an initial estimate of wind and energy potential • for the long-term correlation of wind measurements and turbine production data • to provide wind potential maps on a regional to country wide scale • to provide input data sets for simulation models • to determine the spatial correlation of the wind field in portfolio calculations • to calculate the wind turbine energy loss during prescribed downtimes • to provide information on the temporal variations of the wind and wind turbine energy production The time series of wind speed and wind direction are compared to measurements at offshore and onshore locations.

Direct Numerical Simulations of Reflection-Driven, Reduced MHD Turbulence from the Sun to the Alfvén Critical Point

NASA Astrophysics Data System (ADS)

Perez, J. C.; Chandran, B. D.

2013-12-01

We present direct numerical simulations of inhomogeneous reduced magnetohydrodynamic (RMHD) turbulence between the Sun and the Alfvén critical point. These are the first such simulations that take into account the solar-wind outflow velocity and the radial inhomogeneity of the background solar wind without approximating the nonlinear terms in the governing equations. Our simulation domain is a narrow magnetic flux tube with a square cross section centered on a radial magnetic field line. We impose periodic boundary conditions in the plane perpendicular to the background magnetic field B0. RMHD turbulence is driven by outward-propagating Alfvén waves (z+ fluctuations) launched from the Sun, which undergo partial non-WKB reflection to produce sunward-propagating Alfvén waves (z- fluctuations). Nonlinear interactions between z+ and z- then cause fluctuation energy to cascade from large scales to small scales and dissipate. We present ten simulations with different values of the correlation time τ+c⊙ and perpendicular correlation length L⊥⊙ of outward-propagating Alfvén waves (AWs) at the coronal base. We find that between 15% and 33% of the z+ energy launched into the corona dissipates between the coronal base and Alfvén critical point, which is at rA = 11.1R⊙ in our model solar wind. Between 33% and 40% of this input energy goes into work on the solar-wind outflow, and between 22% and 36% escapes as z+ fluctuations through the simulation boundary at r=rA. Except in the immediate vicinity of r=R⊙, the z× power spectra scale like k⊥-α×, where k⊥ is the wavenumber in the plane perpendicular to B0. In our simulation with the smallest value of τ+c⊙ (~2 min) and largest value of L⊥⊙ (~2×104 km), we find that α+ decreases approximately linearly with increasing ln(r), reaching a value of~1.3 at r=11.1R⊙. Our simulations with larger values of τ+c⊙ exhibit alignment between the contours of constant Φ× and Ω×, where Φ× are the Elsässer potentials and Ω× are the outer-scale parallel Elsässer vorticities. This alignment reduces the efficiency of nonlinear interactions at r≥2R⊙ to a degree that increases with increasing τ+c⊙.

A molecular dynamics simulation study of chloroform

NASA Astrophysics Data System (ADS)

Tironi, Ilario G.; van Gunsteren, Wilfred F.

Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

The influence of idealized surface heterogeneity on virtual turbulent flux measurements

NASA Astrophysics Data System (ADS)

De Roo, Frederik; Mauder, Matthias

2018-04-01

The imbalance of the surface energy budget in eddy-covariance measurements is still an unsolved problem. A possible cause is the presence of land surface heterogeneity, which affects the boundary-layer turbulence. To investigate the impact of surface variables on the partitioning of the energy budget of flux measurements in the surface layer under convective conditions, we set up a systematic parameter study by means of large-eddy simulation. For the study we use a virtual control volume approach, which allows the determination of advection by the mean flow, flux-divergence and storage terms of the energy budget at the virtual measurement site, in addition to the standard turbulent flux. We focus on the heterogeneity of the surface fluxes and keep the topography flat. The surface fluxes vary locally in intensity and these patches have different length scales. Intensity and length scales can vary for the two horizontal dimensions but follow an idealized chessboard pattern. Our main focus lies on surface heterogeneity of the kilometer scale, and one order of magnitude smaller. For these two length scales, we investigate the average response of the fluxes at a number of virtual towers, when varying the heterogeneity length within the length scale and when varying the contrast between the different patches. For each simulation, virtual measurement towers were positioned at functionally different positions (e.g., downdraft region, updraft region, at border between domains, etc.). As the storage term is always small, the non-closure is given by the sum of the advection by the mean flow and the flux-divergence. Remarkably, the missing flux can be described by either the advection by the mean flow or the flux-divergence separately, because the latter two have a high correlation with each other. For kilometer scale heterogeneity, we notice a clear dependence of the updrafts and downdrafts on the surface heterogeneity and likewise we also see a dependence of the energy partitioning on the tower location. For the hectometer scale, we do not notice such a clear dependence. Finally, we seek correlators for the energy balance ratio in the simulations. The correlation with the friction velocity is less pronounced than previously found, but this is likely due to our concentration on effectively strongly to freely convective conditions.

Does children's energy intake at one meal influence their intake at subsequent meals? Or do we just think it does?

PubMed

Hanley, James A; Hutcheon, Jennifer A

2010-05-01

It is widely believed that young children are able to adjust their energy intake across successive meals to compensate for higher or lower intakes at a given meal. This conclusion is based on past observations that although children's intake at individual meals is highly variable, total daily intakes are relatively constant. We investigated how much of this reduction in variability could be explained by the statistical phenomenon of the variability of individual components (each meal) always being relatively larger than the variability of their sum (total daily intake), independent of any physiological compensatory mechanism. We calculated, theoretically and by simulation, how variable a child's daily intake would be if there was no correlation between intakes at individual meals. We simulated groups of children with meal/snack intakes and variability in meal/snack intakes based on previously published values. Most importantly, we assumed that there was no correlation between intakes on successive meals. In both approaches, the coefficient of variation of the daily intakes was roughly 15%, considerably less than the 34% for individual meals. Thus, most of the reduction in variability found in past studies was explained without positing strong 'compensation'. Although children's daily energy intakes are indeed considerably less variable than their individual components, this phenomenon was observed even when intakes at each meal were simulated to be totally independent. We conclude that the commonly held belief that young children have a strong physiological compensatory mechanism to adjust intake at one meal based on intake at prior meals is likely to be based on flawed statistical reasoning.

Dynamic processes in heavy-ion collisions at intermediate energies

NASA Astrophysics Data System (ADS)

Prendergast, E. P.

1999-03-01

This thesis describes the study of the reaction dynamics in heavy-ion collisions of small nuclear systems at intermediate energies. For this, experiments were performed of 24Mg+27A1 at 45 and 95 AMeV. The experiments described in this thesis were performed at the GANIL accelerator facility in Caeri (France) using the Huygens detectors in conjunction with the ‘MUR’. The Huygens detectors consist of the CsI(Tl)-Wall (CIW) covering the backward hemisphere and, located at mid-rapidity, the central trigger detector (CTD), a gas chamber with microstrip read-out backed by 48 plastic scintillators. The forward region is covered by 16 of the plastic scintillators of the CTD and by the MUR, a time-of-flight wall consisting of 96 plastic scintillator sheets. In earlier experiments only fragments with atomic number, Z, greater then two could be identifled in the CTD. Therefore, an investigation was done into the properties of different drift gases. The use of freon (CF4) in the drift chamber, combined with an increase of the gas pressure to 150 mbar, makes it possible to identify all particles with Z ≥ 2. Under these conditions particles with Z = 1 can only be identifled to approximately 25 AMeV. The Isospin Quantum Molecular Dynamics (IQMD) model has been used, to interpret the measured data. This model gives a microscopical description of heavy-ion collisions and simulates collisions on an event by event basis. In IQMD all protons and neutrons are represented as individual Gaussian wave packets. After initialisation the path of each nucleon is calculated for 200 fm/c, after which the simulation is stopped. At this time, nucleons which are close in space are clustered into fragments. The events generated by IQMD can then be processed by a GEANT detector simulation. This calculation takes into account the effects of the detector on the incoming particles. By using the GEANT simulation it is possible to give a direct comparison between the results of IQMD and the experimental data. The impact-parameter selection procedure, based on the charged-particle multiplicity, was studied using IQMD events and the GEANT detector simulation. This showed that indeed an impact-parameter selection can be made with this method. However, the accuracy of this selection for these small systems is not very good. In particular the central-event selection is heavily polluted by mid-central events. Only mid-central events have been studied for 24Mg+27A1 at 45 and 95 AMeV. In order to study the collective flow in heavy-ion collisions, first the event plane has to be reconstructed. Again IQMD events and the GEANT detector simulation were used to investigate the effectiveness of several different event-plane reconstruction methods. It was found that an event plane can be reconstructed. The azimuthal-correlation method gives marginally the best result. With this method to reconstruct the reaction plane, the directed in-plane fiow was studied. The experimental data showed a strongly reduced flow at 95 AMeV compared to 45 AMeV, in accordance with a balancing energy of 114 ± 10 AMeV as derived from literature. Finally, the reaction dynamics were studied using the azimuthal correlations and the polar-angle distributions of intermediate-mass fragments (IMFs) emitted at midrapidity, both of which do not require an event-plane reconstructioh. The azimuthal correlations for the two energies are quite similar, whereas the directed in-plane flow is substantially higher at 45 AMeV than at 95 AMeV. This shows that the azimuthal correlations are insensitive to the magnitude of the directed in-plane flow. At both energies, the azimuthal-correlation functions for the various IMFs show absolute maxima at 180°, which can not be explained by a mid-rapidity source emitting fragments mdependently. However, the distributions are described by IQMD. The maxima are either caused target-projectile correlations (as in IQMD) or by momentum conservation. To describe the momentum-conservation scenario, a second model was introduced, which simulates the prompt multifragmentation of a small source. This model was fitted to the measured azimuthal-correlation functions, resulting in source sizes between 32 and 40 amu, depending on the mass of the emitted IMFs. Subsequently, the polar-angle distributions of the two models were compared to the experimental data. The distributions of the experimental data showed target- and projectile-like maxima, which can not be described by a decaying source, but are described by IQMD. Therefore, it is concluded that the IMF production in these small systems is a dynamic process with no evidence of a mid-rapidity source.

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

Refined Simulation of Satellite Laser Altimeter Full Echo Waveform

NASA Astrophysics Data System (ADS)

Men, H.; Xing, Y.; Li, G.; Gao, X.; Zhao, Y.; Gao, X.

2018-04-01

The return waveform of satellite laser altimeter plays vital role in the satellite parameters designation, data processing and application. In this paper, a method of refined full waveform simulation is proposed based on the reflectivity of the ground target, the true emission waveform and the Laser Profile Array (LPA). The ICESat/GLAS data is used as the validation data. Finally, we evaluated the simulation accuracy with the correlation coefficient. It was found that the accuracy of echo simulation could be significantly improved by considering the reflectivity of the ground target and the emission waveform. However, the laser intensity distribution recorded by the LPA has little effect on the echo simulation accuracy when compared with the distribution of the simulated laser energy. At last, we proposed a refinement idea by analyzing the experimental results, in the hope of providing references for the waveform data simulation and processing of GF-7 satellite in the future.

Simulation of angular-resolved RABBITT measurements in noble-gas atoms

NASA Astrophysics Data System (ADS)

Bray, Alexander W.; Naseem, Faiza; Kheifets, Anatoli S.

2018-06-01

We simulate angular-resolved RABBITT (reconstruction of attosecond beating by interference of two-photon transitions) measurements on valence shells of noble-gas atoms (Ne, Ar, Kr, and Xe). Our nonperturbative numerical simulation is based on solution of the time-dependent Schrödinger equation (TDSE) for a target atom driven by an ionizing XUV and dressing IR fields. From these simulations we extract the angular-dependent magnitude and phase of the RABBITT oscillations and deduce the corresponding angular anisotropy β parameter and Wigner time delay τW for the single XUV photon absorption that initiates the RABBITT process. Said β and τW parameters are compared with calculations in the random-phase approximation with exchange (RPAE), which includes intershell correlation. This comparison is used to test various effective potentials employed in the one-electron TDSE. In lighter atoms (Ne and Ar), several effective potentials are found to provide accurate simulations of RABBITT measurements for a wide range of photon energies up to 100 eV above the valence-shell threshold. In heavier atoms (Kr and Xe), the onset of strong correlation with the d shell restricts the validity of the single active electron approximation to several tens of eV above the valence-shell threshold.

Interactions of anesthetics with the water-hexane interface. A molecular dynamics study

NASA Technical Reports Server (NTRS)

Chipot, C.; Wilson, M. A.; Pohorille, A.

1997-01-01

The free energy profiles characterizing the transfer of nine solutes across the liquid-vapor interfaces of water and hexane and across the water-hexane interface were calculated from molecular dynamics simulations. Among the solutes were n-butane and three of its halogenated derivatives, as well as three halogenated cyclobutanes. The two remaining molecules, dichlorodifluoromethane and 1,2-dichloroperfluoroethane, belong to series of halo-substituted methanes and ethanes, described in previous studies (J. Chem. Phys. 1996, 104, 3760; Chem. Phys. 1996, 204, 337). Each series of molecules contains structurally similar compounds that differ greatly in anesthetic potency. The accuracy of the simulations was tested by comparing the calculated and the experimental free energies of solvation of all nine compounds in water and in hexane. In addition. the calculated and the measured surface excess concentrations of n-butane at the water liquid-vapor interface were compared. In all cases, good agreement with experimental results was found. At the water-hexane interface, the free energy profiles for polar molecules exhibited significant interfacial minima, whereas the profiles for nonpolar molecules did not. The existence of these minima was interpreted in terms of a balance between the free energy contribution arising from solute-solvent interactions and the work to form a cavity that accommodates the solute. These two contributions change monotonically, but oppositely, across the interface. The interfacial solubilities of the solutes, obtained from the free energy profiles, correlate very well with their anesthetic potencies. This is the case even when the Meyer-Overton hypothesis, which predicts a correlation between anesthetic potency and solubility in oil, fails.

Correlation of high energy muons with primary composition in extensive air shower

NASA Technical Reports Server (NTRS)

Chou, C.; Higashi, S.; Hiraoka, N.; Ozaki, S.; Sato, T.; Suwada, T.; Takahasi, T.; Umeda, H.

1985-01-01

An experimental investigation of high energy muons above 200 GeV in extensive air showers has been made for studying high energy interaction and primary composition of cosmic rays of energies in the range 10 to the 14th power approx. 10 to the 15th power eV. The muon energies are estimated from the burst sizes initiated by the muons in the rock, which are measured by four layers of proportional counters, each of area 5 x 2.6 sq m, placed at 30 m.w.e. deep, Funasaka tunnel vertically below the air shower array. These results are compared with Monte Carlo simulations based on the scaling model and the fireball model for two primary compositions, all proton and mixed.

Using experimental data to test an n -body dynamical model coupled with an energy-based clusterization algorithm at low incident energies

NASA Astrophysics Data System (ADS)

Kumar, Rohit; Puri, Rajeev K.

2018-03-01

Employing the quantum molecular dynamics (QMD) approach for nucleus-nucleus collisions, we test the predictive power of the energy-based clusterization algorithm, i.e., the simulating annealing clusterization algorithm (SACA), to describe the experimental data of charge distribution and various event-by-event correlations among fragments. The calculations are constrained into the Fermi-energy domain and/or mildly excited nuclear matter. Our detailed study spans over different system masses, and system-mass asymmetries of colliding partners show the importance of the energy-based clusterization algorithm for understanding multifragmentation. The present calculations are also compared with the other available calculations, which use one-body models, statistical models, and/or hybrid models.

Measuring top-quark polarization in top-pair + missing-energy events.

PubMed

Berger, Edmond L; Cao, Qing-Hong; Yu, Jiang-Hao; Zhang, Hao

2012-10-12

The polarization of a top quark can be sensitive to new physics beyond the standard model. Since the charged lepton from top-quark decay is maximally correlated with the top-quark spin, it is common to measure the polarization from the distribution in the angle between the charged lepton and the top-quark directions. We propose a novel method based on the charged lepton energy fraction and illustrate the method with a detailed simulation of top-quark pairs produced in supersymmetric top squark pair production. We show that the lepton energy ratio distribution that we define is very sensitive to the top-quark polarization but insensitive to the precise measurement of the top-quark energy.

Analytical Simulations of Energy-Absorbing Impact Spheres for a Mars Sample Return Earth Entry Vehicle

NASA Technical Reports Server (NTRS)

Billings, Marcus Dwight; Fasanella, Edwin L. (Technical Monitor)

2002-01-01

Nonlinear dynamic finite element simulations were performed to aid in the design of an energy-absorbing impact sphere for a passive Earth Entry Vehicle (EEV) that is a possible architecture for the Mars Sample Return (MSR) mission. The MSR EEV concept uses an entry capsule and energy-absorbing impact sphere designed to contain and limit the acceleration of collected samples during Earth impact without a parachute. The spherical shaped impact sphere is composed of solid hexagonal and pentagonal foam-filled cells with hybrid composite, graphite-epoxy/Kevlar cell walls. Collected Martian samples will fit inside a smaller spherical sample container at the center of the EEV's cellular structure. Comparisons were made of analytical results obtained using MSC.Dytran with test results obtained from impact tests performed at NASA Langley Research Center for impact velocities from 30 to 40 m/s. Acceleration, velocity, and deformation results compared well with the test results. The correlated finite element model was then used for simulations of various off-nominal impact scenarios. Off-nominal simulations at an impact velocity of 40 m/s included a rotated cellular structure impact onto a flat surface, a cellular structure impact onto an angled surface, and a cellular structure impact onto the corner of a step.

Multichannel-Sensing Scheduling and Transmission-Energy Optimizing in Cognitive Radio Networks with Energy Harvesting.

PubMed

Hoan, Tran-Nhut-Khai; Hiep, Vu-Van; Koo, In-Soo

2016-03-31

This paper considers cognitive radio networks (CRNs) utilizing multiple time-slotted primary channels in which cognitive users (CUs) are powered by energy harvesters. The CUs are under the consideration that hardware constraints on radio devices only allow them to sense and transmit on one channel at a time. For a scenario where the arrival of harvested energy packets and the battery capacity are finite, we propose a scheme to optimize (i) the channel-sensing schedule (consisting of finding the optimal action (silent or active) and sensing order of channels) and (ii) the optimal transmission energy set corresponding to the channels in the sensing order for the operation of the CU in order to maximize the expected throughput of the CRN over multiple time slots. Frequency-switching delay, energy-switching cost, correlation in spectrum occupancy across time and frequency and errors in spectrum sensing are also considered in this work. The performance of the proposed scheme is evaluated via simulation. The simulation results show that the throughput of the proposed scheme is greatly improved, in comparison to related schemes in the literature. The collision ratio on the primary channels is also investigated.

Analysis of competition between transformation pathways in the functioning of biotic abstract dual automata.

PubMed

Popa, Radu; Cimpoiasu, Vily M

2013-05-01

Properties of avenues of transformation and their mutualism with forms of organization in dynamic systems are essential for understanding the evolution of prebiotic order. We have analyzed competition between two avenues of transformation in an A↔B system, using the simulation approach called BiADA (Biotic Abstract Dual Automata). We discuss means of avoiding common pitfalls of abstract system modeling and benefits of BiADA-based simulations. We describe the effect of the availability of free energy, energy sink magnitude, and autocatalysis on the evolution of energy flux and order in the system. Results indicate that prebiotic competition between avenues of transformation was more stringent in energy-limited environments. We predict that in such conditions the efficiency of autocatalysis during competition between alternative system states will increase for systems with forms of organization having short half-lives and thus information that is time-sensitive to energy starvation. Our results also offer a potential solution to Manfred Eigen's error catastrophe dilemma. In the conditions discussed above, the exponential growth of quasi species is curbed through the removal of less competitive "genetic" variants via energy starvation. We propose that one of the most important achievements (and selective edges) of a dynamic network during competition in energy-limited or energy-variable environments was the capacity to correlate the internal energy flux and the need for free energy with the availability of free energy in the environment.

SIMULATION-BASED WEATHER NORMALIZATION APPROACH TO STUDY THE IMPACT OF WEATHER ON ENERGY USE OF BUILDINGS IN THE U.S.

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

Makhmalbaf, Atefe; Srivastava, Viraj; Wang, Na

Weather normalization is a crucial task in several applications related to building energy conservation such as retrofit measurements and energy rating. This paper documents preliminary results found from an effort to determine a set of weather adjustment coefficients that can be used to smooth out impacts of weather on energy use of buildings in 1020 weather location sites available in the U.S. The U.S. Department of Energy (DOE) commercial reference building models are adopted as hypothetical models with standard operations to deliver consistency in modeling. The correlation between building envelop design, HVAC system design and properties for different building typesmore » and the change in heating and cooling energy consumption caused by variations in weather is examined.« less

Numerical and laboratory simulation of fault motion and earthquake occurrence

NASA Technical Reports Server (NTRS)

Cohen, S. C.

1978-01-01

Simple linear rheologies were used with elastic forces driving the main events and viscoelastic forces being important for aftershock and creep occurrence. Friction and its dependence on velocity, stress, and displacement also plays a key role in determining how, when, and where fault motion occurs. The discussion of the qualitative behavior of the simulators focuses on the manner in which energy was stored in the system and released by the unstable and stable sliding processes. The numerical results emphasize the statistics of earthquake occurrence and the correlations among source parameters.

Exploring Hamiltonian dielectric solvent molecular dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-09-01

Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an α-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.

Molecular structures and thermodynamic properties of monohydrated gaseous iodine compounds: Modelling for severe accident simulation

NASA Astrophysics Data System (ADS)

Sudolská, Mária; Cantrel, Laurent; Budzák, Šimon; Černušák, Ivan

2014-03-01

Monohydrated complexes of iodine species (I, I2, HI, and HOI) have been studied by correlated ab initio calculations. The standard enthalpies of formation, Gibbs free energy and the temperature dependence of the heat capacities at constant pressure were calculated. The values obtained have been implemented in ASTEC nuclear accident simulation software to check the thermodynamic stability of hydrated iodine compounds in the reactor coolant system and in the nuclear containment building of a pressurised water reactor during a severe accident. It can be concluded that iodine complexes are thermodynamically unstable by means of positive Gibbs free energies and would be represented by trace level concentrations in severe accident conditions; thus it is well justified to only consider pure iodine species and not hydrated forms.

The evolving energy budget of accretionary wedges

NASA Astrophysics Data System (ADS)

McBeck, Jessica; Cooke, Michele; Maillot, Bertrand; Souloumiac, Pauline

2017-04-01

The energy budget of evolving accretionary systems reveals how deformational processes partition energy as faults slip, topography uplifts, and layer-parallel shortening produces distributed off-fault deformation. The energy budget provides a quantitative framework for evaluating the energetic contribution or consumption of diverse deformation mechanisms. We investigate energy partitioning in evolving accretionary prisms by synthesizing data from physical sand accretion experiments and numerical accretion simulations. We incorporate incremental strain fields and cumulative force measurements from two suites of experiments to design numerical simulations that represent accretionary wedges with stronger and weaker detachment faults. One suite of the physical experiments includes a basal glass bead layer and the other does not. Two physical experiments within each suite implement different boundary conditions (stable base versus moving base configuration). Synthesizing observations from the differing base configurations reduces the influence of sidewall friction because the force vector produced by sidewall friction points in opposite directions depending on whether the base is fixed or moving. With the numerical simulations, we calculate the energy budget at two stages of accretion: at the maximum force preceding the development of the first thrust pair, and at the minimum force following the development of the pair. To identify the appropriate combination of material and fault properties to apply in the simulations, we systematically vary the Young's modulus and the fault static and dynamic friction coefficients in numerical accretion simulations, and identify the set of parameters that minimizes the misfit between the normal force measured on the physical backwall and the numerically simulated force. Following this derivation of the appropriate material and fault properties, we calculate the components of the work budget in the numerical simulations and in the simulated increments of the physical experiments. The work budget components of the physical experiments are determined from backwall force measurements and incremental velocity fields calculated via digital image correlation. Comparison of the energy budget preceding and following the development of the first thrust pair quantifies the tradeoff of work done in distributed deformation and work expended in frictional slip due to the development of the first backthrust and forethrust. In both the numerical and physical experiments, after the pair develops internal work decreases at the expense of frictional work, which increases. Despite the increase in frictional work, the total external work of the system decreases, revealing that accretion faulting leads to gains in efficiency. Comparison of the energy budget of the accretion experiments and simulations with the strong and weak detachments indicate that when the detachment is strong, the total energy consumed in frictional sliding and internal deformation is larger than when the detachment is relatively weak.

Prediction of Environmental Impact of High-Energy Materials with Atomistic Computer Simulations

DTIC Science & Technology

2010-11-01

from a training set of compounds. Other methods include Quantitative Struc- ture-Activity Relationship ( QSAR ) and Quantitative Structure-Property...26 28 the development of QSPR/ QSAR models, in contrast to boiling points and critical parameters derived from empirical correlations, to improve...Quadratic Configuration Interaction Singles Doubles QSAR Quantitative Structure-Activity Relationship QSPR Quantitative Structure-Property

Standardized performance tests of collectors of solar thermal energy - A flat-plate copper collector with parallel mylar striping

NASA Technical Reports Server (NTRS)

Johnson, S. M.

1976-01-01

Basic test results are reported for a flat plate solar collector whose performance was determined in a solar simulator. The collector was tested over ranges of inlet temperatures, fluxes and one coolant flow rate. Collector efficiency is correlated in terms of inlet temperature and flux level.

Standardized performance tests of collectors of solar thermal energy: An evacuated flatplate copper collector with a serpentine flow distribution

NASA Technical Reports Server (NTRS)

Johnson, S. M.

1976-01-01

Basic test results are given for a flat plate solar collector whose performance was determined in the NASA-Lewis solar simulator. The collector was tested over ranges of inlet temperatures, fluxes and one coolant flow rate. Collector efficiency is correlated in terms of inlet temperature and flux level.

Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N.

PubMed

Vorontsov, Ivan I; Miyashita, Osamu

2011-04-30

Complexes of two Cyanovirin-N (CVN) mutants, m4-CVN and P51G-m4-CVN, with deoxy di-mannose analogs were employed as models to generate conformational ensembles using explicit water Molecular Dynamics (MD) simulations in solution and in crystal environment. The results were utilized for evaluation of binding free energies with the molecular mechanics Poisson-Boltzmann (or Generalized Born) surface area, MM/PB(GB)SA, methods. The calculations provided the ranking of deoxy di-mannose ligands affinity in agreement with available qualitative experimental evidences. This confirms the importance of the hydrogen-bond network between di-mannose 3'- and 4'-hydroxyl groups and the protein binding site B(M) as a basis of the CVN activity as an effective HIV fusion inhibitor. Comparison of binding free energies averaged over snapshots from the solution and crystal simulations showed high promises in the use of the crystal matrix for acceleration of the conformational ensemble generation, the most time consuming step in MM/PB(GB)SA approach. Correlation between energy values based on solution versus crystal ensembles is 0.95 for both MM/PBSA and MM/GBSA methods. Copyright © 2010 Wiley Periodicals, Inc.

Transient Spectra in TDDFT: Corrections and Correlations

NASA Astrophysics Data System (ADS)

Parkhill, John; Nguyen, Triet

We introduce an atomistic, all-electron, black-box electronic structure code to simulate transient absorption (TA) spectra and apply it to simulate pyrazole and a GFP chromophore derivative. The method is an application of OSCF2, our dissipative extension of time-dependent density functional theory. We compare our simulated spectra directly with recent ultra-fast spectroscopic experiments, showing that they are usefully predicted. We also relate bleaches in the TA signal to Fermi-blocking which would be missed in a simplified model. An important ingredient in the method is the stationary-TDDFT correction scheme recently put forwards by Fischer, Govind, and Cramer which allows us to overcome a limitation of adiabatic TDDFT. We demonstrate that OSCF2 is able to predict both the energies of bleaches and induced absorptions, as well as the decay of the transient spectrum, with only the molecular structure as input. With remaining time we will discuss corrections which resolve the non-resonant behavior of driven TDDFT, and correlated corrections to mean-field dynamics.

Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

NASA Astrophysics Data System (ADS)

Jana, Biman; Adkar, Bharat V.; Biswas, Rajib; Bagchi, Biman

2011-01-01

The catalytic conversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to adenosine diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of ATP binding domain (LID) and AMP binding domain (NMP) domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motion of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis, and multidimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two-dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed root mean square deviation variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder-type theoretical model to explain the observed dynamic coupling between the motion of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations.

The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum

NASA Astrophysics Data System (ADS)

Kitao, Akio; Hirata, Fumio; Gō, Nobuhiro

1991-12-01

The effects of solvent on the conformation and dynamics of protein is studied by computer simulation. The dynamics is studied by focusing mainly on collective motions of the protein molecule. Three types of simulation, normal mode analysis, molecular dynamics in vacuum, and molecular dynamics in water are applied to melittin, the major component of bee venom. To define collective motions principal, component analysis as well as normal mode analysis has been carried out. The principal components with large fluctuation amplitudes have a very good correspondence with the low-frequency normal modes. Trajectories of the molecular dynamics simulation are projected onto the principal axes. From the projected motions time correlation functions are calculated. The results indicate that the very-low-frequency modes, whose frequencies are less than ≈ 50 cm -1, are overdamping in water with relaxation times roushly twice as long as the period of the oscillatory motion. Effective Langevin mode analysis is carried out by using the friction coefficient matrix determined from the velocity correlation function calculated from the molecular dynamics trajectory in water. This analysis reproduces the results of the simulation in water reasonably well. The presence of the solvent water is found also to affect the shape of the potential energy surface in such a way that it produces many local minima with low-energy barriers in between, the envelope of which is given by the surface in vacuum. Inter-minimum transitions endow the conformational dynamics of proteins in water another diffusive character, which already exists in the intra-minimum collective motions.

Effective screening length and quasiuniversality for the restricted primitive model of an electrolyte solution.

PubMed

Janecek, Jirí; Netz, Roland R

2009-02-21

Monte Carlo simulations for the restricted primitive model of an electrolyte solution above the critical temperature are performed at a wide range of concentrations and temperatures. Thermodynamic properties such as internal energy, osmotic coefficient, activity coefficient, as well as spatial correlation functions are determined. These observables are used to investigate whether quasiuniversality in terms of an effective screening length exists, similar to the role played by the effective electron mass in solid-state physics. To that end, an effective screening length is extracted from the asymptotic behavior of the Fourier-transformed charge-correlation function and plugged into the Debye-Huckel limiting expressions for various thermodynamic properties. Comparison with numerical results is favorable, suggesting that correlation and other effects not captured on the Debye-Huckel limiting level can be successfully incorporated by a single effective parameter while keeping the functional form of Debye-Huckel expressions. We also compare different methods to determine mean ionic activity coefficient in molecular simulations and check the internal consistency of the numerical data.

Footprints of electron correlation in strong-field double ionization of Kr close to the sequential-ionization regime

NASA Astrophysics Data System (ADS)

Li, Xiaokai; Wang, Chuncheng; Yuan, Zongqiang; Ye, Difa; Ma, Pan; Hu, Wenhui; Luo, Sizuo; Fu, Libin; Ding, Dajun

2017-09-01

By combining kinematically complete measurements and a semiclassical Monte Carlo simulation we study the correlated-electron dynamics in the strong-field double ionization of Kr. Interestingly, we find that, as we step into the sequential-ionization regime, there are still signatures of correlation in the two-electron joint momentum spectrum and, more intriguingly, the scaling law of the high-energy tail is completely different from early predictions on the low-Z atom (He). These experimental observations are well reproduced by our generalized semiclassical model adapting a Green-Sellin-Zachor potential. It is revealed that the competition between the screening effect of inner-shell electrons and the Coulomb focusing of nuclei leads to a non-inverse-square central force, which twists the returned electron trajectory at the vicinity of the parent core and thus significantly increases the probability of hard recollisions between two electrons. Our results might have promising applications ranging from accurately retrieving atomic structures to simulating celestial phenomena in the laboratory.

Evaluation of CFD Methods for Simulation of Two-Phase Boiling Flow Phenomena in a Helical Coil Steam Generator

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

Pointer, William David; Shaver, Dillon; Liu, Yang

The U.S. Department of Energy, Office of Nuclear Energy charges participants in the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program with the development of advanced modeling and simulation capabilities that can be used to address design, performance and safety challenges in the development and deployment of advanced reactor technology. The NEAMS has established a high impact problem (HIP) team to demonstrate the applicability of these tools to identification and mitigation of sources of steam generator flow induced vibration (SGFIV). The SGFIV HIP team is working to evaluate vibration sources in an advanced helical coil steam generator using computational fluidmore » dynamics (CFD) simulations of the turbulent primary coolant flow over the outside of the tubes and CFD simulations of the turbulent multiphase boiling secondary coolant flow inside the tubes integrated with high resolution finite element method assessments of the tubes and their associated structural supports. This report summarizes the demonstration of a methodology for the multiphase boiling flow analysis inside the helical coil steam generator tube. A helical coil steam generator configuration has been defined based on the experiments completed by Polytecnico di Milano in the SIET helical coil steam generator tube facility. Simulations of the defined problem have been completed using the Eulerian-Eulerian multi-fluid modeling capabilities of the commercial CFD code STAR-CCM+. Simulations suggest that the two phases will quickly stratify in the slightly inclined pipe of the helical coil steam generator. These results have been successfully benchmarked against both empirical correlations for pressure drop and simulations using an alternate CFD methodology, the dispersed phase mixture modeling capabilities of the open source CFD code Nek5000.« less

Transformation between divacancy defects induced by an energy pulse in graphene.

PubMed

Xia, Jun; Liu, XiaoYi; Zhou, Wei; Wang, FengChao; Wu, HengAn

2016-07-08

The mutual transformations among the four typical divacancy defects induced by a high-energy pulse were studied via molecular dynamics simulation. Our study revealed all six possible mutual transformations and found that defects transformed by absorbing energy to overcome the energy barrier with bonding, debonding, and bond rotations. The reversibility of defect transformations was also investigated by potential energy analysis. The energy difference was found to greatly influence the transformation reversibility. The direct transformation path was irreversible if the energy difference was too large. We also studied the correlation between the transformation probability and the input energy. It was found that the transformation probability had a local maxima at an optimal input energy. The introduction of defects and their structural evolutions are important for tailoring the exceptional properties and thereby performances of graphene-based devices, such as nanoporous membranes for the filtration and desalination of water.

Pressure-strain energy redistribution in compressible turbulence: return-to-isotropy versus kinetic-potential energy equipartition

NASA Astrophysics Data System (ADS)

Lee, Kurnchul; Venugopal, Vishnu; Girimaji, Sharath S.

2016-08-01

Return-to-isotropy and kinetic-potential energy equipartition are two fundamental pressure-moderated energy redistributive processes in anisotropic compressible turbulence. Pressure-strain correlation tensor redistributes energy among various Reynolds stress components and pressure-dilatation is responsible for energy reallocation between dilatational kinetic and potential energies. The competition and interplay between these pressure-based processes are investigated in this study. Direct numerical simulations (DNS) of low turbulent Mach number dilatational turbulence are performed employing the hybrid thermal Lattice Boltzman method (HTLBM). It is found that a tendency towards equipartition precedes proclivity for isotropization. An evolution towards equipartition has a collateral but critical effect on return-to-isotropy. The preferential transfer of energy from strong (rather than weak) Reynolds stress components to potential energy accelerates the isotropization of dilatational fluctuations. Understanding of these pressure-based redistributive processes is critical for developing insight into the character of compressible turbulence.

Craig's XY distribution and the statistics of Lagrangian power in two-dimensional turbulence

NASA Astrophysics Data System (ADS)

Bandi, Mahesh M.; Connaughton, Colm

2008-03-01

We examine the probability distribution function (PDF) of the energy injection rate (power) in numerical simulations of stationary two-dimensional (2D) turbulence in the Lagrangian frame. The simulation is designed to mimic an electromagnetically driven fluid layer, a well-documented system for generating 2D turbulence in the laboratory. In our simulations, the forcing and velocity fields are close to Gaussian. On the other hand, the measured PDF of injected power is very sharply peaked at zero, suggestive of a singularity there, with tails which are exponential but asymmetric. Large positive fluctuations are more probable than large negative fluctuations. It is this asymmetry of the tails which leads to a net positive mean value for the energy input despite the most probable value being zero. The main features of the power distribution are well described by Craig’s XY distribution for the PDF of the product of two correlated normal variables. We show that the power distribution should exhibit a logarithmic singularity at zero and decay exponentially for large absolute values of the power. We calculate the asymptotic behavior and express the asymmetry of the tails in terms of the correlation coefficient of the force and velocity. We compare the measured PDFs with the theoretical calculations and briefly discuss how the power PDF might change with other forcing mechanisms.

Craig's XY distribution and the statistics of Lagrangian power in two-dimensional turbulence.

PubMed

Bandi, Mahesh M; Connaughton, Colm

2008-03-01

We examine the probability distribution function (PDF) of the energy injection rate (power) in numerical simulations of stationary two-dimensional (2D) turbulence in the Lagrangian frame. The simulation is designed to mimic an electromagnetically driven fluid layer, a well-documented system for generating 2D turbulence in the laboratory. In our simulations, the forcing and velocity fields are close to Gaussian. On the other hand, the measured PDF of injected power is very sharply peaked at zero, suggestive of a singularity there, with tails which are exponential but asymmetric. Large positive fluctuations are more probable than large negative fluctuations. It is this asymmetry of the tails which leads to a net positive mean value for the energy input despite the most probable value being zero. The main features of the power distribution are well described by Craig's XY distribution for the PDF of the product of two correlated normal variables. We show that the power distribution should exhibit a logarithmic singularity at zero and decay exponentially for large absolute values of the power. We calculate the asymptotic behavior and express the asymmetry of the tails in terms of the correlation coefficient of the force and velocity. We compare the measured PDFs with the theoretical calculations and briefly discuss how the power PDF might change with other forcing mechanisms.

SKA weak lensing- II. Simulated performance and survey design considerations

NASA Astrophysics Data System (ADS)

Bonaldi, Anna; Harrison, Ian; Camera, Stefano; Brown, Michael L.

2016-12-01

We construct a pipeline for simulating weak lensing cosmology surveys with the Square Kilometre Array (SKA), taking as inputs telescope sensitivity curves; correlated source flux, size and redshift distributions; a simple ionospheric model; source redshift and ellipticity measurement errors. We then use this simulation pipeline to optimize a 2-yr weak lensing survey performed with the first deployment of the SKA (SKA1). Our assessments are based on the total signal to noise of the recovered shear power spectra, a metric that we find to correlate very well with a standard dark energy figure of merit. We first consider the choice of frequency band, trading off increases in number counts at lower frequencies against poorer resolution; our analysis strongly prefers the higher frequency Band 2 (950-1760 MHz) channel of the SKA-MID telescope to the lower frequency Band 1 (350-1050 MHz). Best results would be obtained by allowing the centre of Band 2 to shift towards lower frequency, around 1.1 GHz. We then move on to consider survey size, finding that an area of 5000 deg2 is optimal for most SKA1 instrumental configurations. Finally, we forecast the performance of a weak lensing survey with the second deployment of the SKA. The increased survey size (3π steradian) and sensitivity improves both the signal to noise and the dark energy metrics by two orders of magnitude.

Property-process relations in simulated clinical abrasive adjusting of dental ceramics.

PubMed

Yin, Ling

2012-12-01

This paper reports on property-process correlations in simulated clinical abrasive adjusting of a wide range of dental restorative ceramics using a dental handpiece and diamond burs. The seven materials studied included four mica-containing glass ceramics, a feldspathic porcelain, a glass-infiltrated alumina, and a yttria-stabilized tetragonal zirconia. The abrasive adjusting process was conducted under simulated clinical conditions using diamond burs and a clinical dental handpiece. An attempt was made to establish correlations between process characteristics in terms of removal rate, chipping damage, and surface finish and material mechanical properties of hardness, fracture toughness and Young's modulus. The results show that the removal rate is mainly a function of hardness, which decreases nonlinearly with hardness. No correlations were noted between the removal rates and the complex relations of hardness, Young's modulus and fracture toughness. Surface roughness was primarily a linear function of diamond grit size and was relatively independent of materials. Chipping damage in terms of the average chipping width decreased with fracture toughness except for glass-infiltrated alumina. It also had higher linear correlations with critical strain energy release rates (R²=0.66) and brittleness (R²=0.62) and a lower linear correlation with indices of brittleness (R²=0.32). Implications of these results can provide guidance for the microstructural design of dental ceramics, optimize performance, and guide the proper selection of technical parameters in clinical abrasive adjusting conducted by dental practitioners. Copyright © 2012 Elsevier Ltd. All rights reserved.

Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences

PubMed Central

Whitney, Anna; Shakhnovich, Eugene I.

2015-01-01

Design of proteins with desired thermal properties is important for scientific and biotechnological applications. Here we developed a theoretical approach to predict the effect of mutations on protein stability from non-equilibrium unfolding simulations. We establish a relative measure based on apparent simulated melting temperatures that is independent of simulation length and, under certain assumptions, proportional to equilibrium stability, and we justify this theoretical development with extensive simulations and experimental data. Using our new method based on all-atom Monte-Carlo unfolding simulations, we carried out a saturating mutagenesis of Dihydrofolate Reductase (DHFR), a key target of antibiotics and chemotherapeutic drugs. The method predicted more than 500 stabilizing mutations, several of which were selected for detailed computational and experimental analysis. We find a highly significant correlation of r = 0.65–0.68 between predicted and experimentally determined melting temperatures and unfolding denaturant concentrations for WT DHFR and 42 mutants. The correlation between energy of the native state and experimental denaturation temperature was much weaker, indicating the important role of entropy in protein stability. The most stabilizing point mutation was D27F, which is located in the active site of the protein, rendering it inactive. However for the rest of mutations outside of the active site we observed a weak yet statistically significant positive correlation between thermal stability and catalytic activity indicating the lack of a stability-activity tradeoff for DHFR. By combining stabilizing mutations predicted by our method, we created a highly stable catalytically active E. coli DHFR mutant with measured denaturation temperature 7.2°C higher than WT. Prediction results for DHFR and several other proteins indicate that computational approaches based on unfolding simulations are useful as a general technique to discover stabilizing mutations. PMID:25905910

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.

Jet energy scale and resolution in the CMS experiment in pp collisions at 8 TeV

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Knünz, V.; König, A.; Krammer, M.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Strauss, J.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Lauwers, J.; Luyckx, S.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; De Bruyn, I.; Deroover, K.; Heracleous, N.; Keaveney, J.; Lowette, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Van Parijs, I.; Barria, P.; Brun, H.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Fasanella, G.; Favart, L.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Maerschalk, T.; Marinov, A.; Perniè, L.; Randle-conde, A.; Reis, T.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Yonamine, R.; Zenoni, F.; Zhang, F.; Beernaert, K.; Benucci, L.; Cimmino, A.; Crucy, S.; Dobur, D.; Fagot, A.; Garcia, G.; Gul, M.; Mccartin, J.; Ocampo Rios, A. A.; Poyraz, D.; Ryckbosch, D.; Salva, S.; Sigamani, M.; Strobbe, N.; Tytgat, M.; Van Driessche, W.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Mertens, A.; Nuttens, C.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Beliy, N.; Hammad, G. H.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Hamer, M.; Hensel, C.; Mora Herrera, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Damiao, D. De Jesus; De Oliveira Martins, C.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; De Souza Santos, A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Cheng, T.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Shaheen, S. M.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Micanovic, S.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Bodlak, M.; Finger, M.; Finger, M., Jr.; Assran, Y.; Elgammal, S.; Ellithi Kamel, A.; Mahmoud, M. A.; Mohammed, Y.; Calpas, B.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Machet, M.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Zghiche, A.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Chapon, E.; Charlot, C.; Dahms, T.; Davignon, O.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Lisniak, S.; Mastrolorenzo, L.; Miné, P.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Merlin, J. A.; Skovpen, K.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Bernet, C.; Boudoul, G.; Bouvier, E.; Carrillo Montoya, C. A.; Chierici, R.; Contardo, D.; Courbon, B.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Lagarde, F.; Laktineh, I. B.; Lethuillier, M.; Mirabito, L.; Pequegnot, A. L.; Perries, S.; Ruiz Alvarez, J. D.; Sabes, D.; Sgandurra, L.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Toriashvili, T.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Edelhoff, M.; Feld, L.; Heister, A.; Kiesel, M. K.; Klein, K.; Lipinski, M.; Ostapchuk, A.; Preuten, M.; Raupach, F.; Schael, S.; Schulte, J. F.; Verlage, T.; Weber, H.; Wittmer, B.; Zhukov, V.; Ata, M.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Endres, M.; Erdmann, M.; Erdweg, S.; Esch, T.; Fischer, R.; Güth, A.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Klingebiel, D.; Knutzen, S.; Kreuzer, P.; Merschmeyer, M.; Meyer, A.; Millet, P.; Olschewski, M.; Padeken, K.; Papacz, P.; Pook, T.; Radziej, M.; Reithler, H.; Rieger, M.; Scheuch, F.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Cherepanov, V.; Erdogan, Y.; Flügge, G.; Geenen, H.; Geisler, M.; Hoehle, F.; Kargoll, B.; Kress, T.; Kuessel, Y.; Künsken, A.; Lingemann, J.; Nehrkorn, A.; Nowack, A.; Nugent, I. M.; Pistone, C.; Pooth, O.; Stahl, A.; Aldaya Martin, M.; Asin, I.; Bartosik, N.; Behnke, O.; Behrens, U.; Bell, A. 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M.; Lanza, G.; Lista, L.; Meola, S.; Merola, M.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Bacchetta, N.; Bellato, M.; Benato, L.; Bisello, D.; Boletti, A.; Branca, A.; Carlin, R.; Checchia, P.; Dall'Osso, M.; Dorigo, T.; Dosselli, U.; Fanzago, F.; Gasparini, F.; Gasparini, U.; Gonella, F.; Gozzelino, A.; Kanishchev, K.; Lacaprara, S.; Maron, G.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Tosi, M.; Vanini, S.; Ventura, S.; Zanetti, M.; Zucchetta, A.; Zumerle, G.; Braghieri, A.; Magnani, A.; Montagna, P.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Alunni Solestizi, L.; Biasini, M.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Spiezia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Broccolo, G.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fedi, G.; Foà, L.; Giassi, A.; Grippo, M. 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D.; Symonds, P.; Teodorescu, L.; Turner, M.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Kasmi, A.; Liu, H.; Pastika, N.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; Avetisyan, A.; Bose, T.; Fantasia, C.; Gastler, D.; Lawson, P.; Rankin, D.; Richardson, C.; Rohlf, J.; St. John, J.; Sulak, L.; Zou, D.; Alimena, J.; Berry, E.; Bhattacharya, S.; Cutts, D.; Dhingra, N.; Ferapontov, A.; Garabedian, A.; Hakala, J.; Heintz, U.; Laird, E.; Landsberg, G.; Mao, Z.; Narain, M.; Piperov, S.; Sagir, S.; Sinthuprasith, T.; Syarif, R.; Breedon, R.; Breto, G.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Gardner, M.; Ko, W.; Lander, R.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Farrell, C.; Hauser, J.; Ignatenko, M.; Saltzberg, D.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Ivova PANEVA, M.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Luthra, A.; Malberti, M.; Olmedo Negrete, M.; Shrinivas, A.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; D'Agnolo, R. T.; Holzner, A.; Kelley, R.; Klein, D.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Welke, C.; Würthwein, F.; Yagil, A.; Zevi Della Porta, G.; Barge, D.; Bradmiller-Feld, J.; Campagnari, C.; Dishaw, A.; Dutta, V.; Flowers, K.; Sevilla, M. Franco; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Gran, J.; Incandela, J.; Justus, C.; Mccoll, N.; Mullin, S. D.; Richman, J.; Stuart, D.; Suarez, I.; To, W.; West, C.; Yoo, J.; Anderson, D.; Apresyan, A.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Mott, A.; Newman, H. B.; Pena, C.; Pierini, M.; Spiropulu, M.; Vlimant, J. R.; Xie, S.; Zhu, R. Y.; Andrews, M. B.; Azzolini, V.; Calamba, A.; Carlson, B.; Ferguson, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Gaz, A.; Jensen, F.; Johnson, A.; Krohn, M.; Mulholland, T.; Nauenberg, U.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chatterjee, A.; Chaves, J.; Chu, J.; Dittmer, S.; Eggert, N.; Mirman, N.; Kaufman, G. Nicolas; Patterson, J. R.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Soffi, L.; Sun, W.; Tan, S. M.; Teo, W. D.; Thom, J.; Thompson, J.; Tucker, J.; Weng, Y.; Wittich, P.; Abdullin, S.; Albrow, M.; Anderson, J.; Apollinari, G.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hanlon, J.; Hare, D.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jindariani, S.; Johnson, M.; Joshi, U.; Jung, A. W.; Klima, B.; Kreis, B.; Kwan, S.; Lammel, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lopes De Sá, R.; Lykken, J.; Maeshima, K.; Marraffino, J. M.; Martinez Outschoorn, V. I.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mishra, K.; Mrenna, S.; Nahn, S.; Newman-Holmes, C.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Weber, H. A.; Whitbeck, A.; Yang, F.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Carnes, A.; Carver, M.; Curry, D.; Das, S.; Di Giovanni, G. P.; Field, R. D.; Furic, I. K.; Hugon, J.; Konigsberg, J.; Korytov, A.; Low, J. F.; Ma, P.; Matchev, K.; Mei, H.; Milenovic, P.; Mitselmakher, G.; Rank, D.; Rossin, R.; Shchutska, L.; Snowball, M.; Sperka, D.; Terentyev, N.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Hewamanage, S.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Ackert, A.; Adams, J. R.; Adams, T.; Askew, A.; Bochenek, J.; Diamond, B.; Haas, J.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Khatiwada, A.; Prosper, H.; Weinberg, M.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Kalakhety, H.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Kurt, P.; O'Brien, C.; Sandoval Gonzalez, I. D.; Silkworth, C.; Turner, P.; Varelas, N.; Wu, Z.; Zakaria, M.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tan, P.; Tiras, E.; Wetzel, J.; Yi, K.; Anderson, I.; Barnett, B. A.; Blumenfeld, B.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Osherson, M.; Roskes, J.; Sady, A.; Sarica, U.; Swartz, M.; Xiao, M.; Xin, Y.; You, C.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Kenny, R. P., III; Majumder, D.; Malek, M.; Murray, M.; Sanders, S.; Stringer, R.; Wang, Q.; Ivanov, A.; Kaadze, K.; Khalil, S.; Makouski, M.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Toda, S.; Lange, D.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Gomez, J. A.; Hadley, N. J.; Jabeen, S.; Kellogg, R. G.; Kolberg, T.; Kunkle, J.; Lu, Y.; Mignerey, A. C.; Shin, Y. H.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Baty, A.; Bierwagen, K.; Brandt, S.; Busza, W.; Cali, I. A.; Demiragli, Z.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Marini, A. C.; Mcginn, C.; Mironov, C.; Niu, X.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Sumorok, K.; Varma, M.; Velicanu, D.; Veverka, J.; Wang, J.; Wang, T. W.; Wyslouch, B.; Yang, M.; Zhukova, V.; Dahmes, B.; Evans, A.; Finkel, A.; Gude, A.; Hansen, P.; Kalafut, S.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Fangmeier, C.; Gonzalez Suarez, R.; Kamalieddin, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Meier, F.; Monroy, J.; Ratnikov, F.; Siado, J. E.; Snow, G. R.; Alyari, M.; Dolen, J.; George, J.; Godshalk, A.; Harrington, C.; Iashvili, I.; Kaisen, J.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Teixeira De Lima, R.; Trocino, D.; Wang, R.-J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Trovato, M.; Velasco, M.; Brinkerhoff, A.; Dev, N.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Lynch, S.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Pearson, T.; Planer, M.; Reinsvold, A.; Ruchti, R.; Smith, G.; Taroni, S.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hart, A.; Hill, C.; Hughes, R.; Ji, W.; Kotov, K.; Ling, T. Y.; Liu, B.; Luo, W.; Puigh, D.; Rodenburg, M.; Winer, B. L.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Palmer, C.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Malik, S.; Barnes, V. E.; Benedetti, D.; Bortoletto, D.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, K.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Sun, J.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Redjimi, R.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Betchart, B.; Bodek, A.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Harel, A.; Hindrichs, O.; Khukhunaishvili, A.; Petrillo, G.; Verzetti, M.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Lath, A.; Nash, K.; Panwalkar, S.; Park, M.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Foerster, M.; Riley, G.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Castaneda Hernandez, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Kamon, T.; Krutelyov, V.; Mueller, R.; Osipenkov, I.; Pakhotin, Y.; Patel, R.; Perloff, A.; Rose, A.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Undleeb, S.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Ni, H.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Sun, X.; Wang, Y.; Wolfe, E.; Wood, J.; Xia, F.; Clarke, C.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Dodd, L.; Duric, S.; Friis, E.; Gomber, B.; Grothe, M.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ruggles, T.; Sarangi, T.; Savin, A.; Sharma, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.

2017-02-01

Improved jet energy scale corrections, based on a data sample corresponding to an integrated luminosity of 19.7 fb-1 collected by the CMS experiment in proton-proton collisions at a center-of-mass energy of 8 TeV, are presented. The corrections as a function of pseudorapidity η and transverse momentum pT are extracted from data and simulated events combining several channels and methods. They account successively for the effects of pileup, uniformity of the detector response, and residual data-simulation jet energy scale differences. Further corrections, depending on the jet flavor and distance parameter (jet size) R, are also presented. The jet energy resolution is measured in data and simulated events and is studied as a function of pileup, jet size, and jet flavor. Typical jet energy resolutions at the central rapidities are 15-20% at 30 GeV, about 10% at 100 GeV, and 5% at 1 TeV. The studies exploit events with dijet topology, as well as photon+jet, Z+jet and multijet events. Several new techniques are used to account for the various sources of jet energy scale corrections, and a full set of uncertainties, and their correlations, are provided.The final uncertainties on the jet energy scale are below 3% across the phase space considered by most analyses (pT>30 GeV and 0| η| <5.). In the barrel region (| η| <1.3) an uncertainty below 1% for pT>30 GeV is reached, when excluding the jet flavor uncertainties, which are provided separately for different jet flavors. A new benchmark for jet energy scale determination at hadron colliders is achieved with 0.32% uncertainty for jets with \\pt of the order of 165-330\\GeV, and | η| <0.8.

Determination of the strong coupling constant $$\\alpha _\\mathrm {s}$$ from transverse energy–energy correlations in multijet events at $$\\sqrt{s} = 8~\\hbox {TeV}$$ TeV using the ATLAS detector

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

Aaboud, M.; Aad, G.; Abbott, B.

In this study, measurements of transverse energy–energy correlations and their associated asymmetries in multi-jet events using the ATLAS detector at the LHC are presented. The data used correspond to √s=8 TeV proton–proton collisions with an integrated luminosity of 20.2 fb –1. The results are presented in bins of the scalar sum of the transverse momenta of the two leading jets, unfolded to the particle level and compared to the predictions from Monte Carlo simulations. A comparison with next-to-leading-order perturbative QCD is also performed, showing excellent agreement within the uncertainties. From this comparison, the value of the strong coupling constant ismore » extracted for different energy regimes, thus testing the running of α s(μ) predicted in QCD up to scales over 1 TeV. A global fit to the transverse energy–energy correlation distributions yields α s(m Z) = 0.1162±0.0011(exp.) +0.0084 –0.0070(theo.) , while a global fit to the asymmetry distributions yields a value of α s(m Z) = 0.1196±0.0013(exp.) +0.0075 –0.0045(theo.).« less

Determination of the strong coupling constant $$\\alpha _\\mathrm {s}$$ from transverse energy–energy correlations in multijet events at $$\\sqrt{s} = 8~\\hbox {TeV}$$ TeV using the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2017-12-15

In this study, measurements of transverse energy–energy correlations and their associated asymmetries in multi-jet events using the ATLAS detector at the LHC are presented. The data used correspond to √s=8 TeV proton–proton collisions with an integrated luminosity of 20.2 fb –1. The results are presented in bins of the scalar sum of the transverse momenta of the two leading jets, unfolded to the particle level and compared to the predictions from Monte Carlo simulations. A comparison with next-to-leading-order perturbative QCD is also performed, showing excellent agreement within the uncertainties. From this comparison, the value of the strong coupling constant ismore » extracted for different energy regimes, thus testing the running of α s(μ) predicted in QCD up to scales over 1 TeV. A global fit to the transverse energy–energy correlation distributions yields α s(m Z) = 0.1162±0.0011(exp.) +0.0084 –0.0070(theo.) , while a global fit to the asymmetry distributions yields a value of α s(m Z) = 0.1196±0.0013(exp.) +0.0075 –0.0045(theo.).« less

Characterizing subcritical assemblies with time of flight fixed by energy estimation distributions

NASA Astrophysics Data System (ADS)

Monterial, Mateusz; Marleau, Peter; Pozzi, Sara

2018-04-01

We present the Time of Flight Fixed by Energy Estimation (TOFFEE) as a measure of the fission chain dynamics in subcritical assemblies. TOFFEE is the time between correlated gamma rays and neutrons, subtracted by the estimated travel time of the incident neutron from its proton recoil. The measured subcritical assembly was the BeRP ball, a 4.482 kg sphere of α-phase weapons grade plutonium metal, which came in five configurations: bare, 0.5, 1, and 1.5 in iron, and 1 in nickel closed fitting shell reflectors. We extend the measurement with MCNPX-PoliMi simulations of shells ranging up to 6 inches in thickness, and two new reflector materials: aluminum and tungsten. We also simulated the BeRP ball with different masses ranging from 1 to 8 kg. A two-region and single-region point kinetics models were used to model the behavior of the positive side of the TOFFEE distribution from 0 to 100 ns. The single region model of the bare cases gave positive linear correlations between estimated and expected neutron decay constants and leakage multiplications. The two-region model provided a way to estimate neutron multiplication for the reflected cases, which correlated positively with expected multiplication, but the nature of the correlation (sub or superlinear) changed between material types. Finally, we found that the areal density of the reflector shells had a linear correlation with the integral of the two-region model fit. Therefore, we expect that with knowledge of reflector composition, one could determine the shell thickness, or vice versa. Furthermore, up to a certain amount and thickness of the reflector, the two-region model provides a way of distinguishing bare and reflected plutonium assemblies.

Understanding Plasmas with a High Degree of Correlation Through Modeling: From Rydberg and Fermionic Plasmas to Penning Plasmas

NASA Astrophysics Data System (ADS)

Christlieb, Andrew

2015-09-01

Ultra cold neutral plasmas have gained attention over the past 15 years as being a unique environment for studying moderately to strongly coupled neutral systems. The first ultra cold neutral plasmas were generated by ionizing a Bose Einstein condensate, generating a plasma with .1K ions and 2-4K electrons. These neutral plasmas have the unique property that the ratio of their potential energy to their kinetic energy, (Γ = PE / KE), can greatly exceed 1, leading to a strongly correlated system. The high degree of correlation means that everything from wave propagation through collision dynamics behaves quite differently from their counterpart in traditional neutral plasmas. Currently, a range of gases and different methods for cooling have been used to generate these plasmas from supersonic expansion, through penning trap configurations (reference Tom, Jake and Ed). These systems have time scales form picoseconds to milliseconds have a particle numbers from 105 to 109. These systems present a unique environment for studying the physics of correlation due to their low particle number and small size. We start by reviewing ultra cold plasmas and the current sate of the art in generating these correlated systems. Then we introduce the methods we will use for exploring these systems through direct simulation of Molecular Dynamics models; Momentum Dependent Potentials, Treecodes and Particle-Particle Particle-Mesh methods. We use these tools to look at two key areas of ultra cold plasmas; development of methods to generate a plasma with a Γ >> 1 and the impact of correlation of collisional relaxation. Our eventual goal is to use what we learn to develop models that can simulate correlation in large plasma systems that are outside of the scope of Molecular Dynamics models. In collaboration with Gautham Dharmuman, Mayur Jain, Michael Murillo and John Verboncoeur. This work it supposed by Air Force Office of Scientific Research.

Simulation of water-energy fluxes through small-scale reservoir systems under limited data availability

NASA Astrophysics Data System (ADS)

Papoulakos, Konstantinos; Pollakis, Giorgos; Moustakis, Yiannis; Markopoulos, Apostolis; Iliopoulou, Theano; Dimitriadis, Panayiotis; Koutsoyiannis, Demetris; Efstratiadis, Andreas

2017-04-01

Small islands are regarded as promising areas for developing hybrid water-energy systems that combine multiple sources of renewable energy with pumped-storage facilities. Essential element of such systems is the water storage component (reservoir), which implements both flow and energy regulations. Apparently, the representation of the overall water-energy management problem requires the simulation of the operation of the reservoir system, which in turn requires a faithful estimation of water inflows and demands of water and energy. Yet, in small-scale reservoir systems, this task in far from straightforward, since both the availability and accuracy of associated information is generally very poor. For, in contrast to large-scale reservoir systems, for which it is quite easy to find systematic and reliable hydrological data, in the case of small systems such data may be minor or even totally missing. The stochastic approach is the unique means to account for input data uncertainties within the combined water-energy management problem. Using as example the Livadi reservoir, which is the pumped storage component of the small Aegean island of Astypalaia, Greece, we provide a simulation framework, comprising: (a) a stochastic model for generating synthetic rainfall and temperature time series; (b) a stochastic rainfall-runoff model, whose parameters cannot be inferred through calibration and, thus, they are represented as correlated random variables; (c) a stochastic model for estimating water supply and irrigation demands, based on simulated temperature and soil moisture, and (d) a daily operation model of the reservoir system, providing stochastic forecasts of water and energy outflows. Acknowledgement: This research is conducted within the frame of the undergraduate course "Stochastic Methods in Water Resources" of the National Technical University of Athens (NTUA). The School of Civil Engineering of NTUA provided moral support for the participation of the students in the Assembly.

FY2017 Report on NISC Measurements and Detector Simulations

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

Andrews, Madison Theresa; Meierbachtol, Krista Cruse; Jordan, Tyler Alexander

FY17 work focused on automation, both of the measurement analysis and comparison of simulations. The experimental apparatus was relocated and weeks of continuous measurements of the spontaneous fission source 252Cf was performed. Programs were developed to automate the conversion of measurements into ROOT data framework files with a simple terminal input. The complete analysis of the measurement (which includes energy calibration and the identification of correlated counts) can now be completed with a documented process which involves one simple execution line as well. Finally, the hurdles of slow MCNP simulations resulting in low simulation statistics have been overcome with themore » generation of multi-run suites which make use of the highperformance computing resources at LANL. Preliminary comparisons of measurements and simulations have been performed and will be the focus of FY18 work.« less

Microscopic Electron Variations Measured Simultaneously By The Cluster Spacecraft

NASA Astrophysics Data System (ADS)

Buckley, A. M.; Carozzi, T. D.; Gough, M. P.; Beloff, N.

Data is used from the Particle Correlator experiments running on each of the four Cluster spacecraft so as to determine common microscopic behaviour in the elec- tron population observed over the macroscopic Cluster separations. The Cluster par- ticle correlator experiments operate by forming on board Auto Correlation Functions (ACFs) generated from short time series of electron counts obtained, as a function of electron energy, from the PEACE HEEA sensor. The information on the microscopic variation of the electron flux covers the frequency range DC up to 41 kHz (encom- passing typical electron plasma frequencies and electron gyro frequencies and their harmonics), the electron energy range is that covered by the PEACE HEEA sensor (within the range 1 eV to 26 keV). Results are presented of coherent electron struc- tures observed simultaneously by the four spacecraft in the differing plasma interac- tion regions and boundaries encountered by Cluster. As an aid to understanding the plasma interactions, use is made of numerical simulations which model both the un- derlying statistical properties of the electrons and also the manner in which particle correlator experiments operate.

Computer Simulation of Electron Positron Annihilation Processes

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

Chen, y

2003-10-02

With the launching of the Next Linear Collider coming closer and closer, there is a pressing need for physicists to develop a fully-integrated computer simulation of e{sup +}e{sup -} annihilation process at center-of-mass energy of 1TeV. A simulation program acts as the template for future experiments. Either new physics will be discovered, or current theoretical uncertainties will shrink due to more accurate higher-order radiative correction calculations. The existence of an efficient and accurate simulation will help us understand the new data and validate (or veto) some of the theoretical models developed to explain new physics. It should handle well interfacesmore » between different sectors of physics, e.g., interactions happening at parton levels well above the QCD scale which are described by perturbative QCD, and interactions happening at much lower energy scale, which combine partons into hadrons. Also it should achieve competitive speed in real time when the complexity of the simulation increases. This thesis contributes some tools that will be useful for the development of such simulation programs. We begin our study by the development of a new Monte Carlo algorithm intended to perform efficiently in selecting weight-1 events when multiple parameter dimensions are strongly correlated. The algorithm first seeks to model the peaks of the distribution by features, adapting these features to the function using the EM algorithm. The representation of the distribution provided by these features is then improved using the VEGAS algorithm for the Monte Carlo integration. The two strategies mesh neatly into an effective multi-channel adaptive representation. We then present a new algorithm for the simulation of parton shower processes in high energy QCD. We want to find an algorithm which is free of negative weights, produces its output as a set of exclusive events, and whose total rate exactly matches the full Feynman amplitude calculation. Our strategy is to create the whole QCD shower as a tree structure generated by a multiple Poisson process. Working with the whole shower allows us to include correlations between gluon emissions from different sources. QCD destructive interference is controlled by the implementation of ''angular-ordering,'' as in the HERWIG Monte Carlo program. We discuss methods for systematic improvement of the approach to include higher order QCD effects.« less

Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations

NASA Astrophysics Data System (ADS)

Hao, Ge-Fei; Tan, Ying; Yu, Ning-Xi; Yang, Guang-Fu

2011-03-01

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4), which has been identified as a significant target for a great family of herbicides with diverse chemical structures, is the last common enzyme responsible for the seventh step in the biosynthetic pathway to heme and chlorophyll. Among the existing PPO inhibitors, diphenyl-ether is the first commercial family of PPO inhibitors and used as agriculture herbicides for decades. Most importantly, diphenyl-ether inhibitors have been found recently to possess the potential in Photodynamic therapy (PDT) to treat cancer. Herein, molecular dynamics simulations, approximate free energy calculations and hydrogen bond energy calculations were integrated together to uncover the structure-activity relationships of this type of PPO inhibitors. The calculated binding free energies are correlated very well with the values derived from the experimental k i data. According to the established computational models and the results of approximate free energy calculation, the substitution effects at different position were rationalized from the view of binding free energy. Some outlier ( e.g. LS) in traditional QSAR study can also be explained reasonably. In addition, the hydrogen bond energy calculation and interaction analysis results indicated that the carbonyl oxygen on position-9 and the NO2 group at position-8 are both vital for the electrostatic interaction with Arg98, which made a great contribution to the binding free energy. These insights from computational simulations are not only helpful for understanding the molecular mechanism of PPO-inhibitor interactions, but also beneficial to the future rational design of novel promising PPO inhibitors.

Hydrogen bonds and heat diffusion in α-helices: a computational study.

PubMed

Miño, German; Barriga, Raul; Gutierrez, Gonzalo

2014-08-28

Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we characterized the role of hydrogen bonds in diffusivity of thermal energy for two sets of α-helices with different abilities to form hydrogen bonds. These hydrogen bonds can be a constitutive part of the α-helices or can arise from the lateral chains. In our in vacuo simulations, it was observed that α-helices with a higher possibility of forming hydrogen bonds also had higher rates of thermalization. Our simulations also revealed that heat readily flowed through atoms involved in hydrogen bonds. As a general conclusion, according to our simulations, hydrogen bonds fulfilled an important role in heat diffusion in structural patters of proteins.

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.

Electron and optical properties of fullerene C70 within the conception of a strongly correlated state

NASA Astrophysics Data System (ADS)

Lobanov, B. V.; Murzashev, A. I.

2017-02-01

In the framework of the Hubbard model in the static fluctuation approximation, the energy spectrum of fullerene C70 with allowance for different lengths of the bonds between nonequivalent nodes is calculated. On the basis of the calculated energy spectrum, the optical absorption spectrum in the ultraviolet and visible region is simulated. A good qualitative agreement between the calculated and measured absorption spectra and between the measured and theoretical values of the gap width between the highest occupied and the lowest unoccupied molecular orbital is found.

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

Vaysset, Adrien; Manfrini, Mauricio; Pourtois, Geoffrey

The functionality of a cross-shaped Spin Torque Majority Gate is explored by means of micromagnetic simulations. The different input combinations are simulated varying material parameters, current density and size. The main failure mode is identified: above a critical size, a domain wall can be pinned at the center of the cross, preventing further propagation of the information. By simulating several phase diagrams, the key parameters are obtained and the operating condition is deduced. A simple relation between the domain wall width and the size of the Spin Torque Majority Gate determines the working range. Finally, a correlation is found betweenmore » the energy landscape and the main failure mode. We demonstrate that a macrospin behavior ensures a reliable majority gate operation.« less

Dark Energy Survey Year 1 results: the impact of galaxy neighbours on weak lensing cosmology with IM3SHAPE

DOE PAGES

Samuroff, S.

2017-12-26

We use a suite of simulated images based on Year 1 of the Dark Energy Survey to explore the impact of galaxy neighbours on shape measurement and shear cosmology. The hoopoe image simulations include realistic blending, galaxy positions, and spatial variations in depth and PSF properties. Using the im3shape maximum-likelihood shape measurement code, we identify four mechanisms by which neighbours can have a non-negligible influence on shear estimation. These effects, if ignored, would contribute a net multiplicative bias ofmore » $$m \\sim 0.03 - 0.09$$ in the DES Y1 im3shape catalogue, though the precise impact will be dependent on both the measurement code and the selection cuts applied. This can be reduced to percentage level or less by removing objects with close neighbours, at a cost to the effective number density of galaxies $$n_\\mathrm{eff}$$ of 30%. We use the cosmological inference pipeline of DES Y1 to explore the cosmological implications of neighbour bias and show that omitting blending from the calibration simulation for DES Y1 would bias the inferred clustering amplitude $$S_8\\equiv \\sigma_8 (\\Omega _\\mathrm{m} /0.3)^{0.5}$$ by $$2 \\sigma$$ towards low values. Lastly, we use the hoopoe simulations to test the effect of neighbour-induced spatial correlations in the multiplicative bias. We find the impact on the recovered $$S_8$$ of ignoring such correlations to be subdominant to statistical error at the current level of precision.« less

Dark Energy Survey Year 1 results: the impact of galaxy neighbours on weak lensing cosmology with IM3SHAPE

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

Samuroff, S.

We use a suite of simulated images based on Year 1 of the Dark Energy Survey to explore the impact of galaxy neighbours on shape measurement and shear cosmology. The hoopoe image simulations include realistic blending, galaxy positions, and spatial variations in depth and PSF properties. Using the im3shape maximum-likelihood shape measurement code, we identify four mechanisms by which neighbours can have a non-negligible influence on shear estimation. These effects, if ignored, would contribute a net multiplicative bias ofmore » $$m \\sim 0.03 - 0.09$$ in the DES Y1 im3shape catalogue, though the precise impact will be dependent on both the measurement code and the selection cuts applied. This can be reduced to percentage level or less by removing objects with close neighbours, at a cost to the effective number density of galaxies $$n_\\mathrm{eff}$$ of 30%. We use the cosmological inference pipeline of DES Y1 to explore the cosmological implications of neighbour bias and show that omitting blending from the calibration simulation for DES Y1 would bias the inferred clustering amplitude $$S_8\\equiv \\sigma_8 (\\Omega _\\mathrm{m} /0.3)^{0.5}$$ by $$2 \\sigma$$ towards low values. Lastly, we use the hoopoe simulations to test the effect of neighbour-induced spatial correlations in the multiplicative bias. We find the impact on the recovered $$S_8$$ of ignoring such correlations to be subdominant to statistical error at the current level of precision.« less

Simulation of the Indian Summer Monsoon Using Comprehensive Atmosphere-land Interactions, in the Absence of Two-way Air-sea Interactions

NASA Technical Reports Server (NTRS)

Lim, Young-Kwon; Shin, D. W.; Cocke, Steven; Kang, Sung-Dae; Kim, Hae-Dong

2011-01-01

Community Land Model version 2 (CLM2) as a comprehensive land surface model and a simple land surface model (SLM) were coupled to an atmospheric climate model to investigate the role of land surface processes in the development and the persistence of the South Asian summer monsoon. Two-way air-sea interactions were not considered in order to identify the reproducibility of the monsoon evolution by the comprehensive land model, which includes more realistic vertical soil moisture structures, vegetation and 2-way atmosphere-land interactions at hourly intervals. In the monsoon development phase (May and June). comprehensive land-surface treatment improves the representation of atmospheric circulations and the resulting convergence/divergence through the improvements in differential heating patterns and surface energy fluxes. Coupling with CLM2 also improves the timing and spatial distribution of rainfall maxima, reducing the seasonal rainfall overestimation by approx.60 % (1.8 mm/d for SLM, 0.7 mm/dI for CLM2). As for the interannual variation of the simulated rainfall, correlation coefficients of the Indian seasonal rainfall with observation increased from 0.21 (SLM) to 0.45 (CLM2). However, in the mature monsoon phase (July to September), coupling with the CLM2 does not exhibit a clear improvement. In contrast to the development phase, latent heat flux is underestimated and sensible heat flux and surface temperature over India are markedly overestimated. In addition, the moisture fluxes do not correlate well with lower-level atmospheric convergence, yielding correlation coefficients and root mean square errors worse than those produced by coupling with the SLM. A more realistic representation of the surface temperature and energy fluxes is needed to achieve an improved simulation for the mature monsoon period.

Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

PubMed

Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

2016-05-01

A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives. © 2015 John Wiley & Sons A/S.

Process engineering with planetary ball mills.

PubMed

Burmeister, Christine Friederike; Kwade, Arno

2013-09-21

Planetary ball mills are well known and used for particle size reduction on laboratory and pilot scales for decades while during the last few years the application of planetary ball mills has extended to mechanochemical approaches. Processes inside planetary ball mills are complex and strongly depend on the processed material and synthesis and, thus, the optimum milling conditions have to be assessed for each individual system. The present review focuses on the insight into several parameters like properties of grinding balls, the filling ratio or revolution speed. It gives examples of the aspects of grinding and illustrates some general guidelines to follow for modelling processes in planetary ball mills in terms of refinement, synthesis' yield and contamination from wear. The amount of energy transferred from the milling tools to the powder is significant and hardly measurable for processes in planetary ball mills. Thus numerical simulations based on a discrete-element-method are used to describe the energy transfer to give an adequate description of the process by correlation with experiments. The simulations illustrate the effect of the geometry of planetary ball mills on the energy entry. In addition the imaging of motion patterns inside a planetary ball mill from simulations and video recordings is shown.

Test of interaction models up to 40 PeV by studying hadronic cores of EAS

NASA Astrophysics Data System (ADS)

KASCADE Collaboration; Apel, W. D.; Badea, A. F.; Bekk, K.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Daumiller, K.; Doll, P.; Engel, R.; Engler, J.; Gils, H. J.; Glasstetter, R.; Haungs, A.; Heck, D.; Hörandel, J. R.; Kampert, K.-H.; Klages, H. O.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Oehlschläger, J.; Ostapchenko, S.; Petcu, M.; Pierog, T.; Rebel, H.; Risse, A.; Risse, M.; Roth, M.; Schatz, G.; Schieler, H.; Ulrich, H.; van Buren, J.; Weindl, A.; Wochele, J.; Zabierowski, J.

2007-12-01

The interpretation of extensive air shower measurements often requires a comparison with shower simulations in the atmosphere. These calculations rely on hadronic interaction models which have to extrapolate into kinematical and energy regions not explored by present-day collider experiments. The KASCADE experiment with its large hadron calorimeter and the detector array for the electromagnetic and muonic components provides experimental data to check such interaction models. For the simulations the program CORSIKA is used, which has several hadronic event generators embedded. For high-energy interactions (E_{\\rm{lab}}\\gtrsim100 \\ {\\rm{GeV}}) the models DPMJET, \\{\\sc NEX{\\sc US}} , QGSJET and SIBYLL have been used. Low-energy interactions have been treated by GHEISHA and FLUKA. Different hadronic observables are investigated as well as their correlations with the electromagnetic and muonic shower components up to primary energies of about 40 PeV. Although the predictions of the more recent models are to a large extent compatible with the measured data within the range given by proton and iron primary particles, there are still significant differences between the individual models.

The influence of compressibility on nonlinear spectral energy transfer - Part 1: Fundamental mechanisms

NASA Astrophysics Data System (ADS)

Praturi, Divya Sri; Girimaji, Sharath

2017-11-01

Nonlinear spectral energy transfer by triadic interactions is one of the foundational processes in fluid turbulence. Much of our current knowledge of this process is contingent upon pressure being a Lagrange multiplier with the only function of re-orienting the velocity wave vector. In this study, we examine how the nonlinear spectral transfer is affected in compressible turbulence when pressure is a true thermodynamic variable with a wave character. We perform direct numerical simulations of multi-mode evolution at different turbulent Mach numbers of Mt = 0.03 , 0.6 . Simulations are performed with initial modes that are fully solenoidal, fully dilatational and mixed solenoidal-dilatational. It is shown that solenoidal-solenoidal interactions behave in canonical manner at all Mach numbers. However, dilatational and mixed mode interactions are profoundly different. This is due to the fact that wave-pressure leads to kinetic-internal energy exchange via the pressure-dilatation mechanism. An important consequence of this exchange is that the triple correlation term, responsible for spectral transfer, experiences non-monotonic behavior resulting in inefficient energy transfer to other modes.

Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases.

PubMed

Sadiq, S Kashif; Wright, David W; Kenway, Owain A; Coveney, Peter V

2010-05-24

Accurate calculation of important thermodynamic properties, such as macromolecular binding free energies, is one of the principal goals of molecular dynamics simulations. However, single long simulation frequently produces incorrectly converged quantitative results due to inadequate sampling of conformational space in a feasible wall-clock time. Multiple short (ensemble) simulations have been shown to explore conformational space more effectively than single long simulations, but the two methods have not yet been thermodynamically compared. Here we show that, for end-state binding free energy determination methods, ensemble simulations exhibit significantly enhanced thermodynamic sampling over single long simulations and result in accurate and converged relative binding free energies that are reproducible to within 0.5 kcal/mol. Completely correct ranking is obtained for six HIV-1 protease variants bound to lopinavir with a correlation coefficient of 0.89 and a mean relative deviation from experiment of 0.9 kcal/mol. Multidrug resistance to lopinavir is enthalpically driven and increases through a decrease in the protein-ligand van der Waals interaction, principally due to the V82A/I84V mutation, and an increase in net electrostatic repulsion due to water-mediated disruption of protein-ligand interactions in the catalytic region. Furthermore, we correctly rank, to within 1 kcal/mol of experiment, the substantially increased chemical potency of lopinavir binding to the wild-type protease compared to saquinavir and show that lopinavir takes advantage of a decreased net electrostatic repulsion to confer enhanced binding. Our approach is dependent on the combined use of petascale computing resources and on an automated simulation workflow to attain the required level of sampling and turn around time to obtain the results, which can be as little as three days. This level of performance promotes integration of such methodology with clinical decision support systems for the optimization of patient-specific therapy.

Evaluating MRI based vascular wall motion as a biomarker of Fontan hemodynamic performance

NASA Astrophysics Data System (ADS)

Menon, Prahlad G.; Hong, Haifa

2015-03-01

The Fontan procedure for single-ventricle heart disease involves creation of pathways to divert venous blood from the superior & inferior venacavae (SVC, IVC) directly into the pulmonary arteries (PA), bypassing the right ventricle. For optimal surgical outcomes, venous flow energy loss in the resulting vascular construction must be minimized and ensuring close to equal flow distribution from the Fontan conduit connecting IVC to the left & right PA is paramount. This requires patient-specific hemodynamic evaluation using computational fluid dynamics (CFD) simulations which are often time and resource intensive, limiting applicability for real-time patient management in the clinic. In this study, we report preliminary efforts at identifying a new non-invasive imaging based surrogate for CFD simulated hemodynamics. We establish correlations between computed hemodynamic criteria from CFD modeling and cumulative wall displacement characteristics of the Fontan conduit quantified from cine cardiovascular MRI segmentations over time (i.e. 20 cardiac phases gated from the start of ventricular systole), in 5 unique Fontan surgical connections. To focus our attention on diameter variations while discounting side-to-side swaying motion of the Fontan conduit, the difference between its instantaneous regional expansion and inward contraction (averaged across the conduit) was computed and analyzed. Maximum Fontan conduit-average expansion over the cardiac cycle correlated with the anatomy-specific diametric offset between the axis of the IVC and SVC (r2=0.13, p=0.55) - a known factor correlated with Fontan energy loss and IVC-to-PA flow distribution. Investigation in a larger study cohort is needed to establish stronger statistical correlations.

Scale-invariant structure of energy fluctuations in real earthquakes

NASA Astrophysics Data System (ADS)

Wang, Ping; Chang, Zhe; Wang, Huanyu; Lu, Hong

2017-11-01

Earthquakes are obviously complex phenomena associated with complicated spatiotemporal correlations, and they are generally characterized by two power laws: the Gutenberg-Richter (GR) and the Omori-Utsu laws. However, an important challenge has been to explain two apparently contrasting features: the GR and Omori-Utsu laws are scale-invariant and unaffected by energy or time scales, whereas earthquakes occasionally exhibit a characteristic energy or time scale, such as with asperity events. In this paper, three high-quality datasets on earthquakes were used to calculate the earthquake energy fluctuations at various spatiotemporal scales, and the results reveal the correlations between seismic events regardless of their critical or characteristic features. The probability density functions (PDFs) of the fluctuations exhibit evidence of another scaling that behaves as a q-Gaussian rather than random process. The scaling behaviors are observed for scales spanning three orders of magnitude. Considering the spatial heterogeneities in a real earthquake fault, we propose an inhomogeneous Olami-Feder-Christensen (OFC) model to describe the statistical properties of real earthquakes. The numerical simulations show that the inhomogeneous OFC model shares the same statistical properties with real earthquakes.

Enabling Computational Nanotechnology through JavaGenes in a Cycle Scavenging Environment

NASA Technical Reports Server (NTRS)

Globus, Al; Menon, Madhu; Srivastava, Deepak; Biegel, Bryan A. (Technical Monitor)

2002-01-01

A genetic algorithm procedure is developed and implemented for fitting parameters for many-body inter-atomic force field functions for simulating nanotechnology atomistic applications using portable Java on cycle-scavenged heterogeneous workstations. Given a physics based analytic functional form for the force field, correlated parameters in a multi-dimensional environment are typically chosen to fit properties given either by experiments and/or by higher accuracy quantum mechanical simulations. The implementation automates this tedious procedure using an evolutionary computing algorithm operating on hundreds of cycle-scavenged computers. As a proof of concept, we demonstrate the procedure for evaluating the Stillinger-Weber (S-W) potential by (a) reproducing the published parameters for Si using S-W energies in the fitness function, and (b) evolving a "new" set of parameters using semi-empirical tightbinding energies in the fitness function. The "new" parameters are significantly better suited for Si cluster energies and forces as compared to even the published S-W potential.

Characterization of high energy Xe ion irradiation effects in single crystal molybdenum with depth-resolved synchrotron microbeam diffraction

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

Yun, Di; Miao, Yinbin; Xu, Ruqing

2016-04-01

Microbeam X-ray diffraction experiments were conducted at beam line 34-ID of the Advanced Photon Source (APS) on fission fragment energy Xe heavy ion irradiated single crystal Molybdenum (Mo). Lattice strain measurements were obtained with a depth resolution of 0.7 mu m, which is critical in resolving the peculiar heterogeneity of irradiation damage associated with heavy ion irradiation. Q-space diffraction peak shift measurements were correlated with lattice strain induced by the ion irradiations. Transmission electron microscopy (TEM) characterizations were performed on the as-irradiated materials as well. Nanometer sized Xe bubble microstructures were observed via TEM. Molecular Dynamics (MD) simulations were performedmore » to help interpret the lattice strain measurement results from the experiment. This study showed that the irradiation effects by fission fragment energy Xe ion irradiations can be collaboratively understood with the depth resolved X-ray diffraction and TEM measurements under the assistance of MD simulations. (c) 2015 Elsevier B.V. All rights reserved.« less

Finite Element Simulation for Analysing the Design and Testing of an Energy Absorption System

PubMed Central

Segade, Abraham; López-Campos, José A.; Fernández, José R.; Casarejos, Enrique; Vilán, José A.

2016-01-01

It is not uncommon to use profiles to act as energy absorption parts in vehicle safety systems. This work analyses an impact attenuator based on a simple design and discusses the use of a thermoplastic material. We present the design of the impact attenuator and a mechanical test for the prototype. We develop a simulation model using the finite element method and explicit dynamics, and we evaluate the most appropriate mesh size and integration for describing the test results. Finally, we consider the performance of different materials, metallic ones (steel AISI 4310, Aluminium 5083-O) and a thermoplastic foam (IMPAXX500™). This reflects the car industry’s interest in using new materials to make high-performance, low-mass energy absorbers. We show the strength of the models when it comes to providing reliable results for large deformations and strong non-linearities, and how they are highly correlated with respect to the test results both in value and behaviour. PMID:28773778

Ab Initio Quantum Monte Carlo Simulation of the Warm Dense Electron Gas in the Thermodynamic Limit

DOE PAGES

Dornheim, Tobias; Groth, Simon; Sjostrom, Travis; ...

2016-10-07

Here we perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N = 1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy F xc of the macroscopic electron gas withmore » an unprecedented accuracy of | Δ V | / | V | , | Δ F xc | / | F | xc ~ 10 $-$3. Finally, a comparison of our new data to the recent parametrization of F xc by Karasiev et al. [Phys. Rev. Lett. 112, 076403 (2014)] reveals significant deviations to the latter.« less

Impact of asymmetric martensite and austenite nucleation and growth behavior on the phase stability and hysteresis of freestanding shape-memory nanoparticles

NASA Astrophysics Data System (ADS)

Ko, Won-Seok; Grabowski, Blazej; Neugebauer, Jörg

2018-03-01

Martensitic transformations in nanoscaled shape-memory alloys exhibit characteristic features absent for the bulk counterparts. Detailed understanding is required for applications in micro- and nanoelectromechanical systems, and experimental limitations render atomistic simulation an important complementary approach. Using a recently developed, accurate potential we investigate the phase transformation in freestanding Ni-Ti shape-memory nanoparticles with molecular-dynamics simulations. The results confirm that the decrease in the transformation temperature with decreasing particle size is correlated with an overstabilization of the austenitic surface energy over the martensitic surface energy. However, a detailed atomistic analysis of the nucleation and growth behavior reveals an unexpected difference in the mechanisms determining the austenite finish and martensite start temperature. While the austenite finish temperature is directly affected by a contribution of the surface energy difference, the martensite start temperature is mostly affected by the transformation strain, contrary to general expectations. This insight not only explains the reduced transformation temperature but also the reduced thermal hysteresis in freestanding nanoparticles.

Ab initio molecular dynamics simulations of low energy recoil events in MgO

DOE PAGES

Petersen, B. A.; Liu, B.; Weber, W. J.; ...

2017-01-11

In this paper, low-energy recoil events in MgO are studied using ab initio molecular dynamics simulations to reveal the dynamic displacement processes and final defect configurations. Threshold displacement energies, E d, are obtained for Mg and O along three low-index crystallographic directions, [100], [110], and [111]. The minimum values for E d are found along the [110] direction consisting of the same element, either Mg or O atoms. Minimum threshold values of 29.5 eV for Mg and 25.5 eV for O, respectively, are suggested from the calculations. For other directions, the threshold energies are considerably higher, 65.5 and 150.0 eVmore » for O along [111] and [100], and 122.5 eV for Mg along both [111] and [100] directions, respectively. These results show that the recoil events in MgO are partial-charge transfer assisted processes where the charge transfer plays an important role. Finally, there is a similar trend found in other oxide materials, where the threshold displacement energy correlates linearly with the peak partial-charge transfer, suggesting this behavior might be universal in ceramic oxides.« less

Meso-scale investigation of anaerobic chemical reactivity of Ti-Al-B powder mixtures under impact loading

NASA Astrophysics Data System (ADS)

Gonzales, Manny; Gurumurthy, Ashok; Gokhale, Arun; Thadhani, Naresh N.

2011-06-01

Impact-initiated anaerobic chemical reactions in Ti-Al-B reactive powder mixtures under uniaxial stress conditions are investigated using a coupled experimental/computational approach. In particular, we characterize the effects of bulk composition on the threshold impact energy to initiate reaction using rod-on-anvil type tests performed on Ti-Al-B powder compacts. Statistical volume elements (SVEs) of different bulk compositions of the powder mixtures are analyzed using the continuum hydrocode CTH to quantify the effects of strain confinement and load configuration on the overall energy of the structure. These SVEs are also validated using one-point correlation functions to characterize the volume fraction and surface area of the constituents. Based on the deformation profiles from the continuum simulations, we investigate the effect of particle size distribution and clustering of Ti and B on the threshold energy required for observed reactivity. The deformation and threshold kinetic energy of the simulated system is compared with published values of the activation energy for Ti+B reactions and Al combustion in air to assess the extent of their impact-initiated reactivity. Funded by DTRA grant No. HDTRA1-10-1-0038

New opportunities in the study of in-medium nuclear properties with FAZIA

NASA Astrophysics Data System (ADS)

Gruyer, Diego; Frankland, John D.

2017-11-01

In this contribution we investigate the capabilities (resolution and efficiency) of the FAZIA demonstrator, with a particular emphasis on light cluster structure studies (excited state energy, width, and spin) and emitting source characterization (temperature and density), using multi-particle correlations. This study has been performed on simulated ^{32}{S}+^{12} C collisions from 25 to 80MeV/A.

Standardized performance tests of collectors of solar thermal energy-a flat-plate collector with a single-tube serpentine flow distribution

NASA Technical Reports Server (NTRS)

Johnson, S.

1976-01-01

This preliminary data report gives basic test results of a flat-plate solar collector whose performance was determined in the NASA-Lewis solar simulator. The collector was tested over ranges of inlet temperatures, fluxes and coolant flow rates. Collector efficienty is correlated in terms of inlet temperature and flux level.

Dark Energy Survey Year 1 results: cross-correlation redshifts - methods and systematics characterization

NASA Astrophysics Data System (ADS)

Gatti, M.; Vielzeuf, P.; Davis, C.; Cawthon, R.; Rau, M. M.; DeRose, J.; De Vicente, J.; Alarcon, A.; Rozo, E.; Gaztanaga, E.; Hoyle, B.; Miquel, R.; Bernstein, G. M.; Bonnett, C.; Carnero Rosell, A.; Castander, F. J.; Chang, C.; da Costa, L. N.; Gruen, D.; Gschwend, J.; Hartley, W. G.; Lin, H.; MacCrann, N.; Maia, M. A. G.; Ogando, R. L. C.; Roodman, A.; Sevilla-Noarbe, I.; Troxel, M. A.; Wechsler, R. H.; Asorey, J.; Davis, T. M.; Glazebrook, K.; Hinton, S. R.; Lewis, G.; Lidman, C.; Macaulay, E.; Möller, A.; O'Neill, C. R.; Sommer, N. E.; Uddin, S. A.; Yuan, F.; Zhang, B.; Abbott, T. M. C.; Allam, S.; Annis, J.; Bechtol, K.; Brooks, D.; Burke, D. L.; Carollo, D.; Carrasco Kind, M.; Carretero, J.; Cunha, C. E.; D'Andrea, C. B.; DePoy, D. L.; Desai, S.; Eifler, T. F.; Evrard, A. E.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Goldstein, D. A.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; Hoormann, J. K.; Jain, B.; James, D. J.; Jarvis, M.; Jeltema, T.; Johnson, M. W. G.; Johnson, M. D.; Krause, E.; Kuehn, K.; Kuhlmann, S.; Kuropatkin, N.; Li, T. S.; Lima, M.; Marshall, J. L.; Melchior, P.; Menanteau, F.; Nichol, R. C.; Nord, B.; Plazas, A. A.; Reil, K.; Rykoff, E. S.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sheldon, E.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Tucker, B. E.; Tucker, D. L.; Vikram, V.; Walker, A. R.; Weller, J.; Wester, W.; Wolf, R. C.

2018-06-01

We use numerical simulations to characterize the performance of a clustering-based method to calibrate photometric redshift biases. In particular, we cross-correlate the weak lensing source galaxies from the Dark Energy Survey Year 1 sample with redMaGiC galaxies (luminous red galaxies with secure photometric redshifts) to estimate the redshift distribution of the former sample. The recovered redshift distributions are used to calibrate the photometric redshift bias of standard photo-z methods applied to the same source galaxy sample. We apply the method to two photo-z codes run in our simulated data: Bayesian Photometric Redshift and Directional Neighbourhood Fitting. We characterize the systematic uncertainties of our calibration procedure, and find that these systematic uncertainties dominate our error budget. The dominant systematics are due to our assumption of unevolving bias and clustering across each redshift bin, and to differences between the shapes of the redshift distributions derived by clustering versus photo-zs. The systematic uncertainty in the mean redshift bias of the source galaxy sample is Δz ≲ 0.02, though the precise value depends on the redshift bin under consideration. We discuss possible ways to mitigate the impact of our dominant systematics in future analyses.

Molecular dynamics analysis of a equilibrium nanoscale droplet on a solid surface with periodic roughness

NASA Astrophysics Data System (ADS)

Furuta, Yuma; Surblys, Donatas; Yamaguchi, Yastaka

2016-11-01

Molecular dynamics simulations of the equilibrium wetting behavior of hemi-cylindrical argon droplets on solid surfaces with a periodic roughness were carried out. The rough solid surface is located at the bottom of the calculation cell with periodic boundary conditions in surface lateral directions and mirror boundary condition at the top boundary. Similar to on a smooth surface, the change of the cosine of the droplet contact angle was linearly correlated to the potential well depth of the inter-atomic interaction between liquid and solid on a surface with a short roughness period while the correlation was deviated on one with a long roughness period. To further investigate this feature, solid-liquid, solid-vapor interfacial free energies per unit projected area of solid surface were evaluated by using the thermodynamic integration method in independent quasi-one-dimensional simulation systems with a liquid-solid interface or vapor-solid interface on various rough solid surfaces at a constant pressure. The cosine of the apparent contact angles estimated from the density profile of the droplet systems corresponded well with ones calculated from Young's equation using the interfacial energies evaluated in the quasi-one dimensional systems.

Radial dependence of solar energetic particles derived from the 15 March 2013 solar energetic particle event and global MHD simulation

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

Wu, Chin-Chun, E-mail: chin-chun.wu@nrl.navy.mil; Plunkett, Simon, E-mail: simon.plunkett@nrl.navy.mil; Liou, Kan, E-mail: kan.liou@jhuapl.edu

2016-03-25

We study an unusual solar energetic particle (SEP) event that was associated with the coronal mass ejection (CME) on March 15, 2013. Enhancements of the SEP fluxes were first detected by the ACE spacecraft at 14:00 UT, ∼7 hours after the onset of the CME (07:00 UT), and the SEP’s peak intensities were recorded ∼36 hours after the onset of the CME. Our recent study showed that the CME-driven shock Mach number, based on a global three-dimensional (3-D) magnetohydrodynamic (MHD) simulation, is well correlated with the time-intensity of 10-30 MeV and 30-80 MeV protons. Here we focus on the radial dependence (r{supmore » −α}) of {sup 4}He (3.43-41.2 MeV/n) and O (7.30-89.8 MeV/n) energetic particles from ACE/SIS. It is found that the scaling factor (α) ranges between 2 and 4 for most of the energy channels. We also found that the correlation coefficients tend to increase with SEP energies.« less

Theoretical and numerical analyses of a slit-masked chicane for modulated bunch generation

DOE PAGES

Zhu, Xiaofang; Broemmelsiek, Daniel R.; Shin, Young -Min; ...

2015-10-28

Density modulations on electron beams can improve machine performance of beam-driven accelerators and FELs with resonance beam-wave coupling. The beam modulation is studied with a masked chicane by the analytic model and simulations with the beam parameters of the Fermilab Accelerator Science and Technology (FAST) facility. With the chicane design parameters (bending angle of 18o, bending radius of 0.95 m and R 56 ~ –0.19 m) and a nominal beam of 3 ps bunch length, the analytic model showed that a slit-mask with slit period 900 μ m and aperture width 300 μ m induces a modulation of bunch-to-bunch spacingmore » ~ 100 μ m to the bunch with 2.4% correlated energy spread. With the designed slit mask and a 3 ps bunch, particle-in-cell (PIC) simulations, including nonlinear energy distributions, space charge force, and coherent synchrotron radiation (CSR) effect, also result in beam modulation with bunch-to-bunch distance around 100 μ m and a corresponding modulation frequency of 3 THz. The beam modulation has been extensively examined with three different beam conditions, 2.25 ps (0.25 nC), 3.25 ps (1 nC), and 4.75 ps (3.2 nC), by tracking code Elegant. The simulation analysis indicates that the sliced beam by the slit-mask with 3 ~ 6% correlated energy spread has modulation lengths about 187 μ m (0.25 nC), 270 μ m (1 nC) and 325 μ m (3.2 nC). As a result, the theoretical and numerical data proved the capability of the designed masked chicane in producing modulated bunch train with micro-bunch length around 100 fs.« less

Theoretical and numerical analyses of a slit-masked chicane for modulated bunch generation

NASA Astrophysics Data System (ADS)

Zhu, X.; Broemmelsiek, D. R.; Shin, Y.-M.

2015-10-01

Density modulations on electron beams can improve machine performance of beam-driven accelerators and FELs with resonance beam-wave coupling. The beam modulation is studied with a masked chicane by the analytic model and simulations with the beam parameters of the Fermilab Accelerator Science and Technology (FAST) facility. With the chicane design parameters (bending angle of 18o, bending radius of 0.95 m and R56 ~ -0.19 m) and a nominal beam of 3 ps bunch length, the analytic model showed that a slit-mask with slit period 900 μ m and aperture width 300 μ m induces a modulation of bunch-to-bunch spacing ~ 100 μ m to the bunch with 2.4% correlated energy spread. With the designed slit mask and a 3 ps bunch, particle-in-cell (PIC) simulations, including nonlinear energy distributions, space charge force, and coherent synchrotron radiation (CSR) effect, also result in beam modulation with bunch-to-bunch distance around 100 μ m and a corresponding modulation frequency of 3 THz. The beam modulation has been extensively examined with three different beam conditions, 2.25 ps (0.25 nC), 3.25 ps (1 nC), and 4.75 ps (3.2 nC), by tracking code Elegant. The simulation analysis indicates that the sliced beam by the slit-mask with 3 ~ 6% correlated energy spread has modulation lengths about 187 μ m (0.25 nC), 270 μ m (1 nC) and 325 μ m (3.2 nC). The theoretical and numerical data proved the capability of the designed masked chicane in producing modulated bunch train with micro-bunch length around 100 fs.

Finite-mode spectral model of homogeneous and isotropic Navier-stokes turbulence: a rapidly depleted energy cascade.

PubMed

Lévêque, E; Koudella, C R

2001-04-30

An eddy-viscous term is added to Navier-Stokes dynamics at wave numbers k greater than the inflection point kc of the energy flux F(log(k)). The eddy viscosity is fixed so that the energy spectrum satisfies E(k) = E(kc) (k/kc)(-3) for k>kc. This resulting forcing induces a rapid depletion of the energy cascade at k>kc. It is observed numerically that the model reproduces turbulence energetics at k< or =kc and statistics of two-point velocity correlations at scales r>lambda (Taylor microscale). Compared to a direct numerical simulation of R(lambda) = 130 an equivalent run with the present model results in a gain of a factor 20 in CPU time.

Optimization of design parameters of low-energy buildings

NASA Astrophysics Data System (ADS)

Vala, Jiří; Jarošová, Petra

2017-07-01

Evaluation of temperature development and related consumption of energy required for heating, air-conditioning, etc. in low-energy buildings requires the proper physical analysis, covering heat conduction, convection and radiation, including beam and diffusive components of solar radiation, on all building parts and interfaces. The system approach and the Fourier multiplicative decomposition together with the finite element technique offers the possibility of inexpensive and robust numerical and computational analysis of corresponding direct problems, as well as of the optimization ones with several design variables, using the Nelder-Mead simplex method. The practical example demonstrates the correlation between such numerical simulations and the time series of measurements of energy consumption on a small family house in Ostrov u Macochy (35 km northern from Brno).

Water and Carbon Dioxide Adsorption at Olivine Surfaces

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

Kerisit, Sebastien N.; Bylaska, Eric J.; Felmy, Andrew R.

2013-11-14

Plane-wave density functional theory (DFT) calculations were performed to simulate water and carbon dioxide adsorption at the (010) surface of five olivine minerals, namely, forsterite (Mg2SiO4), calcio-olivine (Ca2SiO4), tephroite (Mn2SiO4), fayalite (Fe2SiO4), and Co-olivine (Co2SiO4). Adsorption energies per water molecule obtained from energy minimizations varied from -78 kJ mol-1 for fayalite to -128 kJ mol-1 for calcio-olivine at sub-monolayer coverage and became less exothermic as coverage increased. In contrast, carbon dioxide adsorption energies at sub-monolayer coverage ranged from -20 kJ mol-1 for fayalite to -59 kJ mol-1 for calcio-olivine. Therefore, the DFT calculations show a strong driving force for carbonmore » dioxide displacement by water at the surface of all olivine minerals in a competitive adsorption scenario. Additionally, adsorption energies for both water and carbon dioxide were found to be more exothermic for the alkaline-earth (AE) olivines than for the transition-metal (TM) olivines and to not correlate with the solvation enthalpies of the corresponding divalent cations. However, a correlation was obtained with the charge of the surface divalent cation indicating that the more ionic character of the AE cations in the olivine structure relative to the TM cations leads to greater interactions with adsorbed water and carbon dioxide molecules at the surface and thus more exothermic adsorption energies for the AE olivines. For calcio-olivine, which exhibits the highest divalent cation charge of the five olivines, ab initio molecular dynamics simulations showed that this effect leads both water and carbon dioxide to react with the surface and form hydroxyl groups and a carbonate-like species, respectively.« less

A time-correlation function approach to nuclear dynamical effects in X-ray spectroscopy

NASA Astrophysics Data System (ADS)

Karsten, Sven; Bokarev, Sergey I.; Aziz, Saadullah G.; Ivanov, Sergei D.; Kühn, Oliver

2017-06-01

Modern X-ray spectroscopy has proven itself as a robust tool for probing the electronic structure of atoms in complex environments. Despite working on energy scales that are much larger than those corresponding to nuclear motions, taking nuclear dynamics and the associated nuclear correlations into account may be of importance for X-ray spectroscopy. Recently, we have developed an efficient protocol to account for nuclear dynamics in X-ray absorption and resonant inelastic X-ray scattering spectra [Karsten et al., J. Phys. Chem. Lett. 8, 992 (2017)], based on ground state molecular dynamics accompanied with state-of-the-art calculations of electronic excitation energies and transition dipoles. Here, we present an alternative derivation of the formalism and elaborate on the developed simulation protocol using gas phase and bulk water as examples. The specific spectroscopic features stemming from the nuclear motions are analyzed and traced down to the dynamics of electronic energy gaps and transition dipole correlation functions. The observed tendencies are explained on the basis of a simple harmonic model, and the involved approximations are discussed. The method represents a step forward over the conventional approaches that treat the system in full complexity and provides a reasonable starting point for further improvements.

A time-correlation function approach to nuclear dynamical effects in X-ray spectroscopy.

PubMed

Karsten, Sven; Bokarev, Sergey I; Aziz, Saadullah G; Ivanov, Sergei D; Kühn, Oliver

2017-06-14

Modern X-ray spectroscopy has proven itself as a robust tool for probing the electronic structure of atoms in complex environments. Despite working on energy scales that are much larger than those corresponding to nuclear motions, taking nuclear dynamics and the associated nuclear correlations into account may be of importance for X-ray spectroscopy. Recently, we have developed an efficient protocol to account for nuclear dynamics in X-ray absorption and resonant inelastic X-ray scattering spectra [Karsten et al., J. Phys. Chem. Lett. 8, 992 (2017)], based on ground state molecular dynamics accompanied with state-of-the-art calculations of electronic excitation energies and transition dipoles. Here, we present an alternative derivation of the formalism and elaborate on the developed simulation protocol using gas phase and bulk water as examples. The specific spectroscopic features stemming from the nuclear motions are analyzed and traced down to the dynamics of electronic energy gaps and transition dipole correlation functions. The observed tendencies are explained on the basis of a simple harmonic model, and the involved approximations are discussed. The method represents a step forward over the conventional approaches that treat the system in full complexity and provides a reasonable starting point for further improvements.

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

Costigliola, Lorenzo; Schrøder, Thomas B.; Dyre, Jeppe C.

The recent theoretical prediction by Maimbourg and Kurchan [e-print http://arxiv.org/abs/1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized bymore » high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.« less

Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors

NASA Astrophysics Data System (ADS)

Underwood, T. S. A.; Sung, W.; McFadden, C. H.; McMahon, S. J.; Hall, D. C.; McNamara, A. L.; Paganetti, H.; Sawakuchi, G. O.; Schuemann, J.

2017-04-01

Whilst Monte Carlo (MC) simulations of proton energy deposition have been well-validated at the macroscopic level, their microscopic validation remains lacking. Equally, no gold-standard yet exists for experimental metrology of individual proton tracks. In this work we compare the distributions of stochastic proton interactions simulated using the TOPAS-nBio MC platform against confocal microscope data for Al2O3:C,Mg fluorescent nuclear track detectors (FNTDs). We irradiated 8× 4× 0.5 mm3 FNTD chips inside a water phantom, positioned at seven positions along a pristine proton Bragg peak with a range in water of 12 cm. MC simulations were implemented in two stages: (1) using TOPAS to model the beam properties within a water phantom and (2) using TOPAS-nBio with Geant4-DNA physics to score particle interactions through a water surrogate of Al2O3:C,Mg. The measured median track integrated brightness (IB) was observed to be strongly correlated to both (i) voxelized track-averaged linear energy transfer (LET) and (ii) frequency mean microdosimetric lineal energy, \\overline{{{y}F}} , both simulated in pure water. Histograms of FNTD track IB were compared against TOPAS-nBio histograms of the number of terminal electrons per proton, scored in water with mass-density scaled to mimic Al2O3:C,Mg. Trends between exposure depths observed in TOPAS-nBio simulations were experimentally replicated in the study of FNTD track IB. Our results represent an important first step towards the experimental validation of MC simulations on the sub-cellular scale and suggest that FNTDs can enable experimental study of the microdosimetric properties of individual proton tracks.

Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors.

PubMed

Underwood, T S A; Sung, W; McFadden, C H; McMahon, S J; Hall, D C; McNamara, A L; Paganetti, H; Sawakuchi, G O; Schuemann, J

2017-04-21

Whilst Monte Carlo (MC) simulations of proton energy deposition have been well-validated at the macroscopic level, their microscopic validation remains lacking. Equally, no gold-standard yet exists for experimental metrology of individual proton tracks. In this work we compare the distributions of stochastic proton interactions simulated using the TOPAS-nBio MC platform against confocal microscope data for Al 2 O 3 :C,Mg fluorescent nuclear track detectors (FNTDs). We irradiated [Formula: see text] mm 3 FNTD chips inside a water phantom, positioned at seven positions along a pristine proton Bragg peak with a range in water of 12 cm. MC simulations were implemented in two stages: (1) using TOPAS to model the beam properties within a water phantom and (2) using TOPAS-nBio with Geant4-DNA physics to score particle interactions through a water surrogate of Al 2 O 3 :C,Mg. The measured median track integrated brightness (IB) was observed to be strongly correlated to both (i) voxelized track-averaged linear energy transfer (LET) and (ii) frequency mean microdosimetric lineal energy, [Formula: see text], both simulated in pure water. Histograms of FNTD track IB were compared against TOPAS-nBio histograms of the number of terminal electrons per proton, scored in water with mass-density scaled to mimic Al 2 O 3 :C,Mg. Trends between exposure depths observed in TOPAS-nBio simulations were experimentally replicated in the study of FNTD track IB. Our results represent an important first step towards the experimental validation of MC simulations on the sub-cellular scale and suggest that FNTDs can enable experimental study of the microdosimetric properties of individual proton tracks.

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Interaction of amino acids with the Au(111) surface: adsorption free energies from molecular dynamics simulations.

PubMed

Hoefling, Martin; Iori, Francesco; Corni, Stefano; Gottschalk, Kay-Eberhard

2010-06-01

Interactions of proteins with inorganic surfaces are of high importance in biological events and in modern biotechnological applications. Therefore, peptides have been engineered to recognize inorganic surfaces with high specificity. However, the underlying interactions are still not well understood. Here, we investigated the adsorption of amino acids as protein building blocks onto a Au(111) surface. In particular, using molecular dynamics simulations, we calculated the potential of mean force between all the 20 amino acids and the gold surface. We found a strong dependence of the binding affinities on the chemical character of the amino acids. Additionally, the interaction free energy is correlated with the propensity of amino acids to form beta-sheets, hinting at design principles for gold binding peptides and induction of beta-sheet formation near surfaces.

ASPEN simulation of a fixed-bed integrated gasification combined-cycle power plant

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

Stone, K.R.

1986-03-01

A fixed-bed integrated gasification combined-cycle (IGCC) power plant has been modeled using the Advanced System for Process ENgineering (ASPEN). The ASPEN simulation is based on a conceptual design of a 509-MW IGCC power plant that uses British Gas Corporation (BGC)/Lurgi slagging gasifiers and the Lurgi acid gas removal process. The 39.3-percent thermal efficiency of the plant that was calculated by the simulation compares very favorably with the 39.4 percent that was reported by EPRI. The simulation addresses only thermal performance and does not calculate capital cost or process economics. Portions of the BGC-IGCC simulation flowsheet are based on the SLAGGERmore » fixed-bed gasifier model (Stefano May 1985), and the Kellogg-Rust-Westinghouse (KRW) iGCC, and the Texaco-IGCC simulations (Stone July 1985) that were developed at the Department of Energy (DOE), Morgantown Energy Technology Center (METC). The simulation runs in 32 minutes of Central Processing Unit (CPU) time on the VAX-11/780. The BGC-IGCC simulation was developed to give accurate mass and energy balances and to track coal tars and environmental species such as SO/sub x/ and NO/sub x/ for a fixed-bed, coal-to-electricity system. This simulation is the third in a series of three IGCC simulations that represent fluidized-bed, entrained-flow, and fixed-bed gasification processes. Alternate process configurations can be considered by adding, deleting, or rearranging unit operation blocks. The gasifier model is semipredictive; it can properly respond to a limited range of coal types and gasifier operating conditions. However, some models in the flowsheet are based on correlations that were derived from the EPRI study, and are therefore limited to coal types and operating conditions that are reasonably close to those given in the EPRI design. 4 refs., 7 figs., 2 tabs.« less

Simulation based energy-resource efficient manufacturing integrated with in-process virtual management

NASA Astrophysics Data System (ADS)

Katchasuwanmanee, Kanet; Cheng, Kai; Bateman, Richard

2016-09-01

As energy efficiency is one of the key essentials towards sustainability, the development of an energy-resource efficient manufacturing system is among the great challenges facing the current industry. Meanwhile, the availability of advanced technological innovation has created more complex manufacturing systems that involve a large variety of processes and machines serving different functions. To extend the limited knowledge on energy-efficient scheduling, the research presented in this paper attempts to model the production schedule at an operation process by considering the balance of energy consumption reduction in production, production work flow (productivity) and quality. An innovative systematic approach to manufacturing energy-resource efficiency is proposed with the virtual simulation as a predictive modelling enabler, which provides real-time manufacturing monitoring, virtual displays and decision-makings and consequentially an analytical and multidimensional correlation analysis on interdependent relationships among energy consumption, work flow and quality errors. The regression analysis results demonstrate positive relationships between the work flow and quality errors and the work flow and energy consumption. When production scheduling is controlled through optimization of work flow, quality errors and overall energy consumption, the energy-resource efficiency can be achieved in the production. Together, this proposed multidimensional modelling and analysis approach provides optimal conditions for the production scheduling at the manufacturing system by taking account of production quality, energy consumption and resource efficiency, which can lead to the key competitive advantages and sustainability of the system operations in the industry.

Structure-based multiscale approach for identification of interaction partners of PDZ domains.

PubMed

Tiwari, Garima; Mohanty, Debasisa

2014-04-28

PDZ domains are peptide recognition modules which mediate specific protein-protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ-peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ-peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ-peptide binding data for training.

Antibacterial drugs as corrosion inhibitors for bronze surfaces in acidic solutions

NASA Astrophysics Data System (ADS)

Rotaru, Ileana; Varvara, Simona; Gaina, Luiza; Muresan, Liana Maria

2014-12-01

The present study is aiming to investigate the effect of four antibiotics (amoxicillin, ciprofloxacin, doxycycline and streptomycin,) belonging to different classes of antibacterial drugs on bronze corrosion in a solution simulating an acid rain (pH 4). Due to their ability to form protective films on the metal surface, the tested antibiotics act as corrosion inhibitors for bronze. The antibiotics were tested at various concentrations in order to determine the optimal concentration range for the best corrosion inhibiting effect. In evaluating the inhibition efficiency, polarization curves, electrochemical impedance spectroscopy, SEM and XPS measurements were used. Moreover, a correlation between the inhibition efficiency of some antibacterial drugs and certain molecular parameters was determined by quantum chemical computations. Parameters like energies EHOMO and ELUMO and HOMO-LUMO energy gap were used for correlation with the corrosion data.

Probabilistic distribution and stochastic P-bifurcation of a hybrid energy harvester under colored noise

NASA Astrophysics Data System (ADS)

Mokem Fokou, I. S.; Nono Dueyou Buckjohn, C.; Siewe Siewe, M.; Tchawoua, C.

2018-03-01

In this manuscript, a hybrid energy harvesting system combining piezoelectric and electromagnetic transduction and subjected to colored noise is investigated. By using the stochastic averaging method, the stationary probability density functions of amplitudes are obtained and reveal interesting dynamics related to the long term behavior of the device. From stationary probability densities, we discuss the stochastic bifurcation through the qualitative change which shows that noise intensity, correlation time and other system parameters can be treated as bifurcation parameters. Numerical simulations are made for a comparison with analytical findings. The Mean first passage time (MFPT) is numerical provided in the purpose to investigate the system stability. By computing the Mean residence time (TMR), we explore the stochastic resonance phenomenon; we show how it is related to the correlation time of colored noise and high output power.

Analytical expressions for the log-amplitude correlation function of a plane wave through anisotropic atmospheric refractive turbulence.

PubMed

Gudimetla, V S Rao; Holmes, Richard B; Smith, Carey; Needham, Gregory

2012-05-01

The effect of anisotropic Kolmogorov turbulence on the log-amplitude correlation function for plane-wave fields is investigated using analysis, numerical integration, and simulation. A new analytical expression for the log-amplitude correlation function is derived for anisotropic Kolmogorov turbulence. The analytic results, based on the Rytov approximation, agree well with a more general wave-optics simulation based on the Fresnel approximation as well as with numerical evaluations, for low and moderate strengths of turbulence. The new expression reduces correctly to previously published analytic expressions for isotropic turbulence. The final results indicate that, as asymmetry becomes greater, the Rytov variance deviates from that given by the standard formula. This deviation becomes greater with stronger turbulence, up to moderate turbulence strengths. The anisotropic effects on the log-amplitude correlation function are dominant when the separation of the points is within the Fresnel length. In the direction of stronger turbulence, there is an enhanced dip in the correlation function at a separation close to the Fresnel length. The dip is diminished in the weak-turbulence axis, suggesting that energy redistribution via focusing and defocusing is dominated by the strong-turbulence axis. The new analytical expression is useful when anisotropy is observed in relevant experiments. © 2012 Optical Society of America

Design of a composite filter realizable on practical spatial light modulators

NASA Technical Reports Server (NTRS)

Rajan, P. K.; Ramakrishnan, Ramachandran

1994-01-01

Hybrid optical correlator systems use two spatial light modulators (SLM's), one at the input plane and the other at the filter plane. Currently available SLM's such as the deformable mirror device (DMD) and liquid crystal television (LCTV) SLM's exhibit arbitrarily constrained operating characteristics. The pattern recognition filters designed with the assumption that the SLM's have ideal operating characteristic may not behave as expected when implemented on the DMD or LCTV SLM's. Therefore it is necessary to incorporate the SLM constraints in the design of the filters. In this report, an iterative method is developed for the design of an unconstrained minimum average correlation energy (MACE) filter. Then using this algorithm a new approach for the design of a SLM constrained distortion invariant filter in the presence of input SLM is developed. Two different optimization algorithms are used to maximize the objective function during filter synthesis, one based on the simplex method and the other based on the Hooke and Jeeves method. Also, the simulated annealing based filter design algorithm proposed by Khan and Rajan is refined and improved. The performance of the filter is evaluated in terms of its recognition/discrimination capabilities using computer simulations and the results are compared with a simulated annealing optimization based MACE filter. The filters are designed for different LCTV SLM's operating characteristics and the correlation responses are compared. The distortion tolerance and the false class image discrimination qualities of the filter are comparable to those of the simulated annealing based filter but the new filter design takes about 1/6 of the computer time taken by the simulated annealing filter design.

Numerical and experimental validation for the thermal transmittance of windows with cellular shades

DOE PAGES

Hart, Robert

2018-02-21

Some highly energy efficient window attachment products are available today, but more rapid market adoption would be facilitated by fair performance metrics. It is important to have validated simulation tools to provide a basis for this analysis. This paper outlines a review and validation of the ISO 15099 center-of-glass zero-solar-load heat transfer correlations for windows with cellular shades. Thermal transmittance was measured experimentally, simulated using computational fluid dynamics (CFD) analysis, and simulated utilizing correlations from ISO 15099 as implemented in Berkeley Lab WINDOW and THERM software. CFD analysis showed ISO 15099 underestimates heat flux of rectangular cavities by up tomore » 60% when aspect ratio (AR) = 1 and overestimates heat flux up to 20% when AR = 0.5. CFD analysis also showed that wave-type surfaces of cellular shades have less than 2% impact on heat flux through the cavities and less than 5% for natural convection of room-side surface. WINDOW was shown to accurately represent heat flux of the measured configurations to a mean relative error of 0.5% and standard deviation of 3.8%. Finally, several shade parameters showed significant influence on correlation accuracy, including distance between shade and glass, inconsistency in cell stretch, size of perimeter gaps, and the mounting hardware.« less

Numerical and experimental validation for the thermal transmittance of windows with cellular shades

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

Hart, Robert

Some highly energy efficient window attachment products are available today, but more rapid market adoption would be facilitated by fair performance metrics. It is important to have validated simulation tools to provide a basis for this analysis. This paper outlines a review and validation of the ISO 15099 center-of-glass zero-solar-load heat transfer correlations for windows with cellular shades. Thermal transmittance was measured experimentally, simulated using computational fluid dynamics (CFD) analysis, and simulated utilizing correlations from ISO 15099 as implemented in Berkeley Lab WINDOW and THERM software. CFD analysis showed ISO 15099 underestimates heat flux of rectangular cavities by up tomore » 60% when aspect ratio (AR) = 1 and overestimates heat flux up to 20% when AR = 0.5. CFD analysis also showed that wave-type surfaces of cellular shades have less than 2% impact on heat flux through the cavities and less than 5% for natural convection of room-side surface. WINDOW was shown to accurately represent heat flux of the measured configurations to a mean relative error of 0.5% and standard deviation of 3.8%. Finally, several shade parameters showed significant influence on correlation accuracy, including distance between shade and glass, inconsistency in cell stretch, size of perimeter gaps, and the mounting hardware.« less

Grain Boundary Character Distributions In Isostructural Materials

NASA Astrophysics Data System (ADS)

Ratanaphan, Sutatch

Anisotropic grain boundary character distributions (GBCDs), which influence macroscopic materials properties, are thought to be controlled by the grain boundary energy anisotropy. Structurally, grain boundary could be viewed as two free surfaces joined together. Grain boundary energy could be simply defined by the total excess energy for creating two free surfaces minus the energy gained when new bonds are formed between these surfaces. This implies that different crystal structure should have different GBEDs and GBCDs. It was recently discovered that grain boundary energy distributions (GBED) in isostructural materials, a class of materials that share the same crystal structure, are directly related to one another. This suggests that GBCDs in isostructural materials might also be related in a similar way. To test this hypothesis, electron backscatter diffraction (EBSD) was used to map grain orientations in Ag, Au, Cu, Fe, and Mo. The GBCDs were determined from the stereological interpretation of EBSD maps containing on the order of 100,000 grains. It was found that the GBCDs of face-centered cubic (FCC) metals are statistically correlated, while the GBCDs of body-centered cubic (BCC) Fe and Mo are not correlated to the GBCD of FCC metals. The degree of the correlations among the FCC metals is weaker if there are significant differences in grain shape or texture. For example, Ag has the weakest correlation to the other FCC materials and also has quantitatively different grain shapes and texture. The relationship between the populations and energies of grain boundaries was also studied. By comparing the GBCDs of Al, Au, Cu, and Ni to the energies of 388 grain boundaries previously calculated by the Embedded Atom Method (EAM), we observed a moderately inverse correlation between the relative areas of grain boundaries and their energies. Interestingly, there are strong inverse correlations between the energies and populations of the most common grain boundaries (Sigma3, Sigma9, and Sigma27). Because the enhancement of twin related boundaries due to the prevalence Sigma3 boundaries results in a decrease in the grain boundary populations for the other boundary types, this inverse correlation is influenced by the crystallographic constraints at triple junctions. In other words, having an anisotropic misorientation distribution with strong maxima for certain boundaries biases the inverse correlation between grain boundary population and energy for other boundaries and causes different slopes at each misorientation. Interestingly, the inverse correlation at each misorientation is consistent with the Boltzmann distribution. Based on our results, it is possible to predict the GBCDs and GBEDs in isostructural polycrystalline materials by using a single GBCD and GBED. This principle is demonstrated by predicting the GBCD and GBED of Actinium (Ac). To investigate the GBED in the isostructural BCC metals, the energies of 408 grain boundaries in Fe and Mo were computed using atomistic simulations based on the embedded-atom method (EAM) potential. We found that the calculated boundary energies in Fe and Mo were strongly correlated and scaled with the ratio of the cohesive energy divided by the square of the lattice constant (Ecoh/a02). We would expect that the GBCD of Fe and Mo might be correlated in a similar manner to that of FCC metals. To test this hypothesis, we compared the GBCDs of Fe and Mo. We found that the GBCDs of Fe and Mo are moderately and strongly correlated when all boundary types and only Sigma3 boundaries were considered, respectively. In this thesis, the results demonstrated that the GBCDs of isostructural materials are correlated with one another and the magnitudes of correlation coefficients varied. Reduced correlations were observed when there were differences in the microstructure and crystallographic texture. The inverse relationship between grain boundary population and energy is more strongly correlated at each misorientation than over the entire five macroscopic parameters of grain boundary, especially when there is significant misorientation texture. This relationship leads to GBCDs of isostructural materials that are also more strongly correlated at each misorientation than over the entire grain boundary space.

Simulation of Energy Response of the ATIC Calorimeter

NASA Technical Reports Server (NTRS)

Batkov, K. E.; Adams, J. H., Jr.; Ahn, H. S.; Bashindzhagyan, G. L.; Case, G.; Christl, M.; Chang, J.; Fazely, A. R.; Ganel, O.; Granger, D.;

Use of Machine Learning Algorithms to Propose a New Methodology to Conduct, Critique and Validate Urban Scale Building Energy Modeling

NASA Astrophysics Data System (ADS)

Pathak, Maharshi

City administrators and real-estate developers have been setting up rather aggressive energy efficiency targets. This, in turn, has led the building science research groups across the globe to focus on urban scale building performance studies and level of abstraction associated with the simulations of the same. The increasing maturity of the stakeholders towards energy efficiency and creating comfortable working environment has led researchers to develop methodologies and tools for addressing the policy driven interventions whether it's urban level energy systems, buildings' operational optimization or retrofit guidelines. Typically, these large-scale simulations are carried out by grouping buildings based on their design similarities i.e. standardization of the buildings. Such an approach does not necessarily lead to potential working inputs which can make decision-making effective. To address this, a novel approach is proposed in the present study. The principle objective of this study is to propose, to define and evaluate the methodology to utilize machine learning algorithms in defining representative building archetypes for the Stock-level Building Energy Modeling (SBEM) which are based on operational parameter database. The study uses "Phoenix- climate" based CBECS-2012 survey microdata for analysis and validation. Using the database, parameter correlations are studied to understand the relation between input parameters and the energy performance. Contrary to precedence, the study establishes that the energy performance is better explained by the non-linear models. The non-linear behavior is explained by advanced learning algorithms. Based on these algorithms, the buildings at study are grouped into meaningful clusters. The cluster "mediod" (statistically the centroid, meaning building that can be represented as the centroid of the cluster) are established statistically to identify the level of abstraction that is acceptable for the whole building energy simulations and post that the retrofit decision-making. Further, the methodology is validated by conducting Monte-Carlo simulations on 13 key input simulation parameters. The sensitivity analysis of these 13 parameters is utilized to identify the optimum retrofits. From the sample analysis, the envelope parameters are found to be more sensitive towards the EUI of the building and thus retrofit packages should also be directed to maximize the energy usage reduction.

Simulation of solution phase electron transfer in a compact donor-acceptor dyad.

PubMed

Kowalczyk, Tim; Wang, Lee-Ping; Van Voorhis, Troy

2011-10-27

Charge separation (CS) and charge recombination (CR) rates in photosynthetic architectures are difficult to control, yet their ratio can make or break photon-to-current conversion efficiencies. A rational design approach to the enhancement of CS over CR requires a mechanistic understanding of the underlying electron-transfer (ET) process, including the role of the environment. Toward this goal, we introduce a QM/MM protocol for ET simulations and use it to characterize CR in the formanilide-anthraquinone dyad (FAAQ). Our simulations predict fast recombination of the charge-transfer excited state, in agreement with recent experiments. The computed electronic couplings show an electronic state dependence and are weaker in solution than in the gas phase. We explore the role of cis-trans isomerization on the CR kinetics, and we find strong correlation between the vertical energy gaps of the full simulations and a collective solvent polarization coordinate. Our approach relies on constrained density functional theory to obtain accurate diabatic electronic states on the fly for molecular dynamics simulations, while orientational and electronic polarization of the solvent is captured by a polarizable force field based on a Drude oscillator model. The method offers a unified approach to the characterization of driving forces, reorganization energies, electronic couplings, and nonlinear solvent effects in light-harvesting systems.

Atomic-scale reversibility in sheared glasses

NASA Astrophysics Data System (ADS)

Fan, Meng; Wang, Minglei; Liu, Yanhui; Schroers, Jan; Shattuck, Mark; O'Hern, Corey

Systems become irreversible on a macroscopic scale when they are sheared beyond the yield strain and begin flowing. Using computer simulations of oscillatory shear, we investigate atomic scale reversibility. We employ molecular dynamics simulations to cool binary Lennard-Jones liquids to zero temperature over a wide range of cooling rates. We then apply oscillatory quasistatic shear at constant pressure to the zero-temperature glasses and identify neighbor-switching atomic rearrangement events. We determine the critical strain γ*, beyond which atoms in the system do not return to their original positions upon reversing the strain. We show that for more slowly cooled glasses, the average potential energy is lower and the typical size of atomic rearrangements is smaller, which correlates with larger γ*. Finally, we connect atomic- and macro-scale reversibility by determining the number of and correlations between the atomic rearrangements that occur as the system reaches the yield strain.

Deorbitalization strategies for meta-generalized-gradient-approximation exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Mejia-Rodriguez, Daniel; Trickey, S. B.

2017-11-01

We explore the simplification of widely used meta-generalized-gradient approximation (mGGA) exchange-correlation functionals to the Laplacian level of refinement by use of approximate kinetic-energy density functionals (KEDFs). Such deorbitalization is motivated by the prospect of reducing computational cost while recovering a strictly Kohn-Sham local potential framework (rather than the usual generalized Kohn-Sham treatment of mGGAs). A KEDF that has been rather successful in solid simulations proves to be inadequate for deorbitalization, but we produce other forms which, with parametrization to Kohn-Sham results (not experimental data) on a small training set, yield rather good results on standard molecular test sets when used to deorbitalize the meta-GGA made very simple, Tao-Perdew-Staroverov-Scuseria, and strongly constrained and appropriately normed functionals. We also study the difference between high-fidelity and best-performing deorbitalizations and discuss possible implications for use in ab initio molecular dynamics simulations of complicated condensed phase systems.

Monte Carlo analysis of tagged neutron beams for cargo container inspection.

PubMed

Pesente, S; Lunardon, M; Nebbia, G; Viesti, G; Sudac, D; Valkovic, V

2007-12-01

Fast neutrons produced via D+T reactions and tagged by the associated particle technique have been recently proposed to inspect cargo containers. The general characteristics of this technique are studied with Monte Carlo simulations by determining the properties of the tagged neutron beams as a function of the relevant design parameters (energy and size of the deuteron beam, geometry of the charged particle detector). Results from simulations, validated by experiments, show that the broadening of the correlation between the alpha-particle and the neutron, induced by kinematical as well as geometrical (beam and detector size) effects, is important and limits the dimension of the minimum voxel to be inspected. Moreover, the effect of the container filling is explored. The material filling produces a sizeable loss of correlation between alpha-particles and neutrons due to scattering and absorption. Conditions in inspecting cargo containers are discussed.

A GPU-based large-scale Monte Carlo simulation method for systems with long-range interactions

NASA Astrophysics Data System (ADS)

Liang, Yihao; Xing, Xiangjun; Li, Yaohang

2017-06-01

In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD) architectures, and adopts the sequential updating scheme of Metropolis algorithm. It makes no approximation in the computation of energy, and reaches a remarkable 440-fold speedup, compared with the serial implementation on CPU. We further use this method to simulate primitive model electrolytes, and measure very precisely all ion-ion pair correlation functions at high concentrations. From these data, we extract the renormalized Debye length, renormalized valences of constituent ions, and renormalized dielectric constants. These results demonstrate unequivocally physics beyond the classical Poisson-Boltzmann theory.

Regional warming of hot extremes accelerated by surface energy fluxes consistent with drying soils

NASA Astrophysics Data System (ADS)

Donat, M.; Pitman, A.; Seneviratne, S. I.

2017-12-01

Strong regional differences exist in how hot temperature extremes increase under global warming. Using an ensemble of coupled climate models, we examine the regional warming rates of hot extremes relative to annual average warming rates in the same regions. We identify hotspots of accelerated warming of model-simulated hot extremes in Europe, North America, South America and Southeast China. These hotspots indicate where the warm tail of a distribution of temperatures increases faster than the average and are robust across most CMIP5 models. Exploring the conditions on the specific day the hot extreme occurs demonstrates the hotspots are explained by changes in the surface energy fluxes consistent with drying soils. Furthermore, in these hotspot regions we find a relationship between the temperature - heat flux correlation under current climate conditions and the magnitude of future projected changes in hot extremes, pointing to a potential emergent constraint for simulations of future hot extremes. However, the model-simulated accelerated warming of hot extremes appears inconsistent with observations of the past 60 years, except over Europe. The simulated acceleration of hot extremes may therefore be unreliable, a result that necessitates a re-evaluation of how climate models resolve the relevant terrestrial processes.

The power of structural modeling of sub-grid scales - application to astrophysical plasmas

NASA Astrophysics Data System (ADS)

Georgiev Vlaykov, Dimitar; Grete, Philipp

2015-08-01

In numerous astrophysical phenomena the dynamical range can span 10s of orders of magnitude. This implies more than billions of degrees-of-freedom and precludes direct numerical simulations from ever being a realistic possibility. A physical model is necessary to capture the unresolved physics occurring at the sub-grid scales (SGS).Structural modeling is a powerful concept which renders itself applicable to various physical systems. It stems from the idea of capturing the structure of the SGS terms in the evolution equations based on the scale-separation mechanism and independently of the underlying physics. It originates in the hydrodynamics field of large-eddy simulations. We apply it to the study of astrophysical MHD.Here, we present a non-linear SGS model for compressible MHD turbulence. The model is validated a priori at the tensorial, vectorial and scalar levels against of set of high-resolution simulations of stochastically forced homogeneous isotropic turbulence in a periodic box. The parameter space spans 2 decades in sonic Mach numbers (0.2 - 20) and approximately one decade in magnetic Mach number ~(1-8). This covers the super-Alfvenic sub-, trans-, and hyper-sonic regimes, with a range of plasma beta from 0.05 to 25. The Reynolds number is of the order of 103.At the tensor level, the model components correlate well with the turbulence ones, at the level of 0.8 and above. Vectorially, the alignment with the true SGS terms is encouraging with more than 50% of the model within 30° of the data. At the scalar level we look at the dynamics of the SGS energy and cross-helicity. The corresponding SGS flux terms have median correlations of ~0.8. Physically, the model represents well the two directions of the energy cascade.In comparison, traditional functional models exhibit poor local correlations with the data already at the scalar level. Vectorially, they are indifferent to the anisotropy of the SGS terms. They often struggle to represent the energy backscatter from small to large scales as well as the turbulent dynamo mechanism.Overall, the new model surpasses the traditional ones in all tests by a large margin.

Molecular simulation studies on chemical reactivity of methylcyclopentadiene.

PubMed

Wang, Qingsheng; Zhang, Yingchun; Rogers, William J; Mannan, M Sam

2009-06-15

Molecular simulations are important to predict thermodynamic values for reactive chemicals especially when sufficient experimental data are not available. Methylcyclopentadiene (MCP) is an example of a highly reactive and hazardous compound in the chemical process industry. In this work, chemical reactivity of 2-methylcyclopentadiene, including isomerization, dimerization, and oxidation reactions, is investigated in detail by theoretical computational chemistry methods and empirical thermodynamic-energy correlation. On the basis of molecular simulations, an average value of -15.2 kcal/mol for overall heat of dimerization and -45.6 kcal/mol for overall heat of oxidation were obtained in gaseous phase at 298 K and 1 atm. These molecular simulation studies can provide guidance for the design of safer chemical processes, safer handling of MCP, and also provide useful information for an investigation of the T2 Laboratories explosion on December 19, 2007, in Florida.

Decorrelation dynamics and spectra in drift-Alfven turbulence

NASA Astrophysics Data System (ADS)

Fernandez Garcia, Eduardo

Motivated by the inability of one-fluid magnetohydrodynamics (MHD) to explain key turbulence characteristics in systems ranging from the solar wind and interstellar medium to fusion devices like the reversed field pinch, this thesis studies magnetic turbulence using a drift-Alfven model that extends MHD by including electron density dynamics. Electron effects play a significant role in the dynamics by changing the structure of turbulent decorrelation in the Alfvenic regime (where fast Alfvenic propagation provides the fastest decorrelation of the system): besides the familiar counter-propagating Alfvenic branches of MHD, an additional branch tied to the diamagnetic and eddy-turn- over rates enters in the turbulent response. This kinematic branch gives hydrodynamic features to turbulence that is otherwise strongly magnetic. Magnetic features are observed in the RMS frequency, energy partitions, cross-field energy transfer and in the turbulent response, whereas hydrodynamic features appear in the average frequency, self-field transfer, turbulent response and finally the wavenumber spectrum. These features are studied via renormalized closure theory and numerical simulation. The closure calculation naturally incorporates the eigenmode structure of the turbulent response in specifying spectral energy balance equations for the magnetic, kinetic and internal (density) energies. Alfvenic terms proportional to cross correlations and involved in cross field transfer compete with eddy-turn-over, self transfer, auto-correlation terms. In the steady state, the kinematic terms dominate the energy balances and yield a 5/3 Kolmogorov spectrum (as observed in the interstellar medium) for the three field energies in the strong turbulence, long wavelength limit. Alfvenic terms establish equipartition of kinetic and magnetic energies. In the limit where wavelengths are short compared to the gyroradius, the Alfvenic terms equipartition the internal and magnetic energies resulting in a steep (-2) spectrum fall-off for those energies while the largely uncoupled kinetic modes still obey a 5/3 law. From the numerical simulations, the response function of drift-Alfven turbulence is measured. Here, a statistical ensemble is constructed from small perturbations of the turbulent amplitudes at fixed wavenumber. The decorrelation structure born out of the eigenmode calculation is verified in the numerical measurement.

Direct Simulation Monte Carlo Investigation of Noncontinuum Couette Flow

NASA Astrophysics Data System (ADS)

Torczynski, J. R.; Gallis, M. A.

2009-11-01

The Direct Simulation Monte Carlo (DSMC) method of molecular gas dynamics is used to study noncontinuum effects in Couette flow. The walls have equal temperatures and equal accommodation coefficients but unequal tangential velocities. Simulations are performed for near-free-molecular to near-continuum gas pressures with accommodation coefficients of 0.25, 0.5, and 1. Ten gases are examined: argon, helium, nitrogen, sea-level air, and six Inverse-Power-Law (IPL) gases with viscosity temperature exponents of 0.5, 0.6, 0.7, 0.8, 0.9, and 1.0, as represented by the Variable Soft Sphere (VSS) interaction. In all cases, the wall shear stress is proportional to the slip velocity. The momentum transfer coefficient relating these two quantities can be accurately correlated in terms of the Knudsen number based on the wall separation. The two dimensionless parameters in the correlation are similar for all gases examined. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Evaluation of Advanced Stirling Convertor Net Heat Input Correlation Methods Using a Thermal Standard

NASA Technical Reports Server (NTRS)

Briggs, Maxwell H.; Schifer, Nicholas A.

2012-01-01

The U.S. Department of Energy (DOE) and Lockheed Martin Space Systems Company (LMSSC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. This generator would use two high-efficiency Advanced Stirling Convertors (ASCs), developed by Sunpower Inc. and NASA Glenn Research Center (GRC). The ASCs convert thermal energy from a radioisotope heat source into electricity. As part of ground testing of these ASCs, different operating conditions are used to simulate expected mission conditions. These conditions require achieving a particular operating frequency, hot end and cold end temperatures, and specified electrical power output for a given net heat input. In an effort to improve net heat input predictions, numerous tasks have been performed which provided a more accurate value for net heat input into the ASCs, including testing validation hardware, known as the Thermal Standard, to provide a direct comparison to numerical and empirical models used to predict convertor net heat input. This validation hardware provided a comparison for scrutinizing and improving empirical correlations and numerical models of ASC-E2 net heat input. This hardware simulated the characteristics of an ASC-E2 convertor in both an operating and non-operating mode. This paper describes the Thermal Standard testing and the conclusions of the validation effort applied to the empirical correlation methods used by the Radioisotope Power System (RPS) team at NASA Glenn.

Communication: Water on hexagonal boron nitride from diffusion Monte Carlo

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

Al-Hamdani, Yasmine S.; Ma, Ming; Michaelides, Angelos, E-mail: angelos.michaelides@ucl.ac.uk

2015-05-14

Despite a recent flurry of experimental and simulation studies, an accurate estimate of the interaction strength of water molecules with hexagonal boron nitride is lacking. Here, we report quantum Monte Carlo results for the adsorption of a water monomer on a periodic hexagonal boron nitride sheet, which yield a water monomer interaction energy of −84 ± 5 meV. We use the results to evaluate the performance of several widely used density functional theory (DFT) exchange correlation functionals and find that they all deviate substantially. Differences in interaction energies between different adsorption sites are however better reproduced by DFT.

Planetary Structures And Simulations Of Large-scale Impacts On Mars

NASA Astrophysics Data System (ADS)

Swift, Damian; El-Dasher, B.

2009-09-01

The impact of large meteroids is a possible cause for isolated orogeny on bodies devoid of tectonic activity. On Mars, there is a significant, but not perfect, correlation between large, isolated volcanoes and antipodal impact craters. On Mercury and the Moon, brecciated terrain and other unusual surface features can be found at the antipodes of large impact sites. On Earth, there is a moderate correlation between long-lived mantle hotspots at opposite sides of the planet, with meteoroid impact suggested as a possible cause. If induced by impacts, the mechanisms of orogeny and volcanism thus appear to vary between these bodies, presumably because of differences in internal structure. Continuum mechanics (hydrocode) simulations have been used to investigate the response of planetary bodies to impacts, requiring assumptions about the structure of the body: its composition and temperature profile, and the constitutive properties (equation of state, strength, viscosity) of the components. We are able to predict theoretically and test experimentally the constitutive properties of matter under planetary conditions, with reasonable accuracy. To provide a reference series of simulations, we have constructed self-consistent planetary structures using simplified compositions (Fe core and basalt-like mantle), which turn out to agree surprisingly well with the moments of inertia. We have performed simulations of large-scale impacts, studying the transmission of energy to the antipodes. For Mars, significant antipodal heating to depths of a few tens of kilometers was predicted from compression waves transmitted through the mantle. Such heating is a mechanism for volcanism on Mars, possibly in conjunction with crustal cracking induced by surface waves. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

A novel laser-collider used to produce monoenergetic 13.3 MeV 7Li (d, n) neutrons

PubMed Central

Zhao, J. R.; Zhang, X. P.; Yuan, D. W.; Li, Y. T.; Li, D. Z.; Rhee, Y. J.; Zhang, Z.; Li, F.; Zhu, B. J.; Li, Yan F.; Han, B.; Liu, C.; Ma, Y.; Li, Yi F.; Tao, M. Z.; Li, M. H.; Guo, X.; Huang, X. G.; Fu, S. Z.; Zhu, J. Q.; Zhao, G.; Chen, L. M.; Fu, C. B.; Zhang, J.

2016-01-01

Neutron energy is directly correlated with the energy of the incident ions in experiments involving laser-driven nuclear reactions. Using high-energy incident ions reduces the energy concentration of the generated neutrons. A novel “laser-collider” method was used at the Shenguang II laser facility to produce monoenergetic neutrons via 7Li (d, n) nuclear reactions. The specially designed K-shaped target significantly increased the numbers of incident d and Li ions at the keV level. Ultimately, 13.3 MeV neutrons were obtained. Considering the time resolution of the neutron detector, we demonstrated that the produced neutrons were monoenergetic. Interferometry and a Multi hydro-dynamics simulation confirmed the monoenergetic nature of these neutrons. PMID:27250660

Fundamental edge broadening effects during focused electron beam induced nanosynthesis

DOE PAGES

Schmied, Roland; Fowlkes, Jason Davidson; Winkler, Robert; ...

2015-02-16

In this study, we explore lateral broadening effects of 3D structures fabricated through focused electron beam induced deposition using MeCpPt(IV)Me 3 precursor. In particular, the scaling behavior of proximity effects as a function of the primary electron energy and the deposit height is investigated through experiments and validated through simulations. Correlated Kelvin force microscopy and conductive atomic force microscopy measurements identified conductive and non-conductive proximity regions. It was determined that the highest primary electron energies enable the highest edge sharpness while lower energies contain a complex convolution of broadening effects. In addition, it is demonstrated that intermediate energies lead tomore » even more complex proximity effects that significantly reduce lateral edge sharpness and thus should be avoided if desiring high lateral resolution.« less

Solute-solvent cavity and bridge functions. I. Varying size of the solute

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

Vyalov, I., E-mail: ivan.vyalov@iit.it; Chuev, G., E-mail: genchuev@rambler.ru; Georgi, N., E-mail: georgi@mis.mpg.de

2014-08-21

In this work we present the results of the extensive molecular simulations of solute-solvent cavity and bridge functions. The mixtures of Lennard-Jones solvent with Lennard-Jones solute at infinite dilution are considered for different solute-solvent size ratios—up to 4:1. The Percus-Yevick and hypernetted chain closures deviate substantially from simulation results in the investigated temperature and density ranges. We also find that the behavior of the indirect and cavity correlation functions is non-monotonous within the hard-core region, but the latter can be successfully approximated by mean-field theory if the solute-solvent interaction energy is divided into repulsive and attractive contribution, according to Weeks-Chandler-Andersenmore » theory. Furthermore, in spite of the non-monotonous behavior of logarithm of the cavity function and the indirect correlation function, their difference, i.e., the bridge function remains constant within the hard-core region. Such behavior of the bridge and indirect correlation functions at small distances and for small values of indirect correlation function is well known from the Duh-Haymet plots, where the non-unique relationship results in loops of the bridge function vs. indirect correlation function graphs. We show that the same pathological behavior appears also when distance is small and indirect correlation function is large. We further show that the unique functional behavior of the bridge function can be established when bridge is represented as a function of the renormalized, repulsive indirect correlation function.« less

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

Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri

Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the basesmore » and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.« less

Nuclear quantum effects in electronically adiabatic quantum time correlation functions: Application to the absorption spectrum of a hydrated electron

NASA Astrophysics Data System (ADS)

Turi, László; Hantal, György; Rossky, Peter J.; Borgis, Daniel

2009-07-01

A general formalism for introducing nuclear quantum effects in the expression of the quantum time correlation function of an operator in a multilevel electronic system is presented in the adiabatic limit. The final formula includes the nuclear quantum time correlation functions of the operator matrix elements, of the energy gap, and their cross terms. These quantities can be inferred and evaluated from their classical analogs obtained by mixed quantum-classical molecular dynamics simulations. The formalism is applied to the absorption spectrum of a hydrated electron, expressed in terms of the time correlation function of the dipole operator in the ground electronic state. We find that both static and dynamic nuclear quantum effects distinctly influence the shape of the absorption spectrum, especially its high energy tail related to transitions to delocalized electron states. Their inclusion does improve significantly the agreement between theory and experiment for both the low and high frequency edges of the spectrum. It does not appear sufficient, however, to resolve persistent deviations in the slow Lorentzian-like decay part of the spectrum in the intermediate 2-3 eV region.

Measurement of the high-energy gamma-ray emission from the Moon with the Fermi Large Area Telescope

DOE PAGES

Ackermann, M.; Ajello, M.; Albert, A.; ...

2016-04-08

We have measured the gamma-ray emission spectrum of the Moon using the data collected by the Large Area Telescope onboard the Fermi satellite during its first seven years of operation, in the energy range from 30 MeV up to a few GeV. We have also studied the time evolution of the flux, finding a correlation with the solar activity. We have developed a full Monte Carlo simulation describing the interactions of cosmic rays with the lunar surface. The results of the present analysis can be explained in the framework of this model, where the production of gamma rays is duemore » to the interactions of cosmic-ray proton and helium nuclei with the surface of the Moon. Lastly, we have used our simulation to derive the cosmic-ray proton and helium spectra near Earth from the Moon gamma-ray data.« less

Measurement of the High-Energy Gamma-Ray Emission from the Moon with the Fermi Large Area Telescope

NASA Technical Reports Server (NTRS)

Ackermann, M.; Ajello, M.; Albert, A.; Atwood, W. B.; Baldini, L.; Barbiellini, G.; Bastieri, D.; Bellazzini, R.; Bissaldi, E.; Blandford, R. D.;

Development of a Polarizable Force Field for Molecular Dynamics Simulations of Poly (Ethylene Oxide) in Aqueous Solution.

PubMed

Starovoytov, Oleg N; Borodin, Oleg; Bedrov, Dmitry; Smith, Grant D

2011-06-14

We have developed a quantum chemistry-based polarizable potential for poly(ethylene oxide) (PEO) in aqueous solution based on the APPLE&P polarizable ether and the SWM4-DP polarizable water models. Ether-water interactions were parametrized to reproduce the binding energy of water with 1,2-dimethoxyethane (DME) determined from high-level quantum chemistry calculations. Simulations of DME-water and PEO-water solutions at room temperature using the new polarizable potentials yielded thermodynamic properties in good agreement with experimental results. The predicted miscibility of PEO and water as a function of the temperature was found to be strongly correlated with the predicted free energy of solvation of DME. The developed nonbonded force field parameters were found to be transferrable to poly(propylene oxide) (PPO), as confirmed by capturing, at least qualitatively, the miscibility of PPO in water as a function of the molecular weight.

Hidden regularity and universal classification of fast side chain motions in proteins

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

Rajeshwar, Rajitha; Smith, Jeremy C.; Krishnam, Marimuthu

Proteins display characteristic dynamical signatures that appear to be universal across all proteins regardless of topology and size. Here, we systematically characterize the universal features of fast side chain motions in proteins by examining the conformational energy surfaces of individual residues obtained using enhanced sampling molecular dynamics simulation (618 free energy surfaces obtained from 0.94 s MD simulation). The side chain conformational free energy surfaces obtained using the adaptive biasing force (ABF) method for a set of eight proteins with different molecular weights and secondary structures are used to determine the methyl axial NMR order parameters (O axis 2), populationsmore » of side chain rotamer states (ρ), conformational entropies (S conf), probability fluxes, and activation energies for side chain inter-rotameric transitions. The free energy barriers separating side chain rotamer states range from 0.3 to 12 kcal/mol in all proteins and follow a trimodal distribution with an intense peak at ~5 kcal/mol and two shoulders at ~3 and ~7.5 kcal/mol, indicating that some barriers are more favored than others by proteins to maintain a balance between their conformational stability and flexibility. The origin and the influences of the trimodal barrier distribution on the distribution of O axis 2 and the side chain conformational entropy are discussed. A hierarchical grading of rotamer states based on the conformational free energy barriers, entropy, and probability flux reveals three distinct classes of side chains in proteins. A unique nonlinear correlation is established between O axis 2 and the side chain rotamer populations (ρ). In conclusion, the apparent universality in O axis 2 versus correlation, trimodal barrier distribution, and distinct characteristics of three classes of side chains observed among all proteins indicates a hidden regularity (or commonality) in the dynamical heterogeneity of fast side chain motions in proteins.« less

Computer model to simulate ionizing radiation effects correlates with experimental data

NASA Astrophysics Data System (ADS)

Perez-Poch, Antoni

Exposure to radiation from high energy protons and particles with ionizing properties is a major challenge for long-term space missions. The specific effect of such radiation on hematopoietic cells is still not fully understood. A number of experiments have been conducted on ground and in space. Those experiments on one hand, measure the extent of damage on blood markers. On the other hand, they intend to quantify the correlation between dose and energy from the radiation particles, with their ability to impair the hematopoietic stem and progenitor function. We present a computer model based on a neural network that intends to assess the relationship between dose, energy and number of hits on a particular cell, to the damage incurred to the human marrow cells. Calibration of the network is performed with the existing experimental data available in bibliography. Different sources of ionizing radiation at different doses (0-90 cGy) and along different patterns of a long-term exposure scenarios are simulated. Results are shown for a continuous variation of doses and are compared with specific data available in the literature. Some predictions are inferred for long-term scenarios of spaceflight, and the risk of jeopardizing a mission due to a major disfunction of the bone marrow is calculated. The method has proved successful in reproducing specific experimental data. We also discuss the significance and validity of the predicted ionizing radiation effects in situations such as long-term missions for a continuous range of dose.

Three-dimensional kinetic simulations of whistler turbulence in solar wind on parallel supercomputers

NASA Astrophysics Data System (ADS)

Chang, Ouliang

The objective of this dissertation is to study the physics of whistler turbulence evolution and its role in energy transport and dissipation in the solar wind plasmas through computational and theoretical investigations. This dissertation presents the first fully three-dimensional (3D) particle-in-cell (PIC) simulations of whistler turbulence forward cascade in a homogeneous, collisionless plasma with a uniform background magnetic field B o, and the first 3D PIC simulation of whistler turbulence with both forward and inverse cascades. Such computationally demanding research is made possible through the use of massively parallel, high performance electromagnetic PIC simulations on state-of-the-art supercomputers. Simulations are carried out to study characteristic properties of whistler turbulence under variable solar wind fluctuation amplitude (epsilon e) and electron beta (betae), relative contributions to energy dissipation and electron heating in whistler turbulence from the quasilinear scenario and the intermittency scenario, and whistler turbulence preferential cascading direction and wavevector anisotropy. The 3D simulations of whistler turbulence exhibit a forward cascade of fluctuations into broadband, anisotropic, turbulent spectrum at shorter wavelengths with wavevectors preferentially quasi-perpendicular to B o. The overall electron heating yields T ∥ > T⊥ for all epsilone and betae values, indicating the primary linear wave-particle interaction is Landau damping. But linear wave-particle interactions play a minor role in shaping the wavevector spectrum, whereas nonlinear wave-wave interactions are overall stronger and faster processes, and ultimately determine the wavevector anisotropy. Simulated magnetic energy spectra as function of wavenumber show a spectral break to steeper slopes, which scales as k⊥lambda e ≃ 1 independent of betae values, where lambdae is electron inertial length, qualitatively similar to solar wind observations. Specific spectral indices from simulated wavevector energy spectra do not match the frequency spectral indices from observations due to the inapplicability of Taylor's hypothesis. In contrast, the direct comparison of simulated frequency energy spectra and solar wind observations shows a closer similarity. Electron density fluctuations power spectra also exhibit a close similarity to solar wind observations and MHD predications, both qualitatively and quantitatively. Linear damping represents an intermediate fraction of the total dissipation of whistler turbulence over a wide range of betae and epsilone. The relative importance of linear damping by comparison to nonlinear dissipation increases with increasing beta e but decreases with increasing epsilone. Correlation coefficient calculations imply that the nonlinear dissipation processes in our simulation are primarily associated with dissipation in regions of intermittent current sheet structures. The simulation results suggest that whistler fluctuations could be the substantial constituent of solar wind turbulence at higher frequencies and short wavelengths, and support the magnetosonic-whistler interpretation of the quasilinear scenario. An even larger scale 3D whistler turbulence simulation exhibits both a forward cascade to shorter wavelengths with wavevectors preferentially k⊥ > k∥, and an inverse cascade to longer wavelengths with wavevectors k ≳ k⊥. The inverse cascade process is primarily driven by the nonlinear wave-wave interaction. It is shown that the energy inverse cascade rate is similar to the energy forward cascade rate at early times although the overall energy in the two cascades is very different. The presence of inverse cascade process does not affect qualitative conclusions established from the whistler turbulence forward cascade simulations.

Spin-resolved correlations in the warm-dense homogeneous electron gas

NASA Astrophysics Data System (ADS)

Arora, Priya; Kumar, Krishan; Moudgil, R. K.

2017-04-01

We have studied spin-resolved correlations in the warm-dense homogeneous electron gas by determining the linear density and spin-density response functions, within the dynamical self-consistent mean-field theory of Singwi et al. The calculated spin-resolved pair-correlation function gσσ'(r) is compared with the recent restricted path-integral Monte Carlo (RPIMC) simulations due to Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)], while interaction energy Eint and exchange-correlation free energy Fxc with the RPIMC and very recent ab initio quantum Monte Carlo (QMC) simulations by Dornheim et al. [Phys. Rev. Lett. 117, 156403 (2016)]. g↑↓(r) is found to be in good agreement with the RPIMC data, while a mismatch is seen in g↑↑(r) at small r where it becomes somewhat negative. As an interesting result, it is deduced that a non-monotonic T-dependence of g(0) is driven primarily by g↑↓(0). Our results of Eint and Fxc exhibit an excellent agreement with the QMC study due to Dornheim et al., which deals with the finite-size correction quite accurately. We observe, however, a visible deviation of Eint from the RPIMC data for high densities ( 8% at rs = 1). Further, we have extended our study to the fully spin-polarized phase. Again, with the exception of high density region, we find a good agreement of Eint with the RPIMC data. This points to the need of settling the problem of finite-size correction in the spin-polarized phase also. Interestingly, we also find that the thermal effects tend to oppose spatial localization as well as spin polarization of electrons. Supplementary material in the form of one zip file available from the Journal web page at http://https://doi.org/10.1140/epjb/e2017-70532-y

Energy dependent track structure parametrisations for protons and carbon ions based on nanometric simulations

NASA Astrophysics Data System (ADS)

Alexander, Frauke; Villagrasa, Carmen; Rabus, Hans; Wilkens, Jan J.

2015-09-01

The BioQuaRT project within the European Metrology Research Programme aims at correlating ion track structure characteristics with the biological effects of radiation and develops measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigate methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Input data sets were generated by simulations of ion tracks of protons and carbon ions in liquid water using the Geant 4 Monte Carlo toolkit with the Geant4-DNA processes. Based on the energy transfer points - recorded with nanometre resolution - we investigated parametrisations of overall properties of ion track structure. Three different track structure parametrisations have been developed using the distances to the 10 next neighbouring ionisations, the radial energy distribution and ionisation cluster size distributions. These parametrisations of nanometric track structure build a basis for deriving biologically relevant mean values which are essential in the clinical situation where each voxel is exposed to a mixed radiation field. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.

PubMed

Hayakawa, Daichi; Nishiyama, Yoshiharu; Mazeau, Karim; Ueda, Kazuyoshi

2017-09-08

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A). Copyright © 2017 Elsevier Ltd. All rights reserved.

Computational Transport Modeling of High-Energy Neutrons Found in the Space Environment

NASA Technical Reports Server (NTRS)

Cox, Brad; Theriot, Corey A.; Rohde, Larry H.; Wu, Honglu

2012-01-01

The high charge and high energy (HZE) particle radiation environment in space interacts with spacecraft materials and the human body to create a population of neutrons encompassing a broad kinetic energy spectrum. As an HZE ion penetrates matter, there is an increasing chance of fragmentation as penetration depth increases. When an ion fragments, secondary neutrons are released with velocities up to that of the primary ion, giving some neutrons very long penetration ranges. These secondary neutrons have a high relative biological effectiveness, are difficult to effectively shield, and can cause more biological damage than the primary ions in some scenarios. Ground-based irradiation experiments that simulate the space radiation environment must account for this spectrum of neutrons. Using the Particle and Heavy Ion Transport Code System (PHITS), it is possible to simulate a neutron environment that is characteristic of that found in spaceflight. Considering neutron dosimetry, the focus lies on the broad spectrum of recoil protons that are produced in biological targets. In a biological target, dose at a certain penetration depth is primarily dependent upon recoil proton tracks. The PHITS code can be used to simulate a broad-energy neutron spectrum traversing biological targets, and it account for the recoil particle population. This project focuses on modeling a neutron beamline irradiation scenario for determining dose at increasing depth in water targets. Energy-deposition events and particle fluence can be simulated by establishing cross-sectional scoring routines at different depths in a target. This type of model is useful for correlating theoretical data with actual beamline radiobiology experiments. Other work exposed human fibroblast cells to a high-energy neutron source to study micronuclei induction in cells at increasing depth behind water shielding. Those findings provide supporting data describing dose vs. depth across a water-equivalent medium. This poster presents PHITS data suggesting an increase in dose, up to roughly 10 cm depth, followed by a continual decrease as neutrons come to a stop in the target.

Atomistic simulation on charge mobility of amorphous tris(8-hydroxyquinoline) aluminum (Alq3): origin of Poole-Frenkel-type behavior.

PubMed

Nagata, Yuki; Lennartz, Christian

2008-07-21

The atomistic simulation of charge transfer process for an amorphous Alq(3) system is reported. By employing electrostatic potential charges, we calculate site energies and find that the standard deviation of site energy distribution is about twice as large as predicted in previous research. The charge mobility is calculated via the Miller-Abrahams formalism and the master equation approach. We find that the wide site energy distribution governs Poole-Frenkel-type behavior of charge mobility against electric field, while the spatially correlated site energy is not a dominant mechanism of Poole-Frenkel behavior in the range from 2x10(5) to 1.4x10(6) V/cm. Also we reveal that randomly meshed connectivities are, in principle, required to account for the Poole-Frenkel mechanism. Charge carriers find a zigzag pathway at low electric field, while they find a straight pathway along electric field when a high electric field is applied. In the space-charge-limited current scheme, the charge-carrier density increases with electric field strength so that the nonlinear behavior of charge mobility is enhanced through the strong charge-carrier density dependence of charge mobility.

Remote control of the dissociative ionization of H2 based on electron-H2 + entanglement

NASA Astrophysics Data System (ADS)

Wang, Jun-Ping; He, Feng

2018-04-01

The single ionization of H2 in strong laser fields creates the correlated electron-H2 + pair. Based on such a correlation, we conceive a strategy to control the energy spectra of the freed electron or dissociative fragments by simulating the time-dependent Schrödinger equation. Two attosecond pulses in a train produce the replica of electron-H2 + pairs, which are to be steered by a time-delayed phase-stabilized (mid)infrared laser pulse. By controlling the behavior of the freed electron, the dissociation of H2 + can be controlled even though there is no direct laser-H2 + coupling. On the other hand, the photoelectron energy spectra can be manipulated via laser-H2 + coupling. This study demonstrates the entanglement of molecular quantum wave packets, and affords a route to remotely control molecular dissociative ionization.

Towards better modelling of drug-loading in solid lipid nanoparticles: Molecular dynamics, docking experiments and Gaussian Processes machine learning.

PubMed

Hathout, Rania M; Metwally, Abdelkader A

2016-11-01

This study represents one of the series applying computer-oriented processes and tools in digging for information, analysing data and finally extracting correlations and meaningful outcomes. In this context, binding energies could be used to model and predict the mass of loaded drugs in solid lipid nanoparticles after molecular docking of literature-gathered drugs using MOE® software package on molecularly simulated tripalmitin matrices using GROMACS®. Consequently, Gaussian processes as a supervised machine learning artificial intelligence technique were used to correlate the drugs' descriptors (e.g. M.W., xLogP, TPSA and fragment complexity) with their molecular docking binding energies. Lower percentage bias was obtained compared to previous studies which allows the accurate estimation of the loaded mass of any drug in the investigated solid lipid nanoparticles by just projecting its chemical structure to its main features (descriptors). Copyright © 2016 Elsevier B.V. All rights reserved.

General Rule of Negative Effective Ueff System & Materials Design of High-Tc Superconductors by ab initio Calculations

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, Hiroshi; Nakanishi, Akitaka; Uede, Hiroki; Takawashi, Yuki; Fukushima, Tetsuya; Sato, Kazunori

2014-03-01

Based upon ab initio electronic structure calculation, I will discuss the general rule of negative effective U system by (1) exchange-correlation-induced negative effective U caused by the stability of the exchange-correlation energy in Hund's rule with high-spin ground states of d5 configuration, and (2) charge-excitation-induced negative effective U caused by the stability of chemical bond in the closed-shell of s2, p6, and d10 configurations. I will show the calculated results of negative effective U systems such as hole-doped CuAlO2 and CuFeS2. Based on the total energy calculations of antiferromagnetic and ferromagnetic states, I will discuss the magnetic phase diagram and superconductivity upon hole doping. I also discuss the computational materials design method of high-Tc superconductors by ab initio calculation to go beyond LDA and multi-scale simulations.

Correlations between emission timescale of fragments and isospin dynamics in 124Sn+64Ni and 112Sn+58Ni reactions at 35A MeV

NASA Astrophysics Data System (ADS)

De Filippo, E.; Pagano, A.; Russotto, P.; Amorini, F.; Anzalone, A.; Auditore, L.; Baran, V.; Berceanu, I.; Borderie, B.; Bougault, R.; Bruno, M.; Cap, T.; Cardella, G.; Cavallaro, S.; Chatterjee, M. B.; Chbihi, A.; Colonna, M.; D'Agostino, M.; Dayras, R.; Di Toro, M.; Frankland, J.; Galichet, E.; Gawlikowicz, W.; Geraci, E.; Grzeszczuk, A.; Guazzoni, P.; Kowalski, S.; La Guidara, E.; Lanzalone, G.; Lanzanò, G.; Le Neindre, N.; Lombardo, I.; Maiolino, C.; Papa, M.; Piasecki, E.; Pirrone, S.; Płaneta, R.; Politi, G.; Pop, A.; Porto, F.; Rivet, M. F.; Rizzo, F.; Rosato, E.; Schmidt, K.; Siwek-Wilczyńska, K.; Skwira-Chalot, I.; Trifirò, A.; Trimarchi, M.; Verde, G.; Vigilante, M.; Wieleczko, J. P.; Wilczyński, J.; Zetta, L.; Zipper, W.

2012-07-01

We present a new experimental method to correlate the isotopic composition of intermediate mass fragments (IMF) emitted at midrapidity in semiperipheral collisions with the emission timescale: IMFs emitted in the early stage of the reaction show larger values of isospin asymmetry, stronger angular anisotropies, and reduced odd-even staggering effects in neutron to proton ratio distributions than those produced in sequential statistical emission. All these effects support the concept of isospin “migration”, that is sensitive to the density gradient between participant and quasispectator nuclear matter, in the so called neck fragmentation mechanism. By comparing the data to a stochastic mean field (SMF) simulation we show that this method gives valuable constraints on the symmetry energy term of nuclear equation of state at subsaturation densities. An indication emerges for a linear density dependence of the symmetry energy.

Compressible Turbulent Channel Flows: DNS Results and Modeling

NASA Technical Reports Server (NTRS)

Huang, P. G.; Coleman, G. N.; Bradshaw, P.; Rai, Man Mohan (Technical Monitor)

1994-01-01

The present paper addresses some topical issues in modeling compressible turbulent shear flows. The work is based on direct numerical simulation of two supersonic fully developed channel flows between very cold isothermal walls. Detailed decomposition and analysis of terms appearing in the momentum and energy equations are presented. The simulation results are used to provide insights into differences between conventional time-and Favre-averaging of the mean-flow and turbulent quantities. Study of the turbulence energy budget for the two cases shows that the compressibility effects due to turbulent density and pressure fluctuations are insignificant. In particular, the dilatational dissipation and the mean product of the pressure and dilatation fluctuations are very small, contrary to the results of simulations for sheared homogeneous compressible turbulence and to recent proposals for models for general compressible turbulent flows. This provides a possible explanation of why the Van Driest density-weighted transformation is so successful in correlating compressible boundary layer data. Finally, it is found that the DNS data do not support the strong Reynolds analogy. A more general representation of the analogy is analysed and shown to match the DNS data very well.

Comparison of an adaptive neuro-fuzzy inference system and an artificial neural network in the cross-talk correction of simultaneous 99 m Tc / 201Tl SPECT imaging using a GATE Monte-Carlo simulation

NASA Astrophysics Data System (ADS)

Heidary, Saeed; Setayeshi, Saeed; Ghannadi-Maragheh, Mohammad

2014-09-01

The aim of this study is to compare the adaptive neuro-fuzzy inference system (ANFIS) and the artificial neural network (ANN) to estimate the cross-talk contamination of 99 m Tc / 201 Tl image acquisition in the 201 Tl energy window (77 ± 15% keV). GATE (Geant4 Application in Emission and Tomography) is employed due to its ability to simulate multiple radioactive sources concurrently. Two kinds of phantoms, including two digital and one physical phantom, are used. In the real and the simulation studies, data acquisition is carried out using eight energy windows. The ANN and the ANFIS are prepared in MATLAB, and the GATE results are used as a training data set. Three indications are evaluated and compared. The ANFIS method yields better outcomes for two indications (Spearman's rank correlation coefficient and contrast) and the two phantom results in each category. The maximum image biasing, which is the third indication, is found to be 6% more than that for the ANN.

Performative building envelope design correlated to solar radiation and cooling energy consumption

NASA Astrophysics Data System (ADS)

Jacky, Thiodore; Santoni

2017-11-01

Climate change as an ongoing anthropogenic environmental challenge is predominantly caused by an amplification in the amount of greenhouse gases (GHGs), notably carbon dioxide (CO2) in building sector. Global CO2 emissions are emitted from HVAC (Heating, Ventilation, and Air Conditioning) occupation to provide thermal comfort in building. In fact, the amount of energy used for cooling or heating building is implication of building envelope design. Building envelope acts as interface layer of heat transfer between outdoor environment and the interior of a building. It appears as wall, window, roof and external shading device. This paper examines performance of various design strategy on building envelope to limit solar radiation and reduce cooling loads in tropical climate. The design strategies are considering orientation, window to wall ratio, material properties, and external shading device. This research applied simulation method using Autodesk Ecotect to investigate simultaneously between variations of wall and window ratio, shading device composition and the implication to the amount of solar radiation, cooling energy consumption. Comparative analysis on the data will determine logical variation between opening and shading device composition and cooling energy consumption. Optimizing the building envelope design is crucial strategy for reducing CO2 emissions and long-term energy reduction in building sector. Simulation technology as feedback loop will lead to better performative building envelope.

Brain tumor segmentation with Vander Lugt correlator based active contour.

PubMed

Essadike, Abdelaziz; Ouabida, Elhoussaine; Bouzid, Abdenbi

2018-07-01

The manual segmentation of brain tumors from medical images is an error-prone, sensitive, and time-absorbing process. This paper presents an automatic and fast method of brain tumor segmentation. In the proposed method, a numerical simulation of the optical Vander Lugt correlator is used for automatically detecting the abnormal tissue region. The tumor filter, used in the simulated optical correlation, is tailored to all the brain tumor types and especially to the Glioblastoma, which considered to be the most aggressive cancer. The simulated optical correlation, computed between Magnetic Resonance Images (MRI) and this filter, estimates precisely and automatically the initial contour inside the tumorous tissue. Further, in the segmentation part, the detected initial contour is used to define an active contour model and presenting the problematic as an energy minimization problem. As a result, this initial contour assists the algorithm to evolve an active contour model towards the exact tumor boundaries. Equally important, for a comparison purposes, we considered different active contour models and investigated their impact on the performance of the segmentation task. Several images from BRATS database with tumors anywhere in images and having different sizes, contrast, and shape, are used to test the proposed system. Furthermore, several performance metrics are computed to present an aggregate overview of the proposed method advantages. The proposed method achieves a high accuracy in detecting the tumorous tissue by a parameter returned by the simulated optical correlation. In addition, the proposed method yields better performance compared to the active contour based methods with the averages of Sensitivity=0.9733, Dice coefficient = 0.9663, Hausdroff distance = 2.6540, Specificity = 0.9994, and faster with a computational time average of 0.4119 s per image. Results reported on BRATS database reveal that our proposed system improves over the recently published state-of-the-art methods in brain tumor detection and segmentation. Copyright © 2018 Elsevier B.V. All rights reserved.

Jet energy scale and resolution in the CMS experiment in pp collisions at 8 TeV

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

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.

Improved jet energy scale corrections, based on a data sample corresponding to an integrated luminosity of 19.7 fbmore » $$^{-1}$$ collected by the CMS experiment in proton-proton collisions at a center-of-mass energy of 8 TeV, are presented. The corrections as a function of pseudorapidity $$\\eta$$ and transverse momentum $$p_{\\mathrm{T}}$$ are extracted from data and simulated events combining several channels and methods. They account successively for the effects of pileup, uniformity of the detector response, and residual data-simulation jet energy scale differences. Further corrections, depending on the jet flavor and distance parameter (jet size) $R$, are also presented. The jet energy resolution is measured in data and simulated events and is studied as a function of pileup, jet size, and jet flavor. Typical jet energy resolutions at the central rapidities are 15-20% at 30 GeV, about 10% at 100 GeV, and 5% at 1 TeV. The studies exploit events with dijet topology, as well as photon+jet, Z+jet and multijet events. Several new techniques are used to account for the various sources of jet energy scale corrections, and a full set of uncertainties, and their correlations, are provided.The final uncertainties on the jet energy scale are below 3% across the phase space considered by most analyses ($$p_{\\mathrm{T}}> $$ 30 GeV and $$| \\eta| < $$ 5.0). In the barrel region ($$| \\eta| < $$ 1.3) an uncertainty below 1% for $$p_{\\mathrm{T}}> $$ 30 GeV is reached, when excluding the jet flavor uncertainties, which are provided separately for different jet flavors. Finally, a new benchmark for jet energy scale determination at hadron colliders is achieved with 0.32% uncertainty for jets with $$p_{\\mathrm{T}}$$ of the order of 165-330 GeV, and $$| \\eta| < $$ 0.8.« less

Jet energy scale and resolution in the CMS experiment in pp collisions at 8 TeV

DOE PAGES

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; ...

2017-02-22

Improved jet energy scale corrections, based on a data sample corresponding to an integrated luminosity of 19.7 fbmore » $$^{-1}$$ collected by the CMS experiment in proton-proton collisions at a center-of-mass energy of 8 TeV, are presented. The corrections as a function of pseudorapidity $$\\eta$$ and transverse momentum $$p_{\\mathrm{T}}$$ are extracted from data and simulated events combining several channels and methods. They account successively for the effects of pileup, uniformity of the detector response, and residual data-simulation jet energy scale differences. Further corrections, depending on the jet flavor and distance parameter (jet size) $R$, are also presented. The jet energy resolution is measured in data and simulated events and is studied as a function of pileup, jet size, and jet flavor. Typical jet energy resolutions at the central rapidities are 15-20% at 30 GeV, about 10% at 100 GeV, and 5% at 1 TeV. The studies exploit events with dijet topology, as well as photon+jet, Z+jet and multijet events. Several new techniques are used to account for the various sources of jet energy scale corrections, and a full set of uncertainties, and their correlations, are provided.The final uncertainties on the jet energy scale are below 3% across the phase space considered by most analyses ($$p_{\\mathrm{T}}> $$ 30 GeV and $$| \\eta| < $$ 5.0). In the barrel region ($$| \\eta| < $$ 1.3) an uncertainty below 1% for $$p_{\\mathrm{T}}> $$ 30 GeV is reached, when excluding the jet flavor uncertainties, which are provided separately for different jet flavors. Finally, a new benchmark for jet energy scale determination at hadron colliders is achieved with 0.32% uncertainty for jets with $$p_{\\mathrm{T}}$$ of the order of 165-330 GeV, and $$| \\eta| < $$ 0.8.« less

Full-dimensional ground- and excited-state potential energy surfaces and state couplings for photodissociation of thioanisole

NASA Astrophysics Data System (ADS)

Li, Shaohong L.; Truhlar, Donald G.

2017-02-01

Analytic potential energy surfaces (PESs) and state couplings of the ground and two lowest singlet excited states of thioanisole (C6H5SCH3) are constructed in a diabatic representation based on electronic structure calculations including dynamic correlation. They cover all 42 internal degrees of freedom and a wide range of geometries including the Franck-Condon region and the reaction valley along the breaking S-CH3 bond with the full ranges of the torsion angles. The parameters in the PESs and couplings are fitted to the results of smooth diabatic electronic structure calculations including dynamic electron correlation by the extended multi-configurational quasi-degenerate perturbation theory method for the adiabatic state energies followed by diabatization by the fourfold way. The fit is accomplished by the anchor points reactive potential method with two reactive coordinates and 40 nonreactive degrees of freedom, where the anchor-point force fields are obtained with a locally modified version of the QuickFF package. The PESs and couplings are suitable for study of the topography of the trilayer potential energy landscape and for electronically nonadiabatic molecular dynamics simulations of the photodissociation of the S-CH3 bond.

Communication: Studies of the Lennard-Jones fluid in 2, 3, and 4 dimensions highlight the need for a liquid-state 1/d expansion.

PubMed

Costigliola, Lorenzo; Schrøder, Thomas B; Dyre, Jeppe C

2016-06-21

The recent theoretical prediction by Maimbourg and Kurchan [e-print arXiv:1603.05023 (2016)] that for regular pair-potential systems the virial potential-energy correlation coefficient increases towards unity as the dimension d goes to infinity is investigated for the standard 12-6 Lennard-Jones fluid. This is done by computer simulations for d = 2, 3, 4 going from the critical point along the critical isotherm/isochore to higher density/temperature. In both cases the virial potential-energy correlation coefficient increases significantly. For a given density and temperature relative to the critical point, with increasing number of dimension the Lennard-Jones system conforms better to the hidden-scale-invariance property characterized by high virial potential-energy correlations (a property that leads to the existence of isomorphs in the thermodynamic phase diagram, implying that it becomes effectively one-dimensional in regard to structure and dynamics). The present paper also gives the first numerical demonstration of isomorph invariance of structure and dynamics in four dimensions. Our findings emphasize the need for a universally applicable 1/d expansion in liquid-state theory; we conjecture that the systems known to obey hidden scale invariance in three dimensions are those for which the yet-to-be-developed 1/d expansion converges rapidly.

The Response of the South Asian Summer Monsoon Circulation to Intensified Irrigation in Global Climate Model Simulations

NASA Technical Reports Server (NTRS)

Shukla, Sonali P.; Puma, Michael J.; Cook, Benjamin I.

2013-01-01

Agricultural intensification in South Asia has resulted in the expansion and intensification of surface irrigation over the twentieth century. The resulting changes to the surface energy balance could affect the temperature contrasts between the South Asian land surface and the equatorial Indian Ocean, potentially altering the South Asian Summer Monsoon (SASM) circulation. Prior studies have noted apparent declines in the monsoon intensity over the twentieth century and have focused on how altered surface energy balances impact the SASM rainfall distribution. Here, we use the coupled Goddard Institute for Space Studies ModelE-R general circulation model to investigate the impact of intensifying irrigation on the large-scale SASM circulation over the twentieth century, including how the effect of irrigation compares to the impact of increasing greenhouse gas (GHG) forcing. We force our simulations with time-varying, historical estimates of irrigation, both alone and with twentieth century GHGs and other forcings. In the irrigation only experiment, irrigation rates correlate strongly with lower and upper level temperature contrasts between the Indian sub-continent and the Indian Ocean (Pearson's r = -0.66 and r = -0.46, respectively), important quantities that control the strength of the SASM circulation. When GHG forcing is included, these correlations strengthen: r = -0.72 and r = -0.47 for lower and upper level temperature contrasts, respectively. Under irrigated conditions, the mean SASM intensity in the model decreases only slightly and insignificantly. However, in the simulation with irrigation and GHG forcing, inter-annual variability of the SASM circulation decreases by *40 %, consistent with trends in the reanalysis products. This suggests that the inclusion of irrigation may be necessary to accurately simulate the historical trends and variability of the SASM system over the last 50 years. These findings suggest that intensifying irrigation, in concert with increased GHG forcing, is capable of reducing the variability of the simulated SASM circulation and altering the regional moisture transport by limiting the surface warming and reducing land-sea temperature gradients.

Standard performance tests of collectors of solar thermal energy: A selectively coated, flat-plate copper collector with one transparent cover and a tube-to-tube spacing of 3-7/8 inches

NASA Technical Reports Server (NTRS)

1976-01-01

Basic test results are given of a flat-plate solar collector whose performance was determined in the NASA-Lewis solar simulator. The collector was tested over ranges of inlet temperatures, fluxes, and coolant flow rates. Collector efficiency is correlated in terms of inlet temperature and flux level.

CL-20/DNB co-crystal based PBX with PEG: molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Gao, Pei; Xiao, Ji Jun; Zhao, Feng; Xiao, He Ming

2016-12-01

Molecular dynamics simulation was carried out for CL-20/DNB co-crystal based PBX (polymer-bonded explosive) blended with polymer PEG (polyethylene glycol). In this paper, the miscibility of the PBX models is investigated through the calculated binding energy. Pair correlation function (PCF) analysis is applied to study the interaction of the interface structures in the PBX models. The mechanical properties of PBXs are also discussed to understand the change of the mechanical properties after adding the polymer. Moreover, the calculated diffusion coefficients of the interfacial explosive molecules are used to discuss the dispersal ability of CL-20 and DNB molecules in the interface layer.

Phase transition in nonuniform Josephson arrays: Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Lozovik, Yu. E.; Pomirchy, L. M.

1994-01-01

Disordered 2D system with Josephson interactions is considered. Disordered XY-model describes the granular films, Josephson arrays etc. Two types of disorder are analyzed: (1) randomly diluted system: Josephson coupling constants J ij are equal to J with probability p or zero (bond percolation problem); (2) coupling constants J ij are positive and distributed randomly and uniformly in some interval either including the vicinity of zero or apart from it. These systems are simulated by Monte Carlo method. Behaviour of potential energy, specific heat, phase correlation function and helicity modulus are analyzed. The phase diagram of the diluted system in T c-p plane is obtained.

Toward Accurate Adsorption Energetics on Clay Surfaces

PubMed Central

2016-01-01

Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and methanol adsorption on the prototypical clay kaolinite. To the best of our knowledge, this is the first time QMC has been used to investigate adsorption at a complex, natural surface such as a clay. As well as being valuable in their own right, the QMC benchmarks obtained provide reference data against which the performance of cheaper DFT methods can be tested. Indeed using various DFT exchange-correlation functionals yields a very broad range of adsorption energies, and it is unclear a priori which evaluation is better. QMC reveals that in the systems considered here it is essential to account for van der Waals (vdW) dispersion forces since this alters both the absolute and relative adsorption energies of water and methanol. We show, via FF simulations, that incorrect relative energies can lead to significant changes in the interfacial densities of water and methanol solutions at the kaolinite interface. Despite the clear improvements offered by the vdW-corrected and the vdW-inclusive functionals, absolute adsorption energies are often overestimated, suggesting that the treatment of vdW forces in DFT is not yet a solved problem. PMID:27917256

Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations.

PubMed

Qian, Haiyan; Chen, Jiongjiong; Pan, Youlu; Chen, Jianzhong

2016-09-19

11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) is a potential target for the treatment of numerous human disorders, such as diabetes, obesity, and metabolic syndrome. In this work, molecular modeling studies combining molecular docking, 3D-QSAR, MESP, MD simulations and free energy calculations were performed on pyridine amides and 1,2,4-triazolopyridines as 11β-HSD1 inhibitors to explore structure-activity relationships and structural requirement for the inhibitory activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by docking strategy. The derived pharmacophoric features were further supported by MESP and Mulliken charge analyses using density functional theory. In addition, MD simulations and free energy calculations were employed to determine the detailed binding process and to compare the binding modes of inhibitors with different bioactivities. The binding free energies calculated by MM/PBSA showed a good correlation with the experimental biological activities. Free energy analyses and per-residue energy decomposition indicated the van der Waals interaction would be the major driving force for the interactions between an inhibitor and 11β-HSD1. These unified results may provide that hydrogen bond interactions with Ser170 and Tyr183 are favorable for enhancing activity. Thr124, Ser170, Tyr177, Tyr183, Val227, and Val231 are the key amino acid residues in the binding pocket. The obtained results are expected to be valuable for the rational design of novel potent 11β-HSD1 inhibitors.

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

Study of Hygrothermal Processes in External Walls with Internal Insulation

NASA Astrophysics Data System (ADS)

Biseniece, Edite; Freimanis, Ritvars; Purvins, Reinis; Gravelsins, Armands; Pumpurs, Aivars; Blumberga, Andra

2018-03-01

Being an important contributor to the final energy consumption, historic buildings built before 1945 have high specific heating energy consumption compared to current energy standards and norms. However, they often cannot be insulated from the outside due to their heritage and culture value. Internal insulation is an alternative. However internal insulation faces challenges related to hygrothermal behaviour leading to mold growth, freezing, deterioration and other risks. The goal of this research is to link hygrothermal simulation results with experimental results for internally insulated historic brick masonry to assess correlation between simulated and measured data as well as the most influential parameters. The study is carried out by both a mathematical simulation tool and laboratory tests of historic masonry with internal insulation with four insulation materials (mineral wool, EPS, wood fiber and granulated aerogel) in a cold climate (average 4000 heating degree days). We found disparity between measured and simulated hygrothermal performance of studied constructions due to differences in material parameters and initial conditions of materials. The latter plays a more important role than material parameters. Under a steady state of conditions, the condensate tolerating system varies between 72.7 % and 80.5 % relative humidity, but in condensate limiting systems relative humidity variates between 73.3 % and 82.3 %. The temperature between the masonry wall and all insulation materials has stabilized on average at +10 °C. Mold corresponding to Mold index 3 was discovered on wood fiber mat.

New perspectives in face correlation: discrimination enhancement in face recognition based on iterative algorithm

NASA Astrophysics Data System (ADS)

Wang, Q.; Alfalou, A.; Brosseau, C.

2016-04-01

Here, we report a brief review on the recent developments of correlation algorithms. Several implementation schemes and specific applications proposed in recent years are also given to illustrate powerful applications of these methods. Following a discussion and comparison of the implementation of these schemes, we believe that all-numerical implementation is the most practical choice for application of the correlation method because the advantages of optical processing cannot compensate the technical and/or financial cost needed for an optical implementation platform. We also present a simple iterative algorithm to optimize the training images of composite correlation filters. By making use of three or four iterations, the peak-to-correlation energy (PCE) value of correlation plane can be significantly enhanced. A simulation test using the Pointing Head Pose Image Database (PHPID) illustrates the effectiveness of this statement. Our method can be applied in many composite filters based on linear composition of training images as an optimization means.

Radiation Protection Effectiveness of Polymeric Based Shielding Materials at Low Earth Orbit

NASA Technical Reports Server (NTRS)

Badavi, Francis F.; Stewart-Sloan, Charlotte R.; Wilson, John W.; Adams, Daniel O.

2008-01-01

Correlations of limited ionizing radiation measurements onboard the Space Transportation System (STS; shuttle) and the International Space Station (ISS) with numerical simulations of charged particle transport through spacecraft structure have indicated that usage of hydrogen rich polymeric materials improves the radiation shielding performance of space structures as compared to the traditionally used aluminum alloys. We discuss herein the radiation shielding correlations between measurements on board STS-81 (Atlantis, 1997) using four polyethylene (PE) spheres of varying radii, and STS-89 (Endeavour, 1998) using aluminum alloy spheres; with numerical simulations of charged particle transport using the Langley Research Center (LaRC)-developed High charge (Z) and Energy TRaNsport (HZETRN) algorithm. In the simulations, the Galactic Cosmic Ray (GCR) component of the ionizing radiation environment at Low Earth Orbit (LEO) covering ions in the 1< or equals Z< or equals 28 range is represented by O'Neill's (2004) model. To compute the transmission coefficient for GCR ions at LEO, O'Neill's model is coupled with the angular dependent LaRC cutoff model. The trapped protons/electrons component of LEO environment is represented by a LaRC-developed time dependent procedure which couples the AP8min/AP8max, Deep River Neutron Monitor (DRNM) and F10.7 solar radio frequency measurements. The albedo neutron environment resulting from interaction of GCR ions with upper atmosphere is modeled through extrapolation of the Atmospheric Ionizing Radiation (AIR) measurements. With the validity of numerical simulations through correlation with PE and aluminum spheres measurements established, we further present results from the expansion of the simulations through the selection of high hydrogen content commercially available polymeric constituents such as PE foam core and Spectra fiber(Registered TradeMark) composite face sheet to assess their radiation shield properties as compared to generic PE.

On the Direct Correlation between Gamma-Rays and PeV Neutrinos from Blazars

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

Gao, Shan; Pohl, Martin; Winter, Walter, E-mail: shan.gao@desy.de

We study the frequently used assumption in multi-messenger astrophysics that the gamma-ray and neutrino fluxes are directly connected because they are assumed to be produced by the same photohadronic production chain. An interesting candidate source for this test is the flat-spectrum radio quasar PKS B1424-418, which recently called attention to a potential correlation between an IceCube PeV neutrino event and its burst phase. We simulate both the multi-waveband photon and the neutrino emission from this source using a self-consistent radiation model. We demonstrate that a simple hadronic model cannot adequately describe the spectral energy distribution for this source, but amore » lepto-hadronic model with a subdominant hadronic component can reproduce the multi-waveband photon spectrum observed during various activity phases of the blazar. As a conclusion, up to about 0.3 neutrino events may coincide with the burst, which implies that the leptonic contribution dominates in the relevant energy band. We also demonstrate that the time-wise correlation between the neutrino event and burst phase is weak.« less

Evaluation and optimization of footwear comfort parameters using finite element analysis and a discrete optimization algorithm

NASA Astrophysics Data System (ADS)

Papagiannis, P.; Azariadis, P.; Papanikos, P.

2017-10-01

Footwear is subject to bending and torsion deformations that affect comfort perception. Following review of Finite Element Analysis studies of sole rigidity and comfort, a three-dimensional, linear multi-material finite element sole model for quasi-static bending and torsion simulation, overcoming boundary and optimisation limitations, is described. Common footwear materials properties and boundary conditions from gait biomechanics are used. The use of normalised strain energy for product benchmarking is demonstrated along with comfort level determination through strain energy density stratification. Sensitivity of strain energy against material thickness is greater for bending than for torsion, with results of both deformations showing positive correlation. Optimization for a targeted performance level and given layer thickness is demonstrated with bending simulations sufficing for overall comfort assessment. An algorithm for comfort optimization w.r.t. bending is presented, based on a discrete approach with thickness values set in line with practical manufacturing accuracy. This work illustrates the potential of the developed finite element analysis applications to offer viable and proven aids to modern footwear sole design assessment and optimization.

Exclusive data-based modeling of neutron-nuclear reactions below 20 MeV

NASA Astrophysics Data System (ADS)

Savin, Dmitry; Kosov, Mikhail

2017-09-01

We are developing CHIPS-TPT physics library for exclusive simulation of neutron-nuclear reactions below 20 MeV. Exclusive modeling reproduces each separate scattering and thus requires conservation of energy, momentum and quantum numbers in each reaction. Inclusive modeling reproduces only selected values while averaging over the others and imposes no such constraints. Therefore the exclusive modeling allows to simulate additional quantities like secondary particle correlations and gamma-lines broadening and avoid artificial fluctuations. CHIPS-TPT is based on the formerly included in Geant4 CHIPS library, which follows the exclusive approach, and extends it to incident neutrons with the energy below 20 MeV. The NeutronHP model for neutrons below 20 MeV included in Geant4 follows the inclusive approach like the well known MCNP code. Unfortunately, the available data in this energy region is mostly presented in ENDF-6 format and semi-inclusive. Imposing additional constraints on secondary particles complicates modeling but also allows to detect inconsistencies in the input data and to avoid errors that may remain unnoticed in inclusive modeling.

Vapor-liquid phase equilibria of water modelled by a Kim-Gordon potential

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

Maerzke, Katie A.; McGrath, M. J.; Kuo, I-F W.

2009-09-07

Gibbs ensemble Monte Carlo simulations were carried out to investigate the properties of a frozen-electron-density (or Kim-Gordon, KG) model of water along the vapor-liquid coexistence curve. Because of its theoretical basis, such a KG model provides for seamless coupling to Kohn-Sham density functional theory for use in mixed quantum mechanics/molecular mechanics (QM/MM) implementations. The Gibbs ensemble simulations indicate rather limited transferability of such a simple KG model to other state points. Specifically, a KG model that was parameterized by Barker and Sprik to the properties of liquid water at 300 K, yields saturated vapor pressures and a critical temperature thatmore » are significantly under- and overestimated, respectively. We present a comprehensive density functional theory study to asses the accuracy of two popular exchange correlation functionals on the structure and density of liquid water at ambient conditions This work was supported by the US Department of Energy Office of Basic Energy Science Chemical Sciences Program. Battelle operates Pacific Northwest National Laboratory for the US Department of Energy.« less

DNA-linked NanoParticle Lattices with Diamond Symmetry: Stability, Shape and Optical Properties

NASA Astrophysics Data System (ADS)

Emamy, Hamed; Tkachenko, Alexei; Gang, Oleg; Starr, Francis

The linking of nanoparticles (NP) by DNA has been proven to be an effective means to create NP lattices with specific order. Lattices with diamond symmetry are predicted to offer novel photonic properties, but self-assembly of such lattices has proven to be challenging due to the low packing fraction, sensitivity to bond orientation, and local heterogeneity. Recently, we reported an approach to create diamond NP lattices based on the association between anisotropic particles with well-defined tetravalent DNA binding topology and isotropically functionalized NP. Here, we use molecular dynamics simulations to evaluate the Gibbs free energy of these lattices, and thereby determine the stability of these lattices as a function of NP size and DNA stiffness. We also predict the equilibrium shape for the cubic diamond crystallite using the Wulff construction method. Specifically, we predict the equilibrium shape using the surface energy for different crystallographic planes. We evaluate surface energy directly form molecular dynamics simulation, which we correlate with theoretical estimates from the expected number of broken DNA bonds along a facet. Furthermore we study the optical properties of this structure, e.g optical bandgap.

Unusual Crystallization Behavior Close to the Glass Transition

NASA Astrophysics Data System (ADS)

Desgranges, Caroline; Delhommelle, Jerome

2018-03-01

Using molecular simulations, we shed light on the mechanism underlying crystal nucleation in metal alloys and unravel the interplay between crystal nucleation and glass transition, as the conditions of crystallization lie close to this transition. While decreasing the temperature of crystallization usually results in a lower free energy barrier, we find an unexpected reversal of behavior for glass-forming alloys as the temperature of crystallization approaches the glass transition. For this purpose, we simulate the crystallization process in two glass-forming Copper alloys, Ag6 Cu4 , which has a positive heat of mixing, and CuZr, characterized by a large negative heat of mixing. Our results allow us to identify this unusual behavior as directly correlated with a nonmonotonic temperature dependence for the formation energy of connected icosahedral structures, which are incompatible with crystalline order and impede the development of the crystal nucleus, leading to an unexpectedly larger free energy barrier at low temperature. This, in turn, promotes the formation of a predominantly closed-packed critical nucleus, with fewer defects, thereby suggesting a new way to control the structure of the crystal nucleus, which is of key importance in catalysis.

Modification of graphene by ion beam

NASA Astrophysics Data System (ADS)

Gawlik, G.; Ciepielewski, P.; Jagielski, J.; Baranowski, J.

2017-09-01

Ion induced defect generation in graphene was analyzed using Raman spectroscopy. A single layer graphene membrane produced by chemical vapor deposition (CVD) on copper foil and then transferred on glass substrate was subjected to helium, carbon, nitrogen, argon and krypton ions bombardment at energies from the range 25 keV to 100 keV. A density of ion induced defects and theirs mean size were estimated by using Raman measurements. Increasing number of defects generated by ion with increase of ion mass and decrease of ion energy was observed. Dependence of ion defect efficiency (defects/ion) on ion mass end energy was proportional to nuclear stopping power simulated by SRIM. No correlation between ion defect efficiency and electronic stopping power was observed.

New Possibilities of Substance Identification Based on THz Time Domain Spectroscopy Using a Cascade Mechanism of High Energy Level Excitation

PubMed Central

Trofimov, Vyacheslav A.; Varentsova, Svetlana A.; Zakharova, Irina G.; Zagursky, Dmitry Yu.

2017-01-01

Using an experiment with thin paper layers and computer simulation, we demonstrate the principal limitations of standard Time Domain Spectroscopy (TDS) based on using a broadband THz pulse for the detection and identification of a substance placed inside a disordered structure. We demonstrate the spectrum broadening of both transmitted and reflected pulses due to the cascade mechanism of the high energy level excitation considering, for example, a three-energy level medium. The pulse spectrum in the range of high frequencies remains undisturbed in the presence of a disordered structure. To avoid false absorption frequencies detection, we apply the spectral dynamics analysis method (SDA-method) together with certain integral correlation criteria (ICC). PMID:29186849

Computer-aided molecular modeling techniques for predicting the stability of drug cyclodextrin inclusion complexes in aqueous solutions

NASA Astrophysics Data System (ADS)

Faucci, Maria Teresa; Melani, Fabrizio; Mura, Paola

2002-06-01

Molecular modeling was used to investigate factors influencing complex formation between cyclodextrins and guest molecules and predict their stability through a theoretical model based on the search for a correlation between experimental stability constants ( Ks) and some theoretical parameters describing complexation (docking energy, host-guest contact surfaces, intermolecular interaction fields) calculated from complex structures at a minimum conformational energy, obtained through stochastic methods based on molecular dynamic simulations. Naproxen, ibuprofen, ketoprofen and ibuproxam were used as model drug molecules. Multiple Regression Analysis allowed identification of the significant factors for the complex stability. A mathematical model ( r=0.897) related log Ks with complex docking energy and lipophilic molecular fields of cyclodextrin and drug.

Analytic Interatomic Forces in the Random Phase Approximation

NASA Astrophysics Data System (ADS)

Ramberger, Benjamin; Schäfer, Tobias; Kresse, Georg

2017-03-01

We discuss that in the random phase approximation (RPA) the first derivative of the energy with respect to the Green's function is the self-energy in the G W approximation. This relationship allows us to derive compact equations for the RPA interatomic forces. We also show that position dependent overlap operators are elegantly incorporated in the present framework. The RPA force equations have been implemented in the projector augmented wave formalism, and we present illustrative applications, including ab initio molecular dynamics simulations, the calculation of phonon dispersion relations for diamond and graphite, as well as structural relaxations for water on boron nitride. The present derivation establishes a concise framework for forces within perturbative approaches and is also applicable to more involved approximations for the correlation energy.

Normal and Tangential Momentum Accommodation for Earth Satellite Conditions

NASA Technical Reports Server (NTRS)

Knechtel, Earl D.; Pitts, William C.

1973-01-01

Momentum accommodation was determined experimentally for gas-surface interactions simulating in a practical way those of near-earth satellites. Throughout the ranges of gas energies and incidence angles of interest for earth-conditions, two components of force were measured by means of a vacuum microbalance to determine the normal and tangential momentum-accommodation coefficients for nitrogen ions on technical-quality aluminum surfaces. For these experimental conditions, the electrodynamics of ion neutralization near the surface indicate that results for nitrogen ions should differ relatively little from those for nitrogen molecules, which comprise the largest component of momentum flux for near-earth satellites. The experimental results indicated that both normal and tangential momentum-accommodation coefficients varied widely with energy, tending to be relatively well accommodated at the higher energies, but becoming progressively less accommodated as the energy was reduced to and below that for earth-satellite speeds. Both coefficients also varied greatly with incidence angle, the normal momentum becoming less accommodated as the incidence angle became more glancing, whereas the tangential momentum generally became more fully accommodated. For each momentum coefficient, an empirical correlation function was obtained which closely approximated the experimental results over the ranges of energy and incidence angle. Most of the observed variations of momentum accommodation with energy and incidence angle were qualitatively indicated by a calculation using a three-dimensional model that simulated the target surface by a one-dimensional attractive potential and hard sphere reflectors.

Characteristic energy range of electron scattering due to plasmaspheric hiss

DOE PAGES

Ma, Q.; Li, W.; Thorne, R. M.; ...

2016-11-15

In this paper, we investigate the characteristic energy range of electron flux decay due to the interaction with plasmaspheric hiss in the Earth's inner magnetosphere. The Van Allen Probes have measured the energetic electron flux decay profiles in the Earth's outer radiation belt during a quiet period following the geomagnetic storm that occurred on 7 November 2015. The observed energy of significant electron decay increases with decreasing L shell and is well correlated with the energy band corresponding to the first adiabatic invariant μ = 4–200 MeV/G. The electron diffusion coefficients due to hiss scattering are calculated at L =more » 2–6, and the modeled energy band of effective pitch angle scattering is also well correlated with the constant μ lines and is consistent with the observed energy range of electron decay. Using the previously developed statistical plasmaspheric hiss model during modestly disturbed periods, we perform a 2-D Fokker-Planck simulation of the electron phase space density evolution at L = 3.5 and demonstrate that plasmaspheric hiss causes the significant decay of 100 keV–1 MeV electrons with the largest decay rate occurring at around 340 keV, forming anisotropic pitch angle distributions at lower energies and more flattened distributions at higher energies. Finally, our study provides reasonable estimates of the electron populations that can be most significantly affected by plasmaspheric hiss and the consequent electron decay profiles.« less

Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases.

PubMed

Hamed, Mazen Y; Arya, Gaurav

2016-05-01

Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of ZF motifs to their sites on DNA. ΔG values were -15.82(12), -3.66(12), and -12.14(11.6) kcal/mol for finger one, finger two, and finger three, respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔG = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔG = 22 kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation (r = .98). The mutations in key amino acids in the ZF motif in positions-1, 2, 3, and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was .99 and with Van der Waal was .93. Results agree with experimentally found selectivity which showed that Arginine in position-1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared ZF motifs bound to triplet bases in other reports (), our results may help in the design of ZF motifs based on the established recognition codes based on energies and contributing energies to the total energy.

Measuring the Scatter of the Mass–Richness Relation in Galaxy Clusters in Photometric Imaging Surveys by Means of Their Correlation Function

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

Campa, Julia; Estrada, Juan; Flaugher, Brenna

2017-02-03

The knowledge of the scatter in the mass-observable relation is a key ingredient for a cosmological analysis based on galaxy clusters in a photometric survey. We demonstrate here how the linear bias measured in the correlation function for clusters can be used to determine the value of the scatter. The new method is tested in simulations of a 5.000 square degrees optical survey up to z~1, similar to the ongoing Dark Energy Survey. The results indicate that the scatter can be measured with a precision of 5% using this technique.

Probabilistic Density Function Method for Stochastic ODEs of Power Systems with Uncertain Power Input

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

Wang, Peng; Barajas-Solano, David A.; Constantinescu, Emil

Wind and solar power generators are commonly described by a system of stochastic ordinary differential equations (SODEs) where random input parameters represent uncertainty in wind and solar energy. The existing methods for SODEs are mostly limited to delta-correlated random parameters (white noise). Here we use the Probability Density Function (PDF) method for deriving a closed-form deterministic partial differential equation (PDE) for the joint probability density function of the SODEs describing a power generator with time-correlated power input. The resulting PDE is solved numerically. A good agreement with Monte Carlo Simulations shows accuracy of the PDF method.

Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

NASA Astrophysics Data System (ADS)

Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

2012-04-01

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

Medical image diagnoses by artificial neural networks with image correlation, wavelet transform, simulated annealing

NASA Astrophysics Data System (ADS)

Szu, Harold H.

1993-09-01

Classical artificial neural networks (ANN) and neurocomputing are reviewed for implementing a real time medical image diagnosis. An algorithm known as the self-reference matched filter that emulates the spatio-temporal integration ability of the human visual system might be utilized for multi-frame processing of medical imaging data. A Cauchy machine, implementing a fast simulated annealing schedule, can determine the degree of abnormality by the degree of orthogonality between the patient imagery and the class of features of healthy persons. An automatic inspection process based on multiple modality image sequences is simulated by incorporating the following new developments: (1) 1-D space-filling Peano curves to preserve the 2-D neighborhood pixels' relationship; (2) fast simulated Cauchy annealing for the global optimization of self-feature extraction; and (3) a mini-max energy function for the intra-inter cluster-segregation respectively useful for top-down ANN designs.

Accurate condensed history Monte Carlo simulation of electron transport. II. Application to ion chamber response simulations.

PubMed

Kawrakow, I

2000-03-01

In this report the condensed history Monte Carlo simulation of electron transport and its application to the calculation of ion chamber response is discussed. It is shown that the strong step-size dependencies and lack of convergence to the correct answer previously observed are the combined effect of the following artifacts caused by the EGS4/PRESTA implementation of the condensed history technique: dose underprediction due to PRESTA'S pathlength correction and lateral correlation algorithm; dose overprediction due to the boundary crossing algorithm; dose overprediction due to the breakdown of the fictitious cross section method for sampling distances between discrete interaction and the inaccurate evaluation of energy-dependent quantities. These artifacts are now understood quantitatively and analytical expressions for their effect are given.

Quantum dynamics in continuum for proton transport—Generalized correlation

NASA Astrophysics Data System (ADS)

Chen, Duan; Wei, Guo-Wei

2012-04-01

As a key process of many biological reactions such as biological energy transduction or human sensory systems, proton transport has attracted much research attention in biological, biophysical, and mathematical fields. A quantum dynamics in continuum framework has been proposed to study proton permeation through membrane proteins in our earlier work and the present work focuses on the generalized correlation of protons with their environment. Being complementary to electrostatic potentials, generalized correlations consist of proton-proton, proton-ion, proton-protein, and proton-water interactions. In our approach, protons are treated as quantum particles while other components of generalized correlations are described classically and in different levels of approximations upon simulation feasibility and difficulty. Specifically, the membrane protein is modeled as a group of discrete atoms, while ion densities are approximated by Boltzmann distributions, and water molecules are represented as a dielectric continuum. These proton-environment interactions are formulated as convolutions between number densities of species and their corresponding interaction kernels, in which parameters are obtained from experimental data. In the present formulation, generalized correlations are important components in the total Hamiltonian of protons, and thus is seamlessly embedded in the multiscale/multiphysics total variational model of the system. It takes care of non-electrostatic interactions, including the finite size effect, the geometry confinement induced channel barriers, dehydration and hydrogen bond effects, etc. The variational principle or the Euler-Lagrange equation is utilized to minimize the total energy functional, which includes the total Hamiltonian of protons, and obtain a new version of generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation and generalized Kohn-Sham equation. A set of numerical algorithms, such as the matched interface and boundary method, the Dirichlet to Neumann mapping, Gummel iteration, and Krylov space techniques, is employed to improve the accuracy, efficiency, and robustness of model simulations. Finally, comparisons between the present model predictions and experimental data of current-voltage curves, as well as current-concentration curves of the Gramicidin A channel, verify our new model.

Impact of Charge Degradation on the Life Cycle Climate Performance of a Residential Air-Conditioning System

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

Beshr, Mohamed; Aute, Vikrant; Abdelaziz, Omar

2014-01-01

Vapor compression systems continuously leak a small fraction of their refrigerant charge to the environment, whether during operation or servicing. As a result of the slow leak rate occurring during operation, the refrigerant charge decreases until the system is serviced and recharged. This charge degradation, after a certain limit, begins to have a detrimental effect on system capacity, energy consumption, and coefficient of performance (COP). This paper presents a literature review and a summary of previous experimental work on the effect of undercharging or charge degradation of different vapor compression systems, especially those without a receiver. These systems include residentialmore » air conditioning and heat pump systems utilizing different components and refrigerants, and water chiller systems. Most of these studies show similar trends for the effect of charge degradation on system performance. However, it is found that although much experimental work exists on the effect of charge degradation on system performance, no correlation or comparison between charge degradation and system performance yet exists. Thus, based on the literature review, three different correlations that characterize the effect of charge on system capacity and energy consumption are developed for different systems as follows: one for air-conditioning systems, one for vapor compression water-to-water chiller systems, and one for heat pumps. These correlations can be implemented in vapor compression cycle simulation tools to obtain a better prediction of the system performance throughout its lifetime. In this paper, these correlations are implemented in an open source tool for life cycle climate performance (LCCP) based design of vapor compression systems. The LCCP of a residential air-source heat pump is evaluated using the tool and the effect of charge degradation on the results is studied. The heat pump is simulated using a validated component-based vapor compression system model and the LCCP results obtained using the three charge degradation correlations are compared.« less

Properties of inhibitors of methane hydrate formation via molecular dynamics simulations.

PubMed

Anderson, Brian J; Tester, Jefferson W; Borghi, Gian Paolo; Trout, Bernhardt L

2005-12-21

Within the framework of a proposed two-step mechanism for hydrate inhibition, the energy of binding of four inhibitor molecules (PEO, PVP, PVCap, and VIMA) to a hydrate surface is estimated with molecular dynamic simulations. One key feature of this proposed mechanism is that the binding of an inhibitor molecule to the surface of an ensuing hydrate crystal disrupts growth and therein crystallization. It is found through the molecular dynamic simulations that inhibitor molecules that experimentally exhibit better inhibition strength also have higher free energies of binding, an indirect confirmation of our proposed mechanism. Inhibitors increasing in effectiveness, PEO < PVP < PVCap < VIMA, have increasingly negative (exothermic) binding energies of -0.2 < -20.6 < -37.5 < -45.8 kcal/mol and binding free energies of increasing favorability (+0.4 approximately = +0.5 < -9.4 < -15.1 kcal/mol). Furthermore, the effect of an inhibitor molecule on the local liquid water structure under hydrate-forming conditions was examined and correlated to the experimental effectiveness of the inhibitors. Two molecular characteristics that lead to strongly binding inhibitors were found: (1) a charge distribution on the edge of the inhibitor that mimics the charge separation in the water molecules on the surface of the hydrate and (2) the congruence of the size of the inhibitor with respect to the available space at the hydrate-surface binding site. Equipped with this molecular-level understanding of the process of hydrate inhibition via low-dosage kinetic hydrate inhibitors we can design new, more effective inhibitor molecules.

Thermal performance - Rangewood Villas. Field monitoring of various conservation construction techniques in the hot-humid area

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

Not Available

1986-06-01

This report, prepared by researchers at Florida Solar Energy Center, describes data acquired over a complete year of comprehensive thermal performance monitoring. The construction details of the house and instrumentation system are clearly documented. Rangewood Villas in Cocoa, Florida, is an innovative townhouse project that incorporates several energy efficient construction techniques developed at FSEC including vent skin roofs and walls utilizing radiant barriers to substantially lower heat gain through radiant transfer of solar energy. The computer simulation model selected as the basis for data acquisition parameters is the Thermal Analysis Research Program (TARP). The TARP model does not contain humiditymore » correlations which are very important in predicting thermal performance in the warm humid area. These correlations are developed for enhancement of the TARP model through extensive relative humidity measurements in various zones, and enthalpy measurements of the heat pump. The data acquisition system devised for this program provides a standard instrumentation system which can be adapted by others working in the hot humid area and intersted in developing comparative performance data.« less

The LAAS network observation for studying time correlations in extensive air showers

NASA Astrophysics Data System (ADS)

Ochi, Nobuaki; Iyono, A.; Kimura, Hitoomi; Konishi, Takeharu; Nakamura, Toru; Nakatsuka, Takao; Ohara, Soji; Ohmori, Nobuharu; Saito, Katsuhiko; Takahashi, Nobusuke; Tsuji, Shuhei; Wada, Tomonori; Yamamoto, Isao; Yamashita, Yoshihiko; Yanagimoto, Yukio

2003-02-01

The Large Area Air Shower (LAAS) group has been performing a network observation of extensive air showers (EAS) since 1996 in Japan. Ten compact EAS arrays are operating simultaneously at distant stations (up to ≍1000 km) and detecting EAS with mean energy of ≍1015 eV. Each station has 4--12 scintillation counters and a Global Positioning System (GPS), which provides time stamps of EAS triggers with an accuracy of 1μs. As a consequence of the comparable time stamps, uniformly-adjusted detectors and a standardized data format among all stations, we can treat the independent observations as a gigantic EAS detector system as a whole. The primary purpose of the network observation is to study large-scale correlations in ultra-high-energy cosmic rays. On the other hand, three nearby stations within 1~km distance at Okayama area have a possibility to detect extremely-high-energy EAS (≍1019 eV) as coincident triggers of the three stations. The present status of the network and some results from computer simulations are reported here.

Dissolution of methane bubbles with hydrate armoring in deep ocean conditions

NASA Astrophysics Data System (ADS)

Kovalchuk, Margarita; Socolofsky, Scott

2017-11-01

The deep ocean is a storehouse of natural gas. Methane bubble moving upwards from marine sediments may become trapped in gas hydrates. It is uncertain precisely how hydrate armoring affects dissolution, or mass transfer from the bubble to the surrounding water column. The Texas A&M Oilspill Calculator was used to simulate a series of gas bubble dissolution experiments conducted in the United States Department of Energy National Energy Technology Laboratory High Pressure Water Tunnel. Several variations of the mass transfer coefficient were calculated based on gas or hydrate phase solubility and clean or dirty bubble correlations. Results suggest the mass transfer coefficient may be most closely modeled with gas phase solubility and dirty bubble correlation equations. Further investigation of hydrate bubble dissolution behavior will refine current numeric models which aid in understanding gas flux to the atmosphere and plumes such as oil spills. Research funded in part by the Texas A&M University 2017 Undergraduate Summer Research Grant and a Grant from the Methane Gas Hydrates Program of the US DOE National Energy Technology Laboratory.

Two new meal- and web-based interactive food frequency questionnaires: validation of energy and macronutrient intake.

PubMed

Christensen, Sara E; Möller, Elisabeth; Bonn, Stephanie E; Ploner, Alexander; Wright, Antony; Sjölander, Arvid; Bälter, Olle; Lissner, Lauren; Bälter, Katarina

2013-06-05

Meal-Q and its shorter version, MiniMeal-Q, are 2 new Web-based food frequency questionnaires. Their meal-based and interactive format was designed to promote ease of use and to minimize answering time, desirable improvements in large epidemiological studies. We evaluated the validity of energy and macronutrient intake assessed with Meal-Q and MiniMeal-Q as well as the reproducibility of Meal-Q. Healthy volunteers aged 20-63 years recruited from Stockholm County filled out the 174-item Meal-Q. The questionnaire was compared to 7-day weighed food records (WFR; n=163), for energy and macronutrient intake, and to doubly labeled water (DLW; n=39), for total energy expenditure. In addition, the 126-item MiniMeal-Q was evaluated in a simulated validation using truncated Meal-Q data. We also assessed the answering time and ease of use of both questionnaires. Bland-Altman plots showed a varying bias within the intake range for all validity comparisons. Cross-classification of quartiles placed 70%-86% in the same/adjacent quartile with WFR and 77% with DLW. Deattenuated and energy-adjusted Pearson correlation coefficients with the WFR ranged from r=0.33-0.74 for macronutrients and was r=0.18 for energy. Correlations with DLW were r=0.42 for Meal-Q and r=0.38 for MiniMeal-Q. Intraclass correlations for Meal-Q ranged from r=0.57-0.90. Median answering time was 17 minutes for Meal-Q and 7 minutes for MiniMeal-Q, and participants rated both questionnaires as easy to use. Meal-Q and MiniMeal-Q are easy to use and have short answering times. The ranking agreement is good for most of the nutrients for both questionnaires and Meal-Q shows fair reproducibility.

Understanding nature's particle accelerators using high energy gamma-ray survey instruments

NASA Astrophysics Data System (ADS)

Abeysekara, Anushka Udara

Nature's particle accelerators, such as Pulsars, Pulsar Wind Nebulae, Active Galactic Nuclei and Supernova Remnants accelerate charged particles to very high energies that then produce high energy photons. The particle acceleration mechanisms and the high energy photon emission mechanisms are poorly understood phenomena. These mechanisms can be understood either by studying individual sources in detail or, alternatively, using the collective properties of a sample of sources. Recent development of GeV survey instruments, such as Fermi-LAT, and TeV survey instruments, such as Milagro, provides a large sample of high energy gamma-ray flux measurements from galactic and extra-galactic sources. In this thesis I provide constraints on GeV and TeV radiation mechanisms using the X-ray-TeV correlations and GeV-TeV correlations. My data sample was obtained from three targeted searches for extragalactic sources and two targeted search for galactic sources, using the existing Milagro sky maps. The first extragalactic candidate list consists of Fermi-LAT GeV extragalactic sources, and the second extragalactic candidate list consists of TeVCat extragalactic sources that have been detected by Imaging Atmospheric Cerenkov Telescopes (IACTs). In both extragalactic candidate lists Markarian 421 was the only source detected by Milagro. A comparison between the Markarian 421 time-averaged flux, measured by Milagro, and the flux measurements of transient states, measured by IACTs, is discussed. The third extragalactic candidate list is a list of potential TeV emitting BL Lac candidates that was synthesized using X-ray observations of BL Lac objects and a Synchrotron Self-Compton model. Milagro's sensitivity was not sufficient to detect any of those candidates. However, the 95% confidence flux upper limits of those sources were above the predicted flux. Therefore, these results provide evidence to conclude that the Synchrotron Self-Compton model for BL Lac objects is still a viable model. Targeted searches for galactic candidates were able to measure TeV emission associated with 14 Fermi-LAT GeV pulsars. In this thesis I also presented a new multi-wavelength technique that I developed to isolate the flux correlation factor (fΩ ) of pulsars as a function of pulsar spin down luminosity. The correlation between fΩ and pulsar spin-down luminosity for a Fermi-LAT GeV pulsar sample was measured using the measurements obtained in the Milagro targeted search performed for galactic sources and from the literature. The measured correlation has some features that favor the Outer Gap model over the Polar Cap, Slot Gap and One Pole Caustic models for pulsar emission in the energy range of 0.1 to 100 GeV. However, these simulated models failed to explain many other important pulsar population characteristics. Therefore, further improvements on the galactic pulsar population simulations are needed to provide tighter constraints.

Molecular dynamics simulation study of nanoscale passive oxide growth on Ni-Al alloy surfaces at low temperatures

NASA Astrophysics Data System (ADS)

Sankaranarayanan, Subramanian K. R. S.; Ramanathan, Shriram

2008-08-01

Oxidation kinetics of Ni-Al (100) alloy surface is investigated at low temperatures (300-600 K) and at different gas pressures using molecular dynamics (MD) simulations with dynamic charge transfer between atoms. Monte Carlo simulations employing the bond order simulation model are used to generate the surface segregated minimum energy initial alloy configurations for use in the MD simulations. In the simulated temperature-pressure-composition regime for Ni-Al alloys, we find that the oxide growth curves follow a logarithmic law beyond an initial transient regime. The oxidation rates for Ni-Al alloys were found to decrease with increasing Ni composition. Structure and dynamical correlations in the metal/oxide/gas environments are used to gain insights into the evolution and morphology of the growing oxide film. Oxidation of Ni-Al alloys is characterized by the absence of Ni-O bond formation. Oxide films formed on the various simulated metal surfaces are amorphous in nature and have a limiting thickness ranging from ˜1.7nm for pure Al to 1.1 nm for 15% Ni-Al surfaces. Oxide scale analysis indicates significant charge transfer as well as variation in the morphology and structure of the oxide film formed on pure Al and 5% Ni-Al alloy. For oxide scales thicker than 1 nm, the oxide structure in case of pure Al exhibits a mixed tetrahedral (AlO4˜37%) and octahedral (AlO6˜19%) environment, whereas the oxide scale on Ni-Al alloy surface is almost entirely composed of tetrahedral environment (AlO4˜60%) with very little AlO6 (<1%) . The oxide growth kinetic curves are fitted to Arrhenius-type plots to get an estimate of the activation energy barriers for metal oxidation. The activation energy barrier for oxidation on pure Al was found to be 0.3 eV lower than that on 5% Ni-Al surface. Atomistic observations as well as calculated dynamical correlation functions indicate a layer by layer growth on pure Al, whereas a transition from an initial island growth mode (<75ps) to a layer by layer mode (>100ps) occurs in case of 5% Ni-Al alloy. The oxide growth on both pure Al and Ni-Al alloy surfaces occurs by inward anion and outward cation diffusions. The cation diffusion in both the cases is similar, whereas the anion diffusion in case of 5% Ni-Al is 25% lower than pure Al, thereby resulting in reduced self-limiting thickness of oxide scale on the alloy surface. The simulation findings agree well with previously reported experimental observations of oxidation on Ni-Al alloy surface.

Impact of spatially correlated pore-scale heterogeneity on drying porous media

NASA Astrophysics Data System (ADS)

Borgman, Oshri; Fantinel, Paolo; Lühder, Wieland; Goehring, Lucas; Holtzman, Ran

2017-07-01

We study the effect of spatially-correlated heterogeneity on isothermal drying of porous media. We combine a minimal pore-scale model with microfluidic experiments with the same pore geometry. Our simulated drying behavior compares favorably with experiments, considering the large sensitivity of the emergent behavior to the uncertainty associated with even small manufacturing errors. We show that increasing the correlation length in particle sizes promotes preferential drying of clusters of large pores, prolonging liquid connectivity and surface wetness and thus higher drying rates for longer periods. Our findings improve our quantitative understanding of how pore-scale heterogeneity impacts drying, which plays a role in a wide range of processes ranging from fuel cells to curing of paints and cements to global budgets of energy, water and solutes in soils.

A climate model diagnostic metric for the Madden-Julian oscillation

NASA Astrophysics Data System (ADS)

Gonzalez, A. O.; Jiang, X.

2016-12-01

Despite its significant impacts on global weather and climate, the Madden-Julian oscillation (MJO) remains a grand challenge for state-of-the-art general circulation models (GCMs). The eastward propagation of the MJO is often poorly simulated in GCMs, represented by a stationary or even westward propagating mode. Recent analyses based on moist static energy processes suggest the horizontal advection of the winter mean moist static energy by the MJO circulation plays a critical role in the observed eastward propagation of the MJO. In this study, we explore relationships between model fidelity in representing the eastward propagation of the MJO and the winter mean lower-tropospheric moisture pattern by analyzing a suite of GCMs from a recent multi-model MJO comparison project. Model capability of reproducing the observed spatial pattern of the 650-900 hPa winter mean specific humidity is a robust indicator of how well they reproduce the MJO's eastward propagation. In particular, model skill in simulating the low-level winter mean specific humidity over the Maritime Continent region (20°S-20°N, 90°-135°E) is highly correlated with model skill of MJO propagation across the 23 GCMs analyzed, with a correlation of about 0.8. Winter mean lower-tropospheric moisture patterns over two other regions, including the western Indian Ocean and an off-equatorial region in the central Indian Ocean, also exhibit high correlations with MJO propagation skill in the model simulations. This study supports recent studies in highlighting the importance of the mean low-level moisture for MJO propagation and it points out a direction for model improvement of the MJO. Meanwhile, it is also suggested that the winter mean low-level moisture pattern over the Indo-Pacific region, particularly over the Maritime Continent region, can serve as a diagnostic metric for the eastward propagation of the MJO in climate model assessments.

Calculation on spectrum of direct DNA damage induced by low-energy electrons including dissociative electron attachment.

PubMed

Liu, Wei; Tan, Zhenyu; Zhang, Liming; Champion, Christophe

2017-03-01

In this work, direct DNA damage induced by low-energy electrons (sub-keV) is simulated using a Monte Carlo method. The characteristics of the present simulation are to consider the new mechanism of DNA damage due to dissociative electron attachment (DEA) and to allow determining damage to specific bases (i.e., adenine, thymine, guanine, or cytosine). The electron track structure in liquid water is generated, based on the dielectric response model for describing electron inelastic scattering and on a free-parameter theoretical model and the NIST database for calculating electron elastic scattering. Ionization cross sections of DNA bases are used to generate base radicals, and available DEA cross sections of DNA components are applied for determining DNA-strand breaks and base damage induced by sub-ionization electrons. The electron elastic scattering from DNA components is simulated using cross sections from different theoretical calculations. The resulting yields of various strand breaks and base damage in cellular environment are given. Especially, the contributions of sub-ionization electrons to various strand breaks and base damage are quantitatively presented, and the correlation between complex clustered DNA damage and the corresponding damaged bases is explored. This work shows that the contribution of sub-ionization electrons to strand breaks is substantial, up to about 40-70%, and this contribution is mainly focused on single-strand break. In addition, the base damage induced by sub-ionization electrons contributes to about 20-40% of the total base damage, and there is an evident correlation between single-strand break and damaged base pair A-T.

Covariances for the 56Fe radiation damage cross sections

NASA Astrophysics Data System (ADS)

Simakov, Stanislav P.; Koning, Arjan; Konobeyev, Alexander Yu.

2017-09-01

The energy-energy and reaction-reaction covariance matrices were calculated for the n + 56Fe damage cross-sections by Total Monte Carlo method using the TENDL-2013 random files. They were represented in the ENDF-6 format and added to the unperturbed evaluation file. The uncertainties for the spectrum averaged radiation quantities in the representative fission, fusion and spallation facilities were first time assessed as 5-25%. Additional 5 to 20% have to be added to the atom displacement rate uncertainties to account for accuracy of the primary defects simulation in materials. The reaction-reaction correlation were shown to be 1% or less.

Novel Method to Characterize and Model the Multiaxial Constitutive and Damage Response of Energetic Materials.

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

Kaneshige, Michael J.; Rabbi, Md Fazle; Kaneshige, Michael J.

2017-12-01

Simulant polymer bonded explosives are widely used to simulate the mechanical response of real energetic materials. In this paper, the fracture resistance of a simulant polymer bo nded explosive (PBX) is experimentally investigated. The simulant is composed of 80 wt.% soda lime glass beads (SLGB) and 20 wt.% high impact Polystyrene 825 (HIPS). Brazilian disk tests are performed to characterize the tensile and compressive properties. Fracture toughness and energy tests are performed in the semi - circular bending (SCB) configuration on 80, 81, 82, and 83 wt % SLGB compositions. Digital image correlation is performed to record the surface displacementsmore » and calculate surface strains during testing. The m icromechanical behavior of ductile and brittle fracture are evaluated using digital microscopy and scanning electron microscopy of the fracture surface. It is determined that (i) the manufacturing process produces a credible simulant of PBX properties, and (ii) the SCB test measures fracture resistance with a reasonable coefficient of variation.« less

Assessment of higher order correlation effects with the help of Moller-Plesset perturbation theory up to sixth order

NASA Astrophysics Data System (ADS)

He, Yuan; Cremer, Dieter

For 30 molecules and two atoms, MP n correlation energies up to n = 6 are computed and used to analyse higher order correlation effects and the initial convergence behaviour of the MP n series. Particularly useful is the analysis of correlation contributions E(n)XY ...( n = 4,5,6; X , Y ,... = S, D, T, Q denoting single, double, triple, and quadruple excitations) in the form of correlation energy spectra. Two classes of system are distinguished, namely class A systems possessing well separated electron pairs and class B systems which are characterized by electron clustering in certain regions of atomic and molecular space. For class A systems, electron pair correlation effects as described by D, Q, DD, DQ, QQ, DDD, etc., contributions are most important, which are stepwise included at MP n with n = 2,... ,6. Class A systems are reasonably described by MP n theory, which is reflected by the fact that convergence of the MP n series is monotonic (but relatively slow) for class A systems. The description of class B systems is difficult since three- and four-electron correlation effects and couplings between two-, three-, and four-electron correlation effects missing for lower order perturbation theory are significant. MP n methods, which do not cover these effects, simulate higher order with lower order correlation effects thus exaggerating the latter, which has to be corrected with increasing n. Consequently, the MP n series oscillates for class B systems at low orders. A possible divergence of the MP n series is mostly a consequence of an unbalanced basis set. For example, diffuse functions added to an unsaturated sp basis lead to an exaggeration of higher order correlation effects, which can cause enhanced oscillations and divergence of the MP n series.

Analysis of Composite Skin-Stiffener Debond Specimens Using a Shell/3D Modeling Technique and Submodeling

NASA Technical Reports Server (NTRS)

OBrien, T. Kevin (Technical Monitor); Krueger, Ronald; Minguet, Pierre J.

2004-01-01

The application of a shell/3D modeling technique for the simulation of skin/stringer debond in a specimen subjected to tension and three-point bending was studied. The global structure was modeled with shell elements. A local three-dimensional model, extending to about three specimen thicknesses on either side of the delamination front was used to model the details of the damaged section. Computed total strain energy release rates and mixed-mode ratios obtained from shell/3D simulations were in good agreement with results obtained from full solid models. The good correlation of the results demonstrated the effectiveness of the shell/3D modeling technique for the investigation of skin/stiffener separation due to delamination in the adherents. In addition, the application of the submodeling technique for the simulation of skin/stringer debond was also studied. Global models made of shell elements and solid elements were studied. Solid elements were used for local submodels, which extended between three and six specimen thicknesses on either side of the delamination front to model the details of the damaged section. Computed total strain energy release rates and mixed-mode ratios obtained from the simulations using the submodeling technique were not in agreement with results obtained from full solid models.

Shuttle orbiter radar cross-sectional analysis

NASA Technical Reports Server (NTRS)

Cooper, D. W.; James, R.

1979-01-01

Theoretical and model simulation studies on signal to noise levels and shuttle radar cross section are described. Pre-mission system calibrations, system configuration, and postmission system calibration of the tracking radars are described. Conversion of target range, azimuth, and elevation into radar centered east north vertical position coordinates are evaluated. The location of the impinging rf energy with respect to the target vehicles body axis triad is calculated. Cross section correlation between the two radars is presented.

Standardized performance tests of collectors of solar thermal energy: A selectively coated, flat-plate copper collector with one transparent cover and a tube-to-tube spacing of 5 5/8 inches

NASA Technical Reports Server (NTRS)

1976-01-01

This preliminary data report gives basic test results of a flat-plate solar collector whose performance was determined in the NASA-Lewis solar simulator. The collector was tested over ranges of inlet temperatures, fluxes and coolant flow rates. Collector efficiency is correlated in terms of inlet temperature and flux level.

Molecular dynamics simulations of plasma-surface interactions

NASA Astrophysics Data System (ADS)

Vegh, Joseph James

Molecular dynamics (MD) simulations are carried out to examine the fundamental mechanisms of plasma-surface interactions for various systems of interest to the semiconductor industry. These include ion and radical bombardment simulations of silicon, model low-k dielectric materials, and hydrocarbon (HC) based model photoresist materials. Simulations of fluorocarbon (FC), fluorine, and argon ion etching of silicon are conducted to find conditions under which the steady state etch of Si in the presence of a FC surface layer occurs. By varying the FC/F/Ar + ratios over a range of conditions, a correlation between FC layer thickness and Si etch yield (EY) is obtained that agrees qualitatively with experimentally observed trends. Further examination of this system allows for a Si etch mechanism to be proposed. This mechanism is similar to that seen in previous Si etching simulations where FC films do not form. The FC layer is observed to fluctuate in thickness during steady state Si etch, as the result of competition between FC deposition and sputtering of relatively large (> 6 C atoms) FC clusters during Ar+ impacts. This cluster ejection process is seen in all of the systems studied, and the properties of these clusters (composition, size, kinetic energy, etc.) are examined and catalogued. Ar+ and H radical and ion bombardment of a methylated Si surface is simulated as a model of plasma etching of low-k dielectric materials. The mechanisms and product distributions observed for 300 K H radical bombardment agree well with experiment. The etch characteristics of Ar+ bombardment are examined as a function of ion energy, and the corresponding variations in surface structure at high ion fluence are characterized. Various HC polymer surfaces are studied under ion and radical bombardment to examine plasma species interactions with model photoresist materials. Simulations of 100 eV Ar+ bombardment of polystyrene (PS), poly(4-methylstyrene) (P4MS), and poly(alpha-methylstyrene) (PalphaMS) show that for all of these materials (which have similar chemical compositions: PS: (C8H 8)x, PalphaMS and P4MS: (C9H 10)x), a densely crosslinked, dehydrogenated damaged layer forms at high ion fluences that greatly reduces the sputter yield of the material. During the initial transient period of bombardment, PalphaMS shows sputter yields nearly twice as high as P4MS or PS; polymer structure can play a role during the early stages of etch. Both the initial and high fluence etch characteristics match those observed experimentally. Further, fluctuations from cell-to-cell are much higher for the PalphaMS simulations, which may correlate to the increased roughening observed experimentally for PalphaMS. Additional simulations are carried out to examine the effects of H and F radical addition during Ar+ bombardment of PS. Both radical species are shown to inhibit and/or reverse the formation of the dehydrogenated layer that forms during bombardment with Ar+ alone. Further studies examine the effect of inert ion mass through simulations of Ar +, Xe+, and He+ bombardment of PS, amorphous C, and nanoscale features on diamond surfaces. The differences in penetration depth, kinetic energy deposition, and scattering patterns are suggestive of the differing etch characteristics that are seen experimentally for these ions. A discussion of dangling bond formation during ion bombardment and longer time-scale dynamics is also offered. A brief review of currently available potential energy functions is presented. Selected results from MD simulations that utilize some of these potentials and are closely related to the work in this dissertation are also discussed. The difficulties of expanding potential energy functions vis-a-vis commonly used ab initio quantum chemical calculations are also addressed.

Self-Consistent Theory of Shot Noise Suppression in Ballistic Conductors

NASA Astrophysics Data System (ADS)

Bulashenko, O. M.; Rubí, J. M.; Kochelap, V. A.

Shot-noise measurements become a fundamental tool to probe carrier interactions in mesoscopic systems [1]. A matter of particular interest is the significance of Coulomb interaction which may keep nearby electrons more regularly spaced rather than strictly at random and lead to the noise reduction. That effect occurs in different physical situations. Among them are charge-limited ballistic transport, resonant tunneling, single-electron tunneling, etc. In this communication we address the problem of Coulomb correlations in ballistic conductors under the space-charge-limited transport conditions, and present for the first time a semiclassical self-consistent theory of shot noise in these conductors by solving analytically the kinetic equation coupled self-consistently with a Poisson equation. Basing upon this theory, exact results for current noise in a two-terminal ballistic conductor under the action of long-range Coulomb correlations has been derived. The noise reduction factor (in respect to the uncorrelated value) is obtained in a closed analytical form for a full range of biases ranging from thermal to shot-noise limits which describe perfectly the results of the Monte Carlo simulations for a nondegenerate electron gas [2]. The magnitude of the noise reduction exceeds 0.01, which is of interest from the point of view of possible applications. Using these analytical results one may estimate a relative contribution to the noise from different groups of carriers (in energy space and/or real space) and to investigate in great detail the correlations between different groups of carriers. This leads us to suggest an electron energy spectroscopy experiment to probe the Coulomb correlations in ballistic conductors. Indeed, while the injected carriers are uncorrelated, those in the volume of the conductor are strongly correlated, as follows from the derived formulas for the fluctuation of the distribution function. Those correlations may be observed experimentally by making use of a combination of two already realized techniques: a hot-electron spectrometer [3,4] which allows one to analyze different energy groups of electrons collected at the contact and shot-noise measurements [5,6]. Such "shot noise reduction spectroscopy" allows one to measure the novel phenomena. In particular, we predict the (anti)correlation of the "tangent" electrons having the energy close to the potential barrier height, to all other electron energy groups collected at the receiving contact.

A Combined Energy Management Algorithm for Wind Turbine/Battery Hybrid System

NASA Astrophysics Data System (ADS)

Altin, Necmi; Eyimaya, Süleyman Emre

2018-03-01

From an energy management standpoint, natural phenomena such as solar irradiation and wind speed are uncontrolled variables, so the correlation between the energy generated by renewable energy sources and energy demand cannot always be predicted. For this reason, energy storage systems are used to provide more efficient renewable energy systems. In these systems, energy management systems are used to control the energy storage system and establish a balance between the generated power and the power demand. In addition, especially in wind turbines, rapidly varying wind speeds cause wind power fluctuations, which threaten the power system stability, especially at high power levels. Energy storage systems are also used to mitigate the power fluctuations and sustain the power system's stability. In these systems, another controller which controls the energy storage system power to mitigate power fluctuations is required. These two controllers are different from each other. In this study, a combined energy management algorithm is proposed which can perform both as an energy control system and a power fluctuation mitigation system. The proposed controller is tested with wind energy conversion system modeled in MATLAB/Simulink. Simulation results show that the proposed controller acts as an energy management system while, at the same time, mitigating power fluctuations.

Combined 3D-QSAR, molecular docking, molecular dynamics simulation, and binding free energy calculation studies on the 5-hydroxy-2H-pyridazin-3-one derivatives as HCV NS5B polymerase inhibitors.

PubMed

Yu, Haijing; Fang, Yu; Lu, Xia; Liu, Yongjuan; Zhang, Huabei

2014-01-01

The NS5B RNA-dependent RNA polymerase (RdRP) is a promising therapeutic target for developing novel anti-hepatitis C virus (HCV) drugs. In this work, a combined molecular modeling study was performed on a series of 193 5-hydroxy-2H-pyridazin-3-one derivatives as inhibitors of HCV NS5B Polymerase. The best 3D-QSAR models, including CoMFA and CoMSIA, are based on receptor (or docking). Furthermore, a 40-ns molecular dynamics (MD) simulation and binding free energy calculations using docked structures of NS5B with ten compounds, which have diverse structures and pIC50 values, were employed to determine the detailed binding process and to compare the binding modes of the inhibitors with different activities. On one side, the stability and rationality of molecular docking and 3D-QSAR results were validated by MD simulation. The binding free energies calculated by the MM-PBSA method gave a good correlation with the experimental biological activity. On the other side, by analyzing some differences between the molecular docking and the MD simulation results, we can find that the MD simulation could also remedy the defects of molecular docking. The analyses of the combined molecular modeling results have identified that Tyr448, Ser556, and Asp318 are the key amino acid residues in the NS5B binding pocket. The results from this study can provide some insights into the development of novel potent NS5B inhibitors. © 2013 John Wiley & Sons A/S.

BLAST: Building energy simulation in Hong Kong

NASA Astrophysics Data System (ADS)

Fong, Sai-Keung

1999-11-01

The characteristics of energy use in buildings under local weather conditions were studied and evaluated using the energy simulation program BLAST-3.0. The parameters used in the energy simulation for the study and evaluation include the architectural features, different internal building heat load settings and weather data. In this study, mathematical equations and the associated coefficients useful to the industry were established. A technology for estimating energy use in buildings under local weather conditions was developed by using the results of this study. A weather data file of Typical Meteorological Years (TMY) has been compiled for building energy studies by analyzing and evaluating the weather of Hong Kong from the year 1979 to 1988. The weather data file TMY and the example weather years 1980 and 1988 were used by BLAST-3.0 to evaluate and study the energy use in different buildings. BLAST-3.0 was compared with other building energy simulation and approximation methods: Bin method and Degree Days method. Energy use in rectangular compartments of different volumes varying from 4,000 m3 to 40,000 m3 with different aspect ratios were analyzed. The use of energy in buildings with concrete roofs was compared with those with glass roofs at indoor temperature 21°C, 23°C and 25°C. Correlation relationships among building energy, space volume, monthly mean temperature and solar radiation were derived and investigated. The effects of space volume, monthly mean temperature and solar radiation on building energy were evaluated. The coefficients of the mathematical relationships between space volume and energy use in a building were computed and found satisfactory. The calculated coefficients can be used for quick estimation of energy use in buildings under similar situations. To study energy use in buildings, the cooling load per floor area against room volume was investigated. The case of an air-conditioned single compartment with 5 m ceiling height was evaluated. It was found that the supply of cool air to the lower portion of the compartment provided significant performance of space cooling. The mathematical relationships between different shading patterns and different glass window to wall ratios of single compartments were established to provide a guide for easy approximation of energy use under similar conditions. In addition, the Overall Thermal Transfer Values (OTTV) for the compartments were studied. The monthly and annual energy use of three realistic buildings were investigated. They were a commercial building, an industrial building and a dual-purpose building. The cooling loads per floor area for the buildings were studied and the OTTV were evaluated by two different methods. Sensitivity analysis was carried out to investigate the impact of the parameters of internal heat gains on the energy use of an academic building. It was found that there was major influence of indoor temperature setting on building energy use The performances of using the local weather data file of TMY and example weather years 1980 and 1989 were evaluated. TMY was found to be the most suitable for energy simulation while the weather years 1980 and 1989 yielded good results.

The role of the attractive and the repulsive interactions in the nonpolar solvation dynamics in simple fluids from the gas-like to the liquid-like densities

NASA Astrophysics Data System (ADS)

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

1999-09-01

We have performed molecular dynamics (MD) simulations of the nonpolar solvation dynamics in simple fluids composed of particles interacting through the Lennard-Jones (LJ) 12-6 potential or its repulsive part. The attractive or the repulsive part of the solute-solvent interaction is assumed to change on the excitation of a solute. We have followed the transition energy fluctuation of the solute by the equilibrium simulation. The division of the LJ potential followed the method of WCA [J. W. Weeks, D. Chandler, and H. C. Andersen, J. Chem. Phys. 54, 5237 (1971)]. We have surveyed over a wide solvent density region from gas-like to liquid-like densities at the constant temperature. When the attractive part changes, the relaxation becomes faster with an increase of the solvent density. This result contradicts with previous theories that treat the nonpolar solvation dynamics in terms of the diffusion of solvent particles. The time scale of the initial part of the relaxation is well correlated with the static fluctuation divided by the static average, which suggests the importance of the curvature of the free energy surface in the initial part of the solvation. When the repulsive part changes, the initial part of the relaxation is almost density independent, determined by the binary motion between solute and solvent. It is consistent with the result that the static fluctuation is almost proportional to the static average, which indicates the absence of the static correlation between solvent particles. On the other hand, the solvation correlation function shows rather complicated density dependence at the longer time scale. In the case of the binary mixture solvent, the relaxation time is inversely proportional to the diffusion coefficient. On the basis of the nonpolar solvation dynamics, the validity of the isolated binary collision model for the vibrational energy relaxation is also discussed, and the recent hydrodynamic theory on the vibrational energy relaxation [B. J. Cherayil and M. D. Feyer, J. Chem. Phys. 107, 7642 (1997)] is critically examined.

A study to compute integrated dpa for neutron and ion irradiation environments using SRIM-2013

NASA Astrophysics Data System (ADS)

Saha, Uttiyoarnab; Devan, K.; Ganesan, S.

2018-05-01

Displacements per atom (dpa), estimated based on the standard Norgett-Robinson-Torrens (NRT) model, is used for assessing radiation damage effects in fast reactor materials. A computer code CRaD has been indigenously developed towards establishing the infrastructure to perform improved radiation damage studies in Indian fast reactors. We propose a method for computing multigroup neutron NRT dpa cross sections based on SRIM-2013 simulations. In this method, for each neutron group, the recoil or primary knock-on atom (PKA) spectrum and its average energy are first estimated with CRaD code from ENDF/B-VII.1. This average PKA energy forms the input for SRIM simulation, wherein the recoil atom is taken as the incoming ion on the target. The NRT-dpa cross section of iron computed with "Quick" Kinchin-Pease (K-P) option of SRIM-2013 is found to agree within 10% with the standard NRT-dpa values, if damage energy from SRIM simulation is used. SRIM-2013 NRT-dpa cross sections applied to estimate the integrated dpa for Fe, Cr and Ni are in good agreement with established computer codes and data. A similar study carried out for polyatomic material, SiC, shows encouraging results. In this case, it is observed that the NRT approach with average lattice displacement energy of 25 eV coupled with the damage energies from the K-P option of SRIM-2013 gives reliable displacement cross sections and integrated dpa for various reactor spectra. The source term of neutron damage can be equivalently determined in the units of dpa by simulating self-ion bombardment. This shows that the information of primary recoils obtained from CRaD can be reliably applied to estimate the integrated dpa and damage assessment studies in accelerator-based self-ion irradiation experiments of structural materials. This study would help to advance the investigation of possible correlations between the damages induced by ions and reactor neutrons.

The effect of abdominal wall morphology on ultrasonic pulse distortion. Part II. Simulations.

PubMed

Mast, T D; Hinkelman, L M; Orr, M J; Waag, R C

1998-12-01

Wavefront propagation through the abdominal wall was simulated using a finite-difference time-domain implementation of the linearized wave propagation equations for a lossless, inhomogeneous, two-dimensional fluid as well as a simplified straight-ray model for a two-dimensional absorbing medium. Scanned images of six human abdominal wall cross sections provided the data for the propagation media in the simulations. The images were mapped into regions of fat, muscle, and connective tissue, each of which was assigned uniform sound speed, density, and absorption values. Propagation was simulated through each whole specimen as well as through each fat layer and muscle layer individually. Wavefronts computed by the finite-difference method contained arrival time, energy level, and wave shape distortion similar to that in measurements. Straight-ray simulations produced arrival time fluctuations similar to measurements but produced much smaller energy level fluctuations. These simulations confirm that both fat and muscle produce significant wavefront distortion and that distortion produced by fat sections differs from that produced by muscle sections. Spatial correlation of distortion with tissue composition suggests that most major arrival time fluctuations are caused by propagation through large-scale inhomogeneities such as fatty regions within muscle layers, while most amplitude and waveform variations are the result of scattering from smaller inhomogeneities such as septa within the subcutaneous fat. Additional finite-difference simulations performed using uniform-layer models of the abdominal wall indicate that wavefront distortion is primarily caused by tissue structures and inhomogeneities rather than by refraction at layer interfaces or by variations in layer thicknesses.

SUNREL Energy Simulation Software | Buildings | NREL

Science.gov Websites

SUNREL Energy Simulation Software SUNREL Energy Simulation Software SUNREL® is a hourly building energy simulation program that aids in the design of small energy-efficient buildings where the loads are

Characterizing and Optimizing the TITAN facility from Energy Spread Determinations with a Retarding Energy Field Analyzer

NASA Astrophysics Data System (ADS)

Champagne, Christian

The TITAN (TRIUMF's Ion Trap for Atomic and Nuclear science) experiment uses a Measurement Penning Trap (MPET) to perform high precision mass measurements (deltam/m ≈ 10--8) on short-lived (t1/2 ≈ 10 ms) isotopes. The ISAC (Isotope Separation and ACceleration) facility provides a 60 keV rare isotope beam to the experiments. A Radio-Frequency Quadrupole (RFQ) ion trap cools and bunches the incoming radioactive beam. An Electron Beam Ion Trap (EBIT) charge breeds the ions to a high charged state q. Since the MPET mass resolution is proportional to the charge state q, an improvement up to two orders of magnitude can be achieved. Further enhancements are obtained by the reduction of the uncertainty on the MPET measurements, such as from the ion bunch longitudinal kinetic energy spread. A Retarding Field energy Analyzer (RFA) was designed and constructed to measure this uncertainty. An energy resolution DeltaE/E ≈ 10--3 was expected from to simulated RFQ ion extraction longitudinal energy spread measurements. An experimental energy resolution DeltaE/E = 2.4x10--3 was obtained. Suggestions to improve the energy resolution are provided. Two testing sessions were undertaken using the RFQ and TITAN ion source to provide a singly charged pulsed ion beam. The first session used a 6Li+ beam with a 1--4 keV energy range. The RFA collimating slits were removed to insure the beam entered the RFA, increasing the energy resolution to DeltaE/E = 5 x 10 --3. An energy resolution DeltaE/E = (1.4 +/- 0.5) x 10--2 was obtained from the longitudinal energy spread measurements as a function of the beam energy. No correlation between the RFQ buffer gas pressure and the longitudinal energy spread was observed. The second session used 6,7Li, 23Na, 39,41K beams with a 1--5 keV energy range and the slits were reincorporated. A linear correlation with the RFQ extraction potentials magnitude is visible with both 2.5 keV 7Li+ and 23Na+ beams. No correlations between the RFQ buffer gas pressure, the space charge, beamgate size and beam composition with respect to the longitudinal energy spread were otherwise found. Further reduction of the RFA energy resolution is necessary to resolve longitudinal energy spread variations under different RFQ parameter settings.

Guidelines and Parameter Selection for the Simulation of Progressive Delamination

NASA Technical Reports Server (NTRS)

Song, Kyongchan; Davila, Carlos G.; Rose, Cheryl A.

2008-01-01

Turon s methodology for determining optimal analysis parameters for the simulation of progressive delamination is reviewed. Recommended procedures for determining analysis parameters for efficient delamination growth predictions using the Abaqus/Standard cohesive element and relatively coarse meshes are provided for single and mixed-mode loading. The Abaqus cohesive element, COH3D8, and a user-defined cohesive element are used to develop finite element models of the double cantilever beam specimen, the end-notched flexure specimen, and the mixed-mode bending specimen to simulate progressive delamination growth in Mode I, Mode II, and mixed-mode fracture, respectively. The predicted responses are compared with their analytical solutions. The results show that for single-mode fracture, the predicted responses obtained with the Abaqus cohesive element correlate well with the analytical solutions. For mixed-mode fracture, it was found that the response predicted using COH3D8 elements depends on the damage evolution criterion that is used. The energy-based criterion overpredicts the peak loads and load-deflection response. The results predicted using a tabulated form of the BK criterion correlate well with the analytical solution and with the results predicted with the user-written element.

Multi-scale modelling to relate beryllium surface temperature, deuterium concentration and erosion in fusion reactor environment

DOE PAGES

Safi, E.; Valles, G.; Lasa, A.; ...

2017-03-27

Beryllium (Be) has been chosen as the plasma-facing material for the main wall of ITER, the next generation fusion reactor. Identifying the key parameters that determine Be erosion under reactor relevant conditions is vital to predict the ITER plasma-facing component lifetime and viability. To date, a certain prediction of Be erosion, focusing on the effect of two such parameters, surface temperature and D surface content, has not been achieved. In this paper, we develop the first multi-scale KMC-MD modeling approach for Be to provide a more accurate database for its erosion, as well as investigating parameters that affect erosion. First,more » we calculate the complex relationship between surface temperature and D concentration precisely by simulating the time evolution of the system using an object kinetic Monte Carlo (OKMC) technique. These simulations provide a D surface concentration profile for any surface temperature and incoming D energy. We then describe how this profile can be implemented as a starting configuration in molecular dynamics (MD) simulations. We finally use MD simulations to investigate the effect of temperature (300–800 K) and impact energy (10–200 eV) on the erosion of Be due to D plasma irradiations. The results reveal a strong dependency of the D surface content on temperature. Increasing the surface temperature leads to a lower D concentration at the surface, because of the tendency of D atoms to avoid being accommodated in a vacancy, and de-trapping from impurity sites diffuse fast toward bulk. At the next step, total and molecular Be erosion yields due to D irradiations are analyzed using MD simulations. The results show a strong dependency of erosion yields on surface temperature and incoming ion energy. The total Be erosion yield increases with temperature for impact energies up to 100 eV. However, increasing temperature and impact energy results in a lower fraction of Be atoms being sputtered as BeD molecules due to the lower D surface concentrations at higher temperatures. Finally, these findings correlate well with different experiments performed at JET and PISCES-B devices.« less

Multi-scale modelling to relate beryllium surface temperature, deuterium concentration and erosion in fusion reactor environment

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

Safi, E.; Valles, G.; Lasa, A.

Beryllium (Be) has been chosen as the plasma-facing material for the main wall of ITER, the next generation fusion reactor. Identifying the key parameters that determine Be erosion under reactor relevant conditions is vital to predict the ITER plasma-facing component lifetime and viability. To date, a certain prediction of Be erosion, focusing on the effect of two such parameters, surface temperature and D surface content, has not been achieved. In this paper, we develop the first multi-scale KMC-MD modeling approach for Be to provide a more accurate database for its erosion, as well as investigating parameters that affect erosion. First,more » we calculate the complex relationship between surface temperature and D concentration precisely by simulating the time evolution of the system using an object kinetic Monte Carlo (OKMC) technique. These simulations provide a D surface concentration profile for any surface temperature and incoming D energy. We then describe how this profile can be implemented as a starting configuration in molecular dynamics (MD) simulations. We finally use MD simulations to investigate the effect of temperature (300–800 K) and impact energy (10–200 eV) on the erosion of Be due to D plasma irradiations. The results reveal a strong dependency of the D surface content on temperature. Increasing the surface temperature leads to a lower D concentration at the surface, because of the tendency of D atoms to avoid being accommodated in a vacancy, and de-trapping from impurity sites diffuse fast toward bulk. At the next step, total and molecular Be erosion yields due to D irradiations are analyzed using MD simulations. The results show a strong dependency of erosion yields on surface temperature and incoming ion energy. The total Be erosion yield increases with temperature for impact energies up to 100 eV. However, increasing temperature and impact energy results in a lower fraction of Be atoms being sputtered as BeD molecules due to the lower D surface concentrations at higher temperatures. Finally, these findings correlate well with different experiments performed at JET and PISCES-B devices.« less

Multi-scale modelling to relate beryllium surface temperature, deuterium concentration and erosion in fusion reactor environment

NASA Astrophysics Data System (ADS)

Safi, E.; Valles, G.; Lasa, A.; Nordlund, K.

2017-05-01

Beryllium (Be) has been chosen as the plasma-facing material for the main wall of ITER, the next generation fusion reactor. Identifying the key parameters that determine Be erosion under reactor relevant conditions is vital to predict the ITER plasma-facing component lifetime and viability. To date, a certain prediction of Be erosion, focusing on the effect of two such parameters, surface temperature and D surface content, has not been achieved. In this work, we develop the first multi-scale KMC-MD modeling approach for Be to provide a more accurate database for its erosion, as well as investigating parameters that affect erosion. First, we calculate the complex relationship between surface temperature and D concentration precisely by simulating the time evolution of the system using an object kinetic Monte Carlo (OKMC) technique. These simulations provide a D surface concentration profile for any surface temperature and incoming D energy. We then describe how this profile can be implemented as a starting configuration in molecular dynamics (MD) simulations. We finally use MD simulations to investigate the effect of temperature (300-800 K) and impact energy (10-200 eV) on the erosion of Be due to D plasma irradiations. The results reveal a strong dependency of the D surface content on temperature. Increasing the surface temperature leads to a lower D concentration at the surface, because of the tendency of D atoms to avoid being accommodated in a vacancy, and de-trapping from impurity sites diffuse fast toward bulk. At the next step, total and molecular Be erosion yields due to D irradiations are analyzed using MD simulations. The results show a strong dependency of erosion yields on surface temperature and incoming ion energy. The total Be erosion yield increases with temperature for impact energies up to 100 eV. However, increasing temperature and impact energy results in a lower fraction of Be atoms being sputtered as BeD molecules due to the lower D surface concentrations at higher temperatures. These findings correlate well with different experiments performed at JET and PISCES-B devices.

Educational Resources | NREL

Science.gov Websites

for Energy Simulation Energy Simulation Games ElectroCity Environmental Science Electro Energy Simulation Games Energy Efficiency Energy Audit Conducting a School Energy Audit presentation Exploration of

Identification and tracking of hairpin vortex auto-generation in turbulent wall-bounded flow

NASA Astrophysics Data System (ADS)

Huang, Yangzi; Green, Melissa

2016-11-01

Hairpin vortices have been widely accepted as component structures of turbulent boundary layers. Their properties (size, vorticity, energy) and dynamic phenomena (origin, growth, breakdown) have been shown to correlate to the complex, multi-scaled turbulent motions observed in both experiments and simulations. As established in the literature, the passage of a hairpin vortex creates a wall-normal ejection of fluid, which encounters the high-speed freestream resulting in near-wall shear and increased drag. A previously generated simulation of an isolated hairpin vortex is used to study the auto-generation of a secondary vortex structure. Eulerian methods such as the Q criterion and Γ2 function, as well as Lagrangian methods are used to visualize the three-dimensional hairpin vortices and the auto-generation process. The circulation development and wall-normal location of both primary and secondary hairpin heads are studied to determine if there is a correlation between the strength and height of the primary hairpin vortex with the secondary hairpin vortex auto-generation.

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)

Frequency and Wavevector Dependence of the Atomic Level Stress-Stress Correlation Function in a Model Supercooled Liquid

NASA Astrophysics Data System (ADS)

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

2012-02-01

Temporal and spatial correlations among the local atomic level shear stresses were studied for a model liquid iron by molecular dynamics simulation [PRL 106,115703]. Integration over time and space of the shear stress correlation function F(r,t) yields viscosity via Green-Kubo relation. The stress correlation function in time and space F(r,t) was Fourier transformed to study the dependence on frequency, E, and wave vector, Q. The results, F(Q,E), showed damped shear stress waves propagating in the liquid for small Q at high and low temperatures. We also observed additional diffuse feature that appears as temperature is reduced below crossover temperature of potential energy landscape at relatively low frequencies at small Q. We suggest that this additional feature might be related to dynamic heterogeneity and boson peaks. We also discuss a relation between the time-scale of the stress-stress correlation function and the alpha-relaxation time of the intermediate self-scattering function S(Q,E).

Quantifying the Energy Landscape Statistics in Proteins - a Relaxation Mode Analysis

NASA Astrophysics Data System (ADS)

Cai, Zhikun; Zhang, Yang

Energy landscape, the hypersurface in the configurational space, has been a useful concept in describing complex processes that occur over a very long time scale, such as the multistep slow relaxations of supercooled liquids and folding of polypeptide chains into structured proteins. Despite extensive simulation studies, its experimental characterization still remains a challenge. To address this challenge, we developed a relaxation mode analysis (RMA) for liquids under a framework analogous to the normal mode analysis for solids. Using RMA, important statistics of the activation barriers of the energy landscape becomes accessible from experimentally measurable two-point correlation functions, e.g. using quasi-elastic and inelastic scattering experiments. We observed a prominent coarsening effect of the energy landscape. The results were further confirmed by direct sampling of the energy landscape using a metadynamics-like adaptive autonomous basin climbing computation. We first demonstrate RMA in a supercooled liquid when dynamical cooperativity emerges in the landscape-influenced regime. Then we show this framework reveals encouraging energy landscape statistics when applied to proteins.

Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition.

PubMed

Paci, Emanuele; Vendruscolo, Michele; Karplus, Martin

2002-12-01

Do Gō-type model potentials provide a valid approach for studying protein folding? They have been widely used for this purpose because of their simplicity and the speed of simulations based on their use. The essential assumption in such models is that only contact interactions existing in the native state determine the energy surface of a polypeptide chain, even for non-native configurations sampled along folding trajectories. Here we use an all-atom molecular mechanics energy function to investigate the adequacy of Gō-type potentials. We show that, although the contact approximation is accurate, non-native contributions to the energy can be significant. The assumed relation between residue-residue interaction energies and the number of contacts between them is found to be only approximate. By contrast, individual residue energies correlate very well with the number of contacts. The results demonstrate that models based on the latter should give meaningful results (e.g., as used to interpret phi values), whereas those that depend on the former are only qualitative, at best.

Optimizing Cellular Networks Enabled with Renewal Energy via Strategic Learning.

PubMed

Sohn, Insoo; Liu, Huaping; Ansari, Nirwan

2015-01-01

An important issue in the cellular industry is the rising energy cost and carbon footprint due to the rapid expansion of the cellular infrastructure. Greening cellular networks has thus attracted attention. Among the promising green cellular network techniques, the renewable energy-powered cellular network has drawn increasing attention as a critical element towards reducing carbon emissions due to massive energy consumption in the base stations deployed in cellular networks. Game theory is a branch of mathematics that is used to evaluate and optimize systems with multiple players with conflicting objectives and has been successfully used to solve various problems in cellular networks. In this paper, we model the green energy utilization and power consumption optimization problem of a green cellular network as a pilot power selection strategic game and propose a novel distributed algorithm based on a strategic learning method. The simulation results indicate that the proposed algorithm achieves correlated equilibrium of the pilot power selection game, resulting in optimum green energy utilization and power consumption reduction.

Role of the Charge-Transfer State in Reduced Langevin Recombination in Organic Solar Cells: A Theoretical Study

PubMed Central

2015-01-01

Reduced Langevin recombination has been observed in organic solar cells (OSCs) for many years, but its origin is still unclear. A recent work by Burke et al. (Adv. Energy Mater.2015, 5, 1500123-1) was inspired by this reduced Langevin recombination, and they proposed an equilibrium model of charge-transfer (CT) states that correlates the open-circuit voltage of OSCs with experimentally available device parameters. In this work, we extend Burke et al.’s CT model further and for the first time directly correlate the reduced Langevin recombination with the energetic and dynamic behavior of the CT state. Recombination through CT states leads in a straightforward manner to a decrease in the Langevin reduction factor with increasing temperature, without explicit consideration of the temperature dependence of the mobility. To verify the correlation between the CT states and reduced Langevin recombination, we incorporated this CT model and the reduced Langevin model into drift-diffusion simulations of a bilayer OSC. The simulations not only successfully reproduced realistic current–voltage (J–V) characteristics of the bilayer OSC, but also demonstrate that the two models consistently lead to same value of the apparent Langevin reduction factor. PMID:26640611

Design of coupled mace filters for optical pattern recognition using practical spatial light modulators

NASA Technical Reports Server (NTRS)

Rajan, P. K.; Khan, Ajmal

1993-01-01

Spatial light modulators (SLMs) are being used in correlation-based optical pattern recognition systems to implement the Fourier domain filters. Currently available SLMs have certain limitations with respect to the realizability of these filters. Therefore, it is necessary to incorporate the SLM constraints in the design of the filters. The design of a SLM-constrained minimum average correlation energy (SLM-MACE) filter using the simulated annealing-based optimization technique was investigated. The SLM-MACE filter was synthesized for three different types of constraints. The performance of the filter was evaluated in terms of its recognition (discrimination) capabilities using computer simulations. The correlation plane characteristics of the SLM-MACE filter were found to be reasonably good. The SLM-MACE filter yielded far better results than the analytical MACE filter implemented on practical SLMs using the constrained magnitude technique. Further, the filter performance was evaluated in the presence of noise in the input test images. This work demonstrated the need to include the SLM constraints in the filter design. Finally, a method is suggested to reduce the computation time required for the synthesis of the SLM-MACE filter.

Impact Damage and Strain Rate Effects for Toughened Epoxy Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Minnetyan, Levon

2006-01-01

Structural integrity of composite systems under dynamic impact loading is investigated herein. The GENOA virtual testing software environment is used to implement the effects of dynamic loading on fracture progression and damage tolerance. Combinations of graphite and glass fibers with a toughened epoxy matrix are investigated. The effect of a ceramic coating for the absorption of impact energy is also included. Impact and post impact simulations include verification and prediction of (1) Load and Impact Energy, (2) Impact Damage Size, (3) Maximum Impact Peak Load, (4) Residual Strength, (5) Maximum Displacement, (6) Contribution of Failure Modes to Failure Mechanisms, (7) Prediction of Impact Load Versus Time, and (8) Damage, and Fracture Pattern. A computer model is utilized for the assessment of structural response, progressive fracture, and defect/damage tolerance characteristics. Results show the damage progression sequence and the changes in the structural response characteristics due to dynamic impact. The fundamental premise of computational simulation is that the complete evaluation of composite fracture requires an assessment of ply and subply level damage/fracture processes as the structure is subjected to loads. Simulation results for the graphite/epoxy composite were compared with the impact and tension failure test data, correlation and verification was obtained that included: (1) impact energy, (2) damage size, (3) maximum impact peak load, (4) residual strength, (5) maximum displacement, and (6) failure mechanisms of the composite structure.

Optimizing physical energy functions for protein folding.

PubMed

Fujitsuka, Yoshimi; Takada, Shoji; Luthey-Schulten, Zaida A; Wolynes, Peter G

2004-01-01

We optimize a physical energy function for proteins with the use of the available structural database and perform three benchmark tests of the performance: (1) recognition of native structures in the background of predefined decoy sets of Levitt, (2) de novo structure prediction using fragment assembly sampling, and (3) molecular dynamics simulations. The energy parameter optimization is based on the energy landscape theory and uses a Monte Carlo search to find a set of parameters that seeks the largest ratio deltaE(s)/DeltaE for all proteins in a training set simultaneously. Here, deltaE(s) is the stability gap between the native and the average in the denatured states and DeltaE is the energy fluctuation among these states. Some of the energy parameters optimized are found to show significant correlation with experimentally observed quantities: (1) In the recognition test, the optimized function assigns the lowest energy to either the native or a near-native structure among many decoy structures for all the proteins studied. (2) Structure prediction with the fragment assembly sampling gives structure models with root mean square deviation less than 6 A in one of the top five cluster centers for five of six proteins studied. (3) Structure prediction using molecular dynamics simulation gives poorer performance, implying the importance of having a more precise description of local structures. The physical energy function solely inferred from a structural database neither utilizes sequence information from the family of the target nor the outcome of the secondary structure prediction but can produce the correct native fold for many small proteins. Copyright 2003 Wiley-Liss, Inc.

Microscopic derivation of IBM and structural evolution in nuclei

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

Nomura, Kosuke

A Hamiltonian of the interacting boson model (IBM) is derived based on the mean-field calculations with nuclear energy density functionals (EDFs). The multi-nucleon dynamics of the surface deformation is simulated in terms of the boson degrees of freedom. The interaction strengths of the IBM Hamiltonian are determined by mapping the potential energy surfaces (PESs) of a given EDF with quadrupole degrees of freedom onto the corresponding PES of IBM. A fermion-to-boson mapping for a rotational nucleus is discussed in terms of the rotational response, which reflects a specific time-dependent feature. Ground-state correlation energy is evaluated as a signature of structuralmore » evolution. Some examples resulting from the present spectroscopic calculations are shown for neutron-rich Pt, Os and W isotopes including exotic ones.« less

Evolution of energy deposition during glass cutting with pulsed femtosecond laser radiation

NASA Astrophysics Data System (ADS)

Kalupka, C.; Großmann, D.; Reininghaus, M.

2017-05-01

We report on investigations of the energy deposition in the volume of thin glass during an ablation cutting process with pulsed femtosecond laser radiation by time-resolved pump-probe shadowgraphy. For a single laser pulse, the temporal evolution of the transient electronic excitation of the glass volume is imaged up to 10 ps after initial excitation. For an increasing number of laser pulses, the spatial excitation of the glass volume significantly changes compared to single pulse irradiation. Sharp spikes are observed, which reduce the transmission of the illuminating probe pulse. This indicates local maxima of the absorption and, therefore, energy deposition of the pump pulse energy in the glass volume. Furthermore, for an increasing number of pulses, different shapes of the surface ablation crater are observed. To study the correlation between the shape of the surface ablation crater and the energy deposition in the glass volume, simulations of the spatial intensity distribution of the pump pulse are executed by means of linear beam propagation method. We show that the transient excitation spikes observed by pump-probe shadowgraphy can be explained by refraction and diffraction of the laser radiation at the surface ablation crater. Our results provide an experimental validation for the physical reason of an ablation stop for an ablation cutting process. Moreover, the simulations allow for the prediction of damage inside the glass volume.

Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2015-06-23

Cell-penetrating and antimicrobial peptides show a remarkable ability to translocate across physiological membranes. Along with factors such as electric-potential-induced perturbations of membrane structure and surface tension effects, experiments invoke porelike membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a nontrivial free-energy cost, thus necessitating a consideration of the factors associated with pore formation and the attendant free energies. Because of experimental and modeling challenges related to the long time scales of the translocation process, we use umbrella sampling molecular dynamics simulations with a lipid-density-based order parameter to investigate membrane-pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of headgroups, charge states, acyl chain lengths, and saturation. We probe the dependence of pore-formation barriers on the area per lipid, lipid bilayer thickness, and membrane bending rigidities in three different lipid classes. The pore-formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. The pore-formation free energy is higher in peptide-lipid systems than in peptide-free lipid systems due to penalties to maintain the solvation of charged hydrophilic solutes within the membrane environment.

A computational analysis of the binding model of MDM2 with inhibitors

NASA Astrophysics Data System (ADS)

Hu, Guodong; Wang, Dunyou; Liu, Xinguo; Zhang, Qinggang

2010-08-01

It is a new and promising strategy for anticancer drug design to block the MDM2-p53 interaction using a non-peptide small-molecule inhibitor. We carry out molecular dynamics simulations to study the binding of a set of six non-peptide small-molecule inhibitors with the MDM2. The relative binding free energies calculated using molecular mechanics Poisson-Boltzmann surface area method produce a good correlation with experimentally determined results. The study shows that the van der Waals energies are the largest component of the binding free energy for each complex, which indicates that the affinities of these inhibitors for MDM2 are dominated by shape complementarity. The A-ligands and the B-ligands are the same except for the conformation of 2,2-dimethylbutane group. The quantum mechanics and the binding free energies calculation also show the B-ligands are the more possible conformation of ligands. Detailed binding free energies between inhibitors and individual protein residues are calculated to provide insights into the inhibitor-protein binding model through interpretation of the structural and energetic results from the simulations. The study shows that G1, G2 and G3 group mimic the Phe19, Trp23 and Leu26 residues in p53 and their interactions with MDM2, but the binding model of G4 group differs from the original design strategy to mimic Leu22 residue in p53.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

KLK14 interactions with HAI-1 and HAI-2 serine protease inhibitors: A molecular dynamics and relative free-energy calculations study.

PubMed

Solís-Calero, Christian; Carvalho, Hernandes F

2017-11-01

Kallikrein 14 (KLK14) is a serine protease linked to several pathologies including prostate cancer and positively correlates with Gleason score. Though KLK14 functioning in cancer is poorly understood, it has been implicated in HGF/Met signaling, given that KLK14 proteolytically inhibits HGF activator-inhibitor 1 (HAI-1), which strongly inhibits pro-HGF activators, thereby contributing to tumor progression. In this work, KLK14 binding to either hepatocyte growth factor activator inhibitor type-1 (HAI-1) or type-2 (HAI-2) was essayed using homology modeling, molecular dynamic simulations and free-energy calculations through MM/PBSA and MM/GBSA. KLK14 was successfully modeled. Calculated free energies suggested higher binding affinity for the KLK14/HAI-1 interaction than for KLK14/HAI-2. This difference in binding affinity is largely explained by the higher stability of the hydrogen-bond networks in KLK14/HAI-1 along the simulation trajectory. A key arginine residue in both HAI-1 and HAI-2 is responsible for their interaction with the S1 pocket in KLK14. Additionally, MM/GBSA free-energy decomposition postulates that KLK14 Asp174 and Trp196 are hotspots for binding HAI-1 and HAI-2. © 2017 International Federation for Cell Biology.

Turbulence and entrainment length scales in large wind farms.

PubMed

Andersen, Søren J; Sørensen, Jens N; Mikkelsen, Robert F

2017-04-13

A number of large wind farms are modelled using large eddy simulations to elucidate the entrainment process. A reference simulation without turbines and three farm simulations with different degrees of imposed atmospheric turbulence are presented. The entrainment process is assessed using proper orthogonal decomposition, which is employed to detect the largest and most energetic coherent turbulent structures. The dominant length scales responsible for the entrainment process are shown to grow further into the wind farm, but to be limited in extent by the streamwise turbine spacing, which could be taken into account when developing farm layouts. The self-organized motion or large coherent structures also yield high correlations between the power productions of consecutive turbines, which can be exploited through dynamic farm control.This article is part of the themed issue 'Wind energy in complex terrains'. © 2017 The Author(s).

Turbulence and entrainment length scales in large wind farms

PubMed Central

2017-01-01

A number of large wind farms are modelled using large eddy simulations to elucidate the entrainment process. A reference simulation without turbines and three farm simulations with different degrees of imposed atmospheric turbulence are presented. The entrainment process is assessed using proper orthogonal decomposition, which is employed to detect the largest and most energetic coherent turbulent structures. The dominant length scales responsible for the entrainment process are shown to grow further into the wind farm, but to be limited in extent by the streamwise turbine spacing, which could be taken into account when developing farm layouts. The self-organized motion or large coherent structures also yield high correlations between the power productions of consecutive turbines, which can be exploited through dynamic farm control. This article is part of the themed issue ‘Wind energy in complex terrains’. PMID:28265028

Numerical investigation of supersonic turbulent boundary layers with high wall temperature

NASA Technical Reports Server (NTRS)

Guo, Y.; Adams, N. A.

1994-01-01

A direct numerical approach has been developed to simulate supersonic turbulent boundary layers. The mean flow quantities are obtained by solving the parabolized Reynolds-averaged Navier-Stokes equations (globally). Fluctuating quantities are computed locally with a temporal direct numerical simulation approach, in which nonparallel effects of boundary layers are partially modeled. Preliminary numerical results obtained at the free-stream Mach numbers 3, 4.5, and 6 with hot-wall conditions are presented. Approximately 5 million grid points are used in all three cases. The numerical results indicate that compressibility effects on turbulent kinetic energy, in terms of dilatational dissipation and pressure-dilatation correlation, are small. Due to the hot-wall conditions the results show significant low Reynolds number effects and large streamwise streaks. Further simulations with a bigger computational box or a cold-wall condition are desirable.

Dissociation and Internal Excitation of Molecular Nitrogen Due to N + N2 Collisions Using Direct Molecular Simulation

NASA Technical Reports Server (NTRS)

Grover, Maninder S.; Schwartzentruber, Thomas E.; Jaffe, Richard L.

2017-01-01

In this work we present a molecular level study of N2+N collisions, focusing on excitation of internal energy modes and non-equilibrium dissociation. The computation technique used here is the direct molecular simulation (DMS) method and the molecular interactions have been modeled using an ab-initio potential energy surface (PES) developed at NASA's Ames Research Center. We carried out vibrational excitation calculations between 5000K and 30000K and found that the characteristic vibrational excitation time for the N + N2 process was an order of magnitude lower than that predicted by the Millikan and White correlation. It is observed that during vibrational excitation the high energy tail of the vibrational energy distribution gets over populated first and the lower energy levels get populated as the system evolves. It is found that the non-equilibrium dissociation rate coefficients for the N + N2 process are larger than those for the N2 + N2 process. This is attributed to the non-equilibrium vibrational energy distributions for the N + N2 process being less depleted than that for the N2 +N2 process. For an isothermal simulation we find that the probability of dissociation goes as 1/T(sub tr) for molecules with internal energy (epsilon(sub int)) less than approximately 9.9eV, while for molecules with epsilon (sub int) greater than 9.9eV the dissociation probability was weakly dependent on translational temperature of the system. We compared non-equilibrium dissociation rate coefficients and characteristic vibrational excitation times obtained by using the ab-initio PES developed at NASA's Ames Research Center to those obtained by using an ab-initio PES developed at the University of Minnesota. Good agreement was found between the macroscopic properties and molecular level description of the system obtained by using the two PESs.

Turbulence and the Formation of Filaments, Loops, and Shock Fronts in NGC 1275

NASA Astrophysics Data System (ADS)

Falceta-Gonçalves, D.; de Gouveia Dal Pino, E. M.; Gallagher, J. S.; Lazarian, A.

2010-01-01

NGC 1275, the central galaxy in the Perseus cluster, is the host of gigantic hot bipolar bubbles inflated by active galactic nucleus (AGN) jets observed in the radio as Perseus A. It presents a spectacular Hα-emitting nebulosity surrounding NGC 1275, with loops and filaments of gas extending to over 50 kpc. The origin of the filaments is still unknown, but probably correlates with the mechanism responsible for the giant buoyant bubbles. We present 2.5 and three-dimensional magnetohydrodynamical (MHD) simulations of the central region of the cluster in which turbulent energy, possibly triggered by star formation and supernovae (SNe) explosions, is introduced. The simulations reveal that the turbulence injected by massive stars could be responsible for the nearly isotropic distribution of filaments and loops that drag magnetic fields upward as indicated by recent observations. Weak shell-like shock fronts propagating into the intracluster medium (ICM) with velocities of 100-500 km s-1 are found, also resembling the observations. The isotropic outflow momentum of the turbulence slows the infall of the ICM, thus limiting further starburst activity in NGC 1275. As the turbulence is subsonic over most of the simulated volume, the turbulent kinetic energy is not efficiently converted into heat and additional heating is required to suppress the cooling flow at the core of the cluster. Simulations combining the MHD turbulence with the AGN outflow can reproduce the temperature radial profile observed around NGC 1275. While the AGN mechanism is the main heating source, the SNe are crucial to isotropize the energy distribution.

Modeling Coupled Processes for Multiphase Fluid Flow in Mechanically Deforming Faults

NASA Astrophysics Data System (ADS)

McKenna, S. A.; Pike, D. Q.

2011-12-01

Modeling of coupled hydrological-mechanical processes in fault zones is critical for understanding the long-term behavior of fluids within the shallow crust. Here we utilize a previously developed cellular-automata (CA) model to define the evolution of permeability within a 2-D fault zone under compressive stress. At each time step, the CA model calculates the increase in fluid pressure within the fault at every grid cell. Pressure surpassing a critical threshold (e.g., lithostatic stress) causes a rupture in that cell, and pressure is then redistributed across the neighboring cells. The rupture can cascade through the spatial domain and continue across multiple time steps. Stress continues to increase and the size and location of rupture events are recorded until a percolating backbone of ruptured cells exists across the fault. Previous applications of this model consider uncorrelated random fields for the compressibility of the fault material. The prior focus on uncorrelated property fields is consistent with development of a number of statistical physics models including percolation processes and fracture propagation. However, geologic materials typically express spatial correlation and this can have a significant impact on the results of the pressure and permeability distributions. We model correlation of the fault material compressibility as a multiGaussian random field with a correlation length defined as the full-width at half maximum (FWHM) of the kernel used to create the field. The FWHM is varied from < 0.001 to approximately 0.47 of the domain size. The addition of spatial correlation to the compressibility significantly alters the model results including: 1) Accumulation of larger amounts of strain prior to the first rupture event; 2) Initiation of the percolating backbone at lower amounts of cumulative strain; 3) Changes in the event size distribution to a combined power-law and exponential distribution with a smaller power; and 4) Evolution of the spatial-temporal distribution of rupture event locations from a purely Poisson process to a complex pattern of clustered events with periodic patterns indicative of emergent phenomena. Switching the stress field from compressive to quiescent, or extensional, during the CA simulation results in a fault zone with a complex permeability pattern and disconnected zones of over-pressured fluid that serves as the initial conditions for simulation of capillary invasion of a separate fluid phase. We use Modified Invasion Percolation to simulate the invasion of a less dense fluid into the fault zone. Results show that the variability in fluid displacement measures caused by the heterogeneous permeability field and initial pressure conditions are significant. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000

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

Diakov, Victor; Brinkman, Gregory; Denholm, Paul

Using production-cost model (PLEXOS), we simulate the Western Interchange (WECC) at several levels of the yearly renewable energy (RE) generation, between 13% and 40% of the total load for the year. We look at the overall energy exchange between a region and the rest of the system (net interchange, NI), and find it useful to examine separately (i) (time-)variable and (ii) year-average components of the NI. Both contribute to inter-regional energy exchange, and are affected by wind and PV generation in the system. We find that net load variability (in relatively large portions of WECC) is the leading factor affectingmore » the variable component of inter-regional energy exchange, and the effect is quantifiable: higher regional net load correlation with the rest of the WECC lowers net interchange variability. Further, as the power mix significantly varies between WECC regions, effects of ‘flexibility import’ (regions ‘borrow’ ramping capability) are also observed.« less

Morphology correlation of craters formed by hypervelocity impacts

NASA Technical Reports Server (NTRS)

Crawford, Gary D.; Rose, M. Frank; Zee, Ralph H.

1993-01-01

Dust-sized olivine particles were fired at a copper plate using the Space Power Institute hypervelocity facility, simulating micrometeoroid damage from natural debris to spacecraft in low-Earth orbit (LEO). Techniques were developed for measuring crater volume, particle volume, and particle velocity, with the particle velocities ranging from 5.6 to 8.7 km/s. A roughly linear correlation was found between crater volume and particle energy which suggested that micrometeoroids follow standard hypervelocity relationships. The residual debris analysis showed that for olivine impacts of up to 8.7 km/s, particle residue is found in the crater. By using the Space Power Institute hypervelocity facility, micrometeoroid damage to satellites can be accurately modeled.

Contact angle of sessile drops in Lennard-Jones systems.

PubMed

Becker, Stefan; Urbassek, Herbert M; Horsch, Martin; Hasse, Hans

2014-11-18

Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.

Hot electron generation under large-signal radio frequency operation of GaN high-electron-mobility transistors

NASA Astrophysics Data System (ADS)

Latorre-Rey, Alvaro D.; Sabatti, Flavio F. M.; Albrecht, John D.; Saraniti, Marco

2017-07-01

In order to assess the underlying physical mechanisms of hot carrier-related degradation such as defect generation in millimeter-wave GaN power amplifiers, we have simulated the electron energy distribution function under large-signal radio frequency conditions in AlGaN/GaN high-electron-mobility transistors. Our results are obtained through a full band Monte Carlo particle-based simulator self-consistently coupled to a harmonic balance circuit solver. At lower frequency, simulations of a Class AB power amplifier at 10 GHz show that the peak hot electron generation is up to 43% lower under RF drive than it is under DC conditions, regardless of the input power or temperature of operation. However, at millimeter-wave operation up to 40 GHz, RF hot carrier generation reaches that from DC biasing and even exceeds it up to 75% as the amplifier is driven into compression. Increasing the temperature of operation also shows that degradation of DC and RF characteristics are tightly correlated and mainly caused by increased phonon scattering. The accurate determination of the electron energy mapping is demonstrated to be a powerful tool for the extraction of compact models used in lifetime and reliability analysis.

Simulations of controlled spectral emission of Al plasmas generated by temporally tailored laser irradiation

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

Colombier, J. P.; Guillermin, M.; Garrelie, F.

2010-10-08

Hydrodynamics simulations and irradiation experiments were performed to correlate ul-trashort intensity envelopes of the laser fields and thermodynamical states reached by the emerging plasma phase in ablation regimes. We discuss the efficiency of energy coupling as a function of different intensity envelopes and the resulting temperature, density and ionization states since the energy delivery rate is an essential factor that predetermines the material thermodynamic evolution. Subsequently, we examine the plasma composition in calculating the proportion of neutral/ion species typical of LIBS signals and comparing it with neutral/ion ratios given by experimental results. Moreover, the calculations allow to investigate the efficiencymore » of nanoparticles generation from materials subjected to different heating rates. These can be related to hydrodynamic ejection of nanosized liquid layers upon the action of mechanic waves. With support from numerical simulations of the hydrodynamic advance of the excited matter, experiments revealed that mastering intensity envelopes of ultrashort laser pulse leads to further control on the ablation products. Emerging plasma phase in a hot state generates specific spectral emission patterns that can serve as indicators for its controlled formation and kinetic evolution.« less

Rubber Impact on 3D Textile Composites

NASA Astrophysics Data System (ADS)

Heimbs, Sebastian; Van Den Broucke, Björn; Duplessis Kergomard, Yann; Dau, Frederic; Malherbe, Benoit

2012-06-01

A low velocity impact study of aircraft tire rubber on 3D textile-reinforced composite plates was performed experimentally and numerically. In contrast to regular unidirectional composite laminates, no delaminations occur in such a 3D textile composite. Yarn decohesions, matrix cracks and yarn ruptures have been identified as the major damage mechanisms under impact load. An increase in the number of 3D warp yarns is proposed to improve the impact damage resistance. The characteristic of a rubber impact is the high amount of elastic energy stored in the impactor during impact, which was more than 90% of the initial kinetic energy. This large geometrical deformation of the rubber during impact leads to a less localised loading of the target structure and poses great challenges for the numerical modelling. A hyperelastic Mooney-Rivlin constitutive law was used in Abaqus/Explicit based on a step-by-step validation with static rubber compression tests and low velocity impact tests on aluminium plates. Simulation models of the textile weave were developed on the meso- and macro-scale. The final correlation between impact simulation results on 3D textile-reinforced composite plates and impact test data was promising, highlighting the potential of such numerical simulation tools.

Interactions of Organics within Hydrated Selective Layer of Reverse Osmosis Desalination Membrane: A Combined Experimental and Computational Study.

PubMed

Ghoufi, Aziz; Dražević, Emil; Szymczyk, Anthony

2017-03-07

In this work we have examined a computational approach in predicting the interactions between uncharged organic solutes and polyamide membranes. We used three model organic molecules with identical molecular weights (100.1 g/mol), 4-aminopiperidine, 3,3-dimethyl-2-butanone (pinacolone) and methylisobutyl ketone for which we obtained experimental data on partitioning, diffusion and separation on a typical seawater reverse osmosis (RO) membrane. The interaction energy between the solutes and the membrane phase (fully aromatic polyamide) was computed from molecular dynamics (MD) simulations and the resulting sequence was found to correlate well with the experimental rejections and sorption data. Sorption of the different organic solutes within the membrane skin layer determined from attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) nicely agreed with interaction energies computed from molecular simulations. Qualitative information about solute diffusivity inside the membrane was also extracted from MD simulations while ATR-FTIR experiments indicated strongly hindered diffusion with diffusion coefficients in the membrane about 10 -15 m 2 /s. The computational approach presented here could be a first step toward predicting rejections trends of, for example, hormones and pharmaceuticals by RO dense membranes.

A Site Density Functional Theory for Water: Application to Solvation of Amino Acid Side Chains.

PubMed

Liu, Yu; Zhao, Shuangliang; Wu, Jianzhong

2013-04-09

We report a site density functional theory (SDFT) based on the conventional atomistic models of water and the universality ansatz of the bridge functional. The excess Helmholtz energy functional is formulated in terms of a quadratic expansion with respect to the local density deviation from that of a uniform system and a universal functional for all higher-order terms approximated by that of a reference hard-sphere system. With the atomistic pair direct correlation functions of the uniform system calculated from MD simulation and an analytical expression for the bridge functional from the modified fundamental measure theory, the SDFT can be used to predict the structure and thermodynamic properties of water under inhomogeneous conditions with a computational cost negligible in comparison to that of brute-force simulations. The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. For theTIP3P model, a comparison of the theoretical predictions with MD simulation and experimental data shows agreement within 0.64 and 1.09 kcal/mol on average, respectively.

Test-particle simulations in increasingly strong turbulence

NASA Technical Reports Server (NTRS)

Pontius, D. H., Jr.; Gray, P. C.; Matthaeus, W. H.

1995-01-01

Quasi-linear theory supposes that the energy in resonant fluctuations is small compared to that in the mean magnetic field. This is evident in the fact that the zeroth-order particle trajectories are helices about a mean field B(sub o) that is spatially uniform over many correlation lengths. However, in the solar wind it is often the case that the fluctuating part of the field is comparable in magnitude to the mean part. It is generally expected that quasi-linear theory remains viable for particles that are in resonance with a region of the fluctuation spectrum having only small energy density, but even so, care must be taken when comparing simulations to theoretical predictions. We have performed a series of test-particle simulations to explore the evolution of ion distributions in turbulent situations with varying levels of magnetic fluctuations. As delta-B/B(sub o) is increased the distinctions among absolute pitch angle (defined relative to B(sub o)), local pitch angle (defined relative to B(x)), and magnetic moment become important, some of them exhibiting periodic sloshing unrelated to the nonadiabatic processes of interest. Comparing and contrasting the various runs illustrates the phenomena that must be considered when the premise underlying quasi-linear theory are relaxed.

Quantifying the nonlocality of Greenberger-Horne-Zeilinger quantum correlations by a bounded communication simulation protocol.

PubMed

Branciard, Cyril; Gisin, Nicolas

2011-07-08

The simulation of quantum correlations with finite nonlocal resources, such as classical communication, gives a natural way to quantify their nonlocality. While multipartite nonlocal correlations appear to be useful resources, very little is known on how to simulate multipartite quantum correlations. We present a protocol that reproduces tripartite Greenberger-Horne-Zeilinger correlations with bounded communication: 3 bits in total turn out to be sufficient to simulate all equatorial Von Neumann measurements on the tripartite Greenberger-Horne-Zeilinger state.

Understanding Building Infrastructure and Building Operation through DOE Asset Score Model: Lessons Learned from a Pilot Project

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

Wang, Na; Goel, Supriya; Gorrissen, Willy J.

2013-06-24

The U.S. Department of Energy (DOE) is developing a national voluntary energy asset score system to help building owners to evaluate the as-built physical characteristics (including building envelope, the mechanical and electrical systems) and overall building energy efficiency, independent of occupancy and operational choices. The energy asset score breaks down building energy use information by simulating building performance under typical operating and occupancy conditions for a given use type. A web-based modeling tool, the energy asset score tool facilitates the implementation of the asset score system. The tool consists of a simplified user interface built on a centralized simulation enginemore » (EnergyPlus). It is intended to reduce both the implementation cost for the users and increase modeling standardization compared with an approach that requires users to build their own energy models. A pilot project with forty-two buildings (consisting mostly offices and schools) was conducted in 2012. This paper reports the findings. Participants were asked to collect a minimum set of building data and enter it into the asset score tool. Participants also provided their utility bills, existing ENERGY STAR scores, and previous energy audit/modeling results if available. The results from the asset score tool were compared with the building energy use data provided by the pilot participants. Three comparisons were performed. First, the actual building energy use, either from the utility bills or via ENERGY STAR Portfolio Manager, was compared with the modeled energy use. It was intended to examine how well the energy asset score represents a building’s system efficiencies, and how well it is correlated to a building’s actual energy consumption. Second, calibrated building energy models (where they exist) were used to examine any discrepancies between the asset score model and the pilot participant buildings’ [known] energy use pattern. This comparison examined the end use breakdowns and more detailed time series data. Third, ASHRAE 90.1 prototype buildings were also used as an industry standard modeling approach to test the accuracy level of the asset score tool. Our analysis showed that the asset score tool, which uses simplified building simulation, could provide results comparable to a more detailed energy model. The buildings’ as-built efficiency can be reflected in the energy asset score. An analysis between the modeled energy use through the asset score tool and the actual energy use from the utility bills can further inform building owners about the effectiveness of their building’s operation and maintenance.« less

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

PubMed

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

High energy neutron transmission analysis of dry cask storage

NASA Astrophysics Data System (ADS)

Greulich, Christopher; Hughes, Christopher; Gao, Yuan; Enqvist, Andreas; Baciak, James

2017-12-01

Since the U.S. currently only approves of storing used nuclear fuel in pools or dry casks, the demand for dry cask storage is on the rise due to the continuous operation of currently existing nuclear plants which are reaching or have reached the capacity of their used fuel pools. With the rising demand comes additional pressure to ensure the integrity of dry cask systems. Visual inspection is costly and man-power intensive, so alternative nondestructive testing techniques are desired to insure the continued safe and effective storage of fuel. One such approach being investigated by the University of Florida is neutron based computed tomography. Simulations in MCNP are preformed where D-T energy neutrons are transmitted through the dry cask and measured on the opposite side. If the transmitted signal is clear enough, the interior of the cask can be reconstructed from the measurement of the alterations of neutron signal intensity using standard mathematical techniques developed for medical imaging. Preliminary efforts show a correlation between energy and number of scatters (which is an indication of retention of position information). Work is ongoing to quantify if the correlation is strong enough that an energy discriminator may be used as a filter in future image reconstruction. The calculated transmission probability suggests that an image could be reconstructed with a week of scanning.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

NASA Astrophysics Data System (ADS)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

The energetic cost of walking: a comparison of predictive methods.

PubMed

Kramer, Patricia Ann; Sylvester, Adam D

2011-01-01

The energy that animals devote to locomotion has been of intense interest to biologists for decades and two basic methodologies have emerged to predict locomotor energy expenditure: those based on metabolic and those based on mechanical energy. Metabolic energy approaches share the perspective that prediction of locomotor energy expenditure should be based on statistically significant proxies of metabolic function, while mechanical energy approaches, which derive from many different perspectives, focus on quantifying the energy of movement. Some controversy exists as to which mechanical perspective is "best", but from first principles all mechanical methods should be equivalent if the inputs to the simulation are of similar quality. Our goals in this paper are 1) to establish the degree to which the various methods of calculating mechanical energy are correlated, and 2) to investigate to what degree the prediction methods explain the variation in energy expenditure. We use modern humans as the model organism in this experiment because their data are readily attainable, but the methodology is appropriate for use in other species. Volumetric oxygen consumption and kinematic and kinetic data were collected on 8 adults while walking at their self-selected slow, normal and fast velocities. Using hierarchical statistical modeling via ordinary least squares and maximum likelihood techniques, the predictive ability of several metabolic and mechanical approaches were assessed. We found that all approaches are correlated and that the mechanical approaches explain similar amounts of the variation in metabolic energy expenditure. Most methods predict the variation within an individual well, but are poor at accounting for variation between individuals. Our results indicate that the choice of predictive method is dependent on the question(s) of interest and the data available for use as inputs. Although we used modern humans as our model organism, these results can be extended to other species.

Application of Free Energy Perturbation for the Design of BACE1 Inhibitors.

PubMed

Ciordia, Myriam; Pérez-Benito, Laura; Delgado, Francisca; Trabanco, Andrés A; Tresadern, Gary

2016-09-26

Novel spiroaminodihydropyrroles probing for optimized interactions at the P3 pocket of β-secretase 1 (BACE1) were designed with the use of free energy perturbation (FEP) calculations. The resulting molecules showed pIC50 potencies in enzymatic BACE1 inhibition assays ranging from approximately 5 to 7. Good correlation was observed between the predicted activity from the FEP calculations and experimental activity. Simulations run with a default 5 ns approach delivered a mean unsigned error (MUE) between prediction and experiment of 0.58 and 0.91 kcal/mol for retrospective and prospective applications, respectively. With longer simulations of 10 and 20 ns, the MUE was in both cases 0.57 kcal/mol for the retrospective application, and 0.69 and 0.59 kcal/mol for the prospective application. Other considerations that impact the quality of the calculations are discussed. This work provides an example of the value of FEP as a computational tool for drug discovery.

Simulation of the single-vibronic-level emission spectrum of HPS.

PubMed

Mok, Daniel K W; Lee, Edmond P F; Chau, Foo-tim; Dyke, John M

2014-05-21

We have computed the potential energy surfaces of the X¹A' and ùA" states of HPS using the explicitly correlated multi-reference configuration interaction (MRCI-F12) method, and Franck-Condon factors between the two states, which include anharmonicity and Duschinsky rotation, with the aim of testing the assignment of the recently reported single-vibronic-level (SVL) emission spectrum of HPS [R. Grimminger, D. J. Clouthier, R. Tarroni, Z. Wang, and T. J. Sears, J. Chem. Phys. 139, 174306 (2013)]. These are the highest level calculations on these states yet reported. It is concluded that our spectral simulation supports the assignments of the molecular carrier, the electronic states involved and the vibrational structure of the experimental laser induced fluorescence, and SVL emission spectra proposed by Grimminger et al. [J. Chem. Phys. 139, 174306 (2013)]. However, there remain questions unanswered regarding the relative electronic energies of the two states and the geometry of the excited state of HPS.

Wide-Field Lensing Mass Maps from Dark Energy Survey Science Verification Data

DOE PAGES

Chang, C.

2015-07-29

We present a mass map reconstructed from weak gravitational lensing shear measurements over 139 deg 2 from the Dark Energy Survey science verification data. The mass map probes both luminous and dark matter, thus providing a tool for studying cosmology. We also find good agreement between the mass map and the distribution of massive galaxy clusters identified using a red-sequence cluster finder. Potential candidates for superclusters and voids are identified using these maps. We measure the cross-correlation between the mass map and a magnitude-limited foreground galaxy sample and find a detection at the 6.8σ level with 20 arc min smoothing.more » These measurements are consistent with simulated galaxy catalogs based on N-body simulations from a cold dark matter model with a cosmological constant. This suggests low systematics uncertainties in the map. Finally, we summarize our key findings in this Letter; the detailed methodology and tests for systematics are presented in a companion paper.« less

Vibrationally resolved photoelectron spectra of lower diamondoids: A time-dependent approach

NASA Astrophysics Data System (ADS)

Xiong, Tao; Włodarczyk, Radosław; Gallandi, Lukas; Körzdörfer, Thomas; Saalfrank, Peter

2018-01-01

Vibrationally resolved lowest-energy bands of the photoelectron spectra (PES) of adamantane, diamantane, and urotropine were simulated by a time-dependent correlation function approach within the harmonic approximation. Geometries and normal modes for neutral and cationic molecules were obtained from B3LYP hybrid density functional theory (DFT). It is shown that the simulated spectra reproduce the experimentally observed vibrational finestructure (or its absence) quite well. Origins of the finestructure are discussed and related to recurrences of autocorrelation functions and dominant vibrations. Remaining quantitative and qualitative errors of the DFT-derived PES spectra refer to (i) an overall redshift by ˜0.5 eV and (ii) the absence of satellites in the high-energy region of the spectra. The former error is shown to be due to the neglect of many-body corrections to ordinary Kohn-Sham methods, while the latter has been argued to be due to electron-nuclear couplings beyond the Born-Oppenheimer approximation [Gali et al., Nat. Commun. 7, 11327 (2016)].

Finite-size effects in simulations of electrolyte solutions under periodic boundary conditions

NASA Astrophysics Data System (ADS)

Thompson, Jeffrey; Sanchez, Isaac

The equilibrium properties of charged systems with periodic boundary conditions may exhibit pronounced system-size dependence due to the long range of the Coulomb force. As shown by others, the leading-order finite-size correction to the Coulomb energy of a charged fluid confined to a periodic box of volume V may be derived from sum rules satisfied by the charge-charge correlations in the thermodynamic limit V -> ∞ . In classical systems, the relevant sum rule is the Stillinger-Lovett second-moment (or perfect screening) condition. This constraint implies that for large V, periodicity induces a negative bias of -kB T(2 V) - 1 in the total Coulomb energy density of a homogeneous classical charged fluid of given density and temperature. We present a careful study of the impact of such finite-size effects on the calculation of solute chemical potentials from explicit-solvent molecular simulations of aqueous electrolyte solutions. National Science Foundation Graduate Research Fellowship Program, Grant No. DGE-1610403.

A percolation approach to study the high electric field effect on electrical conductivity of insulating polymer

NASA Astrophysics Data System (ADS)

Benallou, Amina; Hadri, Baghdad; Martinez-Vega, Juan; El Islam Boukortt, Nour

2018-04-01

The effect of percolation threshold on the behaviour of electrical conductivity at high electric field of insulating polymers has been briefly investigated in literature. Sometimes the dead ends links are not taken into account in the study of the electric field effect on the electrical properties. In this work, we present a theoretical framework and Monte Carlo simulation of the behaviour of the electric conductivity at high electric field based on the percolation theory using the traps energies levels which are distributed according to distribution law (uniform, Gaussian, and power-law). When a solid insulating material is subjected to a high electric field, and during trapping mechanism the dead ends of traps affect with decreasing the electric conductivity according to the traps energies levels, the correlation length of the clusters, the length of the dead ends, and the concentration of the accessible positions for the electrons. A reasonably good agreement is obtained between simulation results and the theoretical framework.

Free energy and entropy of a dipolar liquid by computer simulations

NASA Astrophysics Data System (ADS)

Palomar, Ricardo; Sesé, Gemma

2018-02-01

Thermodynamic properties for a system composed of dipolar molecules are computed. Free energy is evaluated by means of the thermodynamic integration technique, and it is also estimated by using a perturbation theory approach, in which every molecule is modeled as a hard sphere within a square well, with an electric dipole at its center. The hard sphere diameter, the range and depth of the well, and the dipole moment have been calculated from properties easily obtained in molecular dynamics simulations. Connection between entropy and dynamical properties is explored in the liquid and supercooled states by using instantaneous normal mode calculations. A model is proposed in order to analyze translation and rotation contributions to entropy separately. Both contributions decrease upon cooling, and a logarithmic correlation between excess entropy associated with translation and the corresponding proportion of imaginary frequency modes is encountered. Rosenfeld scaling law between reduced diffusion and excess entropy is tested, and the origin of its failure at low temperatures is investigated.

Relaxation of ferroelectric states in 2D distributions of quantum dots: EELS simulation

NASA Astrophysics Data System (ADS)

Cortés, C. M.; Meza-Montes, L.; Moctezuma, R. E.; Carrillo, J. L.

2016-06-01

The relaxation time of collective electronic states in a 2D distribution of quantum dots is investigated theoretically by simulating EELS experiments. From the numerical calculation of the probability of energy loss of an electron beam, traveling parallel to the distribution, it is possible to estimate the damping time of ferroelectric-like states. We generate this collective response of the distribution by introducing a mean field interaction among the quantum dots, and then, the model is extended incorporating effects of long-range correlations through a Bragg-Williams approximation. The behavior of the dielectric function, the energy loss function, and the relaxation time of ferroelectric-like states is then investigated as a function of the temperature of the distribution and the damping constant of the electronic states in the single quantum dots. The robustness of the trends and tendencies of our results indicate that this scheme of analysis can guide experimentalists to develop tailored quantum dots distributions for specific applications.

Modelling Framework and the Quantitative Analysis of Distributed Energy Resources in Future Distribution Networks

NASA Astrophysics Data System (ADS)

Han, Xue; Sandels, Claes; Zhu, Kun; Nordström, Lars

2013-08-01

There has been a large body of statements claiming that the large-scale deployment of Distributed Energy Resources (DERs) could eventually reshape the future distribution grid operation in numerous ways. Thus, it is necessary to introduce a framework to measure to what extent the power system operation will be changed by various parameters of DERs. This article proposed a modelling framework for an overview analysis on the correlation between DERs. Furthermore, to validate the framework, the authors described the reference models of different categories of DERs with their unique characteristics, comprising distributed generation, active demand and electric vehicles. Subsequently, quantitative analysis was made on the basis of the current and envisioned DER deployment scenarios proposed for Sweden. Simulations are performed in two typical distribution network models for four seasons. The simulation results show that in general the DER deployment brings in the possibilities to reduce the power losses and voltage drops by compensating power from the local generation and optimizing the local load profiles.

Wide-Field Lensing Mass Maps from Dark Energy Survey Science Verification Data.

PubMed

Chang, C; Vikram, V; Jain, B; Bacon, D; Amara, A; Becker, M R; Bernstein, G; Bonnett, C; Bridle, S; Brout, D; Busha, M; Frieman, J; Gaztanaga, E; Hartley, W; Jarvis, M; Kacprzak, T; Kovács, A; Lahav, O; Lin, H; Melchior, P; Peiris, H; Rozo, E; Rykoff, E; Sánchez, C; Sheldon, E; Troxel, M A; Wechsler, R; Zuntz, J; Abbott, T; Abdalla, F B; Allam, S; Annis, J; Bauer, A H; Benoit-Lévy, A; Brooks, D; Buckley-Geer, E; Burke, D L; Capozzi, D; Carnero Rosell, A; Carrasco Kind, M; Castander, F J; Crocce, M; D'Andrea, C B; Desai, S; Diehl, H T; Dietrich, J P; Doel, P; Eifler, T F; Evrard, A E; Fausti Neto, A; Flaugher, B; Fosalba, P; Gruen, D; Gruendl, R A; Gutierrez, G; Honscheid, K; James, D; Kent, S; Kuehn, K; Kuropatkin, N; Maia, M A G; March, M; Martini, P; Merritt, K W; Miller, C J; Miquel, R; Neilsen, E; Nichol, R C; Ogando, R; Plazas, A A; Romer, A K; Roodman, A; Sako, M; Sanchez, E; Sevilla, I; Smith, R C; Soares-Santos, M; Sobreira, F; Suchyta, E; Tarle, G; Thaler, J; Thomas, D; Tucker, D; Walker, A R

2015-07-31

We present a mass map reconstructed from weak gravitational lensing shear measurements over 139  deg2 from the Dark Energy Survey science verification data. The mass map probes both luminous and dark matter, thus providing a tool for studying cosmology. We find good agreement between the mass map and the distribution of massive galaxy clusters identified using a red-sequence cluster finder. Potential candidates for superclusters and voids are identified using these maps. We measure the cross-correlation between the mass map and a magnitude-limited foreground galaxy sample and find a detection at the 6.8σ level with 20 arc min smoothing. These measurements are consistent with simulated galaxy catalogs based on N-body simulations from a cold dark matter model with a cosmological constant. This suggests low systematics uncertainties in the map. We summarize our key findings in this Letter; the detailed methodology and tests for systematics are presented in a companion paper.

Predicting the equilibrium solubility of solid polycyclic aromatic hydrocarbons and dibenzothiophene using a combination of MOSCED plus molecular simulation or electronic structure calculations

NASA Astrophysics Data System (ADS)

Phifer, Jeremy R.; Cox, Courtney E.; da Silva, Larissa Ferreira; Nogueira, Gabriel Gonçalves; Barbosa, Ana Karolyne Pereira; Ley, Ryan T.; Bozada, Samantha M.; O'Loughlin, Elizabeth J.; Paluch, Andrew S.

2017-06-01

Methods to predict the equilibrium solubility of non-electrolyte solids are important for the design of novel separation processes. Here we demonstrate how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here SMD or SM8, can be used to predict parameters for the MOdified Separation of Cohesive Energy Density (MOSCED) method. The method is applied to the solutes naphthalene, anthracene, phenanthrene, pyrene and dibenzothiophene, compounds of interested to the petroleum industry and for environmental remediation. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. Comparing to a total of 422 non-aqueous and 193 aqueous experimental solubilities, we find the proposed method is able to well correlate the data. The use of MOSCED is additionally advantageous as it is a solubility parameter-based method useful for intuitive solvent selection and formulation.

Dark Energy Survey Year 1 Results: Cross-Correlation Redshifts - Methods and Systematics Characterization

DOE PAGES

Gatti, M.

2018-02-22

We use numerical simulations to characterize the performance of a clustering-based method to calibrate photometric redshift biases. In particular, we cross-correlate the weak lensing (WL) source galaxies from the Dark Energy Survey Year 1 (DES Y1) sample with redMaGiC galaxies (luminous red galaxies with secure photometric red- shifts) to estimate the redshift distribution of the former sample. The recovered redshift distributions are used to calibrate the photometric redshift bias of standard photo-z methods applied to the same source galaxy sample. We also apply the method to three photo-z codes run in our simulated data: Bayesian Photometric Redshift (BPZ), Directional Neighborhoodmore » Fitting (DNF), and Random Forest-based photo-z (RF). We characterize the systematic uncertainties of our calibration procedure, and find that these systematic uncertainties dominate our error budget. The dominant systematics are due to our assumption of unevolving bias and clustering across each redshift bin, and to differences between the shapes of the redshift distributions derived by clustering vs photo-z's. The systematic uncertainty in the mean redshift bias of the source galaxy sample is z ≲ 0.02, though the precise value depends on the redshift bin under consideration. Here, we discuss possible ways to mitigate the impact of our dominant systematics in future analyses.« less

Dark Energy Survey Year 1 Results: Cross-Correlation Redshifts - Methods and Systematics Characterization

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

Gatti, M.

We use numerical simulations to characterize the performance of a clustering-based method to calibrate photometric redshift biases. In particular, we cross-correlate the weak lensing (WL) source galaxies from the Dark Energy Survey Year 1 (DES Y1) sample with redMaGiC galaxies (luminous red galaxies with secure photometric red- shifts) to estimate the redshift distribution of the former sample. The recovered redshift distributions are used to calibrate the photometric redshift bias of standard photo-z methods applied to the same source galaxy sample. We also apply the method to three photo-z codes run in our simulated data: Bayesian Photometric Redshift (BPZ), Directional Neighborhoodmore » Fitting (DNF), and Random Forest-based photo-z (RF). We characterize the systematic uncertainties of our calibration procedure, and find that these systematic uncertainties dominate our error budget. The dominant systematics are due to our assumption of unevolving bias and clustering across each redshift bin, and to differences between the shapes of the redshift distributions derived by clustering vs photo-z's. The systematic uncertainty in the mean redshift bias of the source galaxy sample is z ≲ 0.02, though the precise value depends on the redshift bin under consideration. Here, we discuss possible ways to mitigate the impact of our dominant systematics in future analyses.« less

Ion Transport and Acceleration at Dipolarization Fronts: High-Resolution MHD/Test-Particle Simulations

NASA Astrophysics Data System (ADS)

Ukhorskiy, A. Y.; Sorathia, K.; Merkin, V. G.; Sitnov, M. I.; Mitchell, D. G.; Wiltberger, M. J.; Lyon, J.

2017-12-01

Much of plasma heating and transport from the magnetotail into the inner magnetosphere occurs in the form of mesoscale discrete injections associated with sharp dipolarizations of magnetic field (dipolarization fronts). In this study we investigate the mechanisms of ion acceleration at dipolarization fronts in a high-resolution global magnetospheric MHD model (LFM). We use large-scale three-dimensional test-particle simulations (CHIMP) to address the following science questions: 1) what are the characteristic scales of dipolarization regions that can stably trap ions? 2) what role does the trapping play in ion transport and acceleration? 3) how does it depend on particle energy and distance from Earth? 4) to what extent ion acceleration is adiabatic? High-resolution LFM was run using idealized solar wind conditions with fixed nominal values of density and velocity and a southward IMF component of -5 nT. To simulate ion interaction with dipolarization fronts, a large ensemble of test particles distributed in energy, pitch-angle, and gyrophase was initialized inside one of the LFM dipolarization channels in the magnetotail. Full Lorentz ion trajectories were then computed over the course of the front inward propagation from the distance of 17 to 6 Earth radii. A large fraction of ions with different initial energies stayed in phase with the front over the entire distance. The effect of magnetic trapping at different energies was elucidated with a correlation of the ion guiding center and the ExB drift velocities. The role of trapping in ion energization was quantified by comparing the partial pressure of ions that exhibit trapping to the pressure of all trapped ions.

Correlation between mechanical and chemical degradation after outdoor and accelerated laboratory aging for multilayer photovoltaic backsheets

NASA Astrophysics Data System (ADS)

Lin, Chiao-Chi; Lyu, Yadong; Yu, Li-Chieh; Gu, Xiaohong

2016-09-01

Channel cracking fragmentation testing and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy were utilized to study mechanical and chemical degradation of a multilayered backsheet after outdoor and accelerated laboratory aging. A model sample of commercial PPE backsheet, namely polyethylene terephthalate/polyethylene terephthalate/ethylene vinyl acetate (PET/PET/EVA) was investigated. Outdoor aging was performed in Gaithersburg, Maryland, USA for up to 510 days, and complementary accelerated laboratory aging was conducted on the NIST (National Institute of Standards and Technology) SPHERE (Simulated Photodegradation via High Energy Radiant Exposure). Fracture energy, mode I stress intensity factor and film strength were analyzed using an analytical model based on channel cracking fragmentation testing results. The correlation between mechanical and chemical degradation was discussed for both outdoor and accelerated laboratory aging. The results of this work provide preliminary understanding on failure mechanism of backsheets after weathering, laying the groundwork for linking outdoor and indoor accelerated laboratory testing for multilayer photovoltaic backsheets.

Clustering redshift distributions for the Dark Energy Survey

NASA Astrophysics Data System (ADS)

Helsby, Jennifer

Accurate determination of photometric redshifts and their errors is critical for large scale structure and weak lensing studies for constraining cosmology from deep, wide imaging surveys. Current photometric redshift methods suffer from bias and scatter due to incomplete training sets. Exploiting the clustering between a sample of galaxies for which we have spectroscopic redshifts and a sample of galaxies for which the redshifts are unknown can allow us to reconstruct the true redshift distribution of the unknown sample. Here we use this method in both simulations and early data from the Dark Energy Survey (DES) to determine the true redshift distributions of galaxies in photometric redshift bins. We find that cross-correlating with the spectroscopic samples currently used for training provides a useful test of photometric redshifts and provides reliable estimates of the true redshift distribution in a photometric redshift bin. We discuss the use of the cross-correlation method in validating template- or learning-based approaches to redshift estimation and its future use in Stage IV surveys.

D-DSC: Decoding Delay-based Distributed Source Coding for Internet of Sensing Things

PubMed Central

Akan, Ozgur B.

2018-01-01

Spatial correlation between densely deployed sensor nodes in a wireless sensor network (WSN) can be exploited to reduce the power consumption through a proper source coding mechanism such as distributed source coding (DSC). In this paper, we propose the Decoding Delay-based Distributed Source Coding (D-DSC) to improve the energy efficiency of the classical DSC by employing the decoding delay concept which enables the use of the maximum correlated portion of sensor samples during the event estimation. In D-DSC, network is partitioned into clusters, where the clusterheads communicate their uncompressed samples carrying the side information, and the cluster members send their compressed samples. Sink performs joint decoding of the compressed and uncompressed samples and then reconstructs the event signal using the decoded sensor readings. Based on the observed degree of the correlation among sensor samples, the sink dynamically updates and broadcasts the varying compression rates back to the sensor nodes. Simulation results for the performance evaluation reveal that D-DSC can achieve reliable and energy-efficient event communication and estimation for practical signal detection/estimation applications having massive number of sensors towards the realization of Internet of Sensing Things (IoST). PMID:29538405

VECC array for Nuclear fast Timing and angUlar corRElation studies (VENTURE)

NASA Astrophysics Data System (ADS)

Alam, S. S.; Bhattacharjee, T.; Banerjee, D.; Saha, A.; Pandit, Deepak; Mondal, D.; Mukhopadhyay, S.; Pal, Surajit; Bhaskar, P.; Das, S. K.; Banerjee, S. R.

2017-12-01

The VECC array for Nuclear fast Timing and angUlar corRElation studies (VENTURE) has been developed using several fast Cerium-Bromide (CeBr3) scintillators coupled to Hamamatsu R9779 Photomultiplier tubes. The CeBr3 detector has been characterised for the spectroscopic properties like energy response, energy resolution, timing resolution and detection efficiency. The response and efficiency of the detector have been compared with the results obtained from a Monte Carlo simulation with GEANT3 package. A time resolution of 144(1) ps and 109(1) ps was obtained for a single detector using 622-512 keV and 1173-1332 keV cascades respectively. The Generalised Centroid Difference (GCD) method has been employed with CeBr3 detectors by measuring the level lifetimes for the 511.9 keV level of 106Pd and the 160.6 and 383.8 keV levels of 133Cs. The angular correlation measurement was performed for the 1173-1332 keV cascade in 60Ni and the 228-49 keV cascade of 132I nucleus, populated from the decay of 132Te produced via 238U(α, f) reaction.

Electromagnetic fields in small systems from a multiphase transport model

NASA Astrophysics Data System (ADS)

Zhao, Xin-Li; Ma, Yu-Gang; Ma, Guo-Liang

2018-02-01

We calculate the electromagnetic fields generated in small systems by using a multiphase transport (AMPT) model. Compared to A +A collisions, we find that the absolute electric and magnetic fields are not small in p +Au and d +Au collisions at energies available at the BNL Relativistic Heavy Ion Collider and in p +Pb collisions at energies available at the CERN Large Hadron Collider. We study the centrality dependencies and the spatial distributions of electromagnetic fields. We further investigate the azimuthal fluctuations of the magnetic field and its correlation with the fluctuating geometry using event-by-event simulations. We find that the azimuthal correlation 〈" close="〉cos(ϕα+ϕβ-2 ΨRP)〉">cos2 (ΨB-Ψ2) between the magnetic field direction and the second-harmonic participant plane is almost zero in small systems with high multiplicities, but not in those with low multiplicities. This indicates that the charge azimuthal correlation is not a valid probe to study the chiral magnetic effect (CME) in small systems with high multiplicities. However, we suggest searching for possible CME effects in small systems with low multiplicities.

D-DSC: Decoding Delay-based Distributed Source Coding for Internet of Sensing Things.

PubMed

Aktas, Metin; Kuscu, Murat; Dinc, Ergin; Akan, Ozgur B

2018-01-01

Spatial correlation between densely deployed sensor nodes in a wireless sensor network (WSN) can be exploited to reduce the power consumption through a proper source coding mechanism such as distributed source coding (DSC). In this paper, we propose the Decoding Delay-based Distributed Source Coding (D-DSC) to improve the energy efficiency of the classical DSC by employing the decoding delay concept which enables the use of the maximum correlated portion of sensor samples during the event estimation. In D-DSC, network is partitioned into clusters, where the clusterheads communicate their uncompressed samples carrying the side information, and the cluster members send their compressed samples. Sink performs joint decoding of the compressed and uncompressed samples and then reconstructs the event signal using the decoded sensor readings. Based on the observed degree of the correlation among sensor samples, the sink dynamically updates and broadcasts the varying compression rates back to the sensor nodes. Simulation results for the performance evaluation reveal that D-DSC can achieve reliable and energy-efficient event communication and estimation for practical signal detection/estimation applications having massive number of sensors towards the realization of Internet of Sensing Things (IoST).

Correlation of current drop, filling gas pressure, and ion beam emission in a low energy Mather-type plasma focus device

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

Behbahani, R. A.; Aghamir, F. M.

The behavior of current drop and its correlation with ion beam emission during the radial phase of a high inductance low energy Mather type plasma focus device have been studied. The study includes two ranges of filling gas pressure, namely the low range of 0.2-0.8 mbar and the high range of 0.8-1.5 mbar. Two different current simulation processes were performed to aid the interpretation of the experimental results. Within the low range of operating pressure, an acceptable match between the computed and experimental current signals was achieved when the effects of anomalous resistances were contemplated. While in the high rangemore » of pressure, the computed and experimental current traces were in line even without considering the effects of anomalous resistances. The analysis shows that by decreasing the filling gas pressure the effects of instabilities are intensified. The computed and experimental current traces, along with ion beam signals gathered from a faraday cup, show that there is a strong correlation between the intensity of ion beam and its duration with the current drop during the radial phase.« less

Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

NASA Astrophysics Data System (ADS)

Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

2018-05-01

We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

PubMed Central

Abramyan, Tigran M.; Snyder, James A.; Yancey, Jeremy A.; Thyparambil, Aby A.; Wei, Yang; Stuart, Steven J.; Latour, Robert A.

2015-01-01

Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG–X–GTGT host–guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5 kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard–Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid–liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122