NASA Astrophysics Data System (ADS)
Pan, Zhao; Whitehead, Jared; Truscott, Tadd
2016-11-01
Little research has been done to investigate the dynamics of error propagation from PIV-based velocity measurements to the pressure calculation. Rather than measure experimental error, we analytically investigate error propagation by examining the properties of the Poisson equation directly. Our results provide two contributions to the PIV community. First, we quantify the error bound in the pressure field by illustrating the mathematical roots of why and how PIV-based pressure calculations propagate. Second, we design the "worst case error" for a pressure Poisson solver. In other words, we provide a systematic example where the relatively small errors in the experimental data can lead to maximum error in the corresponding pressure calculations. The 2D calculation of the worst case error surprisingly leads to the classic Kirchhoff plates problem, and connects the PIV-based pressure calculation, which is a typical fluid problem, to elastic dynamics. The results can be used for optimizing experimental error minimization by avoiding worst case scenarios. More importantly, they can be used to design synthetic velocity error for future PIV-pressure challenges, which can be the hardest test case in the examinations.
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.
Gapsys, Vytautas; Seeliger, Daniel; de Groot, Bert L
2012-07-10
The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the system's Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodynamic cycles involving particle introduction and annihilation. Such alchemical transitions require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft-core potential to be applied in nonequilibrium free energy calculations that alleviates singularities, numerical instabilities, and additional minima in the potential energy for all combinations of nonbonded interactions at all intermediate alchemical states. The method was validated by application to (a) the free energy calculations of a closed thermodynamic cycle, (b) the mutation influence on protein thermostability, (c) calculations of small ligand solvation free energies, and (d) the estimation of binding free energies of trypsin inhibitors. The results show that the novel soft-core function provides a robust and accurate general purpose solution to alchemical free energy calculations.
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
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.
Equation of State of Al Based on Quantum Molecular Dynamics Calculations
NASA Astrophysics Data System (ADS)
Minakov, Dmitry V.; Levashov, Pavel R.; Khishchenko, Konstantin V.
2011-06-01
In this work, we present quantum molecular dynamics calculations of the shock Hugoniots of solid and porous samples as well as release isentropes and values of isentropic sound velocity behind the shock front for aluminum. We use the VASP code with an ultrasoft pseudopotential and GGA exchange-correlation functional. Up to 108 particles have been used in calculations. For the Hugoniots of Al we solve the Hugoniot equation numerically. To calculate release isentropes, we use Zel'dovich's approach and integrate an ordinary differential equation for the temperature thus restoring all thermodynamic parameters. Isentropic sound velocity is calculated by differentiation along isentropes. The results of our calculations are in good agreement with experimental data. Thus, quantum molecular dynamics results can be effectively used for verification or calibration of semiempirical equations of state under conditions of lack of experimental information at high energy densities. This work is supported by RFBR, grants 09-08-01129 and 11-08-01225.
NASA Astrophysics Data System (ADS)
Takaba, Hiromitsu; Kimura, Shou; Alam, Md. Khorshed
2017-03-01
Durability of organo-lead halide perovskite are important issue for its practical application in a solar cells. In this study, using density functional theory (DFT) and molecular dynamics, we theoretically investigated a crystal structure, electronic structure, and ionic diffusivity of the partially substituted cubic MA0.5X0.5PbI3 (MA = CH3NH3+, X = NH4+ or (NH2)2CH+ or Cs+). Our calculation results indicate that a partial substitution of MA induces a lattice distortion, resulting in preventing MA or X from the diffusion between A sites in the perovskite. DFT calculations show that electronic structures of the investigated partially substituted perovskites were similar with that of MAPbI3, while their bandgaps slightly decrease compared to that of MAPbI3. Our results mean that partial substitution in halide perovskite is effective technique to suppress diffusion of intrinsic ions and tune the band gap.
Pan, Zhao; Whitehead, Jared; Thomson, Scott; Truscott, Tadd
2016-01-01
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. PMID:27499587
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.
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.
Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.
Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L; Brooks, Charles L
2017-06-13
λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased estimator and its variance is usually smaller than the current empirical estimator. We also show that the multistate Bennett acceptance ratio equation or the unbinned weighted histogram analysis method equation can be derived using the RBE. We illustrate the use and performance of this new free energy computational framework by application to a simple harmonic system as well as relevant calculations of small molecule relative free energies of solvation and binding to a protein receptor. Our findings demonstrate consistent and improved performance compared with conventional alchemical free energy methods.
NASA Astrophysics Data System (ADS)
Xu, Xue-song; Wang, Sheng-wei
2012-03-01
In re-entry, the drilling riser hanging to the holding vessel takes on a free hanging state, waiting to be moved from the initial random position to the wellhead. For the re-entry, dynamics calculation is often done to predict the riser motion or evaluate the structural safety. A dynamics calculation method based on Flexible Segment Model (FSM) is proposed for free hanging marine risers. In FSM, a riser is discretized into a series of flexible segments. For each flexible segment, its deflection feature and external forces are analyzed independently. For the whole riser, the nonlinear governing equations are listed according to the moment equilibrium at nodes. For the solution of the nonlinear equations, a linearization iteration scheme is provided in the paper. Owing to its flexibility, each segment can match a long part of the riser body, which enables that good results can be obtained even with a small number of segments. Moreover, the linearization iteration scheme can avoid widely used Newton-Rapson iteration scheme in which the calculation stability is influenced by the initial points. The FSM-based dynamics calculation is timesaving and stable, so suitable for the shape prediction or real-time control of free hanging marine risers.
Liu, H H; McCullough, E C; Mackie, T R
1998-01-01
A convolution/superposition based method was developed to calculate dose distributions and wedge factors in photon treatment fields generated by dynamic wedges. This algorithm used a dual source photon beam model that accounted for both primary photons from the target and secondary photons scattered from the machine head. The segmented treatment tables (STT) were used to calculate realistic photon fluence distributions in the wedged fields. The inclusion of the extra-focal photons resulted in more accurate dose calculation in high dose gradient regions, particularly in the beam penumbra. The wedge factors calculated using the convolution method were also compared to the measured data and showed good agreement within 0.5%. The wedge factor varied significantly with the field width along the moving jaw direction, but not along the static jaw or the depth direction. This variation was found to be determined by the ending position of the moving jaw, or the STT of the dynamic wedge. In conclusion, the convolution method proposed in this work can be used to accurately compute dose for a dynamic or an intensity modulated treatment based on the fluence modulation in the treatment field.
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.
Monge-Palacios, M; Corchado, J C; Espinosa-Garcia, J
2013-06-07
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)]. 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 (E(coll) ≥ 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.
Lattice dynamics calculations based on density-functional perturbation theory in real space
NASA Astrophysics Data System (ADS)
Shang, Honghui; Carbogno, Christian; Rinke, Patrick; Scheffler, Matthias
2017-06-01
A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered orbitals as basis functions is demonstrated exemplarily for the all-electron Fritz Haber Institute ab initio molecular simulations (FHI-aims) package. The convergence of the calculations with respect to numerical parameters is carefully investigated and a systematic comparison with finite-difference approaches is performed both for finite (molecules) and extended (periodic) systems. Finally, the scaling tests and scalability tests on massively parallel computer systems demonstrate the computational efficiency.
Comparison of calculated with measured dynamic aperture
Zimmermann, F.
1994-06-01
The measured dynamic aperture of the HERA proton ring and the value expected from simulation studies agree within a factor of 2. A better agreement is achieved if a realistic tune modulation is included in the simulation. The approximate threshold of tune-modulation induced diffusion can be calculated analytically. Its value is in remarkable agreement with the dynamic aperture measured. The calculation is based on parameters of resonances through order 11 which are computed using differential-algebra methods and normal-form algorithms. Modulational diffusion in conjunction with drifting machine parameters appears to be the most important transverse diffusion process.
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 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.
NASA Astrophysics Data System (ADS)
Sharipov, Felix; Yang, Yuanchao; Ricker, Jacob E.; Hendricks, Jay H.
2016-10-01
Currently, the piston-cylinder assembly known as PG39 is used as a primary pressure standard at the National Institute of Standards and Technology (NIST) in the range of 20 kPa to 1 MPa with a standard uncertainty of 3× {{10}-6} as evaluated in 2006. An approximate model of gas flow through the crevice between the piston and sleeve contributed significantly to this uncertainty. The aim of this work is to revise the previous effective cross sectional area of PG39 and its uncertainty by carrying out more exact calculations that consider the effects of rarefied gas flow. The effective cross sectional area is completely determined by the pressure distribution in the crevice. Once the pressure distribution is known, the elastic deformations of both piston and sleeve are calculated by finite element analysis. Then, the pressure distribution is recalculated iteratively for the new crevice dimension. As a result, a new value of the effective area is obtained with a relative difference of 3× {{10}-6} from the previous one. Moreover, this approach allows us to reduce significantly the standard uncertainty related to the gas flow model so that the total uncertainty is decreased by a factor of three.
Kishi, Ryohei; Fujii, Hiroaki; Kishimoto, Shingo; Murata, Yusuke; Ito, Soichi; Okuno, Katsuki; Shigeta, Yasuteru; Nakano, Masayoshi
2012-05-03
We develop novel calculation and analysis methods for the dynamic first hyperpolarizabilities β [the second-order nonlinear optical (NLO) properties at the molecular level] in the second-harmonic generation based on the quantum master equation method combined with the ab initio molecular orbital (MO) configuration interaction method. As examples, we have evaluated off-resonant dynamic β values of donor (NH(2))- and/or acceptor (NO(2))-substituted benzenes using these methods, which are shown to reproduce those by the conventional summation-over-states method well. The spatial contributions of electrons to the dynamic β of these systems are also analyzed using the dynamic β density and its partition into the MO contributions. The present results demonstrate the advantage of these methods in unraveling the mechanism of dynamic NLO properties and in building the structure-dynamic NLO property relationships of real molecules.
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 CH2 (+) 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(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) 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(+)/H containing systems.
Gutierrez, Eric; Quinn, Daniel B; Chin, Diana D; Lentink, David
2016-12-06
There are three common methods for calculating the lift generated by a flying animal based on the measured airflow in the wake. However, these methods might not be accurate according to computational and robot-based studies of flapping wings. Here we test this hypothesis for the first time for a slowly flying Pacific parrotlet in still air using stereo particle image velocimetry recorded at 1000 Hz. The bird was trained to fly between two perches through a laser sheet wearing laser safety goggles. We found that the wingtip vortices generated during mid-downstroke advected down and broke up quickly, contradicting the frozen turbulence hypothesis typically assumed in animal flight experiments. The quasi-steady lift at mid-downstroke was estimated based on the velocity field by applying the widely used Kutta-Joukowski theorem, vortex ring model, and actuator disk model. The calculated lift was found to be sensitive to the applied model and its different parameters, including vortex span and distance between the bird and laser sheet-rendering these three accepted ways of calculating weight support inconsistent. The three models predict different aerodynamic force values mid-downstroke compared to independent direct measurements with an aerodynamic force platform that we had available for the same species flying over a similar distance. Whereas the lift predictions of the Kutta-Joukowski theorem and the vortex ring model stayed relatively constant despite vortex breakdown, their values were too low. In contrast, the actuator disk model predicted lift reasonably accurately before vortex breakdown, but predicted almost no lift during and after vortex breakdown. Some of these limitations might be better understood, and partially reconciled, if future animal flight studies report lift calculations based on all three quasi-steady lift models instead. This would also enable much needed meta studies of animal flight to derive bioinspired design principles for quasi-steady lift
NASA Astrophysics Data System (ADS)
Akbarzadeh, Hamed; Abroshan, Hadi; Taherkhani, Farid; Parsafar, Gholam Abbas
2011-07-01
We present an approach for constant-pressure molecular dynamics simulations. This approach is especially designed for finite systems, for which no periodic boundary condition applies. A molecular dynamics (MD) simulation for Ni nanoclusters is used to calculate their pressure-volume-temperature ( p-v-T) data for the temperature range 200 K≤ T≤400 K, and pressures up to 600 kbar. Isothermal sets of p-v-T data were generated by the simulation; each set was fitted by three equations of state (EoSs): Linear Isotherm Regularity-II (LIRII), Birch-Murnaghan (BM), and EOS III. It is found that the MD data are satisfactorily reproduced by the EoSs with reasonable precision. Some features of the EoSs criteria, such as the temperature dependences of the coefficients, the isothermal bulk modulus and its pressure derivative at the zero-pressure limit, and isobaric thermal expansion for Ni nanoclusters, are investigated. We have found that same EoSs are valid for both bulk Ni and Ni nanoclusters, but with different values of the parameters, which depend on the cluster size and temperature. An increase in bulk modulus with decrease of cluster size can be observed. Also, an increase in isobaric expansion coefficient with decrease of cluster size has been found.
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.
Shiraishi, Fumihide; Tomita, Tomofumi; Iwata, Michio; Berrada, Aziz A; Hirayama, Hiroshi
2009-12-01
Dynamic sensitivity analysis has become an important tool to successfully characterize all sorts of biological systems. However, when the analysis is carried out on large scale systems, it becomes imperative to employ a highly accurate computational method in order to obtain reliable values. Furthermore, the preliminary laborious mathematical operations required by current software before the computation of dynamic sensitivities makes it inconvenient for a significant number of unacquainted users. To satisfy these needs, the present work investigates a newly developed algorithm consisting of a combination of Taylor series method that can directly execute Taylor expansions for simultaneous non-linear-differential equations and a simple but highly-accurate numerical differentiation method based on finite-difference formulas. Applications to three examples of biochemical systems indicate that the proposed method makes it possible to compute the dynamic sensitivity values with highly-reliable accuracies and also allows to readily compute them by setting up only the differential equations for metabolite concentrations in the computer program. Also, it is found that the Padé approximation introduced in the Taylor series method shortens the computation time greatly because it stabilizes the computation so that it allows us to use larger stepsizes in the numerical integration. Consequently, the calculated results suggest that the proposed computational method, in addition to being user-friendly, makes it possible to perform dynamic sensitivity analysis in large-scale metabolic reaction systems both efficiently and reliably.
Cluster dynamical mean-field calculations for TiOCl
NASA Astrophysics Data System (ADS)
Saha-Dasgupta, T.; Lichtenstein, A.; Hoinkis, M.; Glawion, S.; Sing, M.; Claessen, R.; Valentí, R.
2007-10-01
Based on a combination of cluster dynamical mean field theory (DMFT) and density functional calculations, we calculated the angle-integrated spectral density in the layered s=1/2 quantum magnet TiOCl. The agreement with recent photoemission and oxygen K-edge x-ray absorption spectroscopy experiments is found to be good. The improvement achieved with this calculation with respect to previous single-site DMFT calculations is an indication of the correlated nature and low-dimensionality of TiOCl.
Sun, Dong-Ru; Zheng, Qing-Chuan; Zhang, Hong-Xing
2017-03-01
Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation and binding free energy studies were performed to investigate the biochemistry behaviors of two class inhibitors binding to matriptase. The binding free energies predicted by MM/GBSA methods are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. The key residues responsible for achieving strong binding have been identified by the MM/GBSA free energy decomposition analysis. Especially, Trp215 and Phe99 had an important impact on active site architecture and ligand binding. The results clearly identify the two class inhibitors exist different binding modes. Through summarizing the two different modes, we have mastered some important and favorable interaction patterns between matriptase and inhibitors. Our findings would be helpful for understanding the interaction mechanism between the inhibitor and matriptase and afford important guidance for the rational design of potent matriptase inhibitors.
Feliks, Mikolaj; Lafaye, Céline; Shu, Xiaokun; Royant, Antoine; Field, Martin
2016-08-09
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.
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.
NASA Astrophysics Data System (ADS)
Muñoz-Losa, Aurora; Markovitsi, Dimitra; Improta, Roberto
2015-08-01
A State-Specific PCM-DFT method taking into account dynamical solvent effects in the calculation of ionization energies (IEs) is reported. Mono-methylated nucleobases, representative of DNA blocks, are used as a test case. The accuracy of several functionals is tested, the M05-2X functional providing the most consistent performance. The inclusion of some molecules of the first hydration shell does not significantly affect the computed IE. The obtained vertical and adiabatic IEs are in good agreement with the available experimental and computational results, supporting the reliability of our method, enabling the calculation of first and upper ionization energies by using a single approach.
Yang, Xuemei; Friedman, Adam; Nagpal, Shailender; Perrimon, Norbert; Asara, John M
2009-12-01
A label-free quantification strategy including the development of in-house software (NakedQuant) to calculate the average TIC across all spectral counts in tandem affinity purification (TAP)-tagging liquid chromatography-mass spectrometry MS/MS (LC/MS/MS) experiments was applied to a large-scale study of protein complexes in the MAPK portion of the insulin signaling pathway from Drosophila cells. Dynamics were calculated under basal and stimulating conditions as fold changes. These experiments were performed in the context of a core service model with the user performing the TAP immunoprecipitation and the MS core performing the MS and informatics stops. The MS strategy showed excellent coverage of known components in addition to potentially novel interactions.
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.
Modeling Functions with the Calculator Based Ranger.
ERIC Educational Resources Information Center
Sherrill, Donna; Tibbs, Peggy
This paper presents two mathematics activities that model functions studied using the Calculator Based Ranger (CBR) software for TI-82 and TI-83 graphing calculators. The activities concern a bouncing ball experiment and modeling a decaying exponential function. (ASK)
NASA Astrophysics Data System (ADS)
Guan, Zhuohuai; Li, Liang; Wu, Chongyou
2017-06-01
Transmission belt is one of the most likely to fail parts of combine harvester, which affecting the machine reliability seriously. Dynamic strength occurs along with vibration during the operation and must be taken into account when calculating reliability, especially in harsh working environment like harvesting. However, the existing calculation method of reliability on combine harvester transmission belt didn’t take the dynamic strength into account. In this research, a reliability calculation method was proposed based on the dynamic analysis of transmission belt. The nonlinear dynamic equation was built using string and beam model. Through the equation, relationship between belt speed and dynamic stress was deduced. Considering dynamic stress and regarding uncertain parameters as random uncertain parameters, reliability calculation model was built. Finally, an example was presented and the above mentioned dynamic reliability calculation method was simulated to verify the theoretical analysis in this paper and tested by the Monte-Carlo method.
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
NASA Astrophysics Data System (ADS)
Ishii, Hiroyuki; Kobayashi, Nobuhiko; Hirose, Kenji
2017-01-01
We present a wave-packet dynamical approach to charge transport using maximally localized Wannier functions based on density functional theory including van der Waals interactions. We apply it to the transport properties of pentacene and rubrene single crystals and show the temperature-dependent natures from bandlike to thermally activated behaviors as a function of the magnitude of external static disorder. We compare the results with those obtained by the conventional band and hopping models and experiments.
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
Dynamical collective calculation of supernova neutrino signals.
Gava, Jérôme; Kneller, James; Volpe, Cristina; McLaughlin, G C
2009-08-14
We present the first calculations with three flavors of collective and shock wave effects for neutrino propagation in core-collapse supernovae using hydrodynamical density profiles and the S matrix formalism. We explore the interplay between the neutrino-neutrino interaction and the effects of multiple resonances upon the time signal of positrons in supernova observatories. A specific signature is found for the inverted hierarchy and a large third neutrino mixing angle and we predict, in this case, a dearth of lower energy positrons in Cherenkov detectors midway through the neutrino signal and the simultaneous revelation of valuable information about the original fluxes. We show that this feature is also observable with current generation neutrino detectors at the level of several sigmas.
NASA Astrophysics Data System (ADS)
Massobrio, C.; Celino, M.; Pouillon, Y.; Billas, I. M. L.
In both clusters and disordered systems the determination of structural properties often relies on qualitative interpretations of experimental data. First-principles molecular dynamics provides a reliable atomic-scale tool to optimize geometries and follow the dynamical evolution at different temperatures. We present three examples of application of first-principles molecular dynamics to the study of finite systems and disordered, bulk networks. In the first case, devoted to the copper oxide clusters CuO2 and CuO6, the account of temperature effects and a careful search of all isomer allows to complement effectively photoelectron spectroscopy data. In the second example, we analyze the behavior of the C60 fullerene when one or two silicon atoms are inserted in the cage to replace carbon atoms. Silicon atoms correspond to chemically reactive sites of the fullerenes, giving rise to local structural distortions. Then, we describe the determination of the structure for liquid SiSe2 at thermal equilibrium. The microscopic origins of intermediate range order are rationalized in terms of network connectivity and specific features appearing in the structure factors. Overall, first-principles molecular dynamics appears as a convincing method to corroborate experimental work and make reliable predictions based on well-established electronic structure techniques.
Thermal neutron scattering law calculations using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Wormald, Jonathan; Hawari, Ayman I.
2017-09-01
In recent years, methods for the calculation of the thermal scattering law (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables, respectively) were developed based on ab initio lattice dynamics (AILD) and/or classical molecular dynamics (CMD). While these methods are now mature and efficient, further advancement in the application of such atomistic techniques is possible using ab initio molecular dynamics (AIMD) methods. In this case, temperature effects are inherently included in the calculation, e.g. phonon density of states (DOS), while using ab initio force fields that eliminate the need for parameterized semi-empirical force fields. In this work, AIMD simulations were performed to predict the phonon spectra as a function of temperature for beryllium and graphite, which are representative nuclear reactor moderator and reflector materials. Subsequently, the calculated phonon spectra were utilized to predict S(α,β) using the LEAPR module of the NJOY code. The AIMD models of beryllium and graphite were 5 × 5 × 5 crystal unit cells (250 atoms and 500 atoms respectively). Electronic structure calculations for the prediction of Hellman-Feynman forces were performed using density functional theory with a GGA exchange correlation functional and corresponding core electron pseudopotentials. AIMD simulations of 1000-10,000 time-steps were performed with the canonical ensemble (NVT thermostat) for several temperatures between 300 K and 900 K. The phonon DOS were calculated as the power spectrum of the AIMD predicted velocity autocorrelation functions. The resulting AIMD phonon DOS and corresponding inelastic thermal neutron scattering cross sections at 300 K, where anharmonic effects are expected to be small, were found to be in reasonable agreement with the results generated using traditional AILD. This illustrated the validity of the AIMD approach. However, since the impact of the temperature on the phonon DOS (e.g. broadening of
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.
Li, Bin; Han, Ke-Li
2008-03-21
A theoretical investigation on the nonadiabatic processes of the full three-dimensional D(+)+H(2) and H(+)+D(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(2) or D(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(2) or D(2). The calculated results from ZN-TSH method are in good agreement with the exact quantum calculations and the experimental measurements.
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.
NASA Astrophysics Data System (ADS)
Cao, Jun
2015-06-01
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(1ππ*) and S2(1nNπ*) 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.
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.
Robust Biased Brownian Dynamics for Rate Constant Calculation
Zou, Gang; Skeel, Robert D.
2003-01-01
A reaction probability is required to calculate the rate constant of a diffusion-dominated reaction. Due to the complicated geometry and potentially high dimension of the reaction probability problem, it is usually solved by a Brownian dynamics simulation, also known as a random walk or path integral method, instead of solving the equivalent partial differential equation by a discretization method. Building on earlier work, this article completes the development of a robust importance sampling algorithm for Brownian dynamics—i.e., biased Brownian dynamics with weight control—to overcome the high energy and entropy barriers in biomolecular association reactions. The biased Brownian dynamics steers sampling by a bias force, and the weight control algorithm controls sampling by a target weight. This algorithm is optimal if the bias force and the target weight are constructed from the solution of the reaction probability problem. In reality, an approximate reaction probability has to be used to construct the bias force and the target weight. Thus, the performance of the algorithm depends on the quality of the approximation. Given here is a method to calculate a good approximation, which is based on the selection of a reaction coordinate and the variational formulation of the reaction probability problem. The numerically approximated reaction probability is shown by computer experiments to give a factor-of-two speedup over the use of a purely heuristic approximation. Also, the fully developed method is compared to unbiased Brownian dynamics. The tests for human superoxide dismutase, Escherichia coli superoxide dismutase, and antisweetener antibody NC6.8, show speedups of 17, 35, and 39, respectively. The test for reactions between two model proteins with orientations shows speedups of 2578 for one set of configurations and 3341 for another set of configurations. PMID:14507681
Purtov, P.A.; Salikhov, K.M.
1987-09-01
Semiclassical HFI description is applicable to calculating the integral CIDNP effect in weak fields. The HFI has been calculated for radicals with sufficiently numerous magnetically equivalent nuclei (n greater than or equal to 5) in satisfactory agreement with CIDNP calculations based on quantum-mechanical description of radical-pair spin dynamics.
Dynamic Load Balancing of Parallel Monte Carlo Transport Calculations
O'Brien, M; Taylor, J; Procassini, R
2004-12-22
The performance of parallel Monte Carlo transport calculations which use both spatial and particle parallelism is increased by dynamically assigning processors to the most worked domains. Since the particle work load varies over the course of the simulation, this algorithm determines each cycle if dynamic load balancing would speed up the calculation. If load balancing is required, a small number of particle communications are initiated in order to achieve load balance. This method has decreased the parallel run time by more than a factor of three for certain criticality calculations.
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
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.
Calculating Conductance of Ion Channels - Linking Molecular Dynamics and Electrophysiology
NASA Astrophysics Data System (ADS)
Wilson, Michael A.; Pohorille, Andrew
2015-01-01
Molecular dynamics computer simulations were combined with an electrodiffusion model to compute conduction of simple ion channels. The main assumptions of the model, and the consistency, efficiency and accuracy of the ion current calculations were tested and found satisfactory. The calculated current-voltage dependence for a synthetic peptide channel is in agreement with experiments and correctly captures the asymmetry of current with respect to applied field.
Gravitation Field Calculations on a Dynamic Lattice by Distributed Computing
NASA Astrophysics Data System (ADS)
Mähönen, Petri; Punkka, Veikko
A new method of calculating numerically time evolution of a gravitational field in General Relatity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
Gravitational field calculations on a dynamic lattice by distributed computing.
NASA Astrophysics Data System (ADS)
Mähönen, P.; Punkka, V.
A new method of calculating numerically time evolution of a gravitational field in general relativity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
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.
Lončarić, Ivor; Alducin, M; Juaristi, J I
2016-10-05
We perform a detailed study of the static and dynamical properties of molecular oxygen adsorption on Ag(110) based on semi-local density functional theory (DFT) calculations and compare the results to experimental studies. For the classical dynamics calculations we use two complementary approaches, ab initio molecular dynamics and dynamics on a precalculated potential energy surface. In contrast to the molecular beam experiments, at low beam incidence energies we obtain high molecular adsorption probabilities that are related to the physisorption-like adsorption wells at the bridge sites of Ag(110). Semi-local DFT seems to overbind O2 in these wells. Based on our dynamics calculations we propose a model for adsorption in the chemisorption wells via initial adsorption in the bridge wells. In this model the measured low adsorption probabilities at low incidence energies are explained by the existence of energy barriers between the physisorption-like and chemisorption wells.
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.
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
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.
Calculation of Dynamic Coefficients for Multiwound Foil Bearings
NASA Astrophysics Data System (ADS)
Feng, Kai; Kaneko, Shigehiko
Dynamic performance of multiwound foil bearings with the effects of foil local deflection is investigated. The foils, separated and supported by projections on the ir surface are treated as thin plates. Deflections of the foils are solved with a finite element model. The air pressure is calculated with the Reynolds' equation by treating the lubricant as an isothermal idea gas. The effects of foils are simulated with the deflection of top foil added to the film thickness. A finite difference computer program is developed to solve the Reynolds equation and the elastic deflection equation, simultaneously. Perturbation method is used to determine the dynamic coefficients. The effects of foil deflection is discussed by comparing the dynamic coefficients of a foil bearing and a rigid bearing. Experimental data from a test rig supported by two multiwound foil bearings are used to validate this numerical solution.
A Reduced-frequency Approach for Calculating Dynamic Derivatives
NASA Technical Reports Server (NTRS)
Murman, Scott M.
2005-01-01
Computational Fluid Dynamics (CFD) is increasingly being used to both augment and create an aerodynamic performance database for aircraft configurations. This aerodynamic database contains the response of the aircraft to varying flight conditions and control surface deflections. The current work presents a novel method for calculating dynamic stability derivatives which reduces the computational cost over traditional unsteady CFD approaches by an order of magnitude, while still being applicable to arbitrarily complex geometries over a wide range of flow regimes. The primary thesis of this work is that the response to a forced motion can often be represented with a small, predictable number of frequency components without loss of accuracy. By resolving only those frequencies of interest, the computational effort is significantly reduced so that the routine calculation of dynamic derivatives becomes practical. The current implementation uses this same non-linear, frequency-domain approach and extends the application to the 3-D Euler equations. The current work uses a Cartesian, embedded-boundary method to automate the generation of dynamic stability derivatives.
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.
Calculation of Cross Sections in Electron-Nuclear Dynamics
NASA Astrophysics Data System (ADS)
Cabrera-Trujillo, R.; Sabin, John R.; Deumens, E.; Öhrn, Y.
In this work, we present an overview of the study of total and differential cross section calculations within the electron-nuclear dynamics (END). END is a method to solve the time-dependent Schrödinger equation in a non-adiabatic approach to direct dynamics. The method takes advantage of a coherent state representation of the molecular wave function. A quantum-mechanical Lagrangian formulation is employed to approximate the Schrödinger equation, via the time-dependent variational principle, to a set of coupled first-order differential equations in time for the END. We obtain the final wave function for the system allowing the determination of collisional properties of interest, as for example, deflection functions, charge exchange probabilities and amplitudes, and differential cross sections. We discuss the use and selection of basis sets for both the electronic description of the colliding systems as well as for their importance in the description of electron capture. As quantum effects are important in many cases and lacking for classical nuclei, we discuss the Schiff methodology and its advantages over other traditional methods for including semiclassical corrections. Time-lapse rendering of the dynamics of the participating electrons and atomic nuclei provides for a detailed view of dynamical and reactive processes. Comparison to experimental and other theoretical results is provided where appropriate data are available.
Kussmann, Jörg; Ochsenfeld, Christian
2007-11-28
A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.
Calculated Hovering Helicopter Flight Dynamics with a Circulation Controlled Rotor
NASA Technical Reports Server (NTRS)
Johnson, W.; Chopra, I.
1977-01-01
The influence of the rotor blowing coefficient on the calculated roots of the longitudinal and lateral motion was examined for a range of values of the rotor lift and the blade flap frequency. The control characteristics of a helicopter with a circulation controlled rotor are discussed. The principal effect of the blowing is a reduction in the rotor speed stability derivative. Above a critical level of blowing coefficient, which depends on the flap frequency and rotor lift, negative speed stability is produced and the dynamic characteristics of the helicopter are radically altered.
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.
Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation
NASA Astrophysics Data System (ADS)
Stein, Evan G.; Rice, Luke M.; Brünger, Axel T.
1997-01-01
Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances andJ-coupling-constant-derived dihedral angle restraints. Compared to two other commonly used algorithms, molecular dynamics in Cartesian space and metric-matrix distance geometry combined with Cartesian molecular dynamics, the method shows increased computational efficiency and success rate for large proteins, and it shows a dramatically increased radius of convergence for DNA. The torsion-angle molecular dynamics algorithm starts from an extended strand conformation and proceeds in four stages: high-temperature torsion-angle molecular dynamics, slow-cooling torsion-angle molecular dynamics, Cartesian molecular dynamics, and minimization. Tests were carried out using experimental NMR data for protein G, interleukin-8, villin 14T, and a 12 base-pair duplex of DNA, and simulated NMR data for bovine pancreatic trypsin inhibitor. For villin 14T, a monomer consisting of 126 residues, structure determination by torsion-angle molecular dynamics has a success rate of 85%, a more than twofold improvement over other methods. In the case of the 12 base-pair DNA duplex, torsion-angle molecular dynamics had a success rate of 52% while Cartesian molecular dynamics and metric-matrix distance geometry always failed.
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.
Shock Hugoniot calculations of polymers using quantum mechanics and molecular dynamics
NASA Astrophysics Data System (ADS)
Chantawansri, Tanya L.; Sirk, Timothy W.; Byrd, Edward F. C.; Andzelm, Jan W.; Rice, Betsy M.
2012-11-01
Using quantum mechanics (QM) and classical force-field based molecular dynamics (FF), we have calculated the principle shock Hugoniot curves for numerous amorphous polymers including poly[methyl methacrylate] (PMMA), poly[styrene], polycarbonate, as well as both the amorphous and crystalline forms of poly[ethylene]. In the FF calculations, we considered a non-reactive force field (i.e., polymer consistent FF). The QM calculations were performed with density functional theory (DFT) using dispersion corrected atom centered pseudopotentials. Overall, results obtained by DFT show much better agreement with available experimental data than classical force fields. In particular, DFT calculated Hugoniot curves for PMMA up to 74 GPa are in very good agreement with experimental data, where a preliminary study of chain fracture and association was also performed. Structure analysis calculations of the radius of gyration and carbon-carbon radial distribution function were also carried out to elucidate contraction of the polymer chains with increasing pressure.
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
Parallel beam dynamics calculations on high performance computers
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.
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.
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
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
2012-01-01
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.
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
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...
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...
Calculation of heat capacities of light and heavy water by path-integral molecular dynamics
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Shinoda, Wataru
2005-10-01
As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2O at 300 K, 6.9 in the liquid H2O at 300 K, and 4.1 in the ice IhH2O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2O has been calculated to be 10% higher than that of H2O, while it is 13% higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions.
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2000-12-01
We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.
[Biometric bases: basic concepts of probability calculation].
Dinya, E
1998-04-26
The author gives or outline of the basic concepts of probability theory. The bases of the event algebra, definition of the probability, the classical probability model and the random variable are presented.
Lasorne, Benjamin; Sicilia, Fabrizio; Bearpark, Michael J.; Robb, Michael A.; Worth, Graham A.; Blancafort, Lluis
2008-03-28
A new practical method to generate a subspace of active coordinates for quantum dynamics calculations is presented. These reduced coordinates are obtained as the normal modes of an analytical quadratic representation of the energy difference between excited and ground states within the complete active space self-consistent field method. At the Franck-Condon point, the largest negative eigenvalues of this Hessian correspond to the photoactive modes: those that reduce the energy difference and lead to the conical intersection; eigenvalues close to 0 correspond to bath modes, while modes with large positive eigenvalues are photoinactive vibrations, which increase the energy difference. The efficacy of quantum dynamics run in the subspace of the photoactive modes is illustrated with the photochemistry of benzene, where theoretical simulations are designed to assist optimal control experiments.
Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng
2006-12-28
Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.
[Hyponatremia: effective treatment based on calculated outcomes].
Vervoort, G; Wetzels, J F M
2006-09-30
A 78-year-old man was treated for symptomatic hyponatremia. Despite administration of an isotonic NaCl 0.9% solution, plasma sodium remained unchanged due to high concentrations of sodium and potassium in the urine. After infusion of a hypertonic NaCl solution, a satisfactory increase in plasma sodium was reached and symptoms resolved gradually. The hyponatremia was found to be caused by hypothyroidism, which was treated. A 70-year-old female was admitted to the hospital with loss of consciousness and hyponatremia. She was treated initially with a hypertonic NaCl 2.5% solution, which resulted in a steady increase in plasma sodium and a resolution of symptoms. Treatment was changed to an isotonic NaCl 0.9% infusion to attenuate the rise of serum sodium. Nevertheless plasma sodium increased too rapidly due to increased diuresis and reduced urinary sodium and potassium excretion. A slower increase in plasma sodium was achieved by administering a glucose 5% infusion. Hyponatremia is frequently observed in hospitalised patients. It should be treated effectively, and the rate of correction should be adapted to the clinical situation. Effective treatment is determined by calculating changes in effective osmoles and the resulting changes in the distribution of water over extra- and intracellular spaces. Changes in urine production and urinary excretion of sodium and potassium should be taken into account.
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.
Generalized approach to absorbed dose calculations for dynamic tumor and organ masses.
Goddu, S M; Howell, R W; Rao, D V
1995-10-01
Tumor absorbed dose calculations in radionuclide therapy are presently based on the assumption of static tumor mass. This work examines the effect of dynamic tumor mass (growth and/or shrinkage) on the absorbed dose. Tumor mass kinetic characteristics were modeled with the Gompertz equation to simulate tumor growth and an additional exponential term to accommodate tumor shrinkage that may result as a consequence of therapy. Correction factors, defined as the ratio of the absorbed dose, which was calculated by considering tumor mass dynamics, to the absorbed dose, which was calculated by assuming static mass, are presented for 1- and 100-g tumors with different tumor mass kinetics. The dependence of the correction factor on the effective half-life Te of the radioactivity in the tumor and the tumor shrinkage half-time Ts was examined. The correction factors for the 1-g tumor were > 1 for short Ts and Te. In contrast, the correction factor was less than 1 for long Ts ( > 9 days). The dose correction factors for the 100-g tumor were > 1 for all Ts and Te. Finally, the dosimetric method for dynamic masses is illustrated with experimental data on Chinese hamster V79 multicellular spheroids that were treated with 3H. Correction factors as high as about 10 are likely when Te and Ts are short. As Ts increases beyond 20 days, the importance of dynamic mass diminishes because most of the activity decays before the mass changes appreciably. In some cases, mass dynamics should be taken into account when the absorbed dose to tumors is estimated.
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.
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.
Dynamic Properties of Rock Required for Prediction Calculations.
Dynamic loading - unloading experiments were performed on rhyolite from the Nevada Test Site. Impact stresses ranged from about 6 to 18 kbar...paths from the gage records. Three waves were recorded in the rhyolite . The first wave is the Hugoniot elastic precursor. Although there is...the banding in the rhyolite being inclined in the direction of the stress wave propagation. Data on Mt. Helen tuff, Indiana limestone, Essex soil
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.
Calculation of Disease Dynamics in a Population of Households
Ross, Joshua V.; House, Thomas; Keeling, Matt J.
2010-01-01
Early mathematical representations of infectious disease dynamics assumed a single, large, homogeneously mixing population. Over the past decade there has been growing interest in models consisting of multiple smaller subpopulations (households, workplaces, schools, communities), with the natural assumption of strong homogeneous mixing within each subpopulation, and weaker transmission between subpopulations. Here we consider a model of SIRS (susceptible-infectious-recovered-susceptible) infection dynamics in a very large (assumed infinite) population of households, with the simplifying assumption that each household is of the same size (although all methods may be extended to a population with a heterogeneous distribution of household sizes). For this households model we present efficient methods for studying several quantities of epidemiological interest: (i) the threshold for invasion; (ii) the early growth rate; (iii) the household offspring distribution; (iv) the endemic prevalence of infection; and (v) the transient dynamics of the process. We utilize these methods to explore a wide region of parameter space appropriate for human infectious diseases. We then extend these results to consider the effects of more realistic gamma-distributed infectious periods. We discuss how all these results differ from standard homogeneous-mixing models and assess the implications for the invasion, transmission and persistence of infection. The computational efficiency of the methodology presented here will hopefully aid in the parameterisation of structured models and in the evaluation of appropriate responses for future disease outbreaks. PMID:20305791
Ab initio calculations of correlated electron dynamics in ultrashort pulses
NASA Astrophysics Data System (ADS)
Feist, Johannes
2010-03-01
The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.
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.
Durlak, Piotr; Latajka, Zdzisław
2011-09-01
The double proton transfer process in the cyclic dimer of propionic acid in the gas phase was studied using a path integral molecular dynamics method. Structures, energies and proton trajectories were determined. Very large amplitude motions of the skeleton of a propionic acid molecule were observed during the simulations, and almost free rotation of the C(2)H(5) group around the C(α)-C bond. A double-well symmetric potential with a very small energy barrier was determined from the free energy profile for the proton motions. Infrared spectra for different isotopomers were calculated, and comparative vibrational analysis was performed. The vibrational results from CPMD appear to be in qualitative agreement with the experimental ones.
An efficient method for calculation of dynamic logarithmic gains in biochemical systems theory.
Shiraishi, Fumihide; Hatoh, Yuji; Irie, Toshinori
2005-05-07
Biochemical systems theory (BST) characterizes a given biochemical system based on the logarithmic gains, rate-constant sensitivities and kinetic-order sensitivities defined at a steady state. This paper describes an efficient method for calculation of the time courses of logarithmic gains, i.e. dynamic logarithmic gains L(Xi, Xj; t), which expresses the percentage change in the value of a dependent variable Xi at a time t in response to an infinitesimal percentage change in the value of an independent variable Xj at t=0. In this method, one first recasts the ordinary differential equations for the dependent variables into an exact canonical nonlinear representation (GMA system) through appropriate transformations of variables. Owing to the structured mathematical form of this representation, the recast system can be fully described by a set of numeric parameters, and the differential equations for the dynamic logarithmic gains can be set up automatically without resource to computer algebra. A simple general-purpose computer program can thus be written that requires only the relevant numeric parameters as input to calculate the time courses of the variables and of the dynamic logarithmic gains for both concentrations and fluxes. Unlike other methods, the proposed method does not require to derive any expression for the partial differentiation of flux expressions with respect to each independent variable. The proposed method has been applied to two kinds of reaction models to elucidate its usefulness.
NASA Astrophysics Data System (ADS)
Yalouz, Saad; Pouthier, Vincent; Falvo, Cyril
2017-08-01
A method combining perturbation theory with a simplifying ansatz is used to describe the exciton-phonon dynamics in complex networks. This method, called PT*, is compared to exact calculations based on the numerical diagonalization of the exciton-phonon Hamiltonian for eight small-sized networks. It is shown that the accuracy of PT* depends on the nature of the network, and three different situations were identified. For most graphs, PT* yields a very accurate description of the dynamics. By contrast, for the Wheel graph and the Apollonian network, PT* reproduces the dynamics only when the exciton occupies a specific initial state. Finally, for the complete graph, PT* breaks down. These different behaviors originate in the interplay between the degenerate nature of the excitonic energy spectrum and the strength of the exciton-phonon interaction so that a criterion is established to determine whether or not PT* is relevant. When it succeeds, our study shows the undeniable advantage of PT* in that it allows us to perform very fast simulations when compared to exact calculations that are restricted to small-sized networks.
NASA Technical Reports Server (NTRS)
Ray, Ronald J.
1994-01-01
New flight test maneuvers and analysis techniques for evaluating the dynamic response of in-flight thrust models during throttle transients have been developed and validated. The approach is based on the aircraft and engine performance relationship between thrust and drag. Two flight test maneuvers, a throttle step and a throttle frequency sweep, were developed and used in the study. Graphical analysis techniques, including a frequency domain analysis method, were also developed and evaluated. They provide quantitative and qualitative results. Four thrust calculation methods were used to demonstrate and validate the test technique. Flight test applications on two high-performance aircraft confirmed the test methods as valid and accurate. These maneuvers and analysis techniques were easy to implement and use. Flight test results indicate the analysis techniques can identify the combined effects of model error and instrumentation response limitations on the calculated thrust value. The methods developed in this report provide an accurate approach for evaluating, validating, or comparing thrust calculation methods for dynamic flight applications.
Analysis of protein dynamics using local-DME calculations.
Wu, Di; Smith, Stephen; Mahan, Hannah; Jernigan, Robert L
2011-01-01
Flexibility and dynamics of protein structures are reflected in the B-factors and order parameters obtained experimentally with X-ray crystallography and Nuclear Magnetic Resonance (NMR). Methods such as Normal Mode Analysis (NMA) and Elastic Network Models (ENM) can be used to predict the fluctuations of protein structures for either atomic level or coarse-grained structures. Here, we introduce the Local-Distance Matrix Error (DME), an efficient and simple analytic method to study the fluctuations of protein structures, especially for the ensembles of NMR-determined protein structures. Comparisons with the fluctuations obtained by experiments and other by computations show strong correlations.
Raman spectroscopy and lattice-dynamics calculations of mixed layered copper-titanium oxides
NASA Astrophysics Data System (ADS)
Abrashev, M. V.; Thomsen, C.; Popov, V. N.; Bozukov, L. N.
1997-02-01
We report micro-Raman spectra obtained from R 2Ba 2Ti 2Cu 2O 11 (R = Nd, Gd) and Gd 2CaBa 2Ti 2O 12 ceramic samples. The analysis of the spectra was performed using the similarity between the investigated structures and related layered pure copper and titanium oxides. The assignment of the observed lines to definite atomic vibrations is supported by lattice-dynamics calculations, based on a shell model. The calculated frequencies for the IR-active modes are also presented. We stress that in contrast to Gd 2CaBa 2Ti 2Cu 2O 12, where the ceramics consist of optically anisotropic plate-like microcrystals, in the case of the quadruple perovskites R 2Ba 2Ti 2Cu 2O 11 the microcrystals are isotropic, probably due to the fine twinning, rendering it impossible to obtain polarized Raman spectra along different crystal directions.
Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machines
Jia, Weile; Fu, Jiyun; Cao, Zongyan; Wang, Long; Chi, Xuebin; Gao, Weiguo; 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.
Interaction of dynamical fractional branes with background fields: Superstring calculations
NASA Astrophysics Data System (ADS)
Saidy-Sarjoubi, Maryam; Kamani, Davoud
2017-05-01
We compute the boundary state corresponding to a fractional Dp-brane with transverse motion and internal background fields: Kalb-Ramond and a U(1) gauge field. The space-time has the orbifold structure ℝ1,5 × ℂ2/ℤ 2. The calculations are in the superstring theory. Using this boundary state we shall obtain the interaction amplitude between two parallel moving fractional Dp-branes. We shall extract behavior of the interaction amplitude for large distances of the branes.
Calculations of the dynamic dipole polarizabilities for the Li+ ion
NASA Astrophysics Data System (ADS)
Zhang, Yong-Hui; Tang, Li-Yan; Zhang, Xian-Zhou; Shi, Ting-Yun
2016-10-01
The B-spline configuration-interaction method is applied to the investigations of dynamic dipole polarizabilities for the four lowest triplet states (2 3S, 33S, 23P, and 33P) of the Li+ ion. The accurate energies for the triplet states of n 3S, n 3P, and n 3D, the dipole oscillator strengths for 23S(33S) → n 3P, 23P(33P) → n 3S, and 23P(33P) → n 3D transitions, with the main quantum number n up to 10 are tabulated for references. The dynamic dipole polarizabilities for the four triplet states under a wide range of photon energy are also listed, which provide input data for analyzing the Stark shift of the Li+ ion. Furthermore, the tune-out wavelengths in the range from 100 nm to 1.2 μm for the four triplet states, and the magic wavelengths in the range from 100 nm to 600 nm for the 23S → 33S, 23S → 23P, and 23S → 33P transitions are determined accurately for the experimental design of the Li+ ion. Project supported by the National Basic Research Program of China (Grant No. 2012CB821305) and the National Natural Science Foundation of China (Grant Nos. 11474319, 11274348, and 91536102).
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.
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
A Brownian Dynamics Approach to ESR Line Shape Calculations
NASA Astrophysics Data System (ADS)
Wright, Matthew P.
The work presented in this thesis uses a Monte Carlo technique to simulate spectra for 14N spin-labels and 15N spin labels. The algorithm presented here also has the capability to produce simulated spectra for any admixture of 14N and 15N. The algorithm makes use of `iterative loops' to model Brownian rotational diffusion and for the repeated evaluation of the spectral correlation function (relaxation function). The method described in this work starts with a derivation of an angular dependent "Spin Hamiltonian" that when diagonalized yields orientation dependent eigenvalues. The resulting eigenvalue equations are later used to calculate the energy trajectories of a nitroxide spin-label undergoing rotational diffusion. The energy trajectories are then used to evaluate the relaxation function. The absorption spectrum is obtained by applying a Fourier transform to the relaxation function. However, the application of the Fourier transform to the relaxation function produces "leakage" effects that manifest as spurious peaks in the first derivative spectrum. To counter "leakage" effects a data windowing function was applied to the relaxation function prior to the Fourier transform. In order to test the accuracy of this algorithm, simulated spectra for 14N, and 15N spin labels diffusing in a glycerol-water mixture as well as a 14N-15N admixture diffusing in the same solvent were produced and compared to experimental spectra. An attempt to quantify the level of agreement was made by calculating the mean square residual of the simulated and experimental spectra. The main spectral features were reproduced with reasonable fidelity by the simulated spectra.
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
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.
Ab initio molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
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(+), Cl(-), and Ag(+) 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 (DeltaG(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(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(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(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
A rigorous full-dimensional quantum dynamics calculation of the vibrational energies of H3O2-
NASA Astrophysics Data System (ADS)
Yu, Hua-Gen
2006-11-01
The vibrational energy levels of the H3O2- anion have been calculated using a rigorous quantum dynamics method based on an accurate ab initio potential energy surface. The eigenvalue problem is solved using the two-layer Lanczos iterative diagonalization algorithm in a mixed grid/nondirect product basis set, where the system Hamiltonian is expressed in a set of orthogonal polyspherical coordinates. The lowest 312 vibrational energy levels in each inversion symmetry, together with a comparison of fundamental frequencies with previous quantum dynamics calculations, are reported. Finally, a statistical analysis of nearest level spacing distribution is carried out, revealing a strongly chaotic nature.
NASA Astrophysics Data System (ADS)
Ngo, N. H.; Tran, H.; Gamache, R. R.
2012-04-01
It is well known that the Voigt profile does not well describe the (measured) shapes of isolated lines. This is due to the neglect of the intermolecular collision-induced velocity changes and of the speed dependence of the collisional parameters. In this paper, we present a new line profile model for pure H2O which takes both of these effects into account. The speed dependence of the collisional parameters has been calculated by a semi-classical method. The velocity changes have been modeled by using the Keilson-Storer collision kernel with two characteristic parameters. The latter have been deduced from classical molecular dynamics simulations which also indicate that, for pure H2O, the correlation between velocity-changing and state-changing collisions is not negligible, a result confirmed by the analysis of measured spectra. A partially correlated speed-dependent Keilson-Storer model has thus been adopted to describe the line-shape. Comparisons between simulated spectra and measurements for four self-broadened lines in the near-infrared at various pressures show excellent agreements.
Ngo, N H; Tran, H; Gamache, R R
2012-04-21
It is well known that the Voigt profile does not well describe the (measured) shapes of isolated lines. This is due to the neglect of the intermolecular collision-induced velocity changes and of the speed dependence of the collisional parameters. In this paper, we present a new line profile model for pure H(2)O which takes both of these effects into account. The speed dependence of the collisional parameters has been calculated by a semi-classical method. The velocity changes have been modeled by using the Keilson-Storer collision kernel with two characteristic parameters. The latter have been deduced from classical molecular dynamics simulations which also indicate that, for pure H(2)O, the correlation between velocity-changing and state-changing collisions is not negligible, a result confirmed by the analysis of measured spectra. A partially correlated speed-dependent Keilson-Storer model has thus been adopted to describe the line-shape. Comparisons between simulated spectra and measurements for four self-broadened lines in the near-infrared at various pressures show excellent agreements.
Mehrabian, Hatef; Chopra, Rajiv; Martel, Anne L
2013-04-01
Assessing tumor response to therapy is a crucial step in personalized treatments. Pharmacokinetic (PK) modeling provides quantitative information about tumor perfusion and vascular permeability that are associated with prognostic factors. A fundamental step in most PK analyses is calculating the signal that is generated in the tumor vasculature. This signal is usually inseparable from the extravascular extracellular signal. It was shown previously using in vivo and phantom experiments that independent component analysis (ICA) is capable of calculating the intravascular time-intensity curve in dynamic contrast enhanced (DCE)-MRI. A novel adaptive complex independent component analysis (AC-ICA) technique is developed in this study to calculate the intravascular time-intensity curve and separate this signal from the DCE-MR images of tumors. The use of the complex-valued DCE-MRI images rather than the commonly used magnitude images satisfied the fundamental assumption of ICA, i.e., linear mixing of the sources. Using an adaptive cost function in ICA through estimating the probability distribution of the tumor vasculature at each iteration resulted in a more robust and accurate separation algorithm. The AC-ICA algorithm provided a better estimate for the intravascular time-intensity curve than the previous ICA-based method. A simulation study was also developed in this study to realistically simulate DCE-MRI data of a leaky tissue mimicking phantom. The passage of the MR contrast agent through the leaky phantom was modeled with finite element analysis using a diffusion model. Once the distribution of the contrast agent in the imaging field of view was calculated, DCE-MRI data was generated by solving the Bloch equation for each voxel at each time point. The intravascular time-intensity curve calculation results were compared to the previously proposed ICA-based intravascular time-intensity curve calculation method that applied ICA to the magnitude of the DCE-MRI data
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
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 (www.scilab.org) which is an open source software.
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.
Self-consistent calculations of transport and magnetization dynamics
NASA Astrophysics Data System (ADS)
Lee, Kyung-Jin
2010-03-01
In layered structures like spin-valves where the current flows perpendicular to the plane, the direction and magnitude of the spin transfer torque (STT) at a point r is decided by the spin accumulation (SA) and associated spin current at the same point r. Initial STT theories commonly assumed that the dependence of SA on magnetization (M) is local and thus essentially fixed by the local M at the same point r. However, its dependence on M is inherently nonlocal because of the 3-dimensional spin diffusion [1]. In other words, when the conduction electron arrives at a point r on the ferromagnet-normal metal interface, the reflected (transmitted) electron takes the spin direction anti-parallel (parallel) to the local M at the point r, diffuses along the interface, and then transfers its spin-angular momentum to another local M at a far away point from the r. That is, SA at a point r is affected by all local M's at other points. The local assumption becomes really invalid when M is inhomogeneous. Note that micromagnetic and time-resolved imaging studies [2] have revealed excitations of incoherent spin-waves and thus inhomogeneous M due to STT. In this situation, the effect of SA on M (=STT) and the nonlocal effect of M on the SA should be treated on an equal footing. The conventional treatments, which ignore the latter part, actually deal with only half of the relevant parts. Therefore, the self-consistent feedback between inhomogenous M and STT through the nonlocal effect should be considered. In this talk, we present self-consistent calculation results that consider the feedback, which allows us to understand peculiar spin-wave modes in a single ferromagnet and a spin-valve. If time is allowed, we extend our talk to other feedback mechanisms which result in the oscillatory STT due to ballistic spin transport [3] and the damping tensor due to the spin-motive force [4] in a very narrow magnetic domain wall. These works have been done in collaboration with Hyun-Woo Lee
Calculated state densities of aperiodic nucleotide base stacks
NASA Astrophysics Data System (ADS)
Ye, Yuan-Jie; Chen, Run-Shen; Martinez, Alberto; Otto, Peter; Ladik, Janos
2000-05-01
Electronic density of states (DOS) histograms and of the nucleotide base stack regions of a segment of human oncogene (both single and double stranded, in B conformation) and of single-stranded random DNA base stack (also in B conformation), were calculated. The computations were performed with the help of the ab initio matrix block negative factor counting (NFC) method for the DOSs. The neglected effects of the sugar-phosphate chain and the water environment (with the counterions) were assessed on the basis of previous ab initio band structure calculations. Further, in the calculation of single nucleotide base stacks also basis set and correlation effects have been investigated. In the case of a single strand the level spacing widths of the allowed regions and the fundamental gap were calculated also with Clementi's double ς basis and corrected for correlation at the MP2 level. The inverse interaction method was applied for the study of Anderson localization.
Web based brain volume calculation for magnetic resonance images.
Karsch, Kevin; Grinstead, Brian; He, Qing; Duan, Ye
2008-01-01
Brain volume calculations are crucial in modern medical research, especially in the study of neurodevelopmental disorders. In this paper, we present an algorithm for calculating two classifications of brain volume, total brain volume (TBV) and intracranial volume (ICV). Our algorithm takes MRI data as input, performs several preprocessing and intermediate steps, and then returns each of the two calculated volumes. To simplify this process and make our algorithm publicly accessible to anyone, we have created a web-based interface that allows users to upload their own MRI data and calculate the TBV and ICV for the given data. This interface provides a simple and efficient method for calculating these two classifications of brain volume, and it also removes the need for the user to download or install any applications.
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.
Chien; Gau; Chang; Stetsko
1999-07-01
A dynamical calculation scheme that employs Cartesian coordinates with a z axis normal to the crystal surface to define polarization unit vectors and wavefields is applied to interpret the intensity distribution of crystal truncation rods for surfaces and interfaces. A comparison between this calculation scheme and the asymptotic iteration approach using the conventional presentation of the polarization components of the wavefields, with the sigma and pi components perpendicular to the wavevectors, is presented. It is found that the use of Cartesian coordinate systems can provide correct boundary conditions in determining the wavefield amplitudes, thus leading to a rigorous and general calculation scheme for dynamical diffraction from surfaces and interfaces.
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
NASA Astrophysics Data System (ADS)
Hu, Wei-Ping; Lynch, Gillian C.; Liu, Yi-Ping; Rossi, Ivan; Stewart, James J. P.; Steckler, Rozeanne; Garrett, Bruce C.; Isaacson, Alan D.; Lu, Da-hong; Melissas, Vasilios S.; Truhlar, Donald G.
1995-08-01
MORATE (Molecular Orbital RATE calculations) is a computer program for direct dynamics calculations of unimolecular and bimolecular rate constants of gas-phase chemical reactions involving atoms, diatoms, or polyatomic species. The dynamical methods used are conventional or variational transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. Variational transition states are found by a one-dimensional search of generalized-transition-state dividing surfaces perpendicular to the minimum-energy path, and tunneling probabilities are evaluated by multidimensional semiclassical algorithms, including the small-curvature and large-curvature tunneling approximations and the microcanonical optimized multidimensional tunneling approximation. The computer program is a conventiently interfaced package consisting of the POLYRATE program, version 6.5, for dynamical rate constant calculations, and the MOPAC program, version 5.05mn, for semiempirical electronic structure computations. In single-level mode, the potential energies, gradients, and higher derivatives of the potential are computed whenever needed by electronic structure calculations employing semiempirical molecular orbital theory without the intermediary of a global or semiglobal fit. All semiempirical methods available in MOPAC, in particular MINDO/3, MNDO, AM1, and PM3, can be called on to calculate the potential, gradient, or Hessian, as required at various steps of the dynamics calculations, and, in addition, the code has flexible options for electronic structure calculations with neglect of diatomic differential overlap and specific reaction parameters (NDDO-SRP). In dual-level mode, MINDO/3, MNDO, AM1, PM3, or NDDO-SRP is used as a lower level to calculate the reaction path, and interpolated corrections to energies and frequencies are added; these corrections are based on higher-level data read from an external file.
A novel approach to calculate thermal expansion of graphene: Molecular dynamics study
NASA Astrophysics Data System (ADS)
Ghasemi, Hamid; Rajabpour, Ali
2017-05-01
High surface-to-volume ratio is one of the extraordinary physical parameters of graphene which plays a crucial role in its electronic, thermal, mechanical and chemical behavior. Despite a lot of continuing theoretical and experimental researches, there are properties of graphene which are not fully understood and known. One of these properties is the thermal expansion coefficient (TEC) of graphene which shows a quite different behavior from what is expected for ordinary materials and has been reported to have a negative value for a wide range of temperatures. All previous researchers have calculated the TEC of graphene by considering its projected size which decreases when the temperature increases. In this paper, a novel method has been used to report the TEC of graphene based on the calculation of its real surface area using molecular dynamics simulations. Our results make clear how much the real surface area of graphene varies with respect to the temperature which is applicable in designing graphene-based nanodevices.
Naumov, Vladimir S; Ignatov, Stanislav K
2017-08-01
The GROMOS 56ACARBO force field for the description of carbohydrates was modified for calculations of chitosan (poly-1,4-(N-acetyl)-β-D-glucopyranosamine-2) with protonated and non-protonated amino groups and its derivatives. Additional parameterization was developed on the basis of quantum chemical calculations. The modified force field (56ACARBO_CHT) allows performing the molecular dynamic calculations of chitosans with different degrees of protonation corresponding to various acidity of medium. Test calculations of the conformational transitions in the chitosan rings and polymeric chains as well as the chitosan nanocrystal dissolution demonstrate good agreement with experimental data. Graphical abstract The GROMOS 56ACARBO_CHT force field allows performing the molecular dynamic calculations of chitosans with different types of amio-group: free, protonated, substituted.
40 CFR 1066.610 - Mass-based and molar-based exhaust emission calculations.
Code of Federal Regulations, 2012 CFR
2012-07-01
... 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 molar-based exhaust emission calculations. (a) Calculate your total mass of emissions over a test cycle as...
40 CFR 1066.610 - Mass-based and molar-based exhaust emission calculations.
Code of Federal Regulations, 2013 CFR
2013-07-01
... 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 molar-based exhaust emission calculations. (a) Calculate your total mass of emissions over a test cycle as...
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
The effect of walking speed on local dynamic stability is sensitive to calculation methods.
Stenum, Jan; Bruijn, Sjoerd M; Jensen, Bente R
2014-11-28
Local dynamic stability has been assessed by the short-term local divergence exponent (λS), which quantifies the average rate of logarithmic divergence of infinitesimally close trajectories in state space. Both increased and decreased local dynamic stability at faster walking speeds have been reported. This might pertain to methodological differences in calculating λS. Therefore, the aim was to test if different calculation methods would induce different effects of walking speed on local dynamic stability. Ten young healthy participants walked on a treadmill at five speeds (60%, 80%, 100%, 120% and 140% of preferred walking speed) for 3min each, while upper body accelerations in three directions were sampled. From these time-series, λS was calculated by three different methods using: (a) a fixed time interval and expressed as logarithmic divergence per stride-time (λS-a), (b) a fixed number of strides and expressed as logarithmic divergence per time (λS-b) and (c) a fixed number of strides and expressed as logarithmic divergence per stride-time (λS-c). Mean preferred walking speed was 1.16±0.09m/s. There was only a minor effect of walking speed on λS-a. λS-b increased with increasing walking speed indicating decreased local dynamic stability at faster walking speeds, whereas λS-c decreased with increasing walking speed indicating increased local dynamic stability at faster walking speeds. Thus, the effect of walking speed on calculated local dynamic stability was significantly different between methods used to calculate local dynamic stability. Therefore, inferences and comparisons of studies employing λS should be made with careful consideration of the calculation method. Copyright © 2014 Elsevier Ltd. All rights reserved.
Calculations of the Dynamic Stress of Several Airplane Wings in Various Gusts
NASA Technical Reports Server (NTRS)
Pierce, Harold B.
1948-01-01
A series of calculations of the dynamic response of airplane wings to gusts were made with the purpose of showing the relative response of a reference airplane, the DC-3 airplane, and of newer types of airplanes represented by the DC-4, DC-6, and L-49 airplanes. Additional calculations were made for the DC-6 airplane to show the effects of speed and altitude. On the basis of the method of calculation used and the conditions selected for analysis, it is indicated that: 1) The newer airplanes show appreciably greater dynamic stress in gusts then does the reference airplane; 2) Increasing the forward speed or the operating altitude results in an increase of the dynamic stress ratio for the gust with a gradient distance of 10 chords.
Qin, Wu; Li, Xin; Bian, Wen-Wen; Fan, Xiu-Juan; Qi, Jing-Yao
2010-02-01
There is increasing attention in the unique biological and medical properties of graphene, and it is expected that biomaterials incorporating graphene will be developed for the graphene-based drug delivery systems and biomedical devices. Despite the importance of biomolecules-graphene interactions, a detailed understanding of the adsorption mechanism and features of biomolecules onto the surfaces of graphene is lacking. To address this, we have performed density functional theory (DFT) and molecular dynamics (MD) methods exploring the adsorption geometries, adsorption energies, electronic band structures, adsorption isotherms, and adsorption dynamics of l-leucine (model biomolecule)/graphene composite system. DFT calculations confirmed the energetic stability of adsorption model and revealed that electronic structure of graphene can be controlled by the adsorption direction of l-leucine. MD simulations further investigate the potential energy and van der Waals energy for the interaction processes of l-leucine/graphene system at different temperatures and pressures. We find that the van der Waals interaction between the l-leucine and the graphene play a dominant role in the adsorption process under a certain range of temperature and pressure, and the l-leucine molecule could be adsorbed onto graphene spontaneously in aqueous solution.
Muchová, Eva; Slavícek, Petr; Sobolewski, Andrzej L; Hobza, Pavel
2007-06-21
The goal of this study is to explore the photochemical processes following optical excitation of the glycine molecule into its two low-lying excited states. We employed electronic structure methods at various levels to map the PES of the ground state and the two low-lying excited states of glycine. It follows from our calculations that the photochemistry of glycine can be regarded as a combination of photochemical behavior of amines and carboxylic acid. The first channel (connected to the presence of amino group) results in ultrafast decay, while the channels characteristic for the carboxylic group occur on a longer time scale. Dynamical calculations provided the branching ratio for these channels. We also addressed the question whether conformationally dependent photochemistry can be observed for glycine. While electronic structure calculations favor this possibility, the ab initio multiple spawning (AIMS) calculations showed only minor relevance of the reaction path resulting in conformationally dependent dynamics.
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.
Bubble Dynamics Calculations Using the DYSMAS/E Finite Difference Code
1988-07-01
NSWC TR 88-226 AD-A241 549 BUBBLE DYNAMICS CALCULATIONS USING THE DYSMAS/E FINITE DIFFERENCE CODE BY STEPHEN A. WILKERSON (NSWC) DR. HANS SCHITrKE...62314N RJ I4W27 1t. TITLE (include Securfry CJalssticdtti) Bubble Dynamics Calculations Using the l)YSMAS/E Finite D~ifference Code 12, PERSONAL AUTHOR...FIELD GROUP SUB. GR. bubble divnamics DN’SNAS/E, code 19 09 bubble collapse detonation 19. ABSTRACT (Continue on rovotse if noceisary and idenrty by block
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.
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
2015-11-08
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
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
2015-11-01
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
Brittleness index calculation and evaluation for CBM reservoirs based on AVO simultaneous inversion
NASA Astrophysics Data System (ADS)
Wu, Haibo; Dong, Shouhua; Huang, Yaping; Wang, Haolong; Chen, Guiwu
2016-11-01
In this paper, a new approach is proposed for coalbed methane (CBM) reservoir brittleness index (BI) calculations. The BI, as a guide for fracture area selection, is calculated by dynamic elastic parameters (dynamic Young's modulus Ed and dynamic Poisson's ratio υd) obtained from an amplitude versus offset (AVO) simultaneous inversion. Among the three different classes of CBM reservoirs distinguished on the basis of brittleness in the theoretical part of this study, class I reservoirs with high BI values are identified as preferential target areas for fracturing. Therefore, we derive the AVO approximation equation expressed by Ed and υd first. This allows the direct inversion of the dynamic elastic parameters through the pre-stack AVO simultaneous inversion, which is based on Bayes' theorem. Thereafter, a test model with Gaussian white noise and a through-well seismic profile inversion is used to demonstrate the high reliability of the inversion parameters. Accordingly, the BI of a CBM reservoir section from the Qinshui Basin is calculated using the proposed method and a class I reservoir section detected through brittleness evaluation. From the outcome of this study, we believe the adoption of this new approach could act as a guide and reference for BI calculations and evaluations of CBM reservoirs.
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.
NASA Astrophysics Data System (ADS)
Imaoka, Haruna; Kinugawa, Kenichi
2017-03-01
Thermal conductivity, shear viscosity, and bulk viscosity of normal liquid 4He at 1.7-4.0 K are calculated using path integral centroid molecular dynamics (CMD) simulations. The calculated thermal conductivity and shear viscosity above lambda transition temperature are on the same order of magnitude as experimental values, while the agreement of shear viscosity is better. Above 2.3 K the CMD well reproduces the temperature dependences of isochoric shear viscosity and of the time integral of the energy current and off-diagonal stress tensor correlation functions. The calculated bulk viscosity, not known in experiments, is several times larger than shear viscosity.
A method of solid-solid phase equilibrium calculation by molecular dynamics
NASA Astrophysics Data System (ADS)
Karavaev, A. V.; Dremov, V. V.
2016-12-01
A method for evaluation of solid-solid phase equilibrium curves in molecular dynamics simulation for a given model of interatomic interaction is proposed. The method allows to calculate entropies of crystal phases and provides an accuracy comparable with that of the thermodynamic integration method by Frenkel and Ladd while it is much simpler in realization and less intense computationally. The accuracy of the proposed method was demonstrated in MD calculations of entropies for EAM potential for iron and for MEAM potential for beryllium. The bcc-hcp equilibrium curves for iron calculated for the EAM potential by the thermodynamic integration method and by the proposed one agree quite well.
Dynamic condensation approach to calculation of structural responses and response sensitivities
NASA Astrophysics Data System (ADS)
Weng, Shun; Tian, Wei; Zhu, Hongping; Xia, Yong; Gao, Fei; Zhang, Yaoting; Li, Jiajing
2017-05-01
Structural responses and response sensitivities are widely used in the finite element model updating, damage identification and optimization design. Calculation of the responses and response sensitivities of a large-scale structure consumes considerable computation storage and is usually time-consuming. This paper proposes an improved dynamic condensation approach to calculate the structural responses and response sensitivities. The condensed vibration equation is achieved by a simplified iterative scheme. By selecting the DOFs associated with the concerned element to be master DOFs, the response sensitivity is rapidly calculated from the derivatives of the master stiffness and mass matrices. Since the condensed vibration equation has a much smaller size than the original vibration equation, the proposed method is quite efficient in calculating the structural responses and response sensitivities. Finally, applications of the proposed method to an eight-storey frame and a cantilever plate demonstrate its accuracy and efficiency in the calculation of structural responses and response sensitivities.
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.
Content-Based Image Retrieval Based on Shape Similarity Calculation
NASA Astrophysics Data System (ADS)
Jin, Cong; Ke, Shan-Wu
2017-09-01
In the content-based image retrieval technology, the performance of retrieval system using only a single image feature is generally unsatisfactory, and therefore the image retrieval system using two or more image features is more often used. When there is the target deformation or the size variation, the performance of image retrieval system using only shape features is not satisfactory, too. To solve these problems, in this paper, the extraction of image salient region and a shape representation methods of describing the image content are proposed, then they are used with image texture and color features to implement image retrieval. Experimental results show that the proposed image retrieval system can provide very good retrieval performance.
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".
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".
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…
NASA Astrophysics Data System (ADS)
Truong, Thanh N.; Lu, Da-hong; Lynch, Gillian C.; Liu, Yi-Ping; Melissas, Vasilios S.; Stewart, James J. P.; Steckler, Rozeanne; Garrett, Bruce C.; Isaacson, Alan D.; Gonzalez-Lafont, Angels; Rai, Sachchida N.; Hancock, Gene C.; Joseph, Tomi; Truhlar, Donald G.
1993-04-01
We present a computer program, MORATE (Molecular Orbital RATE calculations), for direct dynamics calculations of unimolecular and bimolecular rate constants of gas-phase chemical reactions involving atoms, diatoms, or polyatomic species. The potential energies, gradients, and higher derivatives of the potential are calculated whenever needed by semiempirical molecular orbital theory without the intermediary of a global or semiglobal fit. The dynamical methods used are conventional or variational transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. The computer program is conveniently interfaced package consisting of the POLYRATE program, version 4.5.1, for dynamical rate calculations, and the MOPAC program, version 5.03, for semiempirical electronic structure computations. All semiempirical methods available in MOPAC, in particular MINDO/3, MNDO, AM1, and PM3, can be called on to calculate the potential and gradient. Higher derivatives of the potential are obtained by numerical derivatives of the gradient. Variational transition states are found by a one-dimensional search of generalized-transition-state dividing surfaces perpendicular to the minimum-energy path, and tunneling probabilities are evaluated by numerical quadrature.
Díaz, Natalia; Suárez, Dimas; Sordo, Tomás L
2003-11-30
Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.
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.
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.
Calculating track-based observables for the LHC.
Chang, Hsi-Ming; Procura, Massimiliano; Thaler, Jesse; Waalewijn, Wouter J
2013-09-06
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.
NASA Astrophysics Data System (ADS)
Landry, E. S.; McGaughey, A. J. H.
2009-10-01
The accuracies of two theoretical expressions for thermal boundary resistance are assessed by comparing their predictions to independent predictions from molecular dynamics (MD) simulations. In one expression (RE) , the phonon distributions are assumed to follow the equilibrium, Bose-Einstein distribution, while in the other expression (RNE) , the phonons are assumed to have nonequilibrium, but bulk-like distributions. The phonon properties are obtained using lattice dynamics-based methods, which assume that the phonon interface scattering is specular and elastic. We consider (i) a symmetrically strained Si/Ge interface, and (ii) a series of interfaces between Si and “heavy-Si,” which differs from Si only in mass. All of the interfaces are perfect, justifying the assumption of specular scattering. The MD-predicted Si/Ge thermal boundary resistance is temperature independent and equal to 3.1×10-9m2-K/W below a temperature of ˜500K , indicating that the phonon scattering is elastic, as required for the validity of the theoretical calculations. At higher-temperatures, the MD-predicted Si/Ge thermal boundary resistance decreases with increasing temperature, a trend we attribute to inelastic scattering. For the Si/Ge interface and the Si/heavy-Si interfaces with mass ratios greater than two, RE is in good agreement with the corresponding MD-predicted values at temperatures where the interface scattering is elastic. When applied to a system containing no interface, RE is erroneously nonzero due to the assumption of equilibrium phonon distributions on either side of the interface. While RNE is zero for a system containing no interface, it is 40%-60% less than the corresponding MD-predicted values for the Si/Ge interface and the Si/heavy-Si interfaces at temperatures where the interface scattering is elastic. This inaccuracy is attributed to the assumption of bulk-like phonon distributions on either side of the interface.
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.
Miao, Yinglong; Sinko, William; Pierce, Levi; Bucher, Denis; Walker, Ross C; McCammon, J Andrew
2014-07-08
Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they require proper reweighting for free energy calculation. In this work, we systematically compare the accuracy of different reweighting algorithms including the exponential average, Maclaurin series, and cumulant expansion on three model systems: alanine dipeptide, chignolin, and Trp-cage. Exponential average reweighting can recover the original free energy profiles easily only when the distribution of the boost potential is narrow (e.g., the range ≤20kBT) as found in dihedral-boost aMD simulation of alanine dipeptide. In dual-boost aMD simulations of the studied systems, exponential average generally leads to high energetic fluctuations, largely due to the fact that the Boltzmann reweighting factors are dominated by a very few high boost potential frames. In comparison, reweighting based on Maclaurin series expansion (equivalent to cumulant expansion on the first order) greatly suppresses the energetic noise but often gives incorrect energy minimum positions and significant errors at the energy barriers (∼2-3kBT). Finally, reweighting using cumulant expansion to the second order is able to recover the most accurate free energy profiles within statistical errors of ∼kBT, particularly when the distribution of the boost potential exhibits low anharmonicity (i.e., near-Gaussian distribution), and should be of wide applicability. A toolkit of Python scripts for aMD reweighting "PyReweighting" is distributed free of charge at http://mccammon.ucsd.edu/computing/amdReweighting/.
Lu, Ben Zhuo; Chen, Wei Zu; Wang, Cun Xin; Xu, Xiao-jie
2002-08-15
The electrostatic force including the intramolecular Coulombic interactions and the electrostatic contribution of solvation effect were entirely calculated by using the finite difference Poisson-Boltzmann method (FDPB), which was incorporated into the GROMOS96 force field to complete a new finite difference stochastic dynamics procedure (FDSD). Simulations were performed on an insulin dimer. Different relative dielectric constants were successively assigned to the protein interior; a value of 17 was selected as optimal for our system. The simulation data were analyzed and compared with those obtained from 500-ps molecular dynamics (MD) simulation with explicit water and a 500-ps conventional stochastic dynamics (SD) simulation without the mean solvent force. The results indicate that the FDSD method with GROMOS96 force field is suitable to study the dynamics and structure of proteins in solution if used with the optimal protein dielectric constant. Copyright 2002 Wiley-Liss, Inc.
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.
Molecular dynamics simulation and quantum mechanical calculations on α-D-N-acetylneuraminic acid.
Priyadarzini, Thanu R K; Subashini, Balakrishnan; Selvin, Jeyasigamani F A; Veluraja, Kasinadar
2012-04-01
N-Acetylneuraminic acid is a sugar molecule of biological significance due to its pivotal role in molecular recognition processes. The three dimensional structure and conformation of α-Neu5Ac in biological environments can be clearly observed by molecular dynamics (MD) simulation and quantum mechanical (QM) calculations. A 10ns MD simulation on α-Neu5Ac yields two conformational models which are stabilized by water mediated hydrogen bond between O-8/O-9 hydroxyl oxygen and carbonyl of carboxylate group. The average life time of the conformers and the residual time of water which mediates the hydrogen bonding interactions are computed. Based on the amphiprotic nature of water, water mediation of each conformer is divided into two different modes, one donor-one acceptor mode and two donor modes. According to the analysis of simulation trajectories, the preferred mode of water mediation for conformers is the one donor-one acceptor mode. The energy and geometry of the MD derived conformational models of α-Neu5Ac are optimized using HF/6-31G(∗) basis set of Gaussian03. QM calculations also resulted that α-Neu5Ac is preferentially stabilized by water mediated hydrogen bonding between O-8 hydroxyl and the carboxylate group where the mediation is one donor-one acceptor type. The optimized geometry of α-Neu5Ac which is in good agreement with the crystal structure of α-D-N-acetyl-1-O-methylneuraminic acid methyl ester is deposited in the public domain database 3DSDSCAR (http://3dsdscar.org). This optimized structure can be used by biotechnologists, biophysicists and glycobiologists for modelling the sialylglycans and also to design drugs using sialic acid analog inhibitors. Copyright © 2012 Elsevier Ltd. All rights reserved.
Nakai, Hiromi; Yoshikawa, Takeshi; Nonaka, Yutaro
2017-01-05
This study presents an efficient algorithm to search for the poles of dynamic polarizability to obtain excited states of large systems with nonlocal excitation nature. The present algorithm adopts a homogeneous search with a constant frequency interval and a bisection search to achieve high accuracy. Furthermore, the subtraction process of the information about the detected poles from the total dynamic polarizability is used to extract the undetected pole contributions. Numerical assessments confirmed the accuracy and efficiency of the present algorithm in obtaining the excitation energies and oscillator strengths of all dipole-allowed excited states. A combination of the present pole-search algorithm and divide-and-conquer-based dynamic polarizability calculations was found to be promising to treat nonlocal excitations of large systems. © 2016 Wiley Periodicals, Inc.
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.
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.
Aman, Ken; Westlund, Per-Olof
2007-02-14
Direct calculation of electron spin relaxation and EPR lineshapes, based on Brownian dynamics simulation techniques and the stochastic Liouville equation approach (SLE-L) [Mol. Phys., 2004, 102, 1085-1093], is here generalized to high spin systems with spin quantum number S = 3/2, 2, 5/2, 3 and 7/2. A direct calculation method is demonstrated for electron spin-spin and spin-lattice relaxation, S-, X- and Q-band EPR-lineshapes and paramagnetic enhanced water proton T(1)- NMRD profiles. The main relaxation mechanism for the electron spin system is a stochastic second rank zero field splitting (ZFS). Brownian dynamics simulation techniques are used in describing a fluctuating ZFS interaction which comprises two parts namely the "permanent" part which is modulated by isotropic reorientation diffusion, and the transient part which is modulated by fast local distortion, which is also modelled by the isotropic rotation diffusion model. The SLE-L approach present is applicable both in the perturbation (Redfield) regime as well as outside the perturbation regime, in the so called slow motion regime.
Study of dynamic weighing system based on photoelectric detecting technique
NASA Astrophysics Data System (ADS)
Song, Gui-cai; Na, Yan-xiang; Cao, Shi-hao; Yang, Fei-yu
2011-08-01
Dynamic weighing is a process that it reckons the weight of vehicles according to measuring the tires which are moving. It makes use of sensors and some others auxiliary apparatus to measure the appearance of a certain vehicle and tires, then calculates the weight and the speed of vehicles. Finally it can note and read this information. To analyze the dynamic weighing system at home and abroad, it can be easily discovered that these are based on the sensors of electricity. The disadvantages of those sensors are very obvious. For example, when vehicles are dynamic weighed, the speed and accuracy can not be ensured at the same time. Dynamic weighing system is designed in the research of papers. Linear CCD can be used as Sensor to be applied in the mold of weighing. This paper describes the dynamic weighing system, analyses the dynamic of the system, and also investigates the modules of the dynamic weighing system.
NASA Astrophysics Data System (ADS)
Roondhe, Basant; Upadhyay, Deepak; Som, Narayan; Pillai, Sharad B.; Shinde, Satyam; Jha, Prafulla K.
2017-03-01
The structural, electronic, dynamical and thermodynamical properties of CmX (X = N, P, As, Sb, and Bi) compounds are studied using first principles calculations within density functional theory. The Perdew-Burke-Ernzerhof spin polarized generalized gradient approximation and Perdew-Wang (PW) spin polarized local density approximation as the exchange correlational functionals are used in these calculations. There is a good agreement between the present and previously reported data. The calculated electronic density of states suggests that the curium monopnictides are metallic in nature, which is consistent with earlier studies. The significant values of magnetic moment suggest their magnetic nature. The phonon dispersion curves and phonon density of states are also calculated, which depict the dynamical stability of these compounds. There is a significant separation between the optical and acoustical phonon branches. The temperature dependence of the thermodynamical functions are also calculated and discussed. Internal energy and vibrational contribution to the Helmholtz free energy increases and decreases, respectively, with temperature. The entropy increases with temperature. The specific heat at constant volume and Debye temperature obey Debye theory. The temperature variation of the considered thermodynamical functions is in line with those of other crystalline solids.
NASA Astrophysics Data System (ADS)
Roondhe, Basant; Upadhyay, Deepak; Som, Narayan; Pillai, Sharad B.; Shinde, Satyam; Jha, Prafulla K.
2017-01-01
The structural, electronic, dynamical and thermodynamical properties of CmX (X = N, P, As, Sb, and Bi) compounds are studied using first principles calculations within density functional theory. The Perdew-Burke-Ernzerhof spin polarized generalized gradient approximation and Perdew-Wang (PW) spin polarized local density approximation as the exchange correlational functionals are used in these calculations. There is a good agreement between the present and previously reported data. The calculated electronic density of states suggests that the curium monopnictides are metallic in nature, which is consistent with earlier studies. The significant values of magnetic moment suggest their magnetic nature. The phonon dispersion curves and phonon density of states are also calculated, which depict the dynamical stability of these compounds. There is a significant separation between the optical and acoustical phonon branches. The temperature dependence of the thermodynamical functions are also calculated and discussed. Internal energy and vibrational contribution to the Helmholtz free energy increases and decreases, respectively, with temperature. The entropy increases with temperature. The specific heat at constant volume and Debye temperature obey Debye theory. The temperature variation of the considered thermodynamical functions is in line with those of other crystalline solids.
Techniques for achieving thermal equilibrium in molecular dynamics calculations for solids
NASA Astrophysics Data System (ADS)
Wu, Ernest Yue; Friauf, Robert J.
1990-06-01
We develop techniques for achieving thermal equilibrium in molecular dynamics calculations for solids. Atoms in a Lennard-Jones solid are initially given random velocities and displacements from their equilibrium positions with suitably scaled Maxwellian distributions. A quantitative criterion for thermal equilibrium of the solid is established by using the equipartition of energy theorem. At high temperatures, thermal expansion is studied, and we introduce a method for adjusting the lattice parameter to ensure zero external pressure. The results of molecular dynamics simulations show agreement with experimental data for rare gas and ionic crystals.
[Correction of enhanced dynamic wedge factor and analysis of monitor unit calculation].
Huang, Sijuan; Chen, Lixin; Cao, Wufei; Sun, Wenzhao; Chen, Along; Liu, Bojio; Wang, Bin
2015-02-01
To study the correction of algorithm for Varian enhanced dynamic wedge(EDW) factors and compare the dose/monitor unit (MU) deviation measured at the central axis of EDW field with that obtained by manual calculation or using the treatment planning system. EDW factors and dose were measured with Thimble ion chamber at 10 cm depth under the water for 6 MV and 10 MV photon on Varian linear accelerator. The corresponding calculations were done with the radiation treatment planning system. An analytic formula, namely the MU Fraction model, was used to calculate the EDW factor, which was corrected with a constant factor. The MU of conventional 2-D planning derived from manual calculating, treatment planning system, and actual measurements were compared. With the measured results as the standard, the corrected manual calculation deviation of EDW factors was significantly reduced. For photon 6 MV, the maximum deviation reduced from 4.2% to 1.3% for 60° symmetry fields was, and from -4.7% to -1.8% for asymmetric fields. For photon 10 MV, the maximum deviation for all EDW fields was reduced from -3.0% to 1.1%. Comparison of the manual calculations with the measured results showed a MU deviation for symmetric fields within 2%, and more than 5% for some asymmetric fields. The deviation between the calculations of the treatment planning and the measured results was less than 1.5%. Constant factor correction can effectively reduce the deviation of manual calculation. For MU calculation of EDW field in conventional 2-D dimensional treatment planning, the corrected results of symmetric fields meet clinical requirements. While the minimum distance between the field edge and the central axis was less than 4 cm in asymmetric fields, the corresponding special method, measurement or the treatment planning system should be used to calculate the dose/MU.
NASA Astrophysics Data System (ADS)
Chao, S.; Jiao, C. W.; Liu, S.
2016-08-01
At this stage of the development of China's highway, the quantity and size of traffic signs are growing with the guiding information increasing. In this paper, a calculation method is provided for special sign board with reducing wind load measures to save construction materials and cost. The empirical model widely used in China is introduced for normal sign structure design. After that, this paper shows a computational fluid dynamics method, which can calculate both normal and special sign structures. These two methods are compared and analyzed with examples to ensure the applicability and feasibility of CFD method.
Dynamical Calculations of bar K and MULTI-bar K Nuclei
NASA Astrophysics Data System (ADS)
Gazda, D.; Mareš, J.; Friedman, E.; Gal, A.
We report on our recent calculations of bar K and multi-bar K nuclei. Calculations were performed fully self-consistently across the periodic table using the relativistic mean-field approach. We aimed at detailed analysis of dynamical processes and various thresholds that determine the K- absorption width. Further, we studied the behavior of the nuclear medium under the influence of increasing strangeness in order to search for bar K condensation precursor phenomena. Last, we explored possibly self-bound strange hadronic configurations consisting of neutrons and bar K0 mesons and studied their properties.
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.
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.
Wannier-based calculation of the orbital magnetization in crystals
NASA Astrophysics Data System (ADS)
Lopez, M. G.; Vanderbilt, David; Thonhauser, T.; Souza, Ivo
2012-01-01
We present a first-principles scheme that allows the orbital magnetization of a magnetic crystal to be evaluated accurately and efficiently even in the presence of complex Fermi surfaces. Starting from an initial electronic-structure calculation with a coarse ab initio k-point mesh, maximally localized Wannier functions are constructed and used to interpolate the necessary k-space quantities on a fine mesh, in parallel to a previously developed formalism for the anomalous Hall conductivity [X. Wang, J. Yates, I. Souza, and D. Vanderbilt, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.74.195118 74, 195118 (2006)]. We formulate our new approach in a manifestly gauge-invariant manner, expressing the orbital magnetization in terms of traces over matrices in Wannier space. Since only a few (e.g., of the order of 20) Wannier functions are typically needed to describe the occupied and partially occupied bands, these Wannier matrices are small, which makes the interpolation itself very efficient. The method has been used to calculate the orbital magnetization of bcc Fe, hcp Co, and fcc Ni. Unlike an approximate calculation based on integrating orbital currents inside atomic spheres, our results nicely reproduce the experimentally measured ordering of the orbital magnetization in these three materials.
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.
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.
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
NASA Astrophysics Data System (ADS)
Bonomi, Massimiliano; Branduardi, Davide; Bussi, Giovanni; Camilloni, Carlo; Provasi, Davide; Raiteri, Paolo; Donadio, Davide; Marinelli, Fabrizio; Pietrucci, Fabio; Broglia, Ricardo A.; Parrinello, Michele
2009-10-01
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure. This leaves the possibility for the user to exploit many different MD engines depending on the system simulated and on the computational resources available. Free-energy calculations can be performed as a function of many collective variables, with a particular focus on biological problems, and using state-of-the-art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The present software, written in ANSI-C language, can be easily interfaced with both Fortran and C/C++ codes. Program summaryProgram title: PLUMED Catalogue identifier: AEEE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Lesser GPL No. of lines in distributed program, including test data, etc.: 107 505 No. of bytes in distributed program, including test data, etc.: 2 052 759 Distribution format: tar.gz Programming language: ANSI-C Computer: Any computer capable of running an executable produced by GCC compiler Operating system: Linux/Unix RAM: Depending on the number of atoms, the method chosen and the collective variables used Classification: 23 External routines: Must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER). Nature of problem: Calculation of free-energy surfaces for biological and condensed matter systems. Solution method: Implementation of various enhanced sampling techniques. Unusual features: PLUMED is not a stand-alone program but it must be interfaced with a MD code (such as GROMACS, NAMD, DL_POLY or SANDER) that needs to be recompiled. Each interface is provided in a patch form. Running time: Depending on the number of atoms, the method chosen and the
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.
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
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
NASA Astrophysics Data System (ADS)
Koppisetty, Chaitanya A. K.; Frank, Martin; Lyubartsev, Alexander P.; Nyholm, Per-Georg
2015-01-01
Accurate estimation of protein-carbohydrate binding energies using computational methods is a challenging task. Here we report the use of expanded ensemble molecular dynamics (EEMD) simulation with double decoupling for estimation of binding energies of hevein, a plant lectin with its monosaccharide and disaccharide ligands GlcNAc and (GlcNAc)2, respectively. In addition to the binding energies, enthalpy and entropy components of the binding energy are also calculated. The estimated binding energies for the hevein-carbohydrate interactions are within the range of ±0.5 kcal of the previously reported experimental binding data. For comparison, binding energies were also estimated using thermodynamic integration, molecular dynamics end point calculations (MM/GBSA) and the expanded ensemble methodology is seen to be more accurate. To our knowledge, the method of EEMD simulations has not been previously reported for estimating biomolecular binding energies.
NASA Astrophysics Data System (ADS)
Michel, K. H.; ćakır, D.; Sevik, C.; Peeters, F. M.
2017-03-01
The elastic constant C11 and piezoelectric stress constant e1 ,11 of two-dimensional (2D) dielectric materials comprising h-BN, 2 H -MoS2 , and other transition-metal dichalcogenides and dioxides are calculated using lattice dynamical theory. The results are compared with corresponding quantities obtained with ab initio calculations. We identify the difference between clamped-ion and relaxed-ion contributions with the dependence on inner strains which are due to the relative displacements of the ions in the unit cell. Lattice dynamics allows us to express the inner-strain contributions in terms of microscopic quantities such as effective ionic charges and optoacoustical couplings, which allows us to clarify differences in the piezoelectric behavior between h-BN and MoS2. Trends in the different microscopic quantities as functions of atomic composition are discussed.
Wehrle, Marius; Sulc, Miroslav; Vanícek, Jirí
2011-01-01
We explore three specific approaches for speeding up the calculation of quantum time correlation functions needed for time-resolved electronic spectra. The first relies on finding a minimum set of sufficiently accurate electronic surfaces. The second increases the time step required for convergence of exact quantum simulations by using different split-step algorithms to solve the time-dependent Schrödinger equation. The third approach lowers the number of trajectories needed for convergence of approximate semiclassical dynamics methods.
Calculations on Hard Ferroelectric PbZr1-xTixO3 Dynamic Hysteresis
NASA Astrophysics Data System (ADS)
Hamad, Mahmoud A.
2017-02-01
A phenomenological model was modified for dynamic hysteresis loops of hard ferroelectric PbZr1-xTixO3 (PZT). The comparison with experimental results showed that the modified model can reproduce polarization versus an electric field. A predicted hysteresis loss of hard ferroelectric PZT was formulated and estimated. The calculations showed an increase in hysteresis loss with a decrease of frequency at a 40-kV/cm electric field amplitude.
Towards automated calculation of evidence-based clinical scores
Aakre, Christopher A; Dziadzko, Mikhail A; Herasevich, Vitaly
2017-01-01
AIM To determine clinical scores important for automated calculation in the inpatient setting. METHODS A modified Delphi methodology was used to create consensus of important clinical scores for inpatient practice. A list of 176 externally validated clinical scores were identified from freely available internet-based services frequently used by clinicians. Scores were categorized based on pertinent specialty and a customized survey was created for each clinician specialty group. Clinicians were asked to rank each score based on importance of automated calculation to their clinical practice in three categories - “not important”, “nice to have”, or “very important”. Surveys were solicited via specialty-group listserv over a 3-mo interval. Respondents must have been practicing physicians with more than 20% clinical time spent in the inpatient setting. Within each specialty, consensus was established for any clinical score with greater than 70% of responses in a single category and a minimum of 10 responses. Logistic regression was performed to determine predictors of automation importance. RESULTS Seventy-nine divided by one hundred and forty-four (54.9%) surveys were completed and 72/144 (50%) surveys were completed by eligible respondents. Only the critical care and internal medicine specialties surpassed the 10-respondent threshold (14 respondents each). For internists, 2/110 (1.8%) of scores were “very important” and 73/110 (66.4%) were “nice to have”. For intensivists, no scores were “very important” and 26/76 (34.2%) were “nice to have”. Only the number of medical history (OR = 2.34; 95%CI: 1.26-4.67; P < 0.05) and vital sign (OR = 1.88; 95%CI: 1.03-3.68; P < 0.05) variables for clinical scores used by internists was predictive of desire for automation. CONCLUSION Few clinical scores were deemed “very important” for automated calculation. Future efforts towards score calculator automation should focus on technically feasible
Krykunov, Mykhaylo; Autschbach, Jochen
2007-01-14
We report implementations and results of time-dependent density functional calculations (i) of the frequency-dependent magnetic dipole-magnetic dipole polarizability, (ii) of the (observable) translationally invariant linear magnetic response, and (iii) of a linear intensity differential (LID) which includes the dynamic dipole magnetizability. The density functional calculations utilized density fitting. For achieving gauge-origin independence we have employed time-periodic magnetic-field-dependent basis functions as well as the dipole velocity gauge, and have included explicit density-fit related derivatives of the Coulomb potential. We present the results of calculations of static and dynamic magnetic dipole-magnetic dipole polarizabilities for a set of small molecules, the LID for the SF6 molecule, and dispersion curves for M-hexahelicene of the origin invariant linear magnetic response as well as of three dynamic polarizabilities: magnetic dipole-magnetic dipole, electric dipole-electric dipole, and electric dipole-magnetic dipole. We have also performed comparison of the linear magnetic response and magnetic dipole-magnetic dipole polarizability over a wide range of frequencies for H2O and SF6.
Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study
NASA Astrophysics Data System (ADS)
Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad
2012-03-01
Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.
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 Astrophysics Data System (ADS)
Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida
2009-06-01
A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.
Calculation of Hamilton energy and control of dynamical systems with different types of attractors
NASA Astrophysics Data System (ADS)
Ma, Jun; Wu, Fuqiang; Jin, Wuyin; Zhou, Ping; Hayat, Tasawar
2017-05-01
Strange attractors can be observed in chaotic and hyperchaotic systems. Most of the dynamical systems hold a finite number of attractors, while some chaotic systems can be controlled to present an infinite number of attractors by generating infinite equilibria. Chaos can also be triggered in some dynamical systems that can present hidden attractors, and the attractors in these dynamical systems find no equilibria and the basin of attraction is not connected with any equilibrium (the equilibria position meets certain restriction function). In this paper, Hamilton energy is calculated on the chaotic systems with different types of attractors, and energy modulation is used to control the chaos in these systems. The potential mechanism could be that negative feedback in energy can suppress the phase space and oscillating behaviors, and thus, the chaotic, periodical oscillators can be controlled. It could be effective to control other chaotic, hyperchaotic and even periodical oscillating systems as well.
Calculation of Hamilton energy and control of dynamical systems with different types of attractors.
Ma, Jun; Wu, Fuqiang; Jin, Wuyin; Zhou, Ping; Hayat, Tasawar
2017-05-01
Strange attractors can be observed in chaotic and hyperchaotic systems. Most of the dynamical systems hold a finite number of attractors, while some chaotic systems can be controlled to present an infinite number of attractors by generating infinite equilibria. Chaos can also be triggered in some dynamical systems that can present hidden attractors, and the attractors in these dynamical systems find no equilibria and the basin of attraction is not connected with any equilibrium (the equilibria position meets certain restriction function). In this paper, Hamilton energy is calculated on the chaotic systems with different types of attractors, and energy modulation is used to control the chaos in these systems. The potential mechanism could be that negative feedback in energy can suppress the phase space and oscillating behaviors, and thus, the chaotic, periodical oscillators can be controlled. It could be effective to control other chaotic, hyperchaotic and even periodical oscillating systems as well.
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.
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.
Cao, Bing-Yang; Li, Yuan-Wei
2010-07-14
A uniform source-and-sink (USS) scheme, which combines features of the reverse [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] and improved relaxation [B. Y. Cao, J. Chem. Phys. 129, 074106 (2008)] methods, is developed to calculate the thermal conductivity by nonequilibrium molecular dynamics (NEMD). The uniform internal heat source and sink are realized by exchanging the velocity vectors of individual atoms in the right half and left half systems, and produce a periodically quadratic temperature profile throughout the system. The thermal conductivity can be easily extracted from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. In particular, this scheme greatly increases the relaxation of the exited localized phonon modes which often worsen the calculation accuracy and efficiency in most other NEMD methods. The calculation of the thermal conductivities of solid argon shows that the simple USS scheme gives accurate results with fast convergence.
NASA Astrophysics Data System (ADS)
Cao, Bing-Yang; Li, Yuan-Wei
2010-07-01
A uniform source-and-sink (USS) scheme, which combines features of the reverse [F. Müller-Plathe, J. Chem. Phys. 106, 6082 (1997)] and improved relaxation [B. Y. Cao, J. Chem. Phys. 129, 074106 (2008)] methods, is developed to calculate the thermal conductivity by nonequilibrium molecular dynamics (NEMD). The uniform internal heat source and sink are realized by exchanging the velocity vectors of individual atoms in the right half and left half systems, and produce a periodically quadratic temperature profile throughout the system. The thermal conductivity can be easily extracted from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. In particular, this scheme greatly increases the relaxation of the exited localized phonon modes which often worsen the calculation accuracy and efficiency in most other NEMD methods. The calculation of the thermal conductivities of solid argon shows that the simple USS scheme gives accurate results with fast convergence.
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.
Integration based profile likelihood calculation for PDE constrained parameter estimation problems
NASA Astrophysics Data System (ADS)
Boiger, R.; Hasenauer, J.; Hroß, S.; Kaltenbacher, B.
2016-12-01
Partial differential equation (PDE) models are widely used in engineering and natural sciences to describe spatio-temporal processes. The parameters of the considered processes are often unknown and have to be estimated from experimental data. Due to partial observations and measurement noise, these parameter estimates are subject to uncertainty. This uncertainty can be assessed using profile likelihoods, a reliable but computationally intensive approach. In this paper, we present the integration based approach for the profile likelihood calculation developed by (Chen and Jennrich 2002 J. Comput. Graph. Stat. 11 714-32) and adapt it to inverse problems with PDE constraints. While existing methods for profile likelihood calculation in parameter estimation problems with PDE constraints rely on repeated optimization, the proposed approach exploits a dynamical system evolving along the likelihood profile. We derive the dynamical system for the unreduced estimation problem, prove convergence and study the properties of the integration based approach for the PDE case. To evaluate the proposed method, we compare it with state-of-the-art algorithms for a simple reaction-diffusion model for a cellular patterning process. We observe a good accuracy of the method as well as a significant speed up as compared to established methods. Integration based profile calculation facilitates rigorous uncertainty analysis for computationally demanding parameter estimation problems with PDE constraints.
LRCS calculation and imaging of complex target based on GRECO
NASA Astrophysics Data System (ADS)
Wu, Wen; Xu, Fu-chang; Han, Xiang'e.
2013-09-01
The research on Laser Radar Cross Section(LRCS) is of great significance in many research fields, such as defense, aviation, aerospace, meteorology etc. Current study of LRCS focuses mainly on the full-size target. The LRCS of full-size target, characterized by the scattering properties of the target, is influenced by target material, shape, size, and the wavelength of laser, but it is independent on the size of irradiation beam. In fact, when the target is in large size, and the beam emitted from laser radar is very narrow, it may be in a local rather than a full-size irradiation. In this case, the scattering properties of a target are dependent on not only the size of irradiation beam on the target, but also the direction of irradiation beam. Therefore, it is essential to analyze the scattering properties of a complex target in a local irradiation. Based on the basic theory of Graphic-electromagnetic Computing(GRECO), we improved the method used in the processing of electromagnetic scattering, calculated the monostatic and bistatic LRCS of several targets. The results are consistent with that in the early work done by other researchers. In addition, by changing the divergence angle of the incident beam, the situation of narrow beam in a local irradiation was presented. Under different sizes of irradiation beam, analysis and calculation of local cross section was made in detail. The results indicate that the size of irradiation beam can greatly affect the LRCS for targets. Finally, we calculated scattering cross section per unit of each location point; with color tag, scattering intensity distribution of every location point on the target was displayed, which can be revealed by the color of every pixel point. On the basis of scattering intensity distribution of every location point, the imaging of a target was realized, which provides a reference for quick identification of the target.
Dynamic Buffer Capacity in Acid-Base Systems.
Michałowska-Kaczmarczyk, Anna M; Michałowski, Tadeusz
The generalized concept of 'dynamic' buffer capacity βV is related to electrolytic systems of different complexity where acid-base equilibria are involved. The resulting formulas are presented in a uniform and consistent form. The detailed calculations are related to two Britton-Robinson buffers, taken as examples.
Path integral based calculations of symmetrized time correlation functions. II.
Bonella, S; Monteferrante, M; Pierleoni, C; Ciccotti, G
2010-10-28
Schofield's form of quantum time correlation functions is used as the starting point to derive a computable expression for these quantities. The time composition property of the propagators in complex time is exploited to approximate Schofield's function in terms of a sequence of short time classical propagations interspersed with path integrals that, combined, represent the thermal density of the system. The approximation amounts to linearization of the real time propagators and it becomes exact with increasing number of propagation legs. Within this scheme, the correlation function is interpreted as an expectation value over a probability density defined on the thermal and real path space and calculated by a Monte Carlo algorithm. The performance of the algorithm is tested on a set of benchmark problems. Although the numerical effort required is considerable, we show that the algorithm converges systematically to the exact answer with increasing number of iterations and that it is stable for times longer than those accessible via a brute force, path integral based, calculation of the correlation function. Scaling of the algorithm with dimensionality is also examined and, when the method is combined with commonly used filtering schemes, found to be comparable to that of alternative semiclassical methods.
Dipole-active optical phonons in YTiO3 : Ellipsometry study and lattice-dynamics calculations
NASA Astrophysics Data System (ADS)
Kovaleva, N. