Eged, Katalin; Kis, Zoltán; Voigt, Gabriele
2006-01-01
After an accidental release of radionuclides to the inhabited environment the external gamma irradiation from deposited radioactivity contributes significantly to the radiation exposure of the population for extended periods. For evaluating this exposure pathway, three main model requirements are needed: (i) to calculate the air kerma value per photon emitted per unit source area, based on Monte Carlo (MC) simulations; (ii) to describe the distribution and dynamics of radionuclides on the diverse urban surfaces; and (iii) to combine all these elements in a relevant urban model to calculate the resulting doses according to the actual scenario. This paper provides an overview about the different approaches to calculate photon transport in urban areas and about several dose calculation codes published. Two types of Monte Carlo simulations are presented using the global and the local approaches of photon transport. Moreover, two different philosophies of the dose calculation, the "location factor method" and a combination of relative contamination of surfaces with air kerma values are described. The main features of six codes (ECOSYS, EDEM2M, EXPURT, PARATI, TEMAS, URGENT) are highlighted together with a short model-model features intercomparison. PMID:16095771
Langevin spin dynamics based on ab initio calculations: numerical schemes and applications.
Rózsa, L; Udvardi, L; Szunyogh, L
2014-05-28
A method is proposed to study the finite-temperature behaviour of small magnetic clusters based on solving the stochastic Landau-Lifshitz-Gilbert equations, where the effective magnetic field is calculated directly during the solution of the dynamical equations from first principles instead of relying on an effective spin Hamiltonian. Different numerical solvers are discussed in the case of a one-dimensional Heisenberg chain with nearest-neighbour interactions. We performed detailed investigations for a monatomic chain of ten Co atoms on top of a Au(0 0 1) surface. We found a spiral-like ground state of the spins due to Dzyaloshinsky-Moriya interactions, while the finite-temperature magnetic behaviour of the system was well described by a nearest-neighbour Heisenberg model including easy-axis anisotropy. PMID:24806308
Molecular Dynamics Calculations
NASA Technical Reports Server (NTRS)
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
NASA Astrophysics Data System (ADS)
Pan, Zhao; Whitehead, Jared; Thomson, Scott; Truscott, Tadd
2016-08-01
Obtaining pressure field data from particle image velocimetry (PIV) is an attractive technique in fluid dynamics due to its noninvasive nature. The application of this technique generally involves integrating the pressure gradient or solving the pressure Poisson equation using a velocity field measured with PIV. However, very little research has been done to investigate the dynamics of error propagation from PIV-based velocity measurements to the pressure field calculation. Rather than measure the error through experiment, we investigate the dynamics of the error propagation by examining the Poisson equation directly. We analytically quantify the error bound in the pressure field, and are able to illustrate the mathematical roots of why and how the Poisson equation based pressure calculation propagates error from the PIV data. The results show that the error depends on the shape and type of boundary conditions, the dimensions of the flow domain, and the flow type.
NASA Astrophysics Data System (ADS)
Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios
2015-12-01
We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.
NASA Astrophysics Data System (ADS)
Monge-Palacios, M.; Corchado, J. C.; Espinosa-Garcia, J.
2013-06-01
To understand the reactivity and mechanism of the OH + NH3 → H2O + NH2 gas-phase reaction, which evolves through wells in the entrance and exit channels, a detailed dynamics study was carried out using quasi-classical trajectory calculations. The calculations were performed on an analytical potential energy surface (PES) recently developed by our group, PES-2012 [Monge-Palacios et al. J. Chem. Phys. 138, 084305 (2013)], 10.1063/1.4792719. Most of the available energy appeared as H2O product vibrational energy (54%), reproducing the only experimental evidence, while only the 21% of this energy appeared as NH2 co-product vibrational energy. Both products appeared with cold and broad rotational distributions. The excitation function (constant collision energy in the range 1.0-14.0 kcal mol-1) increases smoothly with energy, contrasting with the only theoretical information (reduced-dimensional quantum scattering calculations based on a simplified PES), which presented a peak at low collision energies, related to quantized states. Analysis of the individual reactive trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (Ecoll ≥ 6 kcal mol-1) all trajectories are direct, at low energies about 20%-30% of trajectories are indirect, i.e., with the mediation of a trapping complex, mainly in the product well. Finally, the effect of the zero-point energy constraint on the dynamics properties was analyzed.
NASA Technical Reports Server (NTRS)
Camarda, C. J.; Adelman, H. M.
1984-01-01
The implementation of static and dynamic structural-sensitivity derivative calculations in a general purpose, finite-element computer program denoted the Engineering Analysis Language (EAL) System is described. Derivatives are calculated with respect to structural parameters, specifically, member sectional properties including thicknesses, cross-sectional areas, and moments of inertia. Derivatives are obtained for displacements, stresses, vibration frequencies and mode shapes, and buckling loads and mode shapes. Three methods for calculating derivatives are implemented (analytical, semianalytical, and finite differences), and comparisons of computer time and accuracy are made. Results are presented for four examples: a swept wing, a box beam, a stiffened cylinder with a cutout, and a space radiometer-antenna truss.
Velocity Based Modulus Calculations
NASA Astrophysics Data System (ADS)
Dickson, W. C.
2007-12-01
A new set of equations are derived for the modulus of elasticity E and the bulk modulus K which are dependent only upon the seismic wave propagation velocities Vp, Vs and the density ρ. The three elastic moduli, E (Young's modulus), the shear modulus μ (Lamé's second parameter) and the bulk modulus K are found to be simple functions of the density and wave propagation velocities within the material. The shear and elastic moduli are found to equal the density of the material multiplied by the square of their respective wave propagation-velocities. The bulk modulus may be calculated from the elastic modulus using Poisson's ratio. These equations and resultant values are consistent with published literature and values in both magnitude and dimension (N/m2) and are applicable to the solid, liquid and gaseous phases. A 3D modulus of elasticity model for the Parkfield segment of the San Andreas Fault is presented using data from the wavespeed model of Thurber et al. [2006]. A sharp modulus gradient is observed across the fault at seismic depths, confirming that "variation in material properties play a key role in fault segmentation and deformation style" [Eberhart-Phillips et al., 1993] [EPM93]. The three elastic moduli E, μ and K may now be calculated directly from seismic pressure and shear wave propagation velocities. These velocities may be determined using conventional seismic reflection, refraction or transmission data and techniques. These velocities may be used in turn to estimate the density. This allows velocity based modulus calculations to be used as a tool for geophysical analysis, modeling, engineering and prospecting.
NASA Astrophysics Data System (ADS)
Amadon, B.; Lechermann, F.; Georges, A.; Jollet, F.; Wehling, T. O.; Lichtenstein, A. I.
2008-05-01
The description of realistic strongly correlated systems has recently advanced through the combination of density functional theory in the local density approximation (LDA) and dynamical mean field theory (DMFT). This LDA+DMFT method is able to treat both strongly correlated insulators and metals. Several interfaces between LDA and DMFT have been used, such as ( Nth order) linear muffin-tin orbitals or maximally localized Wannier functions. Such schemes are, however, either complex in use or additional simplifications are often performed (i.e., the atomic sphere approximation). We present an alternative implementation of LDA+DMFT , which keeps the precision of the Wannier implementation, but which is lighter. It relies on the projection of localized orbitals onto a restricted set of Kohn-Sham states to define the correlated subspace. The method is implemented within the projector augmented wave and within the mixed-basis pseudopotential frameworks. This opens the way to electronic structure calculations within LDA+DMFT for more complex structures with the precision of an all-electron method. We present an application to two correlated systems, namely, SrVO3 and β -NiS (a charge-transfer material), including ligand states in the basis set. The results are compared to calculations done with maximally localized Wannier functions, and the physical features appearing in the orbitally resolved spectral functions are discussed.
Dynamical calculations for RHEED intensity oscillations
NASA Astrophysics Data System (ADS)
Daniluk, Andrzej
2005-03-01
A practical computing algorithm working in real time has been developed for calculating the reflection high-energy electron diffraction from the molecular beam epitaxy growing surface. The calculations are based on the use of a dynamical diffraction theory in which the electrons are taken to be diffracted by a potential, which is periodic in the dimension perpendicular to the surface. The results of the calculations are presented in the form of rocking curves to illustrate how the diffracted beam intensities depend on the glancing angle of the incident beam. Program summaryTitle of program: RHEED Catalogue identifier:ADUY Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUY Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Pentium-based PC Operating systems or monitors under which the program has been tested: Windows 9x, XP, NT, Linux Programming language used: Borland C++ Memory required to execute with typical data: more than 1 MB Number of bits in a word: 64 bits Number of processors used: 1 Distribution format:tar.gz Number of lines in distributed program, including test data, etc.:982 Number of bytes in distributed program, including test data, etc.: 126 051 Nature of physical problem: Reflection high-energy electron diffraction (RHEED) is a very useful technique for studying growth and surface analysis of thin epitaxial structures prepared by the molecular beam epitaxy (MBE). Nowadays, RHEED is used in many laboratories all over the world where researchers deal with the growth of materials by MBE. The RHEED technique can reveal, almost instantaneously, changes either in the coverage of the sample surface by adsorbates or in the surface structure of a thin film. In most cases the interpretation of experimental results is based on the use of dynamical diffraction approaches. Such approaches are said to be quite useful in qualitative and
Mouas, Mohamed; Gasser, Jean-Georges; Hellal, Slimane; Grosdidier, Benoît; Makradi, Ahmed; Belouettar, Salim
2012-03-01
Molecular dynamics (MD) simulations of liquid tin between its melting point and 1600 °C have been performed in order to interpret and discuss the ionic structure. The interactions between ions are described by a new accurate pair potential built within the pseudopotential formalism and the linear response theory. The calculated structure factor that reflects the main information on the local atomic order in liquids is compared to diffraction measurements. Having some confidence in the ability of this pair potential to give a good representation of the atomic structure, we then focused our attention on the investigation of the atomic transport properties through the MD computations of the velocity autocorrelation function and stress autocorrelation function. Using the Green-Kubo formula (for the first time to our knowledge for liquid tin) we determine the macroscopic transport properties from the corresponding microscopic time autocorrelation functions. The selfdiffusion coefficient and the shear viscosity as functions of temperature are found to be in good agreement with the experimental data. PMID:22401446
Molecular dynamics calculations of nuclear stimulated desorption
Glikman, E.; Kelson, I. ); Doan, N.V. )
1991-09-01
Molecular dynamics calculations of nuclear stimulated desorption are carried out for a palladium crystal containing radioactive palladium atoms. The total desorption probability from various sites are computed, as well as the angular distribution of the desorbing atoms. The implications of the results to different experimental scenarios are discussed.
Böttcher, D; Ernst, A; Henk, J
2011-07-27
The magnetization dynamics of Co nanoislands on Cu(111) is studied on the atomic scale by means of the stochastic Landau-Lifshitz-Gilbert equation. The exchange and anisotropy constants of the spin Hamiltonian are computed from first principles. We focus on hysteresis loops and magnetic switching in dependence on temperature, island size, and strength of an external magnetic field. The magnetic switching of nanoislands whose magnetization is reversed on the sub-nanosecond time scale is found consistent with the Stoner-Wohlfarth theory. We separate the superparamagnetic from the ferromagnetic regime and provide evidence that nanodomains can exist at least on a sub-picosecond time scale. PMID:21715954
Bias in Dynamic Monte Carlo Alpha Calculations
Sweezy, Jeremy Ed; Nolen, Steven Douglas; Adams, Terry R.; Trahan, Travis John
2015-02-06
A 1/N bias in the estimate of the neutron time-constant (commonly denoted as α) has been seen in dynamic neutronic calculations performed with MCATK. In this paper we show that the bias is most likely caused by taking the logarithm of a stochastic quantity. We also investigate the known bias due to the particle population control method used in MCATK. We conclude that this bias due to the particle population control method is negligible compared to other sources of bias.
Feliks, Mikolaj; Lafaye, Céline; Shu, Xiaokun; Royant, Antoine; Field, Martin
2016-08-01
Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics simulations, we have studied the structure, protonation behavior, and dynamics of the biliverdin chromophore and its molecular environment in a series of genetically engineered infrared fluorescent proteins (IFPs) based on the chromophore-binding domain of the Deinococcus radiodurans bacteriophytochrome. Our study suggests that the experimentally observed enhancement of fluorescent properties results from the improved rigidity and planarity of the biliverdin chromophore, in particular of the first two pyrrole rings neighboring the covalent linkage to the protein. We propose that the increases in the levels of both motion and bending of the chromophore out of planarity favor the decrease in fluorescence. The chromophore-binding pocket in some of the studied proteins, in particular the weakly fluorescent parent protein, is shown to be readily accessible to water molecules from the solvent. These waters entering the chromophore region form hydrogen bond networks that affect the otherwise planar conformation of the first three rings of the chromophore. On the basis of our simulations, the enhancement of fluorescence in IFPs can be achieved either by reducing the mobility of water molecules in the vicinity of the chromophore or by limiting the interactions of the nearby protein residues with the chromophore. Finally, simulations performed at both low and neutral pH values highlight differences in the dynamics of the chromophore and shed light on the mechanism of fluorescence loss at low pH. PMID:27471775
Biased Brownian dynamics for rate constant calculation.
Zou, G; Skeel, R D; Subramaniam, S
2000-08-01
An enhanced sampling method-biased Brownian dynamics-is developed for the calculation of diffusion-limited biomolecular association reaction rates with high energy or entropy barriers. Biased Brownian dynamics introduces a biasing force in addition to the electrostatic force between the reactants, and it associates a probability weight with each trajectory. A simulation loses weight when movement is along the biasing force and gains weight when movement is against the biasing force. The sampling of trajectories is then biased, but the sampling is unbiased when the trajectory outcomes are multiplied by their weights. With a suitable choice of the biasing force, more reacted trajectories are sampled. As a consequence, the variance of the estimate is reduced. In our test case, biased Brownian dynamics gives a sevenfold improvement in central processing unit (CPU) time with the choice of a simple centripetal biasing force. PMID:10919998
NASA Astrophysics Data System (ADS)
Sementa, L.; Wijzenbroek, M.; van Kolck, B. J.; Somers, M. F.; Al-Halabi, A.; Busnengo, H. F.; Olsen, R. A.; Kroes, G. J.; Rutkowski, M.; Thewes, C.; Kleimeier, N. F.; Zacharias, H.
2013-01-01
We present new experimental and theoretical results for reactive scattering of dihydrogen from Cu(100). In the new experiments, the associative desorption of H2 is studied in a velocity resolved and final rovibrational state selected manner, using time-of-flight techniques in combination with resonance-enhanced multi-photon ionization laser detection. Average desorption energies and rotational quadrupole alignment parameters were obtained in this way for a number of (v = 0, 1) rotational states, v being the vibrational quantum number. Results of quantum dynamics calculations based on a potential energy surface computed with a specific reaction parameter (SRP) density functional, which was derived earlier for dihydrogen interacting with Cu(111), are compared with the results of the new experiments and with the results of previous molecular beam experiments on sticking of H2 and on rovibrationally elastic and inelastic scattering of H2 and D2 from Cu(100). The calculations use the Born-Oppenheimer and static surface approximations. With the functional derived semi-empirically for dihydrogen + Cu(111), a chemically accurate description is obtained of the molecular beam experiments on sticking of H2 on Cu(100), and a highly accurate description is obtained of rovibrationally elastic and inelastic scattering of D2 from Cu(100) and of the orientational dependence of the reaction of (v = 1, j = 2 - 4) H2 on Cu(100). This suggests that a SRP density functional derived for H2 interacting with a specific low index face of a metal will yield accurate results for H2 reactively scattering from another low index face of the same metal, and that it may also yield accurate results for H2 interacting with a defected (e.g., stepped) surface of that same metal, in a system of catalytic interest. However, the description that was obtained of the average desorption energies, of rovibrationally elastic and inelastic scattering of H2 from Cu(100), and of the orientational dependence of
NASA Astrophysics Data System (ADS)
Nakai, T.; Kumagai, T.; Saito, T.; Matsumoto, K.; Kume, T.; Nakagawa, M.; Sato, H.
2015-12-01
Bornean tropical rain forests are among the moistest biomes of the world with abundant rainfall throughout the year, and considered to be vulnerable to a change in the rainfall regime; e.g., high tree mortality was reported in such forests induced by a severe drought associated with the ENSO event in 1997-1998. In order to assess the effect (risk) of future climate change on eco-hydrology in such tropical rain forests, it is important to understand the water use of trees individually, because the vulnerability or mortality of trees against climate change can depend on the size of trees. Therefore, we refined the Spatially Explicit Individual-Based Dynamic Global Vegetation Model (SEIB-DGVM) so that the transpiration and its control by stomata are calculated for each individual tree. By using this model, we simulated the transpiration of each tree and its DBH-size dependency, and successfully reproduced the measured data of sap flow of trees and eddy covariance flux data obtained in a Bornean lowland tropical rain forest in Lambir Hills National Park, Sarawak, Malaysia.
Li, Y. Q.; Zhang, P. Y.; Han, K. L.
2015-03-28
A global many-body expansion potential energy surface is reported for the electronic ground state of CH{sub 2}{sup +} by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH{sup +}(X{sup 1}Σ{sup +})+H({sup 2}S)→C{sup +}({sup 2}P)+H{sub 2}(X{sup 1}Σ{sub g}{sup +}) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C{sup +}/H containing systems.
Hou, Tingjun; Wang, Junmei; Li, Youyong; Wang, Wei
2011-01-01
The Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) and the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free energies for macromolecules by combining molecular mechanics calculations and continuum solvation models. To systematically evaluate the performance of these methods, we report here an extensive study of 59 ligands interacting with six different proteins. First, we explored the effects of the length of the molecular dynamics (MD) simulation, ranging from 400 to 4800 ps, and the solute dielectric constant (1, 2 or 4) to the binding free energies predicted by MM/PBSA. The following three important conclusions could be observed: (1). MD simulation lengths have obvious impact on the predictions, and longer MD simulations are not always necessary to achieve better predictions; (2). The predictions are quite sensitive to solute dielectric constant, and this parameter should be carefully determined according to the characteristics of the protein/ligand binding interface; (3). Conformational entropy showed large fluctuations in MD trajectories and a large number of snapshots are necessary to achieve stable predictions. Next, we evaluated the accuracy of the binding free energies calculated by three Generalized Born (GB) models. We found that the GB model developed by Onufriev and Case was the most successful model in ranking the binding affinities of the studied inhibitors. Finally, we evaluated the performance of MM/GBSA and MM/PBSA in predicting binding free energies. Our results showed that MM/PBSA performed better in calculating absolute, but not necessarily relative, binding free energies than MM/GBSA. Considering its computational efficiency, MM/GBSA can serve as a powerful tool in drug design, where correct ranking of inhibitors is often emphasized. PMID:21117705
Greif, Michael; Nagy, Tibor; Soloviov, Maksym; Castiglioni, Luca; Hengsberger, Matthias; Meuwly, Markus; Osterwalder, Jürg
2015-01-01
A THz-pump and x-ray-probe experiment is simulated where x-ray photoelectron diffraction (XPD) patterns record the coherent vibrational motion of carbon monoxide molecules adsorbed on a Pt(111) surface. Using molecular dynamics simulations, the excitation of frustrated wagging-type motion of the CO molecules by a few-cycle pulse of 2 THz radiation is calculated. From the atomic coordinates, the time-resolved XPD patterns of the C 1s core level photoelectrons are generated. Due to the direct structural information in these data provided by the forward scattering maximum along the carbon-oxygen direction, the sequence of these patterns represents the equivalent of a molecular movie. PMID:26798798
NASA Astrophysics Data System (ADS)
Li, Bin; Han, Ke-Li
2008-03-01
A theoretical investigation on the nonadiabatic processes of the full three-dimensional D++H2 and H++D2 reaction systems has been performed by using trajectory surface hopping (TSH) method based on the Zhu-Nakamura (ZN) theory. This ZN-TSH method refers to not only classically allowed hops but also classically forbidden hops. The potential energy surface constructed by Kamisaka et al. is employed in the calculation. A new iterative method is proposed to yield the two-dimensional seam surface from the topography of the adiabatic potential surfaces, in which the inconvenience of directly solving the first-order partial differential equation is avoided. The cross sections of these two systems are calculated for three competing channels of the reactive charge transfer, the nonreactive charge transfer, and the reactive noncharge transfer, for ground rovibrational state of H2 or D2. Also, this study provides reaction probabilities of these three processes for the total angular momentum J =0 and ground initial vibrational state of H2 or D2. The calculated results from ZN-TSH method are in good agreement with the exact quantum calculations and the experimental measurements.
Sangpheak, Waratchada; Khuntawee, Wasinee; Wolschann, Peter; Pongsawasdi, Piamsook; Rungrotmongkol, Thanyada
2014-05-01
The structure, dynamic behavior and binding affinity of the inclusion complexes between naringenin and the two cyclodextrins (CDs), β-CD and its 2,6-dimethyl derivative (DM-β-CD), were theoretically studied by multiple molecular dynamics simulations and free energy calculations. Naringenin most likely prefers to bind with CDs through the phenyl ring. Although a lower hydrogen bond formation of naringenin with the 3-hydroxyl group of DM-β-CD (relative to β-CD) was observed, the higher cavity could encapsulate almost the whole naringenin molecule. In contrast for the naringenin/β-CD complex, the phenyl ring feasibly passed through the primary rim resulting in the chromone ring binding inside instead. MM-PBSA/GBSA and QM-PBSA/GBSA binding free energies strongly suggested a greater stability of the naringenin/DM-β-CD inclusion complex. Van der Waals force played an important role as the key guest-host interaction for the complexation between naringenin and each cyclodextrin. PMID:24681901
Cao, Jun
2015-06-28
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π(*) transition induces a cleavage of the C-N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π(*) excitation of the imine chromophore results in a cleavage of the C-C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N-O bond cleavages on both S1((1)ππ(*)) and S2((1)nNπ(*)) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles. PMID:26133423
Cao, Jun
2015-06-28
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π{sup *} transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π{sup *} excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S{sub 1}({sup 1}ππ{sup *}) and S{sub 2}({sup 1}n{sub N}π{sup *}) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.
Molecular-dynamics calculations of thermodynamic properties of metastable alloys
Mazzone, G.; Rosato, V.; Pintore, M.; Delogu, F.; Demontis, P.; Suffritti, G.B.
1997-01-01
In order to improve our current understanding of the microscopic structure of metastable alloys of immiscible elements such as Ag-Cu and Co-Cu, the Helmholtz free energy of several microstructures based on an fcc unit cell has been calculated and compared with that of a reference state. The microstructures considered for the free energy calculations at fixed volume are (1) a structure formed by alternating layers of fixed thickness of metal 1 and metal 2 separated by coherent interfaces; (2) an atomically disordered solid solution; (3) a structure comprising a random distribution of elemental cubic grains separated by coherent interfaces. Numerical results show that the Helmholtz free energy of structure (3) decreases with increasing grain size and that its value calculated for a sufficiently large grain size approaches the free energy of structure (1). Further molecular-dynamics simulations for the Ag-Cu system have allowed the calculation of the enthalpy at the equilibrium volume of several microstructures including some of those listed above. A comparison of the calculated values of the enthalpy with the heat release observed experimentally allows the advancement of an hypothesis concerning the reaction path and the structure of the equiatomic Ag-Cu alloy obtained by ball milling.
Knight, Christopher J.; Hub, Jochen S.
2015-01-01
Small- and wide-angle X-ray scattering (SWAXS) has evolved into a powerful tool to study biological macromolecules in solution. The interpretation of SWAXS curves requires their accurate predictions from structural models. Such predictions are complicated by scattering contributions from the hydration layer and by effects from thermal fluctuations. Here, we describe the new web server WAXSiS (WAXS in solvent) that computes SWAXS curves based on explicit-solvent all-atom molecular dynamics (MD) simulations (http://waxsis.uni-goettingen.de/). The MD simulations provide a realistic model for both the hydration layer and the excluded solvent, thereby avoiding any solvent-related fitting parameters, while naturally accounting for thermal fluctuations. PMID:25855813
Upper Subcritical Calculations Based on Correlated Data
Sobes, Vladimir; Rearden, Bradley T; Mueller, Don; Marshall, William BJ J; Scaglione, John M; Dunn, Michael E
2015-01-01
The American National Standards Institute and American Nuclear Society standard for Validation of Neutron Transport Methods for Nuclear Criticality Safety Calculations defines the upper subcritical limit (USL) as “a limit on the calculated k-effective value established to ensure that conditions calculated to be subcritical will actually be subcritical.” Often, USL calculations are based on statistical techniques that infer information about a nuclear system of interest from a set of known/well-characterized similar systems. The work in this paper is part of an active area of research to investigate the way traditional trending analysis is used in the nuclear industry, and in particular, the research is assessing the impact of the underlying assumption that the experimental data being analyzed for USL calculations are statistically independent. In contrast, the multiple experiments typically used for USL calculations can be correlated because they are often performed at the same facilities using the same materials and measurement techniques. This paper addresses this issue by providing a set of statistical inference methods to calculate the bias and bias uncertainty based on the underlying assumption that the experimental data are correlated. Methods to quantify these correlations are the subject of a companion paper and will not be discussed here. The newly proposed USL methodology is based on the assumption that the integral experiments selected for use in the establishment of the USL are sufficiently applicable and that experimental correlations are known. Under the assumption of uncorrelated data, the new methods collapse directly to familiar USL equations currently used. We will demonstrate our proposed methods on real data and compare them to calculations of currently used methods such as USLSTATS and NUREG/CR-6698. Lastly, we will also demonstrate the effect experiment correlations can have on USL calculations.
Exact-exchange-based quasiparticle calculations
Aulbur, Wilfried G.; Staedele, Martin; Goerling, Andreas
2000-09-15
One-particle wave functions and energies from Kohn-Sham calculations with the exact local Kohn-Sham exchange and the local density approximation (LDA) correlation potential [EXX(c)] are used as input for quasiparticle calculations in the GW approximation (GWA) for eight semiconductors. Quasiparticle corrections to EXX(c) band gaps are small when EXX(c) band gaps are close to experiment. In the case of diamond, quasiparticle calculations are essential to remedy a 0.7 eV underestimate of the experimental band gap within EXX(c). The accuracy of EXX(c)-based GWA calculations for the determination of band gaps is as good as the accuracy of LDA-based GWA calculations. For the lowest valence band width a qualitatively different behavior is observed for medium- and wide-gap materials. The valence band width of medium- (wide-) gap materials is reduced (increased) in EXX(c) compared to the LDA. Quasiparticle corrections lead to a further reduction (increase). As a consequence, EXX(c)-based quasiparticle calculations give valence band widths that are generally 1-2 eV smaller (larger) than experiment for medium- (wide-) gap materials. (c) 2000 The American Physical Society.
Advancements in dynamic kill calculations for blowout wells
Kouba, G.E. . Production Fluids Div.); MacDougall, G.R. ); Schumacher, B.W. . Information Technology Dept.)
1993-09-01
This paper addresses the development, interpretation, and use of dynamic kill equations. To this end, three simple calculation techniques are developed for determining the minimum dynamic kill rate. Two techniques contain only single-phase calculations and are independent of reservoir inflow performance. Despite these limitations, these two methods are useful for bracketing the minimum flow rates necessary to kill a blowing well. For the third technique, a simplified mechanistic multiphase-flow model is used to determine a most-probable minimum kill rate.
Numerical inductance calculations based on first principles.
Shatz, Lisa F; Christensen, Craig W
2014-01-01
A method of calculating inductances based on first principles is presented, which has the advantage over the more popular simulators in that fundamental formulas are explicitly used so that a deeper understanding of the inductance calculation is obtained with no need for explicit discretization of the inductor. It also has the advantage over the traditional method of formulas or table lookups in that it can be used for a wider range of configurations. It relies on the use of fast computers with a sophisticated mathematical computing language such as Mathematica to perform the required integration numerically so that the researcher can focus on the physics of the inductance calculation and not on the numerical integration. PMID:25402467
Algorithm for calculating torque base in vehicle traction control system
NASA Astrophysics Data System (ADS)
Li, Hongzhi; Li, Liang; Song, Jian; Wu, Kaihui; Qiao, Yanjuan; Liu, Xingchun; Xia, Yongguang
2012-11-01
Existing research on the traction control system(TCS) mainly focuses on control methods, such as the PID control, fuzzy logic control, etc, aiming at achieving an ideal slip rate of the drive wheel over long control periods. The initial output of the TCS (referred to as the torque base in this paper), which has a great impact on the driving performance of the vehicle in early cycles, remains to be investigated. In order to improve the control performance of the TCS in the first several cycles, an algorithm is proposed to determine the torque base. First, torque bases are calculated by two different methods, one based on states judgment and the other based on the vehicle dynamics. The confidence level of the torque base calculated based on the vehicle dynamics is also obtained. The final torque base is then determined based on the two torque bases and the confidence level. Hardware-in-the-loop(HIL) simulation and vehicle tests emulating sudden start on low friction roads have been conducted to verify the proposed algorithm. The control performance of a PID-controlled TCS with and without the proposed torque base algorithm is compared, showing that the proposed algorithm improves the performance of the TCS over the first several cycles and enhances about 5% vehicle speed by contrast. The proposed research provides a more proper initial value for TCS control, and improves the performance of the first several control cycles of the TCS.
Quantum Parallelism as a Tool for Ensemble Spin Dynamics Calculations
NASA Astrophysics Data System (ADS)
Álvarez, Gonzalo A.; Danieli, Ernesto P.; Levstein, Patricia R.; Pastawski, Horacio M.
2008-09-01
Efficient simulations of quantum evolutions of spin-1/2 systems are relevant for ensemble quantum computation as well as in typical NMR experiments. We propose an efficient method to calculate the dynamics of an observable provided that the initial excitation is “local.” It resorts to a single entangled pure initial state built as a superposition, with random phases, of the pure elements that compose the mixture. This ensures self-averaging of any observable, drastically reducing the calculation time. The procedure is tested for two representative systems: a spin star (cluster with random long range interactions) and a spin ladder.
Dissipative Particle Dynamics interaction parameters from ab initio calculations
NASA Astrophysics Data System (ADS)
Sepehr, Fatemeh; Paddison, Stephen J.
2016-02-01
Dissipative Particle Dynamics (DPD) is a commonly employed coarse-grained method to model complex systems. Presented here is a pragmatic approach to connect atomic-scale information to the meso-scale interactions defined between the DPD particles or beads. Specifically, electronic structure calculations were utilized for the calculation of the DPD pair-wise interaction parameters. An implicit treatment of the electrostatic interactions for charged beads is introduced. The method is successfully applied to derive the parameters for a hydrated perfluorosulfonic acid ionomer with absorbed vanadium cations.
GPU-based fast gamma index calculation.
Gu, Xuejun; Jia, Xun; Jiang, Steve B
2011-03-01
The γ-index dose comparison tool has been widely used to compare dose distributions in cancer radiotherapy. The accurate calculation of γ-index requires an exhaustive search of the closest Euclidean distance in the high-resolution dose-distance space. This is a computational intensive task when dealing with 3D dose distributions. In this work, we combine a geometric method (Ju et al 2008 Med. Phys. 35 879-87) with a radial pre-sorting technique (Wendling et al 2007 Med. Phys. 34 1647-54) and implement them on computer graphics processing units (GPUs). The developed GPU-based γ-index computational tool is evaluated on eight pairs of IMRT dose distributions. The γ-index calculations can be finished within a few seconds for all 3D testing cases on one single NVIDIA Tesla C1060 card, achieving 45-75× speedup compared to CPU computations conducted on an Intel Xeon 2.27 GHz processor. We further investigated the effect of various factors on both CPU and GPU computation time. The strategy of pre-sorting voxels based on their dose difference values speeds up the GPU calculation by about 2.7-5.5 times. For n-dimensional dose distributions, γ-index calculation time on CPU is proportional to the summation of γ(n) over all voxels, while that on GPU is affected by γ(n) distributions and is approximately proportional to the γ(n) summation over all voxels. We found that increasing the resolution of dose distributions leads to a quadratic increase of computation time on CPU, while less-than-quadratic increase on GPU. The values of dose difference and distance-to-agreement criteria also have an impact on γ-index calculation time. PMID:21317484
GPU-based fast gamma index calculation
NASA Astrophysics Data System (ADS)
Gu, Xuejun; Jia, Xun; Jiang, Steve B.
2011-03-01
The γ-index dose comparison tool has been widely used to compare dose distributions in cancer radiotherapy. The accurate calculation of γ-index requires an exhaustive search of the closest Euclidean distance in the high-resolution dose-distance space. This is a computational intensive task when dealing with 3D dose distributions. In this work, we combine a geometric method (Ju et al 2008 Med. Phys. 35 879-87) with a radial pre-sorting technique (Wendling et al 2007 Med. Phys. 34 1647-54) and implement them on computer graphics processing units (GPUs). The developed GPU-based γ-index computational tool is evaluated on eight pairs of IMRT dose distributions. The γ-index calculations can be finished within a few seconds for all 3D testing cases on one single NVIDIA Tesla C1060 card, achieving 45-75× speedup compared to CPU computations conducted on an Intel Xeon 2.27 GHz processor. We further investigated the effect of various factors on both CPU and GPU computation time. The strategy of pre-sorting voxels based on their dose difference values speeds up the GPU calculation by about 2.7-5.5 times. For n-dimensional dose distributions, γ-index calculation time on CPU is proportional to the summation of γn over all voxels, while that on GPU is affected by γn distributions and is approximately proportional to the γn summation over all voxels. We found that increasing the resolution of dose distributions leads to a quadratic increase of computation time on CPU, while less-than-quadratic increase on GPU. The values of dose difference and distance-to-agreement criteria also have an impact on γ-index calculation time.
Calculation of exact vibration modes for plane grillages by the dynamic stiffness method
NASA Technical Reports Server (NTRS)
Hallauer, W. L., Jr.; Liu, R. Y. L.
1982-01-01
A dynamic stiffness method is developed for the calculation of the exact modal parameters for plane grillages which consist of straight and uniform beams with coincident elastic and inertial axes. Elementary bending-torsion beam theory is utilized, and bending translation is restricted to one direction. The exact bending-torsion dynamic stiffness matrix is obtained for a straight and uniform beam element with coincident elastic and inertial axes. The element stiffness matrices are assembled using the standard procedure of the static stiffness method to form the dynamic stiffness matrix of the complete grillage. The exact natural frequencies, mode shapes, and generalized masses of the grillage are then calculated by solving a nonlinear eigenvalue problem based on the dynamic stiffness matrix. The exact modal solutions for an example grillage are calculated and compared with the approximate solutions obtained by using the finite element method.
Electronic Structure and Molecular Dynamics Calculations for KBH4
NASA Astrophysics Data System (ADS)
Papaconstantopoulos, Dimitrios; Shabaev, Andrew; Hoang, Khang; Mehl, Michael; Kioussis, Nicholas
2012-02-01
In the search for hydrogen storage materials, alkali borohydrides MBH4 (M=Li, Na, K) are especially interesting because of their light weight and the high number of hydrogen atoms per metal atom. Electronic structure calculations can give insights into the properties of these complex hydrides and provide understanding of the structural properties and of the bonding of hydrogen. We have performed first-principles density-functional theory (DFT) and tight-binding (TB) calculations for KBH4 in both the high temperature (HT) and low temperature (LT) phases to understand its electronic and structural properties. Our DFT calculations were carried out using the VASP code. The results were then used as a database to develop a tight-binding Hamiltonian using the NRL-TB method. This approach allowed for computationally efficient calculations of phonon frequencies and elastic constants using the static module of the NRL-TB, and also using the molecular dynamics module to calculate mean-square displacements and formation energies of hydrogen vacancies.
Free-energy calculation via mean-force dynamics using a logarithmic energy landscape.
Morishita, Tetsuya; Itoh, Satoru G; Okumura, Hisashi; Mikami, Masuhiro
2012-06-01
A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule. PMID:23005238
Lattice-dynamical calculations for tetracene and pentacene
NASA Astrophysics Data System (ADS)
Filippini, Giuseppe; Gramaccioli, Carlo Maria
1984-01-01
Lattice-dynamical, calculations for evidently non-rigid molecules of aromatic hydrocarbons have been carried out on tetracene and pentacene. In these substances, "out-of plane" vibrations mix extensively with lattice vibrations, and significant differences can be noted between results from a "rigid-body" and a "non-rigid" treatment. For tetracene crystals, whose Raman spectral data are given in the literature, the agreement with experiment is satisfactory. This confirms the validity of such procedures for interpreting and/or predicting spectroscopic behaviour, starting from empirical atom—atom potentials and valence force fields.
Nonlinear damping calculation in cylindrical gear dynamic modeling
NASA Astrophysics Data System (ADS)
Guilbault, Raynald; Lalonde, Sébastien; Thomas, Marc
2012-04-01
The nonlinear dynamic problem posed by cylindrical gear systems has been extensively covered in the literature. Nonetheless, a significant proportion of the mechanisms involved in damping generation remains to be investigated and described. The main objective of this study is to contribute to this task. Overall, damping is assumed to consist of three sources: surrounding element contribution, hysteresis of the teeth, and oil squeeze damping. The first two contributions are considered to be commensurate with the supported load; for its part however, squeeze damping is formulated using expressions developed from the Reynolds equation. A lubricated impact analysis between the teeth is introduced in this study for the minimum film thickness calculation during contact losses. The dynamic transmission error (DTE) obtained from the final model showed close agreement with experimental measurements available in the literature. The nonlinear damping ratio calculated at different mesh frequencies and torque amplitudes presented average values between 5.3 percent and 8 percent, which is comparable to the constant 8 percent ratio used in published numerical simulations of an equivalent gear pair. A close analysis of the oil squeeze damping evidenced the inverse relationship between this damping effect and the applied load.
Chen Shilu; Fang Weihai
2009-08-07
In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH{sub 3}CHO). Stationary structures for H{sub 2} and CO eliminations in the ground state (S{sub 0}) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH{sub 3}CHO (265 nm<{lambda}<318 nm), the T{sub 1} C-C bond fission following intersystem crossing from the S{sub 1} state is the predominant channel and the minor channel, the ground-state elimination to CH{sub 4}+CO after internal conversion (IC) from S{sub 1} to S{sub 0}, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S{sub 1}/S{sub 0} intersection point resulting from the S{sub 1} C-C bond fission, becomes accessible and increases the yield of CH{sub 4}+CO.
GPU-based calculations in digital holography
NASA Astrophysics Data System (ADS)
Madrigal, R.; Acebal, P.; Blaya, S.; Carretero, L.; Fimia, A.; Serrano, F.
2013-05-01
In this work we are going to apply GPU (Graphical Processing Units) with CUDA environment for scientific calculations, concretely high cost computations on the field of digital holography. For this, we have studied three typical problems in digital holography such as Fourier transforms, Fresnel reconstruction of the hologram and the calculation of vectorial diffraction integral. In all cases the runtime at different image size and the corresponding accuracy were compared to the obtained by traditional calculation systems. The programs have been carried out on a computer with a graphic card of last generation, Nvidia GTX 680, which is optimized for integer calculations. As a result a large reduction of runtime has been obtained which allows a significant improvement. Concretely, 15 fold shorter times for Fresnel approximation calculations and 600 times for the vectorial diffraction integral. These initial results, open the possibility for applying such kind of calculations in real time digital holography.
Dynamical coupled channel calculation of pion and omega meson production
Paris, Mark
2009-01-01
A dynamical coupled channel approach is used to study $\\pi$ and $\\omega$--meson production induced by pions and photons scattering from the proton. Six-channels are used to fit unpolarized and polarized scattering data including $\\pi N$, $\\eta N$, $\\pi\\Delta$, $\\sigma N$, $\\rho N$, $\\omega N$. Bare parameters in an effective hadronic Lagrangian are fixed in $\\chi^2$-fits to data from $\\pi N \\to \\pi N$, $\\gamma N \\to \\pi N$, $\\pi^- p \\to \\omega n$, and $\\gamma p \\to \\omega p$ reactions at center-of-mass energies from threshold to $E < 2.0$ GeV. The $T$ matrix determined in these fits is used to calculate the photon beam asymmetry for $\\omega$-meson production and the $\\omega N \\to \\omega N$ total cross section and scattering lengths.
Beam dynamics calculations and particle tracking using massively parallel processors
Ryne, R.D.; Habib, S.
1995-12-31
During the past decade massively parallel processors (MPPs) have slowly gained acceptance within the scientific community. At present these machines typically contain a few hundred to one thousand off-the-shelf microprocessors and a total memory of up to 32 GBytes. The potential performance of these machines is illustrated by the fact that a month long job on a high end workstation might require only a few hours on an MPP. The acceptance of MPPs has been slow for a variety of reasons. For example, some algorithms are not easily parallelizable. Also, in the past these machines were difficult to program. But in recent years the development of Fortran-like languages such as CM Fortran and High Performance Fortran have made MPPs much easier to use. In the following we will describe how MPPs can be used for beam dynamics calculations and long term particle tracking.
Ab Initio Calculations of Excited Carrier Dynamics in Gallium Nitride
NASA Astrophysics Data System (ADS)
Jhalani, Vatsal; Bernardi, Marco
Bulk wurtzite GaN is the primary material for blue light-emission technology. The radiative processes in GaN are regulated by the dynamics of excited (or so-called ``hot'') carriers, through microscopic processes not yet completely understood. We present ab initio calculations of electron-phonon (e-ph) scattering rates for hot carriers in GaN. Our work combines density functional theory to compute the electronic states, and density functional perturbation theory to obtain the phonon dispersions and e-ph coupling matrix elements. These quantities are interpolated on fine Brillouin zone grids with maximally localized Wannier functions, to converge the e-ph scattering rates within 5 eV of the band edges. We resolve the contribution of the different phonon modes to the total scattering rate, and study the impact on the relaxation times of the long-range Fröhlich interaction due to the longitudinal-optical phonon modes.
Flux-vector splitting for unsteady calculations on dynamic meshes
NASA Technical Reports Server (NTRS)
Anderson, W. Kyle; Thomas, James L.; Rumsey, Christopher L.
1989-01-01
The method of flux vector splitting used is that of Van Leer. The fluxes split in this manner have the advantage of being continuously differentiable at eigenvalue sign changes and this allows normal shocks to be captured with at most two interior zones, although in practice only one zone is usually observed. The fluxes as originally derived, however did not include the necessary terms appropriate for calculations on a dynamic mesh. The extension of the splitting to include these terms while retaining the advantages of the original splitting is the main purpose of this investigation. In addition, the use of multiple grids to reduce the computer time is investigated. A subiterative procedure to eliminate factorization and linearization error so that larger time steps can be used is also investigated.
Automating the parallel processing of fluid and structural dynamics calculations
NASA Technical Reports Server (NTRS)
Arpasi, Dale J.; Cole, Gary L.
1987-01-01
The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilties to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.
Automating the parallel processing of fluid and structural dynamics calculations
NASA Technical Reports Server (NTRS)
Arpasi, Dale J.; Cole, Gary L.
1987-01-01
The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilities to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.
Dynamical coupled channels calculation of pion and omega meson production
Paris, Mark W.
2009-02-15
The dynamical coupled-channels approach developed at the Excited Baryon Analysis Center is extended to include the {omega}N channel to study {pi}- and {omega}-meson production induced by scattering pions and photons from the proton. Six intermediate channels, including {pi}N, {eta}N, {pi}{delta}, {sigma}N, {rho}N, and {omega}N, are employed to describe unpolarized and polarized data. Bare parameters in an effective hadronic Lagrangian are determined in a fit to the data for {pi}N{yields}{pi}N, {gamma}N{yields}{pi}N, {pi}{sup -}p{yields}{omega}n, and {gamma}p{yields}{omega}p reactions at center-of-mass energies from threshold to W<2.0 GeV. The T matrix determined in these fits is used to calculate the photon beam asymmetry for {omega}-meson production and the {omega}N{yields}{omega}N total cross section and {omega}N-scattering lengths. The calculated beam asymmetry is in good agreement with the observed in the range of energies near threshold to W < or approx. 2.0 GeV.
Spreadsheet Based Scaling Calculations and Membrane Performance
Wolfe, T D; Bourcier, W L; Speth, T F
2000-12-28
Many membrane element manufacturers provide a computer program to aid buyers in the use of their elements. However, to date there are few examples of fully integrated public domain software available for calculating reverse osmosis and nanofiltration system performance. The Total Flux and Scaling Program (TFSP), written for Excel 97 and above, provides designers and operators new tools to predict membrane system performance, including scaling and fouling parameters, for a wide variety of membrane system configurations and feedwaters. The TFSP development was funded under EPA contract 9C-R193-NTSX. It is freely downloadable at www.reverseosmosis.com/download/TFSP.zip. TFSP includes detailed calculations of reverse osmosis and nanofiltration system performance. Of special significance, the program provides scaling calculations for mineral species not normally addressed in commercial programs, including aluminum, iron, and phosphate species. In addition, ASTM calculations for common species such as calcium sulfate (CaSO{sub 4}{times}2H{sub 2}O), BaSO{sub 4}, SrSO{sub 4}, SiO{sub 2}, and LSI are also provided. Scaling calculations in commercial membrane design programs are normally limited to the common minerals and typically follow basic ASTM methods, which are for the most part graphical approaches adapted to curves. In TFSP, the scaling calculations for the less common minerals use subsets of the USGS PHREEQE and WATEQ4F databases and use the same general calculational approach as PHREEQE and WATEQ4F. The activities of ion complexes are calculated iteratively. Complexes that are unlikely to form in significant concentration were eliminated to simplify the calculations. The calculation provides the distribution of ions and ion complexes that is used to calculate an effective ion product ''Q.'' The effective ion product is then compared to temperature adjusted solubility products (Ksp's) of solids in order to calculate a Saturation Index (SI) for each solid of
Dračínský, Martin; Bouř, Petr; Hodgkinson, Paul
2016-03-01
The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory (DFT) calculations of shielding and electric field gradient (EFG) tensors. An approach based on convoluting calculated shielding or EFG tensor components with probability distributions of selected bond distances and valence angles obtained from DFT-PIMD simulations at several temperatures is used to calculate the temperature effects. The probability distributions obtained from the quantum PIMD simulations, which includes nuclear quantum effects, are significantly broader and less temperature dependent than those obtained with conventional DFT molecular dynamics or with 1D scans through the potential energy surface. Predicted NMR observables for the model systems were in excellent agreement with experimental data. PMID:26857802
NASA Astrophysics Data System (ADS)
Tackley, P. J.; Nakagawa, T.; Deschamps, F.; Connolly, J.
2011-12-01
Phase diagrams of materials in Earth's transition zone (TZ) are complex and composition-dependent and phase transitions have a first-order influence on mantle dynamics, yet simulations of mantle convection typically include only one or two major phase transitions in the olivine system. In our recent work [1,2], phase assemblages of mantle rocks calculated by free energy minimization for MORB and harzburgite compositions expressed as the ratios of 5 or 6 oxides (CaO-FeO-MgO-Al2O3- SiO2-Na2O) are used to calculate the material properties density, thermal expansivity, specific heat capacity, and seismic velocity as a function of temperature and pressure, which are then incorporated into a numerical thermo-chemical mantle convection model in a 2-D spherical annulus or 3-D spherical shell. The advantage of using such an approach is that thermodynamic parameters affecting dynamics and seismic velocities are included implicitly and self-consistently, obviating the need for ad hoc parameterizations. Here we focus on the resulting thermo-chemical structures in the transition zone and their seismic signature. A robust result is some compositional stratification around 660 km depth caused by the inversion of the MORB-harzburgite density difference between ~660-740 km depth [3], with MORB enrichment in the lower TZ and depletion just below the TZ. The extent of this is quite sensitive to variations in MORB composition of the order 1-2% oxide fraction, particularly FeO and Al2O3, which influence the magnitude and depth of this effect and the density difference. The detailed structure also has a strong lateral variation. We plot radial profiles from different parts of our models, characterizing typical structures and the range of structures, and compare to local seismological profiles as well as profiles from regional inversions [4]. [1] Nakagawa, T., P.J. Tackley, F. Deschamps & J.A.D. Connolly (2009) Geochem. Geophys. Geosyst. 10, doi:10.1029/2008GC002280. [2] Nakagawa, T., P
Parellel beam dynamics calculations on high performance computers
Ryne, R.; Habib, S.
1996-12-01
Faced with a backlog of nuclear waste and weapons plutonium, as well as an ever-increasing public concern about safety and environmental issues associated with conventional nuclear reactors, many countries are studying new, accelerator-driven technologies that hold the promise of providing safe and effective solutions to these problems. Proposed projects include accelerator transmutation of waste (ATW), accelerator-based conversion of plutonium (ABC), accelerator-driven energy production (ADEP), and accelerator production of tritium (APT). Also, next-generation spallation neutron sources based on similar technology will play a major role in materials science and biological science research. The design of accelerators for these projects will require a major advance in numerical modeling capability. For example, beam dynamics simulations with approximately 100 million particles will be needed to ensure that extremely stringent beam loss requirements (less than a nanoampere per meter) can be met. Compared with typical present-day modeling using 10,000-100,000 particles, this represents an increase of 3-4 orders of magnitude. High performance computing (HPC) platforms make it possible to perform such large scale simulations, which require 10`s of GBytes of memory. They also make it possible to perform smaller simulations in a matter of hours that would require months to run on a single processor workstation. This paper will describe how HPC platforms can be used to perform the numerically intensive beam dynamics simulations required for development of these new accelerator-driven technologies.
Parallel beam dynamics calculations on high performance computers
NASA Astrophysics Data System (ADS)
Ryne, Robert; Habib, Salman
1997-02-01
Faced with a backlog of nuclear waste and weapons plutonium, as well as an ever-increasing public concern about safety and environmental issues associated with conventional nuclear reactors, many countries are studying new, accelerator-driven technologies that hold the promise of providing safe and effective solutions to these problems. Proposed projects include accelerator transmutation of waste (ATW), accelerator-based conversion of plutonium (ABC), accelerator-driven energy production (ADEP), and accelerator production of tritium (APT). Also, next-generation spallation neutron sources based on similar technology will play a major role in materials science and biological science research. The design of accelerators for these projects will require a major advance in numerical modeling capability. For example, beam dynamics simulations with approximately 100 million particles will be needed to ensure that extremely stringent beam loss requirements (less than a nanoampere per meter) can be met. Compared with typical present-day modeling using 10,000-100,000 particles, this represents an increase of 3-4 orders of magnitude. High performance computing (HPC) platforms make it possible to perform such large scale simulations, which require 10's of GBytes of memory. They also make it possible to perform smaller simulations in a matter of hours that would require months to run on a single processor workstation. This paper will describe how HPC platforms can be used to perform the numerically intensive beam dynamics simulations required for development of these new accelerator-driven technologies.
Roaming dynamics in the MgH + H→Mg + H 2 reaction: Quantum dynamics calculations
NASA Astrophysics Data System (ADS)
Takayanagi, Toshiyuki; Tanaka, Tomokazu
2011-03-01
Reaction mechanisms of the MgH + H→Mg + H 2 reaction have been investigated using quantum reactive scattering methods on a global ab initio potential energy surface. There exist two microscopic mechanisms in the dynamics of this reaction. One is a direct hydrogen abstraction reaction and the other proceeds via initial formation of a HMgH complex in the deep potential well. The result of the present quantum dynamics calculations suggests that the HMgH complex formed in the reaction mainly decays into the Mg + H 2 channel via a 'roaming mechanism' without going through the saddle point region.
SPREADSHEET BASED SCALING CALCULATIONS AND MEMBRANE PERFORMANCE
Many membrane element manufacturers provide a computer program to aid buyers in the use of their elements. However, to date there are few examples of fully integrated public domain software available for calculating reverse osmosis and nanofiltration system performance. The Total...
User's Manual for Computer Program ROTOR. [to calculate tilt-rotor aircraft dynamic characteristics
NASA Technical Reports Server (NTRS)
Yasue, M.
1974-01-01
A detailed description of a computer program to calculate tilt-rotor aircraft dynamic characteristics is presented. This program consists of two parts: (1) the natural frequencies and corresponding mode shapes of the rotor blade and wing are developed from structural data (mass distribution and stiffness distribution); and (2) the frequency response (to gust and blade pitch control inputs) and eigenvalues of the tilt-rotor dynamic system, based on the natural frequencies and mode shapes, are derived. Sample problems are included to assist the user.
Dynamic social power modulates neural basis of math calculation
Harada, Tokiko; Bridge, Donna J.; Chiao, Joan Y.
2013-01-01
Both situational (e.g., perceived power) and sustained social factors (e.g., cultural stereotypes) are known to affect how people academically perform, particularly in the domain of mathematics. The ability to compute even simple mathematics, such as addition, relies on distinct neural circuitry within the inferior parietal and inferior frontal lobes, brain regions where magnitude representation and addition are performed. Despite prior behavioral evidence of social influence on academic performance, little is known about whether or not temporarily heightening a person's sense of power may influence the neural bases of math calculation. Here we primed female participants with either high or low power (LP) and then measured neural response while they performed exact and approximate math problems. We found that priming power affected math performance; specifically, females primed with high power (HP) performed better on approximate math calculation compared to females primed with LP. Furthermore, neural response within the left inferior frontal gyrus (IFG), a region previously associated with cognitive interference, was reduced for females in the HP compared to LP group. Taken together, these results indicate that even temporarily heightening a person's sense of social power can increase their math performance, possibly by reducing cognitive interference during math performance. PMID:23390415
Preliminary result of transport properties calculation molten Ag-based superionics
NASA Astrophysics Data System (ADS)
Oztek, H. O.; Yılmaz, M.; Kavanoz, H. B.
2016-03-01
We studied molten Ag based superionics (AgI, Ag2S and Ag3S I) which are well defined with Vashista-Rahman potential. Molecular Dynamic simulation code is Moldy which is used for canonical ensemble (NPT). Thermal properties are obtained from Green-Kubo formalism with equilibrium molecular dynamics (EMD) simulation. These calculation results are compared with the experimentals results.
Free energy calculations using dual-level Born-Oppenheimer molecular dynamics
NASA Astrophysics Data System (ADS)
Retegan, Marius; Martins-Costa, Marilia; Ruiz-López, Manuel F.
2010-08-01
We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.
Error propagation in PIV-based Poisson pressure calculations
NASA Astrophysics Data System (ADS)
Pan, Zhao; Whitehead, Jared; Thomson, Scott; Truscott, Tadd
2015-11-01
After more than 20 years of development, PIV has become a standard non-invasive velocity field measurement technique, and promises to make PIV-based pressure calculations possible. However, the errors inherent in PIV velocity fields propagate through integration and contaminate the calculated pressure field. We propose an analysis that shows how the uncertainties in the velocity field propagate to the pressure field through the Poisson equation. First we model the dynamics of error propagation using boundary value problems (BVPs). Next, L2-norm and/or L∞-norm are utilized as the measure of error in the velocity and pressure field. Finally, using analysis techniques including the maximum principle, the Poincare inequality pressure field can be bounded by the error level of the data by considering the well-posedness of the BVPs. Specifically, we exam if and how the error in the pressure field depend continually on the BVP data. Factors such as flow field geometry, boundary conditions, and velocity field noise levels will be discussed analytically.
Li Bin; Han Keli
2008-03-21
A theoretical investigation on the nonadiabatic processes of the full three-dimensional D{sup +}+H{sub 2} and H{sup +}+D{sub 2} reaction systems has been performed by using trajectory surface hopping (TSH) method based on the Zhu-Nakamura (ZN) theory. This ZN-TSH method refers to not only classically allowed hops but also classically forbidden hops. The potential energy surface constructed by Kamisaka et al. is employed in the calculation. A new iterative method is proposed to yield the two-dimensional seam surface from the topography of the adiabatic potential surfaces, in which the inconvenience of directly solving the first-order partial differential equation is avoided. The cross sections of these two systems are calculated for three competing channels of the reactive charge transfer, the nonreactive charge transfer, and the reactive noncharge transfer, for ground rovibrational state of H{sub 2} or D{sub 2}. Also, this study provides reaction probabilities of these three processes for the total angular momentum J=0 and ground initial vibrational state of H{sub 2} or D{sub 2}. The calculated results from ZN-TSH method are in good agreement with the exact quantum calculations and the experimental measurements.
Calculation of the lateral-dynamic stability of aircraft
NASA Technical Reports Server (NTRS)
Raikh, A
1952-01-01
Graphs and formulas are given with the aid of which all the aerodynamic coefficients required for computing the lateral dynamic stability can be determined. A number of numerical examples are given for obtaining the stability derivatives and solving the characteristic-stability equation. Approximate formulas are derived with the aid of which rapid preliminary computations may be made and the stability coefficients corrected for certain modifications of the airplane. A derivation of the lateral-dynamic-stability equations is included.
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. PMID:26196228
Kuo, Nathanael; Dehghan, Ehsan; Deguet, Anton; Mian, Omar Y.; Le, Yi; Burdette, E. Clif; Fichtinger, Gabor; Prince, Jerry L.; Song, Danny Y.; Lee, Junghoon
2014-01-01
Purpose: Brachytherapy is a standard option of care for prostate cancer patients but may be improved by dynamic dose calculation based on localized seed positions. The American Brachytherapy Society states that the major current limitation of intraoperative treatment planning is the inability to localize the seeds in relation to the prostate. An image-guidance system was therefore developed to localize seeds for dynamic dose calculation. Methods: The proposed system is based on transrectal ultrasound (TRUS) and mobile C-arm fluoroscopy, while using a simple fiducial with seed-like markers to compute pose from the nonencoded C-arm. Three or more fluoroscopic images and an ultrasound volume are acquired and processed by a pipeline of algorithms: (1) seed segmentation, (2) fiducial detection with pose estimation, (3) seed matching with reconstruction, and (4) fluoroscopy-to-TRUS registration. Results: The system was evaluated on ten phantom cases, resulting in an overall mean error of 1.3 mm. The system was also tested on 37 patients and each algorithm was evaluated. Seed segmentation resulted in a 1% false negative rate and 2% false positive rate. Fiducial detection with pose estimation resulted in a 98% detection rate. Seed matching with reconstruction had a mean error of 0.4 mm. Fluoroscopy-to-TRUS registration had a mean error of 1.3 mm. Moreover, a comparison of dose calculations between the authors’ intraoperative method and an independent postoperative method shows a small difference of 7% and 2% forD90 and V100, respectively. Finally, the system demonstrated the ability to detect cold spots and required a total processing time of approximately 1 min. Conclusions: The proposed image-guidance system is the first practical approach to dynamic dose calculation, outperforming earlier solutions in terms of robustness, ease of use, and functional completeness. PMID:25186387
Kuo, Nathanael Prince, Jerry L.; Dehghan, Ehsan; Deguet, Anton; Mian, Omar Y.; Le, Yi; Song, Danny Y.; Burdette, E. Clif; Fichtinger, Gabor; Lee, Junghoon
2014-09-15
Purpose: Brachytherapy is a standard option of care for prostate cancer patients but may be improved by dynamic dose calculation based on localized seed positions. The American Brachytherapy Society states that the major current limitation of intraoperative treatment planning is the inability to localize the seeds in relation to the prostate. An image-guidance system was therefore developed to localize seeds for dynamic dose calculation. Methods: The proposed system is based on transrectal ultrasound (TRUS) and mobile C-arm fluoroscopy, while using a simple fiducial with seed-like markers to compute pose from the nonencoded C-arm. Three or more fluoroscopic images and an ultrasound volume are acquired and processed by a pipeline of algorithms: (1) seed segmentation, (2) fiducial detection with pose estimation, (3) seed matching with reconstruction, and (4) fluoroscopy-to-TRUS registration. Results: The system was evaluated on ten phantom cases, resulting in an overall mean error of 1.3 mm. The system was also tested on 37 patients and each algorithm was evaluated. Seed segmentation resulted in a 1% false negative rate and 2% false positive rate. Fiducial detection with pose estimation resulted in a 98% detection rate. Seed matching with reconstruction had a mean error of 0.4 mm. Fluoroscopy-to-TRUS registration had a mean error of 1.3 mm. Moreover, a comparison of dose calculations between the authors’ intraoperative method and an independent postoperative method shows a small difference of 7% and 2% forD{sub 90} and V{sub 100}, respectively. Finally, the system demonstrated the ability to detect cold spots and required a total processing time of approximately 1 min. Conclusions: The proposed image-guidance system is the first practical approach to dynamic dose calculation, outperforming earlier solutions in terms of robustness, ease of use, and functional completeness.
Calculational investigation of impact cratering dynamics - Early time material motions
NASA Technical Reports Server (NTRS)
Thomsen, J. M.; Austin, M. G.; Ruhl, S. F.; Schultz, P. H.; Orphal, D. L.
1979-01-01
Early time two-dimensional finite difference calculations of laboratory-scale hypervelocity (6 km/sec) impact of 0.3 g spherical 2024 aluminum projectiles into homogeneous plasticene clay targets were performed and the resulting material motions analyzed. Results show that the initial jetting of vaporized target material is qualitatively similar to experimental observation. The velocity flow field developed within the target is shown to have features quite similar to those found in calculations of near-surface explosion cratering. Specific application of Maxwell's analytic Z-Model (developed to interpret the flow fields of near-surface explosion cratering calculations), shows that this model can be used to describe the flow fields resulting from the impact cratering calculations, provided that the flow field center is located beneath the target surface, and that application of the model is made late enough in time that most of the projectile momentum has been dissipated.
Calculation of structural dynamic forces and stresses using mode acceleration
NASA Technical Reports Server (NTRS)
Blelloch, Paul
1989-01-01
While the standard mode acceleration formulation in structural dynamics has often been interpreted to suggest that the reason for improved convergence obtainable is that the dynamic correction factor is divided by the modal frequencies-squared, an alternative formulation is presented which clearly indicates that the only difference between mode acceleration and mode displacement data recovery is the addition of a static correction term. Attention is given to the advantages in numerical implementation associated with this alternative, as well as to an illustrative example.
NASA Astrophysics Data System (ADS)
Shuvaev, Andrey; Pechurkin, Nickolay
Calculations of the dynamics of biological capacity (BC) and the ecological footprint (EF) is necessary to quantify the predictions and options to both natural and artificial ecosystems at different levels of the hierarchy. The magnitude of the BC as characteristic of the potential possibilities of the system is determined according to the integrated monitoring of physiological state, or photosynthetic activity, "green area" of the ecosystem. The quantity of the EF is defined as the amount required in the functioning of the system, including the production of the required products and degradation disposal unit. In our study we consider an example of the algorithm for calculating the dynamics of BC and EF for the quantification of the Krasnoyarsk Territory loaded as the natural ecosystem. The main burden was determined by EF, non-utilized emissions of carbon dioxide in the operation of energy businesses in the region. To verify the relevant calculations for BC processed data to ground and space monitor vegetation core areas of the province. In particular, the net primary production is calculated on the basis of the relative normalized vegetation index - NDVI (Normalized Difference Vegetation Index) based on satellite data A comparative evaluation of the contribution of each of the ways to generate energy (thermal and hydro ) in environmental load was made. A comparison of natural ecosystems and loaded specially created life-support systems in space and on the dynamics of BC/EF gives perspective to quantify the predictions and options for development of systems of different levels of the hierarchy. This work was supported by the Russian Foundation for Basic Research, project number 13-06-00060.
New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations.
Fleming, Kelly L; Tiwary, Pratyush; Pfaendtner, Jim
2016-01-21
Herein, we demonstrate a convenient approach to systematically investigate chemical reaction dynamics using the metadynamics (MetaD) family of enhanced sampling methods. Using a symmetric SN2 reaction as a model system, we applied infrequent metadynamics, a theoretical framework based on acceleration factors, to quantitatively estimate the rate of reaction from biased and unbiased simulations. A systematic study of the algorithm and its application to chemical reactions was performed by sampling over 5000 independent reaction events. Additionally, we quantitatively reweighed exhaustive free-energy calculations to obtain the reaction potential-energy surface and showed that infrequent metadynamics works to effectively determine Arrhenius-like activation energies. Exact agreement with unbiased high-temperature kinetics is also shown. The feasibility of using the approach on actual ab initio molecular dynamics calculations is then presented by using Car-Parrinello MD+MetaD to sample the same reaction using only 10-20 calculations of the rare event. Owing to the ease of use and comparatively low-cost of computation, the approach has extensive potential applications for catalysis, combustion, pyrolysis, and enzymology. PMID:26690335
Cryptosystems based on chaotic dynamics
McNees, R.A.; Protopopescu, V.; Santoro, R.T.; Tolliver, J.S.
1993-08-01
An encryption scheme based on chaotic dynamics is presented. This scheme makes use of the efficient and reproducible generation of cryptographically secure pseudo random numbers from chaotic maps. The result is a system which encrypts quickly and possesses a large keyspace, even in small precision implementations. This system offers an excellent solution to several problems including the dissemination of key material, over the air rekeying, and other situations requiring the secure management of information.
Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machines
Jia, Weile; University of Chinese Academy of Sciences, Beijing ; Fu, Jiyun; University of Chinese Academy of Sciences, Beijing ; Cao, Zongyan; Wang, Long; Chi, Xuebin; Gao, Weiguo; MOE Key Laboratory of Computational Physical Sciences, Fudan University, Shanghai ; Wang, Lin-Wang
2013-10-15
Plane wave pseudopotential (PWP) density functional theory (DFT) calculation is the most widely used method for material simulations, but its absolute speed stagnated due to the inability to use large scale CPU based computers. By a drastic redesign of the algorithm, and moving all the major computation parts into GPU, we have reached a speed of 12 s per molecular dynamics (MD) step for a 512 atom system using 256 GPU cards. This is about 20 times faster than the CPU version of the code regardless of the number of CPU cores used. Our tests and analysis on different GPU platforms and configurations shed lights on the optimal GPU deployments for PWP-DFT calculations. An 1800 step MD simulation is used to study the liquid phase properties of GaInP.
Wang, Jiyao; Deng, Yuqing; Roux, Benoît
2006-01-01
The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining
Molecular-dynamics calculations of energetic displacement cascades
Guinan, M.W.; Kinney, J.H.
1981-08-07
The results of fully dynamic computer simulations of collision cascades show an abrupt decrease in defect production efficiency beginning at energies about 10 times the minimum threshold energy in agreement with experimental results on resistivity damage rates at 4.2 K. A detailed analysis of the time development of a typical cascade reveals that this drop in efficiency is primarily due to recombination by defect transport during the cascade cooling phase. This transport is an order of magnitude larger than that predicted from equilibrium transport theory.
Belyaev, Andrey K; Domcke, Wolfgang; Lasser, Caroline; Trigila, Giulio
2015-03-14
The Landau-Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected for the nuclear dynamics: Ultrafast Jahn-Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent. PMID:25770540
NASA Astrophysics Data System (ADS)
Belyaev, Andrey K.; Domcke, Wolfgang; Lasser, Caroline; Trigila, Giulio
2015-03-01
The Landau-Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected for the nuclear dynamics: Ultrafast Jahn-Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.
Belyaev, Andrey K.; Domcke, Wolfgang; Lasser, Caroline Trigila, Giulio
2015-03-14
The Landau–Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected for the nuclear dynamics: Ultrafast Jahn–Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.
Proton dose calculation based on in-air fluence measurements.
Schaffner, Barbara
2008-03-21
Proton dose calculation algorithms--as well as photon and electron algorithms--are usually based on configuration measurements taken in a water phantom. The exceptions to this are proton dose calculation algorithms for modulated scanning beams. There, it is usual to measure the spot profiles in air. We use the concept of in-air configuration measurements also for scattering and uniform scanning (wobbling) proton delivery techniques. The dose calculation includes a separate step for the calculation of the in-air fluence distribution per energy layer. The in-air fluence calculation is specific to the technique and-to a lesser extent-design of the treatment machine. The actual dose calculation uses the in-air fluence as input and is generic for all proton machine designs and techniques. PMID:18367787
Proton dose calculation based on in-air fluence measurements
NASA Astrophysics Data System (ADS)
Schaffner, Barbara
2008-03-01
Proton dose calculation algorithms—as well as photon and electron algorithms—are usually based on configuration measurements taken in a water phantom. The exceptions to this are proton dose calculation algorithms for modulated scanning beams. There, it is usual to measure the spot profiles in air. We use the concept of in-air configuration measurements also for scattering and uniform scanning (wobbling) proton delivery techniques. The dose calculation includes a separate step for the calculation of the in-air fluence distribution per energy layer. The in-air fluence calculation is specific to the technique and—to a lesser extent—design of the treatment machine. The actual dose calculation uses the in-air fluence as input and is generic for all proton machine designs and techniques.
Some dynamic A-n, S-2n analytic calculations
Coppa, G.; Ravetto, P.; Sumini, M.
1987-11-01
A-n, S-2n dynamic equations in neutron transport theory are given an analytic solution, suitable for numerical safety code validation. Some numerical results are presented for plane geometry with periodic boundary conditions, within the monokinetic isotropic scattering case. They turn out to be very interesting and physically well interpretable and seem to give a deep insight into the transport effects connected with the finite velocity space migration of localized neutron signals. Balance equations are solved by means of a space Helmholtz series expansion connected to a time-variable Laplace transformation technique. The equations that are to be solved for the considered slab geometry, although perfectly equivalent to S-2n equations, are actually the ones corresponding to the typical second-order A-n model. The given fully analytic solution can be used to yield standard reference results for peculiar space transients, against which any numerical safety code exploiting the same discrete ordinate model can be validated.
Computational methods. [Calculation of dynamic loading to offshore platforms
Maeda, H. . Inst. of Industrial Science)
1993-02-01
With regard to the computational methods for hydrodynamic forces, first identification of marine hydrodynamics in offshore technology is discussed. Then general computational methods, the state of the arts and uncertainty on flow problems in offshore technology in which developed, developing and undeveloped problems are categorized and future works follow. Marine hydrodynamics consists of water surface and underwater fluid dynamics. Marine hydrodynamics covers, not only hydro, but also aerodynamics such as wind load or current-wave-wind interaction, hydrodynamics such as cavitation, underwater noise, multi-phase flow such as two-phase flow in pipes or air bubble in water or surface and internal waves, and magneto-hydrodynamics such as propulsion due to super conductivity. Among them, two key words are focused on as the identification of marine hydrodynamics in offshore technology; they are free surface and vortex shedding.
A basic insight to FEM_based temperature distribution calculation
NASA Astrophysics Data System (ADS)
Purwaningsih, A.; Khairina
2012-06-01
A manual for finite element method (FEM)-based temperature distribution calculation has been performed. The code manual is written in visual basic that is operated in windows. The calculation of temperature distribution based on FEM has three steps namely preprocessor, processor and post processor. Therefore, three manuals are produced namely a preprocessor to prepare the data, a processor to solve the problem, and a post processor to display the result. In these manuals, every step of a general procedure is described in detail. It is expected, by these manuals, the understanding of calculating temperature distribution be better and easier.
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
NASA Technical Reports Server (NTRS)
Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew
2000-01-01
One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous
Ab initio molecular dynamics calculations of ion hydration free energies
Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.
Transmission Loss Calculation using A and B Loss Coefficients in Dynamic Economic Dispatch Problem
NASA Astrophysics Data System (ADS)
Jethmalani, C. H. Ram; Dumpa, Poornima; Simon, Sishaj P.; Sundareswaran, K.
2016-04-01
This paper analyzes the performance of A-loss coefficients while evaluating transmission losses in a Dynamic Economic Dispatch (DED) Problem. The performance analysis is carried out by comparing the losses computed using nominal A loss coefficients and nominal B loss coefficients in reference with load flow solution obtained by standard Newton-Raphson (NR) method. Density based clustering method based on connected regions with sufficiently high density (DBSCAN) is employed in identifying the best regions of A and B loss coefficients. Based on the results obtained through cluster analysis, a novel approach in improving the accuracy of network loss calculation is proposed. Here, based on the change in per unit load values between the load intervals, loss coefficients are updated for calculating the transmission losses. The proposed algorithm is tested and validated on IEEE 6 bus system, IEEE 14 bus, system IEEE 30 bus system and IEEE 118 bus system. All simulations are carried out using SCILAB 5.4 (
Nonlinear dynamics based digital logic and circuits
Kia, Behnam; Lindner, John. F.; Ditto, William L.
2015-01-01
We discuss the role and importance of dynamics in the brain and biological neural networks and argue that dynamics is one of the main missing elements in conventional Boolean logic and circuits. We summarize a simple dynamics based computing method, and categorize different techniques that we have introduced to realize logic, functionality, and programmability. We discuss the role and importance of coupled dynamics in networks of biological excitable cells, and then review our simple coupled dynamics based method for computing. In this paper, for the first time, we show how dynamics can be used and programmed to implement computation in any given base, including but not limited to base two. PMID:26029096
Nonlinear dynamics based digital logic and circuits.
Kia, Behnam; Lindner, John F; Ditto, William L
2015-01-01
We discuss the role and importance of dynamics in the brain and biological neural networks and argue that dynamics is one of the main missing elements in conventional Boolean logic and circuits. We summarize a simple dynamics based computing method, and categorize different techniques that we have introduced to realize logic, functionality, and programmability. We discuss the role and importance of coupled dynamics in networks of biological excitable cells, and then review our simple coupled dynamics based method for computing. In this paper, for the first time, we show how dynamics can be used and programmed to implement computation in any given base, including but not limited to base two. PMID:26029096
Numerical calculations of coastal flow with turbulent dynamics
NASA Astrophysics Data System (ADS)
Kundu, Pijush K.
1984-01-01
A two-dimensional numerical model of coastal flow, in which the eddy fluxes are computed by a second-order turbulence model, has been developed. The behaviour of the inertial oscillations due to an impulsive start is in excellent agreement with the analytical solution of KUNDUet al. ( Deep-Sea Research, 30, 1059-1082, 1983). Much of the inertial energy gain in the deep ocean is due to the downward leakage from the coast-surface corner and is accompanied by an upward phase propagation. The low-frequency upwelling solutions develop gravitationally unstable regions in the surface layer, even in the presence of realistic surface heating. But the thickness of the surface layer without surface cooling is never very large, so the analytical models driven by a sink at the coast-surface corner give realistic subsurface solutions. The upwelling solutions generate flow reversal across a strong thermocline, but no 'closed' double cells. Frictional turning, as suggested by several workers, is responsible for the flow reversal. These open double cell persist in the presence of surface heating but not in the presence of an alongshore pressure gradient, p γ = τ γ/( maximum depth) . The imposition of pγ creates a poleward undercurrent on a flat shelf but not on a sloping shelf. The alongshore jet moves offshore due to the nonlinear advection of the thermocline, so that the width of the jet is larger than the Rossby radius. An approximate expression has been derived for predicting the offshore frontal location; the numerical calculation is in fair agreement with it.
Calculated dynamical evolution of the nucleus of comet Hartley 2
NASA Astrophysics Data System (ADS)
Ksanfomality, Leonid
2013-04-01
The nucleus of comet Hartley 2 has a relatively regular dumbbell shape with unequal heads. The narrow part of elongated shape contains a relatively smooth region whose covering material is highly different in its shallow structure compared to other parts of this celestial body. The surface of crudely spherical parts of the nucleus is different from the surface of the "neck", which implies a hypothesis that the shape of the nucleus of Hartley 2 is indicative of destruction of this celestial body occurring in our days. The nucleus rotates around its axis passing through the center of mass, and centrifugal forces arise. This process is hindered by gravitation between parts of the nucleus and gradual slowing of rotation due to body lengthening because of the increase in the moment of inertia (proportional to R2) and due to friction losses in the neck material. We posed the task to determine centrifugal and gravitational forces in the neck (and, respectively, the strains of stretching and compression), the moment of inertia of the body and supply of its rotational energy E, the volume of the nucleus and its average density, and the position of the barycenter and center of rotation. It can be assumed that these forces cause slow but progressive lengthening of the neck which should eventually result in fragmentation of the nucleus. Centrifugal forces can be found as a result of summation of forces produced by parts of the body. According to the calculation model, the total stretching forces in the section passing through the narrowest cut of the neck are 1.21E6 N. The corresponding compression forces in the section passing through the narrow section are 1.04E6 N. The comparison of these values indicates a paradoxical result: stretching strains dominate in the neck, while compressions are dominant in the section passing through the common center of mass. The excess of stretching strains in the neck is 11%. The inference is as follows: the right part of the neck and the
Fluorescent color factor calculation using dBASE-II.
King, R L; Carter, H A; Birckbichler, P J
1986-06-01
A software system utilizing dBASE-II operating on a dual-drive Apple II+ computer is described. Color factors and retention times for 15 amino acids and epsilon-(gamma-glutamyl)lysine dipeptide are calculated following high performance liquid chromatography. The software package produces a listing of acceptable limits for these parameters calculated as plus and minus 2 standard deviations of the mean. The code is distributed in source form. PMID:3450360
Code System to Calculate Transient 2-Dimensional 2-Fluid Flow Dynamics.
Energy Science and Technology Software Center (ESTSC)
1999-07-19
Version 00 The transient dynamics of two-dimensional, two-phase flow with interfacial exchange are calculated at all flow speeds. Each phase is described in terms of its own density, velocity, and temperature. Separate sets of field equations govern the gas and liquid phase dynamics. The six field equations for the two phases couple through mass, momentum, and energy exchange.
Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance
NASA Astrophysics Data System (ADS)
Wilson, Michael A.; Nguyen, Thuy Hien; Pohorille, Andrew
2014-12-01
Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation.
Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance.
Wilson, Michael A; Nguyen, Thuy Hien; Pohorille, Andrew
2014-12-14
Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation. PMID:25494790
Optimal caching algorithm based on dynamic programming
NASA Astrophysics Data System (ADS)
Guo, Changjie; Xiang, Zhe; Zhong, Yuzhuo; Long, Jidong
2001-07-01
With the dramatic growth of multimedia streams, the efficient distribution of stored videos has become a major concern. There are two basic caching strategies: the whole caching strategy and the caching strategy based on layered encoded video, the latter can satisfy the requirement of the highly heterogeneous access to the Internet. Conventional caching strategies assign each object a cache gain by calculating popularity or density popularity, and determine which videos and which layers should be cached. In this paper, we first investigate the delivery model of stored video based on proxy, and propose two novel caching algorithms, DPLayer (for layered encoded caching scheme) and DPWhole (for whole caching scheme) for multimedia proxy caching. The two algorithms are based on the resource allocation model of dynamic programming to select the optimal subset of objects to be cached in proxy. Simulation proved that our algorithms achieve better performance than other existing schemes. We also analyze the computational complexity and space complexity of the algorithms, and introduce a regulative parameter to compress the states space of the dynamic programming problem and reduce the complexity of algorithms.
Austrian Carbon Calculator (ACC) - modelling soil carbon dynamics in Austrian soils
NASA Astrophysics Data System (ADS)
Sedy, Katrin; Freudenschuss, Alexandra; Zethner, Gehard; Spiegel, Heide; Franko, Uwe; Gründling, Ralf; Xaver Hölzl, Franz; Preinstorfer, Claudia; Haslmayr, Hans Peter; Formayer, Herbert
2014-05-01
Austrian Carbon Calculator (ACC) - modelling soil carbon dynamics in Austrian soils. The project funded by the Klima- und Energiefonds, Austrian Climate Research Programme, 4th call Authors: Katrin Sedy, Alexandra Freudenschuss, Gerhard Zethner (Environment Agency Austria), Heide Spiegel (Austrian Agency for Health and Food Safety), Uwe Franko, Ralf Gründling (Helmholtz Centre for Environmental Research) Climate change will affect plant productivity due to weather extremes. However, adverse effects could be diminished and satisfying production levels may be maintained with proper soil conditions. To sustain and optimize the potential of agricultural land for plant productivity it will be necessary to focus on preserving and increasing soil organic carbon (SOC). Carbon sequestration in agricultural soils is strongly influenced by management practice. The present management is affected by management practices that tend to speed up carbon loss. Crop rotation, soil cultivation and the management of crop residues are very important measures to influence carbon dynamics and soil fertility. For the future it will be crucial to focus on practical measures to optimize SOC and to improve soil structure. To predict SOC turnover the existing humus balance model the application of the "Carbon Candy Balance" was verified by results from Austrian long term field experiments and field data of selected farms. Thus the main aim of the project is to generate a carbon balancing tool box that can be applied in different agricultural production regions to assess humus dynamics due to agricultural management practices. The toolbox will allow the selection of specific regional input parameters for calculating the C-balance at field level. However farmers or other interested user can also apply their own field data to receive the result of C-dynamics under certain management practises within the next 100 years. At regional level the impact of predefined changes in agricultural management
Skyrmion-Based Dynamic Magnonic Crystal.
Ma, Fusheng; Zhou, Yan; Braun, H B; Lew, W S
2015-06-10
A linear array of periodically spaced and individually controllable skyrmions is introduced as a magnonic crystal. It is numerically demonstrated that skyrmion nucleation and annihilation can be accurately controlled by a nanosecond spin polarized current pulse through a nanocontact. Arranged in a periodic array, such nanocontacts allow the creation of a skyrmion lattice that causes a periodic modulation of the waveguide's magnetization, which can be dynamically controlled by changing either the strength of an applied external magnetic field or the density of the injected spin current through the nanocontacts. The skyrmion diameter is highly dependent on both the applied field and the injected current. This implies tunability of the lowest band gap as the skyrmion diameter directly affects the strength of the pinning potential. The calculated magnonic spectra thus exhibit tunable allowed frequency bands and forbidden frequency bandgaps analogous to that of conventional magnonic crystals where, in contrast, the periodicity is structurally induced and static. In the dynamic magnetic crystal studied here, it is possible to dynamically turn on and off the artificial periodic structure, which allows switching between full rejection and full transmission of spin waves in the waveguide. These findings should stimulate further research activities on multiple functionalities offered by magnonic crystals based on periodic skyrmion lattices. PMID:25989181
Dynamic Digital Channelizer Based on Spectrum Sensing.
Hu, Junpeng; Zuo, Zhen; Huang, Zhiping; Dong, Zhi
2015-01-01
The ability to efficiently channelize a received signal with dynamic sub-channel bandwidths is a key requirement of software defined radio (SDR) systems. The digital channelizer, which is used to split the received signal into a number of sub-channels, plays an important role in SDR systems. In this paper, a design of dynamic digital channelizer is presented. The proposed method is novel in that it employs a cosine modulated filter bank (CMFB) to divide the received signal into multiple frequency sub-bands and a spectrum sensing technique, which is mostly used in cognitive radio, is introduced to detect the presence of signal of each sub-band. The method of spectrum sensing is carried out based on the eigenvalues of covariance matrix of received signal. The ratio of maximum-minimum eigenvalue of each sub-band is vulnerable to noise fluctuation. This paper suggests an optimized method to calculate the ratio of maximum-minimum eigenvalue. The simulation results imply that the design of digital channelizer can effectively separate the received signal with dynamically changeable sub-channel signals. PMID:26308210
Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin
2015-07-01
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin
2015-01-01
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806
Putting Math in Motion with Calculator-Based Labs.
ERIC Educational Resources Information Center
Doerr, Helen M.; Rieff, Cathieann; Tabor, Jason
1999-01-01
Many students have difficulties in interpreting position versus time graphs. Presents an activity involving calculator-based motion labs that allows students to bring these graphs to life by turning their own motion into a graph that can be analyzed, investigated, and interpreted in terms of how they actually moved. (ASK)
Software-Based Visual Loan Calculator For Banking Industry
NASA Astrophysics Data System (ADS)
Isizoh, A. N.; Anazia, A. E.; Okide, S. O. 3; Onyeyili, T. I.; Okwaraoka, C. A. P.
2012-03-01
industry is very necessary in modern day banking system using many design techniques for security reasons. This paper thus presents the software-based design and implementation of a Visual Loan calculator for banking industry using Visual Basic .Net (VB.Net). The fundamental approach to this is to develop a Graphical User Interface (GUI) using VB.Net operating tools, and then developing a working program which calculates the interest of any loan obtained. The VB.Net programming was done, implemented and the software proved satisfactory.
Tripathi, Sunil Kumar; Muttineni, Ravikumar; Singh, Sanjeev Kumar
2013-10-01
Molecular docking, free energy calculation and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 3,5-diaminoindazoles, imidazo(1,2-b)pyridazines and triazolo(1,5-a) pyridazines series of Cyclin-dependent kinase (CDK2) inhibitors. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviations (RMSDs). We found different binding sites namely catalytic, inhibitory phosphorylation, cyclin binding and CKS-binding site of the CDK2 contributing towards the binding of these compounds. Moreover, correlation between free energy of binding and biological activity yielded a statistically significant correlation coefficient. Finally, three representative protein-ligand complexes were subjected to molecular dynamics simulation to determine the stability of the predicted conformations. The low value of the RMSDs between the initial complex structure and the energy minimized final average complex structure suggests that the derived docked complexes are close to equilibrium. We suggest that the phenylacetyl type of substituents and cyclohexyl moiety make the favorable interactions with a number of residues in the active site, and show better inhibitory activity to improve the pharmacokinetic profile of compounds against CDK2. The structure-based drug design strategy described in this study will be highly useful for the development of new inhibitors with high potency and selectivity. PMID:23727278
Gamma Knife radiosurgery with CT image-based dose calculation.
Xu, Andy Yuanguang; Bhatnagar, Jagdish; Bednarz, Greg; Niranjan, Ajay; Kondziolka, Douglas; Flickinger, John; Lunsford, L Dade; Huq, M Saiful
2015-01-01
The Leksell GammaPlan software version 10 introduces a CT image-based segmentation tool for automatic skull definition and a convolution dose calculation algorithm for tissue inhomogeneity correction. The purpose of this work was to evaluate the impact of these new approaches on routine clinical Gamma Knife treatment planning. Sixty-five patients who underwent CT image-guided Gamma Knife radiosurgeries at the University of Pittsburgh Medical Center in recent years were retrospectively investigated. The diagnoses for these cases include trigeminal neuralgia, meningioma, acoustic neuroma, AVM, glioma, and benign and metastatic brain tumors. Dose calculations were performed for each patient with the same dose prescriptions and the same shot arrangements using three different approaches: 1) TMR 10 dose calculation with imaging skull definition; 2) convolution dose calculation with imaging skull definition; 3) TMR 10 dose calculation with conventional measurement-based skull definition. For each treatment matrix, the total treatment time, the target coverage index, the selectivity index, the gradient index, and a set of dose statistics parameters were compared between the three calculations. The dose statistics parameters investigated include the prescription isodose volume, the 12 Gy isodose volume, the minimum, maximum and mean doses on the treatment targets, and the critical structures under consideration. The difference between the convolution and the TMR 10 dose calculations for the 104 treatment matrices were found to vary with the patient anatomy, location of the treatment shots, and the tissue inhomogeneities around the treatment target. An average difference of 8.4% was observed for the total treatment times between the convolution and the TMR algorithms. The maximum differences in the treatment times, the prescription isodose volumes, the 12 Gy isodose volumes, the target coverage indices, the selectivity indices, and the gradient indices from the convolution
Calculation of the coefficient and dynamics of water diffusion in graphite joints
NASA Astrophysics Data System (ADS)
Wang, Jun; Liu, Wen-Bin
2006-06-01
The coefficient and dynamics of water diffusion in adhesive-graphite joints were calculated insitu with energy dispersive X-ray (EDX) analysis, a method that is significantly simpler than elemental analysis. Water diffusion coefficient and dynamics of adhesive-graphite joints treated by different surface treatment menthods were also investigated. Calculation results indicated that the water diffusion rate in adhesive-graphite joints treated by sandpaper was higher than that treated by chemical oxidation or by silane couple agent. Also the durability of graphite joints treated by coupling agent is superior to that treated by chemical oxidation or sandpaper burnishing.
Shaughnessy, M C; Jones, R E
2016-02-01
We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825
40 CFR 1066.610 - Mass-based and molar-based exhaust emission calculations.
Code of Federal Regulations, 2013 CFR
2013-07-01
... specified in 40 CFR 86.144 or 40 CFR part 1065, subpart G. (b) For composite emission calculations over... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Mass-based and molar-based exhaust... (CONTINUED) AIR POLLUTION CONTROLS VEHICLE-TESTING PROCEDURES Calculations § 1066.610 Mass-based and...
40 CFR 1066.610 - Mass-based and molar-based exhaust emission calculations.
Code of Federal Regulations, 2012 CFR
2012-07-01
... specified in 40 CFR 86.144 or 40 CFR part 1065, subpart G. (b) For composite emission calculations over... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Mass-based and molar-based exhaust... (CONTINUED) AIR POLLUTION CONTROLS VEHICLE-TESTING PROCEDURES Calculations § 1066.610 Mass-based and...
NASA Technical Reports Server (NTRS)
Campbell, John P; Mckinney, Marion O
1952-01-01
A summary of methods for making dynamic lateral stability and response calculations and for estimating the aerodynamic stability derivatives required for use in these calculations is presented. The processes of performing calculations of the time histories of lateral motions, of the period and damping of these motions, and of the lateral stability boundaries are presented as a series of simple straightforward steps. Existing methods for estimating the stability derivatives are summarized and, in some cases, simple new empirical formulas are presented. Detailed estimation methods are presented for low-subsonic-speed conditions but only a brief discussion and a list of references are given for transonic and supersonic speed conditions.
Electronic Structure Calculations of delta-Pu Based Alloys
Landa, A; Soderlind, P; Ruban, A
2003-11-13
First-principles methods are employed to study the ground-state properties of {delta}-Pu-based alloys. The calculations show that an alloy component larger than {delta}-Pu has a stabilizing effect. Detailed calculations have been performed for the {delta}-Pu{sub 1-c}Am{sub c} system. Calculated density of Pu-Am alloys agrees well with the experimental data. The paramagnetic {yields} antiferromagnetic transition temperature (T{sub c}) of {delta}-Pu{sub 1-c}Am{sub c} alloys is calculated by a Monte-Carlo technique. By introducing Am into the system, one could lower T{sub c} from 548 K (pure Pu) to 372 K (Pu{sub 70}Am{sub 30}). We also found that, contrary to pure Pu where this transition destabilizes {delta}-phase, Pu{sub 3}Am compound remains stable in the antiferromagnetic phase that correlates with the recent discovery of a Curie-Weiss behavior of {delta}-Pu{sub 1-c}Am{sub c} at c {approx} 24 at. %.
Mechanical and dynamical stability of TiAsTe compound from ab initio calculations
NASA Astrophysics Data System (ADS)
Deligoz, E.; Ozisik, H.
2015-07-01
The first-principles calculations are employed to provide a fundamental understanding of the structural features and relative thermodynamical, mechanical and phonon stability of TiAsTe compound. The calculated lattice parameters are in good agreement with available experimental results. We have computed elastic constants, its derived moduli and ratios that characterize mechanical properties for the first time. The calculated elastic constants indicate that these materials are mechanically stable at ambient condition. The minimum thermal conductivities of TiAsTe are calculated using both Clarke's model and Cahill's model. Furthermore, the elastic anisotropy has been visualized in detail by plotting the directional dependence of compressibility, Young's modulus and shear modulus. Our results suggest strong elastic anisotropy for this compound. Additionally, the phonon spectra and phonon density of states are also obtained and discussed. The full phonon dispersion calculations confirm the dynamic stability of TiAsTe.
Červinka, Ctirad; Pádua, Agilio A H; Fulem, Michal
2016-03-10
This work presents a molecular dynamics simulation study concerning the thermodynamic data of ionic liquids (ILs) including phase change enthalpies, liquid phase densities, radial and spatial distribution functions, and diffusive properties. Three homologous series of ILs were selected for this study, namely, 1-alkyl-3-methylimidazolium tetrafluoroborates, hexafluorophosphates, and 1,1,2,2-tetrafluoroethanesulfonates, so that properties of 36 ILs are calculated in total. The trends of calculated properties are compared to available experimental data and thoroughly discussed in context of the homologous series. The calculated trends of the vaporization enthalpies within the series are supported by analyzing the structural properties of the ILs. An excellent agreement of calculated structural properties (liquid phase density) with the experimental counterparts is reached. The calculated enthalpic properties are overestimated considerably; thus, further development of the force fields for ILs is required. PMID:26848831
NASA Technical Reports Server (NTRS)
Svizhenko, Alexel; Anantram, M. P.; Maiti, Amitesh
2003-01-01
This paper presents viewgraphs on the modeling of the electromechanical response of carbon nanotubes, utilizing molecular dynamics and transport calculations. The topics include: 1) Simulations of the experiment; 2) Effect of diameter, length and temperature; and 3) Study of sp3 coordination-"The Table experiment".
Comparison of computer codes for calculating dynamic loads in wind turbines
NASA Technical Reports Server (NTRS)
Spera, D. A.
1978-01-01
The development of computer codes for calculating dynamic loads in horizontal axis wind turbines was examined, and a brief overview of each code was given. The performance of individual codes was compared against two sets of test data measured on a 100 KW Mod-0 wind turbine. All codes are aeroelastic and include loads which are gravitational, inertial and aerodynamic in origin.
ERIC Educational Resources Information Center
Seethaler, Pamela M.; Fuchs, Lynn S.; Fuchs, Douglas; Compton, Donald L.
2012-01-01
The purpose of this study was to assess the value of dynamic assessment (DA; degree of scaffolding required to learn unfamiliar mathematics content) for predicting 1st-grade calculations (CAs) and word problems (WPs) development, while controlling for the role of traditional assessments. Among 184 1st graders, predictors (DA, Quantity…
Calculating track-based observables for the LHC.
Chang, Hsi-Ming; Procura, Massimiliano; Thaler, Jesse; Waalewijn, Wouter J
2013-09-01
By using observables that only depend on charged particles (tracks), one can efficiently suppress pileup contamination at the LHC. Such measurements are not infrared safe in perturbation theory, so any calculation of track-based observables must account for hadronization effects. We develop a formalism to perform these calculations in QCD, by matching partonic cross sections onto new nonperturbative objects called track functions which absorb infrared divergences. The track function Ti(x) describes the energy fraction x of a hard parton i which is converted into charged hadrons. We give a field-theoretic definition of the track function and derive its renormalization group evolution, which is in excellent agreement with the pythia parton shower. We then perform a next-to-leading order calculation of the total energy fraction of charged particles in e+ e-→ hadrons. To demonstrate the implications of our framework for the LHC, we match the pythia parton shower onto a set of track functions to describe the track mass distribution in Higgs plus one jet events. We also show how to reduce smearing due to hadronization fluctuations by measuring dimensionless track-based ratios. PMID:25166657
Vertical emission profiles for Europe based on plume rise calculations.
Bieser, J; Aulinger, A; Matthias, V; Quante, M; Denier van der Gon, H A C
2011-10-01
The vertical allocation of emissions has a major impact on results of Chemistry Transport Models. However, in Europe it is still common to use fixed vertical profiles based on rough estimates to determine the emission height of point sources. This publication introduces a set of new vertical profiles for the use in chemistry transport modeling that were created from hourly gridded emissions calculated by the SMOKE for Europe emission model. SMOKE uses plume rise calculations to determine effective emission heights. Out of more than 40,000 different vertical emission profiles 73 have been chosen by means of hierarchical cluster analysis. These profiles show large differences to those currently used in many emission models. Emissions from combustion processes are released in much lower altitudes while those from production processes are allocated to higher altitudes. The profiles have a high temporal and spatial variability which is not represented by currently used profiles. PMID:21561695
Helium diffusion in olivine based on first principles calculations
NASA Astrophysics Data System (ADS)
Wang, Kai; Brodholt, John; Lu, Xiancai
2015-05-01
As a key trace element involved in mantle evolution, the transport properties of helium in the mantle are important for understanding the thermal and chemical evolution of the Earth. However, the mobility of helium in the mantle is still unclear due to the scarcity of measured diffusion data from minerals under mantle conditions. In this study, we used first principles calculations based on density functional theory to calculate the absolute diffusion coefficients of the helium in olivine. Using the climbing images nudged elastic band method, we defined the diffusion pathways, the activation energies (Ea), and the prefactors. Our results demonstrate that the diffusion of helium has moderate anisotropy. The directionally dependent diffusion of helium in olivine can be written in Arrhenius form as follows.
NASA Astrophysics Data System (ADS)
Cao, Jun; Xie, Zhi-Zhong; Yu, Xiaodong
2016-08-01
In the present work, the combined electronic structure calculations and surface hopping simulations have been performed to investigate the excited-state decay of the parent oxazole in the gas phase. Our calculations show that the S2 state decay of oxazole is an ultrafast process characterized by the ring-opening and ring-closure of the five-membered oxazole ring, in which the triplet contribution is minor. The ring-opening involves the Osbnd C bond cleavage affording the nitrile ylide and airine intermediates, while the ring-closure gives rise to a bicyclic species through a 2sbnd 5 bond formation. The azirine and bicyclic intermediates in the S0 state are very likely involved in the phototranspositions of oxazoles. This is different from the previous mechanism in which these intermediates in the T1 state have been proposed for these phototranspositions.
Advancing QCD-based calculations of energy loss
NASA Astrophysics Data System (ADS)
Tywoniuk, Konrad
2013-08-01
We give a brief overview of the basics and current developments of QCD-based calculations of radiative processes in medium. We put an emphasis on the underlying physics concepts and discuss the theoretical uncertainties inherently associated with the fundamental parameters to be extracted from data. An important area of development is the study of the single-gluon emission in medium. Moreover, establishing the correct physical picture of multi-gluon emissions is imperative for comparison with data. We will report on progress made in both directions and discuss perspectives for the future.
Supersampling method for efficient grid-based electronic structure calculations
NASA Astrophysics Data System (ADS)
Ryu, Seongok; Choi, Sunghwan; Hong, Kwangwoo; Kim, Woo Youn
2016-03-01
The egg-box effect, the spurious variation of energy and force due to the discretization of continuous space, is an inherent vexing problem in grid-based electronic structure calculations. Its effective suppression allowing for large grid spacing is thus crucial for accurate and efficient computations. We here report that the supersampling method drastically alleviates it by eliminating the rapidly varying part of a target function along both radial and angular directions. In particular, the use of the sinc filtering function performs best because as an ideal low pass filter it clearly cuts out the high frequency region beyond allowed by a given grid spacing.
Supersampling method for efficient grid-based electronic structure calculations.
Ryu, Seongok; Choi, Sunghwan; Hong, Kwangwoo; Kim, Woo Youn
2016-03-01
The egg-box effect, the spurious variation of energy and force due to the discretization of continuous space, is an inherent vexing problem in grid-based electronic structure calculations. Its effective suppression allowing for large grid spacing is thus crucial for accurate and efficient computations. We here report that the supersampling method drastically alleviates it by eliminating the rapidly varying part of a target function along both radial and angular directions. In particular, the use of the sinc filtering function performs best because as an ideal low pass filter it clearly cuts out the high frequency region beyond allowed by a given grid spacing. PMID:26957151
Sensor Based Engine Life Calculation: A Probabilistic Perspective
NASA Technical Reports Server (NTRS)
Guo, Ten-Huei; Chen, Philip
2003-01-01
It is generally known that an engine component will accumulate damage (life usage) during its lifetime of use in a harsh operating environment. The commonly used cycle count for engine component usage monitoring has an inherent range of uncertainty which can be overly costly or potentially less safe from an operational standpoint. With the advance of computer technology, engine operation modeling, and the understanding of damage accumulation physics, it is possible (and desirable) to use the available sensor information to make a more accurate assessment of engine component usage. This paper describes a probabilistic approach to quantify the effects of engine operating parameter uncertainties on the thermomechanical fatigue (TMF) life of a selected engine part. A closed-loop engine simulation with a TMF life model is used to calculate the life consumption of different mission cycles. A Monte Carlo simulation approach is used to generate the statistical life usage profile for different operating assumptions. The probabilities of failure of different operating conditions are compared to illustrate the importance of the engine component life calculation using sensor information. The results of this study clearly show that a sensor-based life cycle calculation can greatly reduce the risk of component failure as well as extend on-wing component life by avoiding unnecessary maintenance actions.
Seibt, Joachim; Pullerits, Tõnu
2014-09-21
While the theoretical description of population transfer subsequent to electronic excitation in combination with a line shape function description of vibrational dynamics in the context of 2D-spectroscopy is well-developed under the assumption of different timescales of population transfer and fluctuation dynamics, the treatment of the interplay between both kinds of processes lacks a comprehensive description. To bridge this gap, we use the cumulant expansion approach to derive response functions, which account for fluctuation dynamics and population transfer simultaneously. We compare 2D-spectra of a model system under different assumptions about correlations between fluctuations and point out under which conditions a simplified treatment is justified. Our study shows that population transfer and dissipative fluctuation dynamics cannot be described independent of each other in general. Advantages and limitations of the proposed calculation method and its compatibility with the modified Redfield description are discussed.
MRNet-based Dynamic Probe Class Library
Energy Science and Technology Software Center (ESTSC)
2006-12-19
The Dynamic Probe Class Library (DPCL) is an API that allows for the modification of running code, or dynamic instrumentation. Dynamic instruction is an attractive technique for implementing performance analysis tools, debugging, or process steering because this method doesn't require the modification of the application's source code and hence avoids recompiling, re-linking, and restarting the application. The DPCL API is machine independent; hence DPCL-based tools built on one platform will work on another platform
Bernstein, N.; Feldman, J. L.; Singh, David J.
2010-04-05
While the thermal conductivity of the filled skutterudites has been of great interest it had not been calculated within a microscopic theory. Here a central force, Guggenheim-McGlashen, model with parameters largely extracted from first-principles calculations and from spectroscopic data, specific to LaFe{sub 4} Sb{sub 12} or CoSb{sub 3} , is employed in a Green-Kubo/molecular dynamics calculation of thermal conductivity as a function of temperature. We find that the thermal conductivity of a filled solid is more than a factor of two lower than that of an unfilled solid, assuming the “framework” interatomic force parameters are the same between filled and unfilled solids, and that this decrease is almost entirely due to the cubic anharmonic interaction between filling and framework atoms. In addition, partially as a test of our models, we calculate thermal expansivity and isotropic atomic mean-square displacements using both molecular dynamics and lattice dynamics methods. These quantities are in reasonable agreement with experiment, increasing our confidence in the anharmonic parameters of our models. We also find an anomalously large filling-atom mode Gruneisen parameter that is apparently observed for a filled skutterudite and is observed in a clathrate.
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.
2014-10-28
Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
NASA Astrophysics Data System (ADS)
Zapol, Peter; Karpeyev, Dmitry; Maheshwari, Ketan; Zhong, Xiaoliang; Narayanan, Badri; Sankaranarayanan, Subramanian; Wilde, Michael; Heinonen, Olle; Rungger, Ivan
2015-03-01
The electronic conduction in Hf-oxide heterostructures for use in, e.g., resistive switching devices, depends sensitively on local oxygen stoichiometry and interactions at interfaces with metal electrodes. In order to model the electronic structure of different disordered configurations near interfaces, we have combined molecular dynamics (MD) simulations with first-principle based non-equilibrium Green's functions (NEGF) methods, including self-interaction corrections. We have developed an approach to generating automated workflows that combine MD and NEGF computations over many parameter values using the Swift parallel scripting language. A sequence of software tools transforms the result of one calculation into the input of the next allowing for a high-throughput concurrent parameter sweep. MD simulations generate systems with quenched disorder, which are then directly fed to NEGF and on to postprocessing. Different computations can be run on different computer platforms matching the computational load to the hardware resources. We will demonstrate results for metal-HfO2-metal heterostructures obtained using this workflow. Argonne National Laboratory's work was supported under U.S. Department of Energy Contract DE-AC02-06CH11357.
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
NASA Astrophysics Data System (ADS)
Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.
2014-10-01
Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
Probabilistic Study Conducted on Sensor-Based Engine Life Calculation
NASA Technical Reports Server (NTRS)
Guo, Ten-Huei
2004-01-01
Turbine engine life management is a very complicated process to ensure the safe operation of an engine subjected to complex usage. The challenge of life management is to find a reasonable compromise between the safe operation and the maximum usage of critical parts to reduce maintenance costs. The commonly used "cycle count" approach does not take the engine operation conditions into account, and it oversimplifies the calculation of the life usage. Because of the shortcomings, many engine components are regularly pulled for maintenance before their usable life is over. And, if an engine has been running regularly under more severe conditions, components might not be taken out of service before they exceed their designed risk of failure. The NASA Glenn Research Center and its industrial and academic partners have been using measurable parameters to improve engine life estimation. This study was based on the Monte Carlo simulation of 5000 typical flights under various operating conditions. First a closed-loop engine model was developed to simulate the engine operation across the mission profile and a thermomechanical fatigue (TMF) damage model was used to calculate the actual damage during takeoff, where the maximum TMF accumulates. Next, a Weibull distribution was used to estimate the implied probability of failure for a given accumulated cycle count. Monte Carlo simulations were then employed to find the profiles of the TMF damage under different operating assumptions including parameter uncertainties. Finally, probabilities of failure for different operating conditions were analyzed to demonstrate the importance of a sensor-based damage calculation in order to better manage the risk of failure and on-wing life.
Dynamics and Structure of Point Defects in Forsterite: ab initio calculations
NASA Astrophysics Data System (ADS)
Churakov, S.; Khisina, N.; Urusov, V.; Wirth, R.
2001-12-01
OH-bearing fluid inclusions in Fo92 forsterite samples from peridotite nodule 9206 (Udachnaja kimberlite pipe)[1] were documented recently based on TEM and IR studies. The Fourier transform of diffraction pattern from the inclusions exhibited a pattern, which is interpreted as ordered planar (2H)xMg defects. In this study the structure and dynamics of protons associated with Mg(1), Mg(2) vacancies and interstitial polyhedrons ordered in a (100) plane corresponding to double unite cell periodicity of the forsterite lattice has been investigated by ab initio quantum mechanic calculations. Static structure optimizations and ab-initio molecular dynamics (MD) simulations have been performed using the CPMD density functional code[2]. The calculations were accomplished with the BLYP-functional utilizing the generalized gradient approximation. Non-local Goedecker-type pseudopotentials[3] have been applied to account for core electrons. Valence electron orbitals were approximated by plane wave expansion up to 70 Ry energy cutoff. The energy of static structures was sampled on 2x2x2 Monkhorst-Pack mesh[4]. During the structure relaxation parameters of an orthorhombic 2x1x2 supercell contaning 116 atoms corresponding to Mg28Si16O64H8 hydrous olivine was fixed at experimental values of a=9.524Å b=10.225Å and c=11.988Å relative to the Pbnm space group. Series of NVT-MD calculations were performed at 1000 K on 2x1x1 supercell with 58 atoms using four chain Nose thermostat. Randomly disturbed optimized structures were used as initial configuration for MD runs. The 1ps system equilibration is followed by trajectory production over 5 ps interval. A point energy sampling was applied in all MD calculations. A series of geometry optimizations, starting with various initial position of protons in Mg(1), Mg(2) and interstitial sites were carried out to obtain a structure with the lowest lattice energy. It was found that structures with protons completely located within the M1
Application of Dynamic Grey-Linear Auto-regressive Model in Time Scale Calculation
NASA Astrophysics Data System (ADS)
Yuan, H. T.; Don, S. W.
2009-01-01
Because of the influence of different noise and the other factors, the running of an atomic clock is very complex. In order to forecast the velocity of an atomic clock accurately, it is necessary to study and design a model to calculate its velocity in the near future. By using the velocity, the clock could be used in the calculation of local atomic time and the steering of local universal time. In this paper, a new forecast model called dynamic grey-liner auto-regressive model is studied, and the precision of the new model is given. By the real data of National Time Service Center, the new model is tested.
A 3-dimensional finite-difference method for calculating the dynamic coefficients of seals
NASA Technical Reports Server (NTRS)
Dietzen, F. J.; Nordmann, R.
1989-01-01
A method to calculate the dynamic coefficients of seals with arbitrary geometry is presented. The Navier-Stokes equations are used in conjunction with the k-e turbulence model to describe the turbulent flow. These equations are solved by a full 3-dimensional finite-difference procedure instead of the normally used perturbation analysis. The time dependence of the equations is introduced by working with a coordinate system rotating with the precession frequency of the shaft. The results of this theory are compared with coefficients calculated by a perturbation analysis and with experimental results.
Born Oppenheimer Molecular Dynamics calculation of the νO-H IR spectra for acetic acid cyclic dimers
NASA Astrophysics Data System (ADS)
El Amine Benmalti, Mohamed; Krallafa, Abdelghani; Gaigeot, Marie-Pierre
2015-01-01
Both ab initio molecular dynamics simulations based on the Born-Oppenheimer approach calculations and a quantum theoretical model are used in order to study the IR spectrum of the acetic acid dimer in the gas phase. The theoretical model is taking into account the strong anharmonic coupling, Davydov coupling, multiple Fermi resonances between the first harmonics of some bending modes and the first excited state of the symmetric combination of the two vO-H modes and the quantum direct and indirect relaxation. The IR spectra obtained from DFT-based molecular dynamics is compared with our theoretical lineshape and with experiment. Note that in a previous work we have shown that our approach reproduces satisfactorily the main futures of the IR experimental lineshapes of the acetic acid dimer [Mohamed el Amine Benmalti, Paul Blaise, H. T. Flakus, Olivier Henri-Rousseau, Chem Phys, 320(2006) 267-274.].
NASA Technical Reports Server (NTRS)
Austin, M. G.; Thomsen, J. M.; Ruhl, S. F.; Orphal, D. L.; Schultz, P. H.
1980-01-01
The considered investigation was conducted in connection with studies which are to provide a better understanding of the detailed dynamics of impact cratering processes. Such an understanding is vital for a comprehension of planetary surfaces. The investigation is the continuation of a study of impact dynamics in a uniform, nongeologic material at impact velocities achievable in laboratory-scale experiments conducted by Thomsen et al. (1979). A calculation of a 6 km/sec impact of a 0.3 g spherical 2024 aluminum projectile into low strength (50 kPa) homogeneous plasticene clay has been continued from 18 microseconds to past 600 microseconds. The cratering flow field, defined as the material flow field in the target beyond the transient cavity but well behind the outgoing shock wave, has been analyzed in detail to see how applicable the Maxwell Z-Model, developed from analysis of near-surface explosion cratering calculations, is to impact cratering
Calculation of Dynamic Loads Due to Random Vibration Environments in Rocket Engine Systems
NASA Technical Reports Server (NTRS)
Christensen, Eric R.; Brown, Andrew M.; Frady, Greg P.
2007-01-01
An important part of rocket engine design is the calculation of random dynamic loads resulting from internal engine "self-induced" sources. These loads are random in nature and can greatly influence the weight of many engine components. Several methodologies for calculating random loads are discussed and then compared to test results using a dynamic testbed consisting of a 60K thrust engine. The engine was tested in a free-free condition with known random force inputs from shakers attached to three locations near the main noise sources on the engine. Accelerations and strains were measured at several critical locations on the engines and then compared to the analytical results using two different random response methodologies.
Method of calculating gas dynamics and heat transfer in single stage refrigeration units
NASA Technical Reports Server (NTRS)
Zhitomirskiy, I. S.; Popolskiy, A. B.
1974-01-01
A generalized mathematical model of gas-dynamic and heat transfer processes in single-stage regenerative installations operating in Stirling, MacMahon, Gifford-MacMahon, and pulsating tube cycles is proposed. A numerical method os solving initial equations on a digital computer is given. This makes it possible to calculate the change in the thermodynamic parameters in the working cycle in different machine components, as well as the dependence of cold productivity on the temperature level in the steady regime.
NASA Astrophysics Data System (ADS)
Belkacem, Ali; Slaughter, Daniel
2015-05-01
Understanding electron-driven chemical reactions is important for improving a variety of technological applications such as materials processing and the important role they play in the radiation damage in bulk matter. Furthermore, dissociative electron attachment often exhibits site-selective bond cleavage, which holds promise for prediction and precise control of electron-driven chemical reactions. Recent dynamical studies of these reactions have demonstrated that an understanding of anion dissociation dynamics beyond simple one-dimensional models is crucial in interpreting the measured fragment angular distributions. We combine ion fragment momentum imaging experiments with electron attachment entrance amplitude calculations to interrogate the non-Born-Oppenheimer dynamics of dissociative electron attachment in polyatomic molecules. We will report recent experimental developments in molecules of technological interest including methanol, methane and uracil. Work supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.
Water on the sun: line assignments based on variational calculations.
Polyansky, O L; Zobov, N F; Viti, S; Tennyson, J; Bernath, P F; Wallace, L
1997-07-18
The infrared spectrum of hot water observed in a sunspot has been assigned. The high temperature of the sunspot (3200 K) gave rise to a highly congested pure rotational spectrum in the 10-micrometer region that involved energy levels at least halfway to dissociation. Traditional spectroscopy, based on perturbation theory, is inadequate for this problem. Instead, accurate variational solutions of the vibration-rotation Schrödinger equation were used to make assignments, revealing unexpected features, including rotational difference bands and fewer degeneracies than anticipated. These results indicate that a shift away from perturbation theory to first principles calculations is necessary in order to assign spectra of hot polyatomic molecules such as water. PMID:9219686
Wavelet-Based DFT calculations on Massively Parallel Hybrid Architectures
NASA Astrophysics Data System (ADS)
Genovese, Luigi
2011-03-01
In this contribution, we present an implementation of a full DFT code that can run on massively parallel hybrid CPU-GPU clusters. Our implementation is based on modern GPU architectures which support double-precision floating-point numbers. This DFT code, named BigDFT, is delivered within the GNU-GPL license either in a stand-alone version or integrated in the ABINIT software package. Hybrid BigDFT routines were initially ported with NVidia's CUDA language, and recently more functionalities have been added with new routines writeen within Kronos' OpenCL standard. The formalism of this code is based on Daubechies wavelets, which is a systematic real-space based basis set. As we will see in the presentation, the properties of this basis set are well suited for an extension on a GPU-accelerated environment. In addition to focusing on the implementation of the operators of the BigDFT code, this presentation also relies of the usage of the GPU resources in a complex code with different kinds of operations. A discussion on the interest of present and expected performances of Hybrid architectures computation in the framework of electronic structure calculations is also adressed.
Peter, Christine; Hummer, Gerhard
2005-01-01
Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic membrane pores by molecular dynamics simulation of model membranes formed of hexagonally packed carbon nanotubes. We focus on the factors that determine the energetics of ion translocation through such nonpolar nanopores and compare the resulting free-energy barriers for pores with different diameters corresponding to the gating regions in closed and open forms of potassium channels. Our model system also allows us to compare the results from molecular dynamics simulations directly to continuum electrostatics calculations. Both simulations and continuum calculations show that subnanometer wide pores pose a huge free-energy barrier for ions, but a small increase in the pore diameter to ∼1 nm nearly eliminates that barrier. We also find that in those wider channels the ion mobility is comparable to that in the bulk phase. By calculating local electrostatic potentials, we show that the long range Coulomb interactions of ions are strongly screened in the wide water-filled channels. Whereas continuum calculations capture the overall energetics reasonably well, the local water structure, which is not accounted for in this model, leads to interesting effects such as the preference of hydrated ions to move along the pore wall rather than through the center of the pore. PMID:16006629
NASA Technical Reports Server (NTRS)
Campbell, John P; Mckinney, Marion O
1951-01-01
A summary of methods for making dynamic lateral stability and response calculations and for estimating the aerodynamic stability derivatives required for use in these calculations is presented. The processes of performing calculations of the time histories of lateral motions, of the period and damping of these motions, and of the lateral stability boundaries are presented as a series of simple straightforward steps. Existing methods for estimating the stability derivatives are summarized and, in some cases, simple new empirical formulas are presented. Reference is also made to reports presenting experimental data that should be useful in making estimates of the derivatives. Detailed estimating methods are presented for low-subsonic-speed conditions but only a brief discussion and a list of references are given for transonic- and supersonic-speed conditions.
Bernard, F.; Borovnicar, I.; Ghirlanda, M.
1996-12-01
The windows based computer program for gasket calculation was presented. C++ computer language was used. On the basis of experimental results and data sets available in the literature and calculated with the help of FSA and PVRC method, the assembly parameters were determined. The result is DONIT TESNITI Diskette, a smart tool to select gaskets on the basis of service conditions and tightness requirements.
The effect of molecular dynamics sampling on the calculated observable gas-phase structures.
Tikhonov, Denis S; Otlyotov, Arseniy A; Rybkin, Vladimir V
2016-07-21
In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory. PMID:27331660
Eradication of Ebola Based on Dynamic Programming.
Zhu, Jia-Ming; Wang, Lu; Liu, Jia-Bao
2016-01-01
This paper mainly studies the eradication of the Ebola virus, proposing a scientific system, including three modules for the eradication of Ebola virus. Firstly, we build a basic model combined with nonlinear incidence rate and maximum treatment capacity. Secondly, we use the dynamic programming method and the Dijkstra Algorithm to set up M-S (storage) and several delivery locations in West Africa. Finally, we apply the previous results to calculate the total cost, production cost, storage cost, and shortage cost. PMID:27313655
Eradication of Ebola Based on Dynamic Programming
Zhu, Jia-Ming; Wang, Lu; Liu, Jia-Bao
2016-01-01
This paper mainly studies the eradication of the Ebola virus, proposing a scientific system, including three modules for the eradication of Ebola virus. Firstly, we build a basic model combined with nonlinear incidence rate and maximum treatment capacity. Secondly, we use the dynamic programming method and the Dijkstra Algorithm to set up M-S (storage) and several delivery locations in West Africa. Finally, we apply the previous results to calculate the total cost, production cost, storage cost, and shortage cost. PMID:27313655
Cheluvaraja, Srinath; Meirovitch, Hagai
2006-07-14
Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed. PMID:16848609
Using molecular dynamics and quantum mechanics calculations to model fluorescence observables
Speelman, Amy L.; Muñoz-Losa, Aurora; Hinkle, Katie L.; VanBeek, Darren B.; Mennucci, Benedetta; Krueger, Brent P.
2011-01-01
We provide a critical examination of two different methods for generating a donor-acceptor electronic coupling trajectory from a molecular dynamics (MD) trajectory and three methods for sampling that coupling trajectory, allowing the modeling of experimental observables directly from the MD simulation. In the first coupling method we perform a single quantum-mechanical (QM) calculation to characterize the excited state behavior, specifically the transition dipole moment, of the fluorescent probe, which is then mapped onto the configuration space sampled by MD. We then utilize these transition dipoles within the ideal dipole approximation (IDA) to determine the electronic coupling between the probes that mediates the transfer of energy. In the second method we perform a QM calculation on each snapshot and use the complete transition densities to calculate the electronic coupling without need for the IDA. The resulting coupling trajectories are then sampled using three methods ranging from an independent sampling of each trajectory point (the Independent Snapshot Method) to a Markov chain treatment that accounts for the dynamics of the coupling in determining effective rates. The results show that the IDA significantly overestimates the energy transfer rate (by a factor of 2.6) during the portions of the trajectory in which the probes are close to each other. Comparison of the sampling methods shows that the Markov chain approach yields more realistic observables at both high and low FRET efficiencies. Differences between the three sampling methods are discussed in terms of the different mechanisms for averaging over structural dynamics in the system. Convergence of the Markov chain method is carefully examined. Together, the methods for estimating coupling and for sampling the coupling provide a mechanism for directly connecting the structural dynamics modeled by MD with fluorescence observables determined through FRET experiments. PMID:21417498
Calculating gravitationally self-consistent sea level changes driven by dynamic topography
NASA Astrophysics Data System (ADS)
Austermann, J.; Mitrovica, J. X.
2015-12-01
We present a generalized formalism for computing gravitationally self-consistent sea level changes driven by the combined effects of dynamic topography, geoid perturbations due to mantle convection, ice mass fluctuations and sediment redistribution on a deforming Earth. Our mathematical treatment conserves mass of the surface (ice plus ocean) load and the solid Earth. Moreover, it takes precise account of shoreline migration and the associated ocean loading. The new formalism avoids a variety of approximations adopted in previous models of sea level change driven by dynamic topography, including the assumption that a spatially fixed isostatic amplification of `air-loaded' dynamic topography accurately accounts for ocean loading effects. While our approach is valid for Earth models of arbitrary complexity, we present numerical results for a set of simple cases in which a pattern of dynamic topography is imposed, the response to surface mass loading assumes that Earth structure varies only with depth and that isostatic equilibrium is maintained at all times. These calculations, involving fluid Love number theory, indicate that the largest errors in previous predictions of sea level change driven by dynamic topography occur in regions of shoreline migration, and thus in the vicinity of most geological markers of ancient sea level. We conclude that a gravitationally self-consistent treatment of long-term sea level change is necessary in any effort to use such geological markers to estimate ancient ice volumes.
Photophysics of Auramine-O: electronic structure calculations and nonadiabatic dynamics simulations.
Xie, Bin-Bin; Xia, Shu-Hua; Chang, Xue-Ping; Cui, Ganglong
2016-01-01
Diphenylmethane dyes are very useful photoinduced molecular rotors; however, their photophysical mechanisms are still elusive until now. In this work, we adopted combined static electronic structure calculations (MS-CASPT2//CASSCF) and trajectory-based surface-hopping dynamics simulations (OM2/MRCI) to study the S1 excited-state relaxation mechanism of a representative diphenylmethane dye Auramine-O. On the basis of the optimized S1 minima and the computed emission bands, we have for the first time assigned experimentally proposed three transient states (i.e. S1-LE, S1-I1 or S1-I2, and S1-II). Mechanistically, upon irradiation to the S1 state, the system first relaxes to the locally excited S1 minimum (S1-LE). Starting from this point, there exist two kinds of relaxation paths to S1-II. In the sequential path, the system first evolves into S1-I1 or S1-I2 and then runs into S1-II; in the concerted one, the system, bypassing S1-I1 and S1-I2, directly runs into S1-II. In addition, the system can decay to the S0 state in the vicinity of three S1/S0 conical intersections i.e. S1S0-I1, S1S0-I2, and S1S0-II. In the S1 dynamic simulations, 54% trajectories decay to the S0 state via S1S0-II; the remaining trajectories are de-excited to the S0 state via S1S0-I1 (11%) and S1S0-I2 (35%). Our present theoretical investigation does not support the experimentally proposed S1 excited-state hypothesis that the intramolecular rotation of the two dimethyl groups around the C-N bond is responsible for the rapid decay of the emission band at about 500 nm; instead, it should be heavily interrelated with the rotation of the two dimethylanilino groups. Finally, this work provides important mechanistic insights into similar diphenylmethane dyes. PMID:26615798
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.
Map-based models in neuronal dynamics
NASA Astrophysics Data System (ADS)
Ibarz, B.; Casado, J. M.; Sanjuán, M. A. F.
2011-04-01
Ever since the pioneering work of Hodgkin and Huxley, biological neuron models have consisted of ODEs representing the evolution of the transmembrane voltage and the dynamics of ionic conductances. It is only recently that discrete dynamical systems-also known as maps-have begun to receive attention as valid phenomenological neuron models. The present review tries to provide a coherent perspective of map-based biological neuron models, describing their dynamical properties; stressing the similarities and differences, both among them and in relation to continuous-time models; exploring their behavior in networks; and examining their wide-ranging possibilities of application in computational neuroscience.
Code System to Calculate Three-Dimensional Extension Two-Phase Flow Dynamics.
Energy Science and Technology Software Center (ESTSC)
1999-04-28
Version 00 This package consists of two programs K-FIX(3D) and K-FIX(3D, FLX) which extend the transient, two-dimensional, two-fluid program K-FIX to perform three-dimensional calculations. The transient dynamics of three-dimensional, two-phase flow with interfacial exchange are calculated at all flow speeds. Each phase is described in terms of its own density, velocity, and temperature. The application is to flow in the annulus between two cylinders where the inner cylinder moves periodically perpendicular to its axis. K-FIX(3D)more » is easily adaptable to a variety of two phase flow problems while K-FIX (3D,FLX) combines KFIX(3D), the three-dimensional version of the KFIX code, with the three-dimensional, elastic shell code FLX for application to a very specific class of problems. KFIX(3D,FLX) was developed specifically to calculate the coupled fluid-structure dynamics of a light water reactor core support barrel under accident conditions. Motion may be induced by blowdown, prescribed displacement, or seismic action. This package was released by NESC in 1982 then transferred to ESTSC and then to RSICC in January 1999. Files were not retrievable from the media, but the NEA Data Bank in France graciously submitted their package which was obtained from NESC. Hence, the files in this package are from the NEADB NESC-0877/01 package.« less
Rapid Parallel Calculation of shell Element Based On GPU
NASA Astrophysics Data System (ADS)
Wanga, Jian Hua; Lia, Guang Yao; Lib, Sheng; Li, Guang Yao
2010-06-01
Long computing time bottlenecked the application of finite element. In this paper, an effective method to speed up the FEM calculation by using the existing modern graphic processing unit and programmable colored rendering tool was put forward, which devised the representation of unit information in accordance with the features of GPU, converted all the unit calculation into film rendering process, solved the simulation work of all the unit calculation of the internal force, and overcame the shortcomings of lowly parallel level appeared ever before when it run in a single computer. Studies shown that this method could improve efficiency and shorten calculating hours greatly. The results of emulation calculation about the elasticity problem of large number cells in the sheet metal proved that using the GPU parallel simulation calculation was faster than using the CPU's. It is useful and efficient to solve the project problems in this way.
Fast calculation of object infrared spectral scattering based on CUDA
NASA Astrophysics Data System (ADS)
Li, Liang-chao; Niu, Wu-bin; Wu, Zhen-sen
2010-11-01
Computational unified device architecture (CUDA) is used for paralleling the spectral scattering calculation from non-Lambertian object of sky and earth background irradiation. The bidirectional reflectance distribution function (BRDF) of five parameter model is utilized in object surface element scattering calculation. The calculation process is partitioned into many threads running in GPU kernel and each thread computes a visible surface element infrared spectral scattering intensity in a specific incident direction, all visible surface elements' intensity are weighted and averaged to obtain the object surface scattering intensity. The comparison of results of the CPU calculation and CUDA parallel calculation of a cylinder shows that the CUDA parallel calculation speed improves more than two hundred times in meeting the accuracy, with a high engineering value.
Efficient Error Calculation for Multiresolution Texture-Based Volume Visualization
LaMar, E; Hamann, B; Joy, K I
2001-10-16
Multiresolution texture-based volume visualization is an excellent technique to enable interactive rendering of massive data sets. Interactive manipulation of a transfer function is necessary for proper exploration of a data set. However, multiresolution techniques require assessing the accuracy of the resulting images, and re-computing the error after each change in a transfer function is very expensive. They extend their existing multiresolution volume visualization method by introducing a method for accelerating error calculations for multiresolution volume approximations. Computing the error for an approximation requires adding individual error terms. One error value must be computed once for each original voxel and its corresponding approximating voxel. For byte data, i.e., data sets where integer function values between 0 and 255 are given, they observe that the set of error pairs can be quite large, yet the set of unique error pairs is small. instead of evaluating the error function for each original voxel, they construct a table of the unique combinations and the number of their occurrences. To evaluate the error, they add the products of the error function for each unique error pair and the frequency of each error pair. This approach dramatically reduces the amount of computation time involved and allows them to re-compute the error associated with a new transfer function quickly.
Trajectory Based Heating and Ablation Calculations for MESUR Pathfinder Aeroshell
NASA Technical Reports Server (NTRS)
Chen, Y. K.; Henline, W. D.; Tauber, M. E.; Arnold, James O. (Technical Monitor)
1994-01-01
Based on the geometry of Mars Environment Survey (MESUR) Pathfinder aeroshell and an estimated Mars entry trajectory, two-dimensional axisymmetric time dependent calculations have been obtained using GIANTS (Gauss-Siedel Implicit Aerothermodynamic Navier-Stokes code with Thermochemical Surface Conditions) code and CMA (Charring Material Thermal Response and Ablation) Program for heating analysis and heat shield material sizing. These two codes are interfaced using a loosely coupled technique. The flowfield and convective heat transfer coefficients are computed by the GIANTS code with a species balance condition for an ablating surface, and the time dependent in-depth conduction with surface blowing is simulated by the CMA code with a complete surface energy balance condition. In this study, SLA-561V has been selected as heat shield material. The solutions, including the minimum heat shield thicknesses over aeroshell forebody, pyrolysis gas blowing rates, surface heat fluxes and temperature distributions, flowfield, and in-depth temperature history of SLA-561V, are presented and discussed in detail.
Nonideal thermoequilibrium calculations using a large product species data base
Hobbs, M.L.; Baer, M.R.
1992-06-01
Thermochemical data fits for approximately 900 gaseous and 600 condensed species found in the JANAF tables (Chase et al., 1985) have been completed for use with the TIGER nonideal thermoequilibrium code (Cowperthwaite and Zwisler, 1973). The TIGER code has been modified to allow systems containing up to 400 gaseous and 100 condensed constituents composed of up to 50 elements. Gaseous covolumes have been estimated following the procedure outlined by Mader (1979) using estimates of van der Waals radii for 48 elements and three-dimensional molecular mechanics. Molecular structures for all gaseous components were explicitly defined in terms of atomic coordinates in {Angstrom}. The Becker-Kistiakowsky-Wilson equation of state (BKW-EOS) has been calibrated near C-J states using detonation temperatures measured in liquid and solid explosives and a large product species data base. Detonation temperatures for liquid and solid explosives were predicted adequately with a single set of BKW parameters. Values for the empirical BKW constants {alpha}, {beta}, k, and {theta} were 0.5, 0.174, 11.85, and 5160, respectively. Values for the covolume factors, k{sub i}, were assumed to be invariant. The liquid explosives included mixtures of hydrazine nitrate with hydrazine, hydrazine hydrate, and water; mixtures of tetranitromethane with nitromethane; liquid isomers ethyl nitrate and 2-nitroethanol; and nitroglycerine. The solid explosives included HMX, RDX, PETN, Tetryl, and TNT. Color contour plots of HMX equilibrium products as well as thermodynamic variables are shown in pressure and temperature space. Similar plots for a pyrotechnic reaction composed of TiH{sub 2} and KC1O{sub 4} are also reported. Calculations for a typical HMX-based propellant are also discussed.
NASA Astrophysics Data System (ADS)
Li, Qiang; Yu, Guichang; Liu, Shulian; Zheng, Shuiying
2012-09-01
Journal bearings are important parts to keep the high dynamic performance of rotor machinery. Some methods have already been proposed to analysis the flow field of journal bearings, and in most of these methods simplified physical model and classic Reynolds equation are always applied. While the application of the general computational fluid dynamics (CFD)-fluid structure interaction (FSI) techniques is more beneficial for analysis of the fluid field in a journal bearing when more detailed solutions are needed. This paper deals with the quasi-coupling calculation of transient fluid dynamics of oil film in journal bearings and rotor dynamics with CFD-FSI techniques. The fluid dynamics of oil film is calculated by applying the so-called "dynamic mesh" technique. A new mesh movement approach is presented while the dynamic mesh models provided by FLUENT are not suitable for the transient oil flow in journal bearings. The proposed mesh movement approach is based on the structured mesh. When the journal moves, the movement distance of every grid in the flow field of bearing can be calculated, and then the update of the volume mesh can be handled automatically by user defined function (UDF). The journal displacement at each time step is obtained by solving the moving equations of the rotor-bearing system under the known oil film force condition. A case study is carried out to calculate the locus of the journal center and pressure distribution of the journal in order to prove the feasibility of this method. The calculating results indicate that the proposed method can predict the transient flow field of a journal bearing in a rotor-bearing system where more realistic models are involved. The presented calculation method provides a basis for studying the nonlinear dynamic behavior of a general rotor-bearing system.
Cao Jun; Fang Weihai; Fang Qiu
2011-01-28
In the present paper, different electronic structure methods have been used to determine stationary and intersection structures on the ground (S{sub 0}) and {sup 1}{pi}{pi}* (S{sub 2}) states of 4-methylpyridine, which is followed by adiabatic and nonadiabatic dynamics simulations to explore the mechanistic photoisomerization of 4-methylpyridine. Photoisomerization starts from the S{sub 2}({sup 1}{pi}{pi}*) state and overcomes a small barrier, leading to formation of the prefulvene isomer in the S{sub 0} state via a S{sub 2}/S{sub 0} conical intersection. The ultrafast S{sub 2}{yields} S{sub 0} nonradiative decay and low quantum yield for the photoisomerization reaction were well reproduced by the combined electronic structure calculation and dynamics simulation. The prefulvene isomer was assigned as a long-lived intermediate and suggested to isomerize to 4-methylpyridine directly in the previous study, which is not supported by the present calculation. The nonadiabatic dynamics simulation and electronic structure calculation reveal that the prefulvene isomer is a short-lived intermediate and isomerizes to benzvalene form very easily. The benzvalene form was predicted as the stable isomer in the present study and is probably the long-lived intermediate observed experimentally. A consecutive light and thermal isomerization cycle via Dewar isomer was determined and this cycle mechanism is different from that reported in the previous study. It should be pointed out that formation of Dewar isomer from the S{sub 2}({sup 1}{pi}{pi}*) state is not in competition with the isomerization to the prefulvene form. The Dewar structure observed experimentally may originate from other excited states.
NASA Astrophysics Data System (ADS)
Cartoixà, Xavier; Dettori, Riccardo; Melis, Claudio; Colombo, Luciano; Rurali, Riccardo
2016-07-01
We study thermal transport in porous Si nanowires (SiNWs) by means of approach-to-equilibrium molecular dynamics simulations. We show that the presence of pores greatly reduces the thermal conductivity, κ, of the SiNWs as long mean free path phonons are suppressed. We address explicitly the dependence of κ on different features of the pore topology—such as the porosity and the pore diameter—and on the nanowire (NW) geometry—diameter and length. We use the results of the molecular dynamics calculations to tune an effective model, which is capable of capturing the dependence of κ on porosity and NW diameter. The model illustrates the failure of Matthiessen's rule to describe the coupling between boundary and pore scattering, which we account for by the inclusion of an additional empirical term.
Structure and dynamics of nanofluids: Theory and simulations to calculate viscosity
NASA Astrophysics Data System (ADS)
Pozhar, Liudmila A.
2000-02-01
The simplified expression of the Pozhar-Gubbins (PG) rigorous, nonequilibrium statistical mechanical theory of dense, strongly inhomogeneous fluids is used to calculate the viscosity of model fluids confined in a slit pore of several molecular diameters in width in terms of the equilibrium structure factors (i.e., the number density and pair correlation functions) of these nanofluids obtained by means of the equilibrium molecular dynamic simulations. These results are compared to those obtained by means of the nonequilibrium molecular dynamic simulations of the planar Poiseuille flow of the model nanofluids, and to the results supplied by several heuristic expressions for the nanofluid viscosity. This comparison proves that the PG transport theory provides a reliable, quantitatively accurate description of the viscosity coefficients of the model nanofluids while all the heauristic approaches fail. This success of the PG prediction of the nanofluid viscosity is because the theoretical expression accounts accurately for the nanofluid structure.
NASA Astrophysics Data System (ADS)
Lazzeretti, P.; Malagoli, M.; Turci, L.; Zanasi, R.
1993-10-01
Theoretical methods based on the random-phase approximation have been applied to evaluate near Hartree-Fock dynamic electric polarizability and shielding tensors of carbon and hydrogen nuclei in the benzene molecule. Cauchy moments of the various properties have been determined. The results obtained in different gauges (dipole length, velocity, and acceleration) are reported.
First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum
Ono, Shigeaki
2009-01-01
The equation of state of tantalum (Ta) has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state. PMID:20057949
An easy implementation of displacement calculations in 3D discrete dislocation dynamics codes
NASA Astrophysics Data System (ADS)
Fivel, Marc; Depres, Christophe
2014-10-01
Barnett's coordinate-free expression of the displacement field of a triangular loop in an isotropic media is revisited in a view to be implemented in 3D discrete dislocation dynamics codes. A general meshing procedure solving the problems of non-planar loops is presented. The method is user-friendly and can be used in numerical simulations since it gives the contribution of each dislocation segment to the global displacement field without defining the connectivity of closed loops. Easy to implement in parallel calculations, this method is successfully applied to large-scale simulations.
Diffusion Rates for Hydrogen on Pd(111) from Molecular Quantum Dynamics Calculations.
Firmino, Thiago; Marquardt, Roberto; Gatti, Fabien; Dong, Wei
2014-12-18
The van Hove formula for the dynamical structure factor (DSF) related to particle scattering at mobile adsorbates is extended to include the relaxation of the adsorbates' vibrational states. The total rate obtained from the DSF is assumed to be the sum of a diffusion and a relaxation rate. A simple kinetic model to support this assumption is presented. To illustrate its potential applicability, the formula is evaluated using wave functions, energies, and lifetimes of vibrational states obtained for H/Pd(111) from first-principle calculations. Results show that quantum effects can be expected to be important even at room temperature. PMID:26273973
Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J
2008-06-19
Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.
Kirkwood-Buff Thermodynamics Derived from Grand Canonical Molecular Dynamics and DRISM Calculations
NASA Astrophysics Data System (ADS)
Lynch, Gillian C.; Perkyns, John S.; Pettitt, B. Montgomery
1999-05-01
The grand canonical ensemble techniques—both Monte Carlo and molecular dynamics—have become very popular in recent years, but no direct link between the number fluctuation results from these simulation methods and a Kirkwood-Buff theory has been established. In this article we look at Kirkwood-Buff integrals computed using thermodynamic averages derived from grand canonical ensemble molecular dynamics simulations and compare them to similar quantities derived from the dielectrically consistent reference interaction site model many-body theory. These calculations will be carried out for three different water models, SPC, SPC/E, and TIP3P.
Method of characteristics - Based sensitivity calculations for international PWR benchmark
Suslov, I. R.; Tormyshev, I. V.; Komlev, O. G.
2013-07-01
Method to calculate sensitivity of fractional-linear neutron flux functionals to transport equation coefficients is proposed. Implementation of the method on the basis of MOC code MCCG3D is developed. Sensitivity calculations for fission intensity for international PWR benchmark are performed. (authors)
An Analysis of Differential Item Functioning Based on Calculator Type.
ERIC Educational Resources Information Center
Schwarz, Richard; Rich, Changhua; Arenson, Ethan; Podrabsky, Tracy; Cook, Gary
The effect of calculator type on student performance on a mathematics examination was studied. Differential item functioning (DIF) methodology was applied to examine group differences (calculator use) on item performance while conditioning on the relevant ability. Other survey questions were developed to ask students the extent to which they used…
Fluorescence spectra shape based dynamic thermometry
NASA Astrophysics Data System (ADS)
Liu, Liwang; Creten, Sebastiaan; Firdaus, Yuliar; Agustin Flores Cuautle, Jose Jesus; Kouyaté, Mansour; Van der Auweraer, Mark; Glorieux, Christ
2014-01-01
An entirely optical, dynamic thermometry technique based on the temperature dependence of a fluorescence spectrum is presented. Different from conventional intensity-based fluorescence thermometry, in this work, neural network recognition is employed to extract the sample temperature from the magnitude and shape of recorded fluorescence spectra. As a demonstration to determine the depth profile of dynamical temperature variations and of the thermal and optical properties of semitransparent samples, in-depth photothermally induced periodical temperature oscillations of a rhodamine B and copper chloride dyed glycerol sample were measured with an accuracy of 4.2 mK.Hz-1/2 and fitted well by a 1D thermal diffusion model.
NASA Astrophysics Data System (ADS)
Cai, Yufei; Zhang, Jianhui; Zhu, Chunling; Huang, Jun; Jiang, Feng
2016-05-01
The atomizer with micro cone apertures has advantages of ultra-fine atomized droplets, low power consumption and low temperature rise. The current research of this kind of atomizer mainly focuses on the performance and its application while there is less research of the principle of the atomization. Under the analysis of the dispenser and its micro-tapered aperture's deformation, the volume changes during the deformation and vibration of the micro-tapered aperture on the dispenser are calculated by coordinate transformation. Based on the characters of the flow resistance in a cone aperture, it is found that the dynamic cone angle results from periodical changes of the volume of the micro-tapered aperture of the atomizer and this change drives one-way flows. Besides, an experimental atomization platform is established to measure the atomization rates with different resonance frequencies of the cone aperture atomizer. The atomization performances of cone aperture and straight aperture atomizers are also measured. The experimental results show the existence of the pumping effect of the dynamic tapered angle. This effect is usually observed in industries that require low dispersion and micro- and nanoscale grain sizes, such as during production of high-pressure nozzles and inhalation therapy. Strategies to minimize the pumping effect of the dynamic cone angle or improve future designs are important concerns. This research proposes that dynamic micro-tapered angle is an important cause of atomization of the atomizer with micro cone apertures.
Calculation of the neutron electric dipole moment with two dynamical flavors of domain wall fermions
F. Berruto; T. Blum; K. Orginos; A. Soni
2005-12-08
We present a study of the neutron electric dipole moment ({rvec d}{sub N}) within the framework of lattice QCD with two flavors of dynamical light quarks. The dipole moment is sensitive to the topological structure of the gauge fields, and accuracy can only be achieved by using dynamical, or sea quark, calculations. However, the topological charge evolves slowly in these calculations, leading to a relatively large uncertainty in {rvec d}{sub N}. It is shown, using quenched configurations, that a better sampling of the charge distribution reduces this problem, but because the CP even part of the fermion determinant is absent, both the topological charge distribution and {rvec d}{sub N} are pathological in the chiral limit. We discuss the statistical and systematic uncertainties arising from the topological charge distribution and unphysical size of the quark mass in our calculations and prospects for eliminating them. Our calculations employ the RBC collaboration two flavor domain wall fermion and DBW2 gauge action lattices with inverse lattice spacing a{sup -1} {approx} 1.7 GeV, physical volume V {approx} (2 fm){sup 3}, and light quark mass roughly equal to the strange quark mass (m{sub sea} = 0.03 and 0.04). We determine a value of the electric dipole moment that is zero within (statistical) errors, |{rvec d}{sub N}| = -0.04(20) e-{theta}-fm at the smaller sea quark mass. Satisfactory results for the magnetic and electric form factors of the proton and neutron are also obtained and presented.
Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics
NASA Astrophysics Data System (ADS)
Donev, Aleksandar; Stillinger, Frank H.; Torquato, Salvatore
2007-07-01
We present a new event-driven molecular dynamics (MD) algorithm for measuring the free energy of nearly jammed packings of spherical and non-spherical hard particles. This Bounding Cell Molecular Dynamics (BCMD) algorithm exactly calculates the free-energy of a single-occupancy cell (SOC) model in which each particle is restricted to a neighborhood of its initial position using a hard-wall bounding cell. Our MD algorithm generalizes previous ones in the literature by enabling us to study non-spherical particles as well as to measure the free-energy change during continuous irreversible transformations. Moreover, we make connections to the well-studied problem of computing the volume of convex bodies in high dimensions using random walks. We test and verify the numerical accuracy of the method by comparing against rigorous asymptotic results for the free energy of jammed and isostatic disordered packings of both hard spheres and ellipsoids, for which the free energy can be calculated directly as the volume of a high-dimensional simplex. We also compare our results to previously published Monte Carlo results for hard-sphere crystals near melting and jamming and find excellent agreement. We have successfully used the BCMD algorithm to determine the configurational and free-volume contributions to the free energy of glassy states of binary hard disks [A. Donev, F.H. Stillinger, S. Torquato, Do binary hard disks exhibit an ideal glass transition? Phys. Rev. Lett. 96 (22) (2006) 225502]. The algorithm can also be used to determine phases with locally- or globally-minimal free energy, to calculate the free-energy cost of point and extended crystal defects, or to calculate the elastic moduli of glassy or crystalline solids, among other potential applications.
Haptics-based dynamic implicit solid modeling.
Hua, Jing; Qin, Hong
2004-01-01
This paper systematically presents a novel, interactive solid modeling framework, Haptics-based Dynamic Implicit Solid Modeling, which is founded upon volumetric implicit functions and powerful physics-based modeling. In particular, we augment our modeling framework with a haptic mechanism in order to take advantage of additional realism associated with a 3D haptic interface. Our dynamic implicit solids are semi-algebraic sets of volumetric implicit functions and are governed by the principles of dynamics, hence responding to sculpting forces in a natural and predictable manner. In order to directly manipulate existing volumetric data sets as well as point clouds, we develop a hierarchical fitting algorithm to reconstruct and represent discrete data sets using our continuous implicit functions, which permit users to further design and edit those existing 3D models in real-time using a large variety of haptic and geometric toolkits, and visualize their interactive deformation at arbitrary resolution. The additional geometric and physical constraints afford more sophisticated control of the dynamic implicit solids. The versatility of our dynamic implicit modeling enables the user to easily modify both the geometry and the topology of modeled objects, while the inherent physical properties can offer an intuitive haptic interface for direct manipulation with force feedback. PMID:15794139
Calculation of transport properties of liquid metals and their alloys via molecular dynamics
NASA Astrophysics Data System (ADS)
Cherne, Frank Joseph, III
The advanced casting modeler requires accurate viscosity and diffusivity data of liquid metals and their alloys. The present work discusses the use of equilibrium and non-equilibrium molecular dynamics techniques to obtain such data without having to rely on oversimplified phenomenological expressions or difficult and expensive experiments. Utilizing the embedded atom method (EAM), the viscosities and diffusivities for a series of equilibrium and non-equilibrium molecular dynamics simulations of nickel, aluminum, and nickel-aluminum alloys are presented. A critical comparison between the equilibrium and non-equilibrium methods is presented. Besides the transport properties, structural data for the liquids are also evaluated. EAM does a poor job of describing the transport properties of nickel-aluminum alloys, particularly near the equiatomic concentration. It has been suggested that charge transfer between nickel and aluminum atoms is responsible for the discrepancy between numerical calculations and available experimental data. A modified electronic distribution function has been developed to simulate the charge transfer associated with compound formation. The effects of such a "charge transfer" modification to the embedded atom method are evaluated. The results of these simulations indicate that the embedded atom method combined with molecular dynamics may be used as a method to predict reasonably the transport properties.
Mihaylov, I. B.; Lerma, F. A.; Fatyga, M.; Siebers, J. V.
2007-04-15
This study quantifies the dose prediction errors (DPEs) in dynamic IMRT dose calculations resulting from (a) use of an intensity matrix to estimate the multi-leaf collimator (MLC) modulated photon fluence (DPE{sub IGfluence}) instead of an explicit MLC particle transport, and (b) handling of tissue heterogeneities (DPE{sub hetero}) by superposition/convolution (SC) and pencil beam (PB) dose calculation algorithms. Monte Carlo (MC) computed doses are used as reference standards. Eighteen head-and-neck dynamic MLC IMRT treatment plans are investigated. DPEs are evaluated via comparing the dose received by 98% of the GTV (GTV D{sub 98%}), the CTV D{sub 95%}, the nodal D{sub 90%}, the cord and the brainstem D{sub 02%}, the parotid D{sub 50%}, the parotid mean dose (D{sub Mean}), and generalized equivalent uniform doses (gEUDs) for the above structures. For the MC-generated intensity grids, DPE{sub IGfluence} is within {+-}2.1% for all targets and critical structures. The SC algorithm DPE{sub hetero} is within {+-}3% for 98.3% of the indices tallied, and within {+-}3.4% for all of the tallied indices. The PB algorithm DPE{sub hetero} is within {+-}3% for 92% of the tallied indices. Statistical equivalence tests indicate that PB DPE{sub hetero} requires a {+-}3.6% interval to state equivalence with the MC standard, while the intervals are <1.5% for SC DPE{sub hetero} and DPE{sub IGfluence}. Overall, these results indicate that SC and MC IMRT dose calculations which use MC-derived intensity matrices for fluence prediction do not introduce significant dose errors compared with full Monte Carlo dose computations; however, PB algorithms may result in clinically significant dose deviations.
Tosso, Rodrigo D; Andujar, Sebastian A; Gutierrez, Lucas; Angelina, Emilio; Rodríguez, Ricaurte; Nogueras, Manuel; Baldoni, Héctor; Suvire, Fernando D; Cobo, Justo; Enriz, Ricardo D
2013-08-26
A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC₅₀ values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper. PMID:23834278
Lattice dynamics and electron-phonon coupling calculations using nondiagonal supercells
NASA Astrophysics Data System (ADS)
Lloyd-Williams, Jonathan H.; Monserrat, Bartomeu
2015-11-01
We study the direct calculation of total energy derivatives for lattice dynamics and electron-phonon coupling calculations using supercell matrices with nonzero off-diagonal elements. We show that it is possible to determine the response of a periodic system to a perturbation characterized by a wave vector with reduced fractional coordinates (m1/n1,m2/n2,m3/n3) using a supercell containing a number of primitive cells equal to the least common multiple of n1,n2, and n3. If only diagonal supercell matrices are used, a supercell containing n1n2n3 primitive cells is required. We demonstrate that the use of nondiagonal supercells significantly reduces the computational cost of obtaining converged zero-point energies and phonon dispersions for diamond and graphite. We also perform electron-phonon coupling calculations using the direct method to sample the vibrational Brillouin zone with grids of unprecedented size, which enables us to investigate the convergence of the zero-point renormalization to the thermal and optical band gaps of diamond.
Molecular dynamics calculation of rotational diffusion coefficient of a carbon nanotube in fluid
NASA Astrophysics Data System (ADS)
Cao, Bing-Yang; Dong, Ruo-Yu
2014-01-01
Rotational diffusion processes are correlated with nanoparticle visualization and manipulation techniques, widely used in nanocomposites, nanofluids, bioscience, and so on. However, a systematical methodology of deriving this diffusivity is still lacking. In the current work, three molecular dynamics (MD) schemes, including equilibrium (Green-Kubo formula and Einstein relation) and nonequilibrium (Einstein-Smoluchowski relation) methods, are developed to calculate the rotational diffusion coefficient, taking a single rigid carbon nanotube in fluid argon as a case. We can conclude that the three methods produce same results on the basis of plenty of data with variation of the calculation parameters (tube length, diameter, fluid temperature, density, and viscosity), indicative of the validity and accuracy of the MD simulations. However, these results have a non-negligible deviation from the theoretical predictions of Tirado et al. [J. Chem. Phys. 81, 2047 (1984)], which may come from several unrevealed factors of the theory. The three MD methods proposed in this paper can also be applied to other situations of calculating rotational diffusion coefficient.
Molecular dynamics calculation of rotational diffusion coefficient of a carbon nanotube in fluid.
Cao, Bing-Yang; Dong, Ruo-Yu
2014-01-21
Rotational diffusion processes are correlated with nanoparticle visualization and manipulation techniques, widely used in nanocomposites, nanofluids, bioscience, and so on. However, a systematical methodology of deriving this diffusivity is still lacking. In the current work, three molecular dynamics (MD) schemes, including equilibrium (Green-Kubo formula and Einstein relation) and nonequilibrium (Einstein-Smoluchowski relation) methods, are developed to calculate the rotational diffusion coefficient, taking a single rigid carbon nanotube in fluid argon as a case. We can conclude that the three methods produce same results on the basis of plenty of data with variation of the calculation parameters (tube length, diameter, fluid temperature, density, and viscosity), indicative of the validity and accuracy of the MD simulations. However, these results have a non-negligible deviation from the theoretical predictions of Tirado et al. [J. Chem. Phys. 81, 2047 (1984)], which may come from several unrevealed factors of the theory. The three MD methods proposed in this paper can also be applied to other situations of calculating rotational diffusion coefficient. PMID:25669403
Eisenbach, Markus; Perera, Meewanage Dilina N.; Landau, David P; Nicholson, Don M.; Yin, Junqi; Brown, Greg
2015-01-01
We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles-derived simulations.
Cao, Jun; Xie, Zhi-Zhong
2016-03-01
The ab initio electronic structure calculations and CASSCF-based nonadiabatic dynamics simulations have been used to investigate the internal conversion and intersystem crossing process of both trans-acrolein and 2-cyclopentenone in the gas phase. Our calculation results show that relaxation from the Franck-Condon region to an S1 minimum is ultrafast and that the S1 state will dominantly undergo intersystem crossing to triplet states due to the existence of significant barriers to access the S1/S0 intersection points and of energetically close-lying triplet states. The S1/T2/T1 three-state intersection is observed in our dynamics simulations to play an important role in the population of the lowest triplet state, which is consistent with previous suggestions. Although the evolution into triplet states involves a similar path and gives rise to a similar triplet quantum yield for these two molecules, the intersystem crossing rate of 2-cyclopentenone is lower owing to the ring constraint that results in a smaller spin-orbital coupling in the singlet-triplet crossing region. The present theoretical study reproduces the experimental results and gives an explanation about the structural factors that govern the excited-state decay of some types of α,β-enones. PMID:26882275
Calculating excess chemical potentials using dynamic simulations in the fourth dimension
Pomes, R.; Eisenmesser, E.; Post, C.B.; Roux, B.
1999-08-01
A general method for computing excess chemical potentials is presented. The excess chemical potential of a solute or ligand molecule is estimated from the potential of mean-force (PMF) calculated along a nonphysical fourth spatial dimension, {ital w}, into which the molecule is gradually inserted or from which it is gradually abstracted. According to this {open_quotes}4D-PMF{close_quotes} (four dimensional) scheme, the free energy difference between two limiting states defines the excess chemical potential: At w={plus_minus}{infinity}, the molecule is not interacting with the rest of the system, whereas at w=0, it is fully interacting. Use of a fourth dimension avoids the numerical instability in the equations of motion encountered upon growing or shrinking solute atoms in conventional free energy perturbation simulations performed in three dimensions, while benefiting from the efficient sampling of configurational space afforded by PMF calculations. The applicability and usefulness of the method are illustrated with calculations of the hydration free energy of simple Lennard-Jones (LJ) solutes, a water molecule, and camphor, using molecular dynamics simulations and umbrella sampling. Physical insight into the nature of the PMF profiles is gained from a continuum treatment of short- and long-range interactions. The short-range barrier for dissolution of a LJ solute in the added dimension provides an apparent surface tension of the solute. An approximation to the long-range behavior of the PMF profiles is made in terms of a continuum treatment of LJ dispersion and electrostatic interactions. Such an analysis saves the need for configurational sampling in the long-range limit of the fourth dimension. The 4D-PMF method of calculating excess chemical potentials should be useful for neutral solute and ligand molecules with a wide range of sizes, shapes, and polarities. {copyright} {ital 1999 American Institute of Physics.}
Procedure for calculating general aircraft noise based on ISO 3891
Hediger, J.R.
1982-01-01
The standard ISO-3891 specifies the presentation of aircraft noise heard on the ground or of noise exposure by succession of aircraft, without giving any details on different parameters required to their calculation. The following study provides some of these parameters considering acoustic measurements as well as laboratory analysis realized in co-operation with the Swiss Federal Office for Civil Aviation.
Independent calculation-based verification of IMRT plans using a 3D dose-calculation engine
Arumugam, Sankar; Xing, Aitang; Goozee, Gary; Holloway, Lois
2013-01-01
Independent monitor unit verification of intensity-modulated radiation therapy (IMRT) plans requires detailed 3-dimensional (3D) dose verification. The aim of this study was to investigate using a 3D dose engine in a second commercial treatment planning system (TPS) for this task, facilitated by in-house software. Our department has XiO and Pinnacle TPSs, both with IMRT planning capability and modeled for an Elekta-Synergy 6 MV photon beam. These systems allow the transfer of computed tomography (CT) data and RT structures between them but do not allow IMRT plans to be transferred. To provide this connectivity, an in-house computer programme was developed to convert radiation therapy prescription (RTP) files as generated by many planning systems into either XiO or Pinnacle IMRT file formats. Utilization of the technique and software was assessed by transferring 14 IMRT plans from XiO and Pinnacle onto the other system and performing 3D dose verification. The accuracy of the conversion process was checked by comparing the 3D dose matrices and dose volume histograms (DVHs) of structures for the recalculated plan on the same system. The developed software successfully transferred IMRT plans generated by 1 planning system into the other. Comparison of planning target volume (TV) DVHs for the original and recalculated plans showed good agreement; a maximum difference of 2% in mean dose, − 2.5% in D95, and 2.9% in V95 was observed. Similarly, a DVH comparison of organs at risk showed a maximum difference of +7.7% between the original and recalculated plans for structures in both high- and medium-dose regions. However, for structures in low-dose regions (less than 15% of prescription dose) a difference in mean dose up to +21.1% was observed between XiO and Pinnacle calculations. A dose matrix comparison of original and recalculated plans in XiO and Pinnacle TPSs was performed using gamma analysis with 3%/3 mm criteria. The mean and standard deviation of pixels passing
Independent calculation-based verification of IMRT plans using a 3D dose-calculation engine.
Arumugam, Sankar; Xing, Aitang; Goozee, Gary; Holloway, Lois
2013-01-01
Independent monitor unit verification of intensity-modulated radiation therapy (IMRT) plans requires detailed 3-dimensional (3D) dose verification. The aim of this study was to investigate using a 3D dose engine in a second commercial treatment planning system (TPS) for this task, facilitated by in-house software. Our department has XiO and Pinnacle TPSs, both with IMRT planning capability and modeled for an Elekta-Synergy 6MV photon beam. These systems allow the transfer of computed tomography (CT) data and RT structures between them but do not allow IMRT plans to be transferred. To provide this connectivity, an in-house computer programme was developed to convert radiation therapy prescription (RTP) files as generated by many planning systems into either XiO or Pinnacle IMRT file formats. Utilization of the technique and software was assessed by transferring 14 IMRT plans from XiO and Pinnacle onto the other system and performing 3D dose verification. The accuracy of the conversion process was checked by comparing the 3D dose matrices and dose volume histograms (DVHs) of structures for the recalculated plan on the same system. The developed software successfully transferred IMRT plans generated by 1 planning system into the other. Comparison of planning target volume (TV) DVHs for the original and recalculated plans showed good agreement; a maximum difference of 2% in mean dose, - 2.5% in D95, and 2.9% in V95 was observed. Similarly, a DVH comparison of organs at risk showed a maximum difference of +7.7% between the original and recalculated plans for structures in both high- and medium-dose regions. However, for structures in low-dose regions (less than 15% of prescription dose) a difference in mean dose up to +21.1% was observed between XiO and Pinnacle calculations. A dose matrix comparison of original and recalculated plans in XiO and Pinnacle TPSs was performed using gamma analysis with 3%/3mm criteria. The mean and standard deviation of pixels passing gamma
Poirier, Bill; Salam, A
2004-07-22
In a previous paper [J. Theo. Comput. Chem. 2, 65 (2003)], one of the authors (B.P.) presented a method for solving the multidimensional Schrodinger equation, using modified Wilson-Daubechies wavelets, and a simple phase space truncation scheme. Unprecedented numerical efficiency was achieved, enabling a ten-dimensional calculation of nearly 600 eigenvalues to be performed using direct matrix diagonalization techniques. In a second paper [J. Chem. Phys. 121, 1690 (2004)], and in this paper, we extend and elaborate upon the previous work in several important ways. The second paper focuses on construction and optimization of the wavelength functions, from theoretical and numerical viewpoints, and also examines their localization. This paper deals with their use in representations and eigenproblem calculations, which are extended to 15-dimensional systems. Even higher dimensionalities are possible using more sophisticated linear algebra techniques. This approach is ideally suited to rovibrational spectroscopy applications, but can be used in any context where differential equations are involved. PMID:15260721
Monte Carlo calculation of dynamical properties of the two-dimensional Hubbard model
NASA Technical Reports Server (NTRS)
White, S. R.; Scalapino, D. J.; Sugar, R. L.; Bickers, N. E.
1989-01-01
A new method is introduced for analytically continuing imaginary-time data from quantum Monte Carlo calculations to the real-frequency axis. The method is based on a least-squares-fitting procedure with constraints of positivity and smoothness on the real-frequency quantities. Results are shown for the single-particle spectral-weight function and density of states for the half-filled, two-dimensional Hubbard model.
Amaro, Rommie E; Cheng, Xiaolin; Ivanov, Ivaylo N; Xu, Dong; McCammon, Jonathan
2009-01-01
The comparative dynamics and inhibitor binding free energies of group-1 and group-2 pathogenic influenza A subtype neuraminidase (NA) enzymes are of fundamental biological interest and relevant to structure-based drug design studies for antiviral compounds. In this work, we present seven generalized Born molecular dynamics simulations of avian (N1)- and human (N9)-type NAs in order to probe the comparative flexibility of the two subtypes, both with and without the inhibitor oseltamivir bound. The enhanced sampling obtained through the implicit solvent treatment suggests several provocative insights into the dynamics of the two subtypes, including that the group-2 enzymes may exhibit similar motion in the 430-binding site regions but different 150-loop motion. End-point free energy calculations elucidate the contributions to inhibitor binding free energies and suggest that entropic considerations cannot be neglected when comparing across the subtypes. We anticipate the findings presented here will have broad implications for the development of novel antiviral compounds against both seasonal and pandemic influenza strains.
Classification of CMEs Based on Their Dynamics
NASA Astrophysics Data System (ADS)
Nicewicz, J.; Michalek, G.
2016-05-01
A large set of coronal mass ejections CMEs (6621) has been selected to study their dynamics seen with the Large Angle and Spectroscopic Coronagraph (LASCO) onboard the Solar and Heliospheric Observatory (SOHO) field of view (LFOV). These events were selected based on having at least six height-time measurements so that their dynamic properties, in the LFOV, can be evaluated with reasonable accuracy. Height-time measurements (in the SOHO/LASCO catalog) were used to determine the velocities and accelerations of individual CMEs at successive distances from the Sun. Linear and quadratic functions were fitted to these data points. On the basis of the best fits to the velocity data points, we were able to classify CMEs into four groups. The types of CMEs do not only have different dynamic behaviors but also different masses, widths, velocities, and accelerations. We also show that these groups of events are initiated by different onset mechanisms. The results of our study allow us to present a consistent classification of CMEs based on their dynamics.
Strobl, Andreas N.; Vickers, Andrew J.; Van Calster, Ben; Steyerberg, Ewout; Leach, Robin J.; Thompson, Ian M.; Ankerst, Donna P.
2015-01-01
Clinical risk calculators are now widely available but have generally been implemented in a static and one-size-fits-all fashion. The objective of this study was to challenge these notions and show via a case study concerning risk-based screening for prostate cancer how calculators can be dynamically and locally tailored to improve on-site patient accuracy. Yearly data from five international prostate biopsy cohorts (3 in the US, 1 in Austria, 1 in England) were used to compare 6 methods for annual risk prediction: static use of the online US-developed Prostate Cancer Prevention Trial Risk Calculator (PCPTRC); recalibration of the PCPTRC; revision of the PCPTRC; building a new model each year using logistic regression, Bayesian prior-to-posterior updating, or random forests. All methods performed similarly with respect to discrimination, except for random forests, which were worse. All methods except for random forests greatly improved calibration over the static PCPTRC in all cohorts except for Austria, where the PCPTRC had the best calibration followed closely by recalibration. The case study shows that a simple annual recalibration of a general online risk tool for prostate cancer can improve its accuracy with respect to the local patient practice at hand. PMID:25989018
Kingsley, Laura J; Esquivel-Rodríguez, Juan; Yang, Ying; Kihara, Daisuke; Lill, Markus A
2016-07-01
Crystallization of protein-protein complexes can often be problematic and therefore computational structural models are often relied on. Such models are often generated using protein-protein docking algorithms, where one of the main challenges is selecting which of several thousand potential predictions represents the most near-native complex. We have developed a novel technique that involves the use of steered molecular dynamics (sMD) and umbrella sampling to identify near-native complexes among protein-protein docking predictions. Using this technique, we have found a strong correlation between our predictions and the interface RMSD (iRMSD) in ten diverse test systems. On two of the systems, we investigated if the prediction results could be further improved using potential of mean force calculations. We demonstrated that a near-native (<2.0 Å iRMSD) structure could be identified in the top-1 ranked position for both systems. © 2016 Wiley Periodicals, Inc. PMID:27232548
E-beam dynamics calculations and comparison with measurements of a high duty accelerator at Boeing
Parazzoli, C.G.; Dowell, D.H.
1995-12-31
The electron dynamics in the photoinjector cavities and through the beamline for a high duty factor electron accelerator are computed. The particle in a cell code ARGUS, is first used in the low energy (< 2 MeV) region of the photoinjector, then the ARGUS-generated phase space at the photoinjector exit is used as input in the standard particle pusher code PARMELA, and the electron beam properties at the end of the beamline computed. Comparisons between the calculated and measured electron bea mradial profiles and emittances are presented for different values of the electron pulse charge. A discussion of the methodology used and on the accuracy of PARMELA in the low energy region of the photoinjector is given.
Dynamic aperture calculation for the RHIC 2010 100 GeV Au-Au run lattices
Luo, Y.; Brown, K.; Fischer, W.; Ptitsyn, V.; Roser, T.; Schoefer, V.; Tepikian, S.; Trbojevic, D.
2010-08-01
In this note we summarize the dynamic aperture calculation with the 2010 RHIC 100 GeV Au-Au run lattices. This study was initiated to understand the observed large beam decay in the Yellow ring after rf re-bucketing in the beginning of this run. The off-line linear lattice models and the interaction region non-linearity models are used. The large beam decay in the Yellow ring after re-bucketing was eventually eliminated by lowering the Yellow tunes to 0.21 from 0.235 with {beta}* = 0.7m lattice. In this note we only focus on the numeric simulation instead of the beam experiments.
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach
Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A
2015-01-01
Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. PMID:26418190
D'Agosta, Roberto
2013-02-14
Research on thermoelectrical energy conversion, the reuse of waste heat produced by some mechanical or chemical processes to generate electricity, has recently gained some momentum. The calculation of the electronic parameters entering the figure of merit of this energy conversion, and therefore the discovery of efficient materials, is usually performed starting from Landauer's approach to quantum transport coupled with Onsager's linear response theory. As it is well known, this approach suffers from certain serious drawbacks. Here, we discuss alternative dynamical methods that can go beyond the validity of Landauer's/Onsager's approach for electronic transport. They can be used to validate the predictions of Landauer's/Onsager's approach and to investigate systems for which this approach has been shown to be unsatisfactory. PMID:23212579
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
NASA Astrophysics Data System (ADS)
Xu, Zheng; Yasuda, Keiji; Liu, Xiao-Jun
2015-10-01
In order to design a sonochemical reactor with high reaction efficiency, it is important to clarify the size and intensity of the sonochemical reaction field. In this study, the reaction field in a sonochemical reactor is estimated from the distribution of pressure above the threshold for cavitation. The quantitation of hydroxide radical in a sonochemical reactor is obtained from the calculation of bubble dynamics and reaction equations. The distribution of the reaction field of the numerical simulation is consistent with that of the sonochemical luminescence. The sound absorption coefficient of liquid in the sonochemical reactor is much larger than that attributed to classical contributions which are heat conduction and shear viscosity. Under the dual irradiation, the reaction field becomes extensive and intensive because the acoustic pressure amplitude is intensified by the interference of two ultrasonic waves. Project supported by the National Natural Science Foundation of China (Grant Nos. 11404245, 11204129, and 11211140039).
Calculations of NMR chemical shifts with APW-based methods
NASA Astrophysics Data System (ADS)
Laskowski, Robert; Blaha, Peter
2012-01-01
We present a full potential, all electron augmented plane wave (APW) implementation of first-principles calculations of NMR chemical shifts. In order to obtain the induced current we follow a perturbation approach [Pickard and Mauri, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.63.245101 63, 245101 (2001)] and extended the common APW + local orbital (LO) basis by several LOs at higher energies. The calculated all-electron current is represented in traditional APW manner as Fourier series in the interstitial region and with a spherical harmonics representation inside the nonoverlapping atomic spheres. The current is integrated using a “pseudocharge” technique. The implementation is validated by comparison of the computed chemical shifts with some “exact” results for spherical atoms and for a set of solids and molecules with available published data.
Using a laser vibrometer for monitoring dynamic strain, modal analysis, and calculating damping
NASA Astrophysics Data System (ADS)
Camden, Michael P.; Simmons, Larry W.
1998-07-01
With the renewed interest in hypervelocity vehicles, component testing in extreme thermoacoustic and thermovibration environments is now required. This requires new test facilities and new instrumentation techniques be developed to test and evaluate these new structures, components and sub- components. To collect data in these extreme environments new instrumentation is needed. In a dynamic test environment use of strain gages is limited to low temperature testing. This paper describes how room temperature and high temperature (greater than 2000 degrees F) strain data is collected, using a laser vibrometer, on cantilevered coupons. This paper also describes the use of a laser vibrometer to obtain mode shapes and damping information. With new structural components, many manufactured from new composite materials such as ceramic matrix composites (CMC), there is a need to acquire accurate mode shapes and damping information. Traditionally modal analysis is done using accelerometers to map out the responses of a structure. This is time consuming, expensive and on small structures the weight of the accelerometers could affect the results. Through the use of a laser vibrometer accurate mode shapes can be obtained quickly. This information can be used to validate finite element models and to determine instrumentation locations on test components. With complex structures it is essential to determine the correct locations to install instrumentation when performing high level dynamic testing, the vibrometer is ideally suited for this. While the mode shapes are being mapped using a vibrometer it is an easy and logical step to calculate the damping of the structural component. Damping is calculated using the half-power bandwidth method that provides accurate results when using a vibrometer.
Keystroke Dynamics-Based Credential Hardening Systems
NASA Astrophysics Data System (ADS)
Bartlow, Nick; Cukic, Bojan
abstract Keystroke dynamics are becoming a well-known method for strengthening username- and password-based credential sets. The familiarity and ease of use of these traditional authentication schemes combined with the increased trustworthiness associated with biometrics makes them prime candidates for application in many web-based scenarios. Our keystroke dynamics system uses Breiman’s random forests algorithm to classify keystroke input sequences as genuine or imposter. The system is capable of operating at various points on a traditional ROC curve depending on application-specific security needs. As a username/password authentication scheme, our approach decreases the system penetration rate associated with compromised passwords up to 99.15%. Beyond presenting results demonstrating the credential hardening effect of our scheme, we look into the notion that a user’s familiarity to components of a credential set can non-trivially impact error rates.
NASA Astrophysics Data System (ADS)
Wei, Xing
2016-09-01
To understand magnetic effects on dynamical tides, we study the rotating magnetohydrodynamic (MHD) flow driven by harmonic forcing. The linear responses are analytically derived in a periodic box under the local WKB approximation. Both the kinetic and Ohmic dissipations at the resonant frequencies are calculated, and the various parameters are investigated. Although magnetic pressure may be negligible compared to thermal pressure, the magnetic field can be important for the first-order perturbation, e.g., dynamical tides. It is found that the magnetic field splits the resonant frequency, namely the rotating hydrodynamic flow has only one resonant frequency, but the rotating MHD flow has two, one positive and the other negative. In the weak field regime the dissipations are asymmetric around the two resonant frequencies and this asymmetry is more striking with a weaker magnetic field. It is also found that both the kinetic and Ohmic dissipations at the resonant frequencies are inversely proportional to the Ekman number and the square of the wavenumber. The dissipation at the resonant frequency on small scales is almost equal to the dissipation at the non-resonant frequencies, namely the resonance takes its effect on the dissipation at intermediate length scales. Moreover, the waves with phase propagation that is perpendicular to the magnetic field are much more damped. It is also interesting to find that the frequency-averaged dissipation is constant. This result suggests that in compact objects, magnetic effects on tidal dissipation should be considered.
NASA Astrophysics Data System (ADS)
Komatsu, Yu; Umemura, Masayuki; Shoji, Mitsuo; Kayanuma, Megumi; Yabana, Kazuhiro; Shiraishi, Kenji
For detecting life from reflectance spectra on extrasolar planets, several indicators called surface biosignatures have been proposed. One of them is the vegetation red edge (VRE) which derives from surface vegetation. VRE is observed in 700-750 nm on the Earth, but there is no guarantee that exovegetation show the red edge in this wavelength. Therefore it is necessary to check the validity of current standards of VRE as the signatures. In facts, M stars (cooler than Sun) will be the main targets in future missions, it is significantly important to know on the fundamental mechanisms in photosynthetic organism such as purple bacteria which absorb longer wavelength radiation. We investigated light absorptions and excitation energy transfers (EETs) in light harvesting complexes in purple bacteria (LH2s) by using quantum dynamics simulations. In LH2, effective EET is accomplished by corporative electronic excitation of the pigments. In our theoretical model, a dipole-dipole approximation was used for the electronic interactions between pigment excitations. Quantum dynamics simulations were performed according to Liouville equation to examine the EET process. The calculated oscillator strength and the transfer time between LH2 were good agreement with the experimental values. As the system size increases, the absorption bands shifted longer and the transfer velocities became larger. When two pigments in a LHC were exchanged to another pigments with lower excitation energy, faster and intensive light collection were observed.
NASA Astrophysics Data System (ADS)
Armbruster, Matthew; Soto, Patricia
2012-02-01
This project proposes to test the hypothesis that the physicochemical milieu modulates the conformational dynamics of synthetic Alzheimer's Ab protofilament structures, the main component of Alzheimer's senile plaques. To this end, 3D solid-state NMR structures of Ab protofilaments were used as initial structures for molecular dynamics simulations in explicit water and a water/hexane environment. The initial structures of the simulations and representative structures from the simulation-generated trajectories were taken to perform computational normal mode analysis. We developed a code in python with a graphical user-friendly interface. The program incorporated the ProDy (0.7.1) package. With the application, we examined cross-correlation plots of Ca positions of the 2-fold Ab protofilaments along the most collective mode and the slowest mode. The protofilament structures were highly correlated in the water environment. We hypothesized the protofilament would move as one in water because of the viscosity. The square fluctuation of Ca positions was calculated for the slowest mode for the hexane model and the MD generated ensemble. The two plots match up until midway through the structure. At the midway point a phase shift emerged between the two structures most likely where the surrounding changes. The in-house developed code made it easy to perform analysis and will be used by other students in the research group.
Svrčková, Pavla; Pysanenko, Andriy; Lengyel, Jozef; Rubovič, Peter; Kočišek, Jaroslav; Poterya, Viktoriya; Slavíček, Petr; Fárník, Michal
2015-10-21
We investigate the solvent effects on photodissociation dynamics of the S-H bond in ethanethiol CH3CH2SH (EtSH). The H fragment images are recorded by velocity map imaging (VMI) at 243 nm in various expansion regimes ranging from isolated molecules to clusters of different sizes and compositions. The VMI experiment is accompanied by electron ionization mass spectrometry using a reflectron time-of-flight mass spectrometer (RTOFMS). The experimental data are interpreted using ab initio calculations. The direct S-H bond fission results in a peak of fast fragments at Ekin(H) ≈ 1.25 eV with a partly resolved structure corresponding to vibrational levels of the CH3CH2S cofragment. Clusters of different nature ranging from dimers to large (EtSH)N, N ≥ 10, clusters and to ethanethiol clusters embedded in larger argon "snowballs" are investigated. In the clusters a sharp peak of near-zero kinetic energy fragments occurs due to the caging. The dynamics of the fragment caging is pictured theoretically, using multi-reference ab initio theory for the ethanethiol dimer. The larger cluster character is revealed by the simultaneous analysis of the VMI and RTOFMS experiments; none of these tools alone can provide the complete picture. PMID:25743944
Nam, Kwangho
2013-08-13
The implementation and performance of the atom-centered density matrix propagation (ADMP) [J. Chem. Phys. 2001, 114, 9758] and the curvy-steps (CURV) methods [J. Chem. Phys. 2004, 121, 1152] are described. These methods solve the electronic Schrödinger equation approximately by propagating the electronic degrees of freedom using the extended Lagrangian molecular dynamics (ELMD) simulation approach. The ADMP and CURV methods are implemented and parallelized to accelerate semiempirical quantum mechanical (QM) methods (such as the MNDO, AM1, PM3, MNDO/d, and AM1/d methods). Test calculations show that both the ADMP and the CURV methods are 2∼4 times faster than the Born-Oppenheimer molecular dynamics (BOMD) method and conserve the total energy well. The accuracy of the ADMP and CURV simulations is comparable to the BOMD simulations. The parallel implementation accelerates the MD simulation by up to 28 fold for the ADMP method and 25 fold for the CURV method, respectively, relative to the speed of the single core BOMD. In addition, a multiple time scale (MTS) approach is introduced to further speed up the semiempirical QM and QM/MM ELMD simulations. Since a larger integration time step is used for the propagation of the nuclear coordinates than that for the electronic degrees of freedom, the MTS approach allows the ELMD simulation to be carried out with a time step that is larger than the time step accessible by the original ADMP and CURV methods. It renders MD simulation to be carried out about 20 times faster than the BOMD simulation, and yields results that are comparable to the single time scale simulation results. The use of the methods introduced in the present work provides an efficient way to extend the length of the QM and QM/MM molecular dynamics simulations beyond the length accessible by BOMD simulation. PMID:26584095
Mathematical simulation and calculation of the soil compaction under dynamic loads
NASA Astrophysics Data System (ADS)
Zolotarevskaya, D. I.
2011-04-01
The deformation and compaction of loamy sandy soddy-podzolic soils under linear dynamic changes in the compressive stresses and in the course of the soil creeping were studied in field experiments. The rheological properties of these soils occurring in the viscoelastic state were described by a first-order differential equation relating the compressive stresses, the rates of their changes, and the velocities of the relative vertical compressive deformation. Regression equations were derived for the viscoelastic properties of the studied soil as functions of its density, moisture, and linear compaction velocity. Methods were proposed for the calculation of indices of the stress-strain state and the compaction of soils under specified conditions of changes in their compressive stresses with time and in the course of the soil creeping after the initial linear increase in load. Corresponding computer programs were developed. The effect of the main factors due to the linear increase in the compressive loads and in the course of the soil creeping on the rheological properties, the stress-strain state, and the density of soils was quantitatively estimated. The calculation showed that the values of the soil deformation and the density under compressive stresses lower than the ultimate strength were stabilized with time, and the properties of the viscoelastic soil approached elastic ones.
Yang, Benhui; Chen, Wenwu; Poirier, Bill
2011-09-01
Exact quantum dynamics calculations of the eigenstate energy levels and wavefunctions for all bound rovibrational states of the Ne(3) trimer (J = 0-18) have been performed using the ScalIT suite of parallel codes. These codes employ a combination of highly efficient methods, including phase-space optimized discrete variable representation, optimal separable basis, and preconditioned inexact spectral transform methods, together with an effective massive parallelization scheme. The Ne(3) energy levels and wavefunctions were computed using a pair-wise Lennard-Jones potential. Jacobi coordinates were used for the calculations, but to identify just those states belonging to the totally symmetric irreducible representation of the G(12) complete nuclear permutation-inversion group, wavefunctions were plotted in hyperspherical coordinates. "Horseshoe" states were observed above the isomerization barrier, but the horseshoe localization effect is weaker than in Ar(3). The rigid rotor model is found to be applicable for only the ground and first excited vibrational states at low J; fitted rotational constant values are presented. PMID:21913762
Teo, Ivan; Mayne, Christopher G; Schulten, Klaus; Lelièvre, Tony
2016-06-14
Adaptive multilevel splitting (AMS) is a rare event sampling method that requires minimal parameter tuning and allows unbiased sampling of transition pathways of a given rare event. Previous simulation studies have verified the efficiency and accuracy of AMS in the calculation of transition times for simple systems in both Monte Carlo and molecular dynamics (MD) simulations. Now, AMS is applied for the first time to an MD simulation of protein-ligand dissociation, representing a leap in complexity from the previous test cases. Of interest is the dissociation rate, which is typically too low to be accessible to conventional MD. The present study joins other recent efforts to develop advanced sampling techniques in MD to calculate dissociation rates, which are gaining importance in the pharmaceutical field as indicators of drug efficacy. The system investigated here, benzamidine bound to trypsin, is an example common to many of these efforts. The AMS estimate of the dissociation rate was found to be (2.6 ± 2.4) × 10(2) s(-1), which compares well with the experimental value. PMID:27159059
Halverson, Thomas; Poirier, Bill
2012-12-14
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003); B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004); and ibid. 121, 1704 (2004)], a new method was introduced for performing exact quantum dynamics calculations. The method uses a 'weylet' basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality-the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions).
NASA Astrophysics Data System (ADS)
Howell, P. C.
2012-12-01
We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity κ, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate κ(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si.
Howell, P C
2012-12-14
We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity κ, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate κ(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si. PMID:23248991
NASA Astrophysics Data System (ADS)
Halverson, Thomas; Poirier, Bill
2012-12-01
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003);, 10.1142/S0219633603000380 B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004);, 10.1063/1.1767511 B. Poirier and A. Salam, J. Chem. Phys. 121, 1704 (2004), 10.1063/1.1767512], a new method was introduced for performing exact quantum dynamics calculations. The method uses a "weylet" basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality—the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions).
Halverson, Thomas; Poirier, Bill
2012-12-14
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003); B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004); and ibid. 121, 1704 (2004)], a new method was introduced for performing exact quantum dynamics calculations. The method uses a "weylet" basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality--the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions). PMID:23248981
NASA Astrophysics Data System (ADS)
Alman, D. A.; Ruzic, D. N.; Brooks, J. N.
2001-10-01
Reflection coefficients of carbon and hydrocarbon molecules have been calculated with a molecular dynamics code. The code uses the Brenner hydrocarbon potential, an empirical many-body potential that can model the chemical bonding in small hydrocarbon molecules and graphite surfaces. A variety of incident energies and angles have been studied. Typical results for carbon show reflection coefficients 0.4 at thermal energy, decreasing to a minimum of 0.15 at 10-20 eV, and then increasing again. Distributed computing is used to distribute the work among 10-20 desktop PCs in the laboratory. The system consists of a client application run on all of the PCs and a single server machine that distributes work and compiles the results sent back from the clients. The client-server software is written in Java and requires no commercial software packages. Thus, the MD code benefits from multiprocessor-like speed-up at no additional cost by using the idle CPU cycles that would otherwise be wasted. These calculations represent an important improvement to the WBC code, which has been used to model surface erosion, core plasma contamination, and tritium codeposition in many fusion design studies and experiments.
Self-consistency based control scheme for magnetization dynamics
Albuquerque, G.; Miltat, J.; Thiaville, A.
2001-06-01
A numerical framework is presented for the solution of the Landau{endash}Lifshitz{endash}Gilbert equation of magnetization motion using a semi-implicit Crank{endash}Nicholson integration scheme. Along with the details of both space and time domain discretizations, we report on the development of a physically based self-consistency criterion that allows for a quantitative measurement of error in dynamic micromagnetic simulations. In essence, this criterion relies in recalculating from actual magnetization motion the imposed phenomenological damping constant. Test calculations were performed with special attention paid to the determination of suitable integration time steps. {copyright} 2001 American Institute of Physics.
NASA Technical Reports Server (NTRS)
Geyser, L. C.
1978-01-01
A digital computer program, DYGABCD, was developed that generates linearized, dynamic models of simulated turbofan and turbojet engines. DYGABCD is based on an earlier computer program, DYNGEN, that is capable of calculating simulated nonlinear steady-state and transient performance of one- and two-spool turbojet engines or two- and three-spool turbofan engines. Most control design techniques require linear system descriptions. For multiple-input/multiple-output systems such as turbine engines, state space matrix descriptions of the system are often desirable. DYGABCD computes the state space matrices commonly referred to as the A, B, C, and D matrices required for a linear system description. The report discusses the analytical approach and provides a users manual, FORTRAN listings, and a sample case.
Optimizing legacy molecular dynamics software with directive-based offload
NASA Astrophysics Data System (ADS)
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-10-01
Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-05-14
The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-05-14
The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less
Space resection model calculation based on Random Sample Consensus algorithm
NASA Astrophysics Data System (ADS)
Liu, Xinzhu; Kang, Zhizhong
2016-03-01
Resection has been one of the most important content in photogrammetry. It aims at the position and attitude information of camera at the shooting point. However in some cases, the observed values for calculating are with gross errors. This paper presents a robust algorithm that using RANSAC method with DLT model can effectually avoiding the difficulties to determine initial values when using co-linear equation. The results also show that our strategies can exclude crude handicap and lead to an accurate and efficient way to gain elements of exterior orientation.
A probability-based formula for calculating interobserver agreement1
Yelton, Ann R.; Wildman, Beth G.; Erickson, Marilyn T.
1977-01-01
Estimates of observer agreement are necessary to assess the acceptability of interval data. A common method for assessing observer agreement, per cent agreement, includes several major weaknesses and varies as a function of the frequency of behavior recorded and the inclusion or exclusion of agreements on nonoccurrences. Also, agreements that might be expected to occur by chance are not taken into account. An alternative method for assessing observer agreement that determines the exact probability that the obtained number of agreements or better would have occurred by chance is presented and explained. Agreements on both occurrences and nonoccurrences of behavior are considered in the calculation of this probability. PMID:16795541
Wang, Guo-Xiang; Dong, Shuai; Hou, Jing-Min
2016-03-31
The lattice structures and topological properties of [Formula: see text] (X = C, Si, Ge, Sn, Pb) under hydrostatic strain have been investigated based on first-principle calculations. Among the materials, [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] are dynamically stable with negative formation energy and no imaginary phonon frequency. We find that the hydrostatic strain cannot induce a quantum phase transition between topological trivial and nontrivial state for both [Formula: see text] and [Formula: see text], while for [Formula: see text] and [Formula: see text] the tensile strain can play a unique role in tuning the band topology, which will lead to a topological nontrivial state with Z 2 invariants (1;111). Although the topological transition occurs above the Fermi level, the Fermi level can be tuned by applying electrostatic gating voltage. PMID:26932939
Freeway travel speed calculation model based on ETC transaction data.
Weng, Jiancheng; Yuan, Rongliang; Wang, Ru; Wang, Chang
2014-01-01
Real-time traffic flow operation condition of freeway gradually becomes the critical information for the freeway users and managers. In fact, electronic toll collection (ETC) transaction data effectively records operational information of vehicles on freeway, which provides a new method to estimate the travel speed of freeway. First, the paper analyzed the structure of ETC transaction data and presented the data preprocess procedure. Then, a dual-level travel speed calculation model was established under different levels of sample sizes. In order to ensure a sufficient sample size, ETC data of different enter-leave toll plazas pairs which contain more than one road segment were used to calculate the travel speed of every road segment. The reduction coefficient α and reliable weight θ for sample vehicle speed were introduced in the model. Finally, the model was verified by the special designed field experiments which were conducted on several freeways in Beijing at different time periods. The experiments results demonstrated that the average relative error was about 6.5% which means that the freeway travel speed could be estimated by the proposed model accurately. The proposed model is helpful to promote the level of the freeway operation monitoring and the freeway management, as well as to provide useful information for the freeway travelers. PMID:25580107
Freeway Travel Speed Calculation Model Based on ETC Transaction Data
Weng, Jiancheng; Yuan, Rongliang; Wang, Ru; Wang, Chang
2014-01-01
Real-time traffic flow operation condition of freeway gradually becomes the critical information for the freeway users and managers. In fact, electronic toll collection (ETC) transaction data effectively records operational information of vehicles on freeway, which provides a new method to estimate the travel speed of freeway. First, the paper analyzed the structure of ETC transaction data and presented the data preprocess procedure. Then, a dual-level travel speed calculation model was established under different levels of sample sizes. In order to ensure a sufficient sample size, ETC data of different enter-leave toll plazas pairs which contain more than one road segment were used to calculate the travel speed of every road segment. The reduction coefficient α and reliable weight θ for sample vehicle speed were introduced in the model. Finally, the model was verified by the special designed field experiments which were conducted on several freeways in Beijing at different time periods. The experiments results demonstrated that the average relative error was about 6.5% which means that the freeway travel speed could be estimated by the proposed model accurately. The proposed model is helpful to promote the level of the freeway operation monitoring and the freeway management, as well as to provide useful information for the freeway travelers. PMID:25580107
Calculating Nozzle Side Loads using Acceleration Measurements of Test-Based Models
NASA Technical Reports Server (NTRS)
Brown, Andrew M.; Ruf, Joe
2007-01-01
As part of a NASA/MSFC research program to evaluate the effect of different nozzle contours on the well-known but poorly characterized "side load" phenomena, we attempt to back out the net force on a sub-scale nozzle during cold-flow testing using acceleration measurements. Because modeling the test facility dynamics is problematic, new techniques for creating a "pseudo-model" of the facility and nozzle directly from modal test results are applied. Extensive verification procedures were undertaken, resulting in a loading scale factor necessary for agreement between test and model based frequency response functions. Side loads are then obtained by applying a wide-band random load onto the system model, obtaining nozzle response PSD's, and iterating both the amplitude and frequency of the input until a good comparison of the response with the measured response PSD for a specific time point is obtained. The final calculated loading can be used to compare different nozzle profiles for assessment during rocket engine nozzle development and as a basis for accurate design of the nozzle and engine structure to withstand these loads. The techniques applied within this procedure have extensive applicability to timely and accurate characterization of all test fixtures used for modal test.A viewgraph presentation on a model-test based pseudo-model used to calculate side loads on rocket engine nozzles is included. The topics include: 1) Side Loads in Rocket Nozzles; 2) Present Side Loads Research at NASA/MSFC; 3) Structural Dynamic Model Generation; 4) Pseudo-Model Generation; 5) Implementation; 6) Calibration of Pseudo-Model Response; 7) Pseudo-Model Response Verification; 8) Inverse Force Determination; 9) Results; and 10) Recent Work.
A Dynamic Attitude Measurement System Based on LINS
Li, Hanzhou; Pan, Quan; Wang, Xiaoxu; Zhang, Juanni; Li, Jiang; Jiang, Xiangjun
2014-01-01
A dynamic attitude measurement system (DAMS) is developed based on a laser inertial navigation system (LINS). Three factors of the dynamic attitude measurement error using LINS are analyzed: dynamic error, time synchronization and phase lag. An optimal coning errors compensation algorithm is used to reduce coning errors, and two-axis wobbling verification experiments are presented in the paper. The tests indicate that the attitude accuracy is improved 2-fold by the algorithm. In order to decrease coning errors further, the attitude updating frequency is improved from 200 Hz to 2000 Hz. At the same time, a novel finite impulse response (FIR) filter with three notches is designed to filter the dither frequency of the ring laser gyro (RLG). The comparison tests suggest that the new filter is five times more effective than the old one. The paper indicates that phase-frequency characteristics of FIR filter and first-order holder of navigation computer constitute the main sources of phase lag in LINS. A formula to calculate the LINS attitude phase lag is introduced in the paper. The expressions of dynamic attitude errors induced by phase lag are derived. The paper proposes a novel synchronization mechanism that is able to simultaneously solve the problems of dynamic test synchronization and phase compensation. A single-axis turntable and a laser interferometer are applied to verify the synchronization mechanism. The experiments results show that the theoretically calculated values of phase lag and attitude error induced by phase lag can both match perfectly with testing data. The block diagram of DAMS and physical photos are presented in the paper. The final experiments demonstrate that the real-time attitude measurement accuracy of DAMS can reach up to 20″ (1σ) and the synchronization error is less than 0.2 ms on the condition of three axes wobbling for 10 min. PMID:25177802
A dynamic attitude measurement system based on LINS.
Li, Hanzhou; Pan, Quan; Wang, Xiaoxu; Zhang, Juanni; Li, Jiang; Jiang, Xiangjun
2014-01-01
A dynamic attitude measurement system (DAMS) is developed based on a laser inertial navigation system (LINS). Three factors of the dynamic attitude measurement error using LINS are analyzed: dynamic error, time synchronization and phase lag. An optimal coning errors compensation algorithm is used to reduce coning errors, and two-axis wobbling verification experiments are presented in the paper. The tests indicate that the attitude accuracy is improved 2-fold by the algorithm. In order to decrease coning errors further, the attitude updating frequency is improved from 200 Hz to 2000 Hz. At the same time, a novel finite impulse response (FIR) filter with three notches is designed to filter the dither frequency of the ring laser gyro (RLG). The comparison tests suggest that the new filter is five times more effective than the old one. The paper indicates that phase-frequency characteristics of FIR filter and first-order holder of navigation computer constitute the main sources of phase lag in LINS. A formula to calculate the LINS attitude phase lag is introduced in the paper. The expressions of dynamic attitude errors induced by phase lag are derived. The paper proposes a novel synchronization mechanism that is able to simultaneously solve the problems of dynamic test synchronization and phase compensation. A single-axis turntable and a laser interferometer are applied to verify the synchronization mechanism. The experiments results show that the theoretically calculated values of phase lag and attitude error induced by phase lag can both match perfectly with testing data. The block diagram of DAMS and physical photos are presented in the paper. The final experiments demonstrate that the real-time attitude measurement accuracy of DAMS can reach up to 20″ (1σ) and the synchronization error is less than 0.2 ms on the condition of three axes wobbling for 10 min. PMID:25177802
Wang, Junmei; Hou, Tingjun
2012-05-25
It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, the conformational entropy, which is usually calculated through normal-mode analysis (NMA), is needed to calculate the absolute binding free energies. Unfortunately, NMA is computationally demanding and becomes a bottleneck of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast approach to estimate the conformational entropy based upon solvent accessible surface area calculations. In our approach, the conformational entropy of a molecule, S, can be obtained by summing up the contributions of all atoms, no matter they are buried or exposed. Each atom has two types of surface areas, solvent accessible surface area (SAS) and buried SAS (BSAS). The two types of surface areas are weighted to estimate the contribution of an atom to S. Atoms having the same atom type share the same weight and a general parameter k is applied to balance the contributions of the two types of surface areas. This entropy model was parametrized using a large set of small molecules for which their conformational entropies were calculated at the B3LYP/6-31G* level taking the solvent effect into account. The weighted solvent accessible surface area (WSAS) model was extensively evaluated in three tests. For convenience, TS values, the product of temperature T and conformational entropy S, were calculated in those tests. T was always set to 298.15 K through the text. First of all, good correlations were achieved between WSAS TS and NMA TS for 44 protein or nucleic acid systems sampled with molecular dynamics simulations (10 snapshots were collected for postentropy calculations): the mean correlation coefficient squares (R²) was 0.56. As to the 20 complexes, the TS
Dynamic based damage detection in composite structures
NASA Astrophysics Data System (ADS)
Banerjee, Sauvik; Ricci, Fabrizio; Baid, Harsh; Mal, Ajit K.
2009-03-01
Advanced composites are being used increasingly in state-of-the-art aircraft and aerospace structures. In spite of their many advantages, composite materials are highly susceptible to hidden flaws that may occur at any time during the life cycle of a structure, and if undetected, may cause sudden and catastrophic failure of the entire structure. This paper is concerned with the detection and characterization of hidden defects in composite structures before they grow to a critical size. A methodology for automatic damage identification and localization is developed using a combination of vibration and wave propagation data. The structure is assumed to be instrumented with an array of actuators and sensors to excite and record its dynamic response, including vibration and wave propagation effects. A damage index, calculated from the measured dynamical response of the structure in a previous (reference) state and the current state, is introduced as a determinant of structural damage. The indices are used to identify low velocity impact damages in increasingly complex composite structural components. The potential application of the approach in developing health monitoring systems in defects-critical structures is indicated.
Integral-transport-based deterministic brachytherapy dose calculations
NASA Astrophysics Data System (ADS)
Zhou, Chuanyu; Inanc, Feyzi
2003-01-01
We developed a transport-equation-based deterministic algorithm for computing three-dimensional brachytherapy dose distributions. The deterministic algorithm has been based on the integral transport equation. The algorithm provided us with the capability of computing dose distributions for multiple isotropic point and/or volumetric sources in a homogenous/heterogeneous medium. The algorithm results have been benchmarked against the results from the literature and MCNP results for isotropic point sources and volumetric sources.
The calculation of the dynamics of interaction between intense electron beams and dielectrics
Milyavskii, V.V.; Skvortsov, V.A.
1995-09-01
A mathematical model is constructed and a numerical investigation performed of the interaction between an intense relativistic electron beam and a solid high-molecular dielectric. The model is based on the equations of mechanics of continuum, electrodynamics, and kinetics, describing the accumulation and relaxation of space charge and shock-wave processes, as well as the evolution of electric field in the sample. A semiempirical procedure is proposed for the calculation of energy deposition by an electron beam in a target in the presence of a nonuniform electric field.
Grid-based electronic structure calculations: The tensor decomposition approach
NASA Astrophysics Data System (ADS)
Rakhuba, M. V.; Oseledets, I. V.
2016-05-01
We present a fully grid-based approach for solving Hartree-Fock and all-electron Kohn-Sham equations based on low-rank approximation of three-dimensional electron orbitals. Due to the low-rank structure the total complexity of the algorithm depends linearly with respect to the one-dimensional grid size. Linear complexity allows for the usage of fine grids, e.g. 81923 and, thus, cheap extrapolation procedure. We test the proposed approach on closed-shell atoms up to the argon, several molecules and clusters of hydrogen atoms. All tests show systematical convergence with the required accuracy.
Furnish, M.D.; Boslough, M.B.; Gray, G.T. III; Remo, J.L.
1994-07-01
We describe methods for measuring dynamical properties for two material categories of interest in understanding large-scale extraterrestrial impacts: iron-nickel and underdense materials (e.g. snow). Particular material properties measured by the present methods include Hugoniot release paths and constitutive properties (stress vs. strain). The iron-nickel materials lend themselves well to conventional shock and quasi-static experiments. As examples, a suite of experiments is described including six impact tests (wave profile compression/release) over the stress range 2--20 GPa, metallography, quasi-static and split Hopkinson pressure bar (SHPB) mechanical testing, and ultrasonic mapping and sound velocity measurements. Temperature sensitivity of the dynamic behavior was measured at high and low strain rates. Among the iron-nickel materials tested, an octahedrite was found to have behavior close to that of Armco iron under shock and quasi-static conditions, while an ataxite exhibited a significantly larger quasi-static yield strength than did the octahedrite or a hexahedrite. The underdense materials pose three primary experimental difficulties. First, the samples are friable; they can melt or sublimate during storage, preparation and testing. Second, they are brittle and crushable; they cannot withstand such treatment as traditional machining or launch in a gun system. Third, with increasing porosity the calculated Hugoniot density becomes rapidly more sensitive to errors in wave time-of-arrival measurements. Carefully chosen simulants eliminate preservation (friability) difficulties, but the other difficulties remain. A family of 36 impact tests was conducted on snow and snow simulants at Sandia, yielding reliable Hugoniot and reshock states, but limited release property information. Other methods for characterizing these materials are discussed.
Formation flying benefits based on vortex lattice calculations
NASA Technical Reports Server (NTRS)
Maskew, B.
1977-01-01
A quadrilateral vortex-lattice method was applied to a formation of three wings to calculate force and moment data for use in estimating potential benefits of flying aircraft in formation on extended range missions, and of anticipating the control problems which may exist. The investigation led to two types of formation having virtually the same overall benefits for the formation as a whole, i.e., a V or echelon formation and a double row formation (with two staggered rows of aircraft). These formations have unequal savings on aircraft within the formation, but this allows large longitudinal spacings between aircraft which is preferable to the small spacing required in formations having equal benefits for all aircraft. A reasonable trade-off between a practical formation size and range benefit seems to lie at about three to five aircraft with corresponding maximum potential range increases of about 46 percent to 67 percent. At this time it is not known what fraction of this potential range increase is achievable in practice.
Coupled-cluster based basis sets for valence correlation calculations
NASA Astrophysics Data System (ADS)
Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.
2016-03-01
Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via
Coupled-cluster based basis sets for valence correlation calculations.
Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J
2016-03-14
Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via ⟨r(n)⟩ (-3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within "chemical accuracy" of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers. PMID:26979680
Ray-Based Calculations of Backscatter in Laser Fusion Targets
Strozzi, D J; Williams, E A; Hinkel, D E; Froula, D H; London, R A; Callahan, D A
2008-02-26
A steady-state model for Brillouin and Raman backscatter along a laser ray path is presented. The daughter plasma waves are treated in the strong damping limit, and have amplitudes given by the (linear) kinetic response to the ponderomotive drive. Pump depletion, inverse-bremsstrahlung damping, bremsstrahlung emission, Thomson scattering off density fluctuations, and whole-beam focusing are included. The numerical code deplete, which implements this model, is described. The model is compared with traditional linear gain calculations, as well as 'plane-wave' simulations with the paraxial propagation code pf3d. Comparisons with Brillouin-scattering experiments at the OMEGA Laser Facility [T. R. Boehly et al., Opt. Commun. 133, p. 495 (1997)] show that laser speckles greatly enhance the reflectivity over the deplete results. An approximate upper bound on this enhancement, motivated by phase conjugation, is given by doubling the deplete coupling coefficient. Analysis with deplete of an ignition design for the National Ignition Facility (NIF) [J. A. Paisner, E. M. Campbell, and W. J. Hogan, Fusion Technol. 26, p. 755 (1994)], with a peak radiation temperature of 285 eV, shows encouragingly low reflectivity. Doubling the coupling to bound the speckle enhancement suggests a less optimistic picture. Re-absorption of Raman light is seen to be significant in this design.
Yeh, In-Chul; Lee, Michael S; Olson, Mark A
2008-11-27
The heat capacity has played a major role in relating microscopic and macroscopic properties of proteins and their disorder-order phase transition of folding. Its calculation by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of protein structures, their solvent environment, and configurational averaging. To better understand these factors on calculating a protein heat capacity, we provide a comparative analysis of simulation models that differ in their implicit solvent description and force-field resolution. Our model protein system is the src Homology 3 (SH3) domain of alpha-spectrin, and we report a series of 10 ns replica-exchange molecular dynamics simulations performed at temperatures ranging from 298 to 550 K, starting from the SH3 native structure. We apply the all-atom CHARMM22 force field with different modified analytical generalized Born solvent models (GBSW and GBMV2) and compare these simulation models with the distance-dependent dielectric screening of charge-charge interactions. A further comparison is provided with the united-atom CHARMM19 plus a pairwise GB model. Unfolding-folding transition temperatures of SH3 were estimated from the temperature-dependent profiles of the heat capacity, root-mean-square distance from the native structure, and the fraction of native contacts, each calculated from the density of states by using the weighted histogram analysis method. We observed that, for CHARMM22, the unfolding transition and energy probability density were quite sensitive to the implicit solvent description, in particular, the treatment of the protein-solvent dielectric boundary in GB models and their surface-area-based hydrophobic term. Among the solvent models tested, the calculated melting temperature varied in the range 353-438 K and was higher than the experimental value near 340 K. A reformulated GBMV2 model of employing a smoother molecular-volume dielectric interface was the most accurate
NASA Astrophysics Data System (ADS)
Pennacchi, Paolo
2008-04-01
The modelling of the unbalanced magnetic pull (UMP) in generators and the experimental validation of the proposed method are presented in this paper. The UMP is one of the most remarkable effects of electromechanical interactions in rotating machinery. As a consequence of the rotor eccentricity, the imbalance of the electromagnetic forces acting between rotor and stator generates a net radial force. This phenomenon can be avoided by means of a careful assembly and manufacture in small and stiff machines, like electrical motors. On the contrary, the eccentricity of the active part of the rotor with respect to the stator is unavoidable in big generators of power plants, because they operate above their first critical speed and are supported by oil-film bearings. In the first part of the paper, a method aimed to calculate the UMP force is described. This model is more general than those available in literature, which are limited to circular orbits. The model is based on the actual position of the rotor inside the stator, therefore on the actual air-gap distribution, regardless of the orbit type. The closed form of the nonlinear UMP force components is presented. In the second part, the experimental validation of the proposed model is presented. The dynamical behaviour in the time domain of a steam turbo-generator of a power plant is considered and it is shown that the model is able to reproduce the dynamical effects due to the excitation of the magnetic field in the generator.
Dynamics-based centrality for directed networks
NASA Astrophysics Data System (ADS)
Masuda, Naoki; Kori, Hiroshi
2010-11-01
Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this respect is the PageRank. In this work, we focus on another class of centrality derived from the Laplacian of the network. We extend the Laplacian-based centrality, which has mainly been applied to strongly connected networks, to the case of general directed networks such that we can quantitatively compare arbitrary nodes. Toward this end, we adopt the idea used in the PageRank to introduce global connectivity between all the pairs of nodes with a certain strength. Numerical simulations are carried out on some networks. We also offer interpretations of the Laplacian-based centrality for general directed networks in terms of various dynamical and structural properties of networks. Importantly, the Laplacian-based centrality defined as the stationary density of the continuous-time random walk with random jumps is shown to be equivalent to the absorption probability of the random walk with sinks at each node but without random jumps. Similarly, the proposed centrality represents the importance of nodes in dynamics on the original network supplied with sinks but not with random jumps.
Molecular Dynamics and Energy Minimization Based on Embedded Atom Method
Energy Science and Technology Software Center (ESTSC)
1995-03-01
This program performs atomic scale computer simulations of the structure and dynamics of metallic system using energetices based on the Embedded Atom Method. The program performs two types of calculations. First, it performs local energy minimization of all atomic positions to determine ground state and saddle point energies and structures. Second, it performs molecular dynamics simulations to determine thermodynamics or miscroscopic dynamics of the system. In both cases, various constraints can be applied to themore » system. The volume of the system can be varied automatically to achieve any desired external pressure. The temperature in molecular dynamics simulations can be controlled by a variety of methods. Further, the temperature control can be applied either to the entire system or just a subset of the atoms that would act as a thermal source/sink. The motion of one or more of the atoms can be constrained to either simulate the effects of bulk boundary conditions or to facilitate the determination of saddle point configurations. The simulations are performed with periodic boundary conditions.« less
NASA Technical Reports Server (NTRS)
Vinokur, M.
1979-01-01
The class of one-dimensional stretching functions used in finite-difference calculations is studied. For solutions containing a highly localized region of rapid variation, simple criteria for a stretching function are derived using a truncation error analysis. These criteria are used to investigate two types of stretching functions. One is an interior stretching function, for which the location and slope of an interior clustering region are specified. The simplest such function satisfying the criteria is found to be one based on the inverse hyperbolic sine. The other type of function is a two-sided stretching function, for which the arbitrary slopes at the two ends of the one-dimensional interval are specified. The simplest such general function is found to be one based on the inverse tangent.
NASA Astrophysics Data System (ADS)
Mozafari, E.; Shulumba, N.; Steneteg, P.; Alling, B.; Abrikosov, Igor A.
2016-08-01
We present a theoretical scheme to calculate the elastic constants of magnetic materials in the high-temperature paramagnetic state. Our approach is based on a combination of disordered local moments picture and ab initio molecular dynamics (DLM-MD). Moreover, we investigate a possibility to enhance the efficiency of the simulations of elastic properties using the recently introduced method: symmetry imposed force constant temperature-dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as a model system. This is done due to its technological importance and its demonstrated strong coupling between magnetic and lattice degrees of freedom. We have studied the temperature-dependent single-crystal and polycrystalline elastic constants of paramagentic CrN up to 1200 K. The obtained results at T = 300 K agree well with the experimental values of polycrystalline elastic constants as well as the Poisson ratio at room temperature. We observe that the Young's modulus is strongly dependent on temperature, decreasing by ˜14 % from T = 300 K to 1200 K. In addition we have studied the elastic anisotropy of CrN as a function of temperature and we observe that CrN becomes substantially more isotropic as the temperature increases. We demonstrate that the use of Birch law may lead to substantial errors for calculations of temperature induced changes of elastic moduli. The proposed methodology can be used for accurate predictions of mechanical properties of magnetic materials at temperatures above their magnetic order-disorder phase transition.
Li, Xianfeng; Hassan, Sergio A.; Mehler, Ernest L.
2006-01-01
Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP–ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding Cα root mean square deviations (RMSD) of about 1.0 and 0.8 Å respectively along the entire simulation time, compared to 0.8 Å for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a Cα RMSD of ≈ 1.4 Å, while the PAR22/LD trajectory became unstable
NASA Technical Reports Server (NTRS)
Haskins, Justin; Kinaci, Alper; Sevik, Cem; Cagin, Tahir
2012-01-01
It is widely known that graphene and many of its derivative nanostructures have exceedingly high reported thermal conductivities (up to 4000 W/mK at 300 K). Such attractive thermal properties beg the use of these structures in practical devices; however, to implement these materials while preserving transport quality, the influence of structure on thermal conductivity should be thoroughly understood. For graphene nanostructures, having average phonon mean free paths on the order of one micron, a primary concern is how size influences the potential for heat conduction. To investigate this, we employ a novel technique to evaluate the lattice thermal conductivity from the Green-Kubo relations and equilibrium molecular dynamics in systems where phonon-boundary scattering dominates heat flow. Specifically, the thermal conductivities of graphene nanoribbons and carbon nanotubes are calculated in sizes up to 3 microns, and the relative influence of boundary scattering on thermal transport is determined to be dominant at sizes less than 1 micron, after which the thermal transport largely depends on the quality of the nanostructure interface. The method is also extended to carbon nanostructures (fullerenes) where phonon confinement, as opposed to boundary scattering, dominates, and general trends related to the influence of curvature on thermal transport in these materials are discussed.
Grandits, Melanie; Michlmayr, Herbert; Sygmund, Christoph; Oostenbrink, Chris
2013-01-01
Ram2 from Pediococcus acidilactici is a rhamnosidase from the glycoside hydrolase family 78. It shows remarkable selectivity for rutinose rather than para-nitrophenyl-alpha-l-rhamnopyranoside (p-NPR). Molecular dynamics simulations were performed using a homology model of this enzyme, in complex with both substrates. Free energy calculations lead to predicted binding affinities of −34.4 and −30.6 kJ mol−1 respectively, agreeing well with an experimentally estimated relative free energy of 5.4 kJ mol−1. Further, the most relevant binding poses could be determined. While p-NPR preferably orients its rhamnose moiety toward the active site, rutinose interacts most strongly with its glucose moiety. A detailed hydrogen bond analysis confirms previously implicated residues in the active site (Asp217, Asp222, Trp226, Asp229 and Glu488) and quantifies the importance of individual residues for the binding. The most important amino acids are Asp229 and Phe339 which are involved in many interactions during the simulations. While Phe339 was observed in more simulations, Asp229 was involved in more persistent interactions (forming an average of at least 2 hydrogen bonds during the simulation). These analyses directly suggest mutations that could be used in a further experimental characterization of the enzyme. This study shows once more the strength of computer simulations to rationalize and guide experiments at an atomic level. PMID:23914137
Adaptation of GEANT4 to Monte Carlo dose calculations based on CT data.
Jiang, H; Paganetti, H
2004-10-01
The GEANT4 Monte Carlo code provides many powerful functions for conducting particle transport simulations with great reliability and flexibility. However, as a general purpose Monte Carlo code, not all the functions were specifically designed and fully optimized for applications in radiation therapy. One of the primary issues is the computational efficiency, which is especially critical when patient CT data have to be imported into the simulation model. In this paper we summarize the relevant aspects of the GEANT4 tracking and geometry algorithms and introduce our work on using the code to conduct dose calculations based on CT data. The emphasis is focused on modifications of the GEANT4 source code to meet the requirements for fast dose calculations. The major features include a quick voxel search algorithm, fast volume optimization, and the dynamic assignment of material density. These features are ready to be used for tracking the primary types of particles employed in radiation therapy such as photons, electrons, and heavy charged particles. Recalculation of a proton therapy treatment plan generated by a commercial treatment planning program for a paranasal sinus case is presented as an example. PMID:15543788
UAV-based NDVI calculation over grassland: An alternative approach
NASA Astrophysics Data System (ADS)
Mejia-Aguilar, Abraham; Tomelleri, Enrico; Asam, Sarah; Zebisch, Marc
2016-04-01
The Normalised Difference Vegetation Index (NDVI) is one of the most widely used indicators for monitoring and assessing vegetation in remote sensing. The index relies on the reflectance difference between the near infrared (NIR) and red light and is thus able to track variations of structural, phenological, and biophysical parameters for seasonal and long-term monitoring. Conventionally, NDVI is inferred from space-borne spectroradiometers, such as MODIS, with moderate resolution up to 250 m ground resolution. In recent years, a new generation of miniaturized radiometers and integrated hyperspectral sensors with high resolution became available. Such small and light instruments are particularly adequate to be mounted on airborne unmanned aerial vehicles (UAV) used for monitoring services reaching ground sampling resolution in the order of centimetres. Nevertheless, such miniaturized radiometers and hyperspectral sensors are still very expensive and require high upfront capital costs. Therefore, we propose an alternative, mainly cheaper method to calculate NDVI using a camera constellation consisting of two conventional consumer-grade cameras: (i) a Ricoh GR modified camera that acquires the NIR spectrum by removing the internal infrared filter. A mounted optical filter additionally obstructs all wavelengths below 700 nm. (ii) A Ricoh GR in RGB configuration using two optical filters for blocking wavelengths below 600 nm as well as NIR and ultraviolet (UV) light. To assess the merit of the proposed method, we carry out two comparisons: First, reflectance maps generated by the consumer-grade camera constellation are compared to reflectance maps produced with a hyperspectral camera (Rikola). All imaging data and reflectance maps are processed using the PIX4D software. In the second test, the NDVI at specific points of interest (POI) generated by the consumer-grade camera constellation is compared to NDVI values obtained by ground spectral measurements using a
Calculation of thermomechanical fatigue life based on isothermal behavior
NASA Technical Reports Server (NTRS)
Halford, Gary R.; Saltsman, James F.
1987-01-01
The isothermal and thermomechanical fatigue (TMF) crack initiation response of a hypothetical material was analyzed. Expected thermomechanical behavior was evaluated numerically based on simple, isothermal, cyclic stress-strain - time characteristics and on strainrange versus cyclic life relations that have been assigned to the material. The attempt was made to establish basic minimum requirements for the development of a physically accurate TMF life-prediction model. A worthy method must be able to deal with the simplest of conditions: that is, those for which thermal cycling, per se, introduces no damage mechanisms other than those found in isothermal behavior. Under these assumed conditions, the TMF life should be obtained uniquely from known isothermal behavior. The ramifications of making more complex assumptions will be dealt with in future studies. Although analyses are only in their early stages, considerable insight has been gained in understanding the characteristics of several existing high-temperature life-prediction methods. The present work indicates that the most viable damage parameter is based on the inelastic strainrange.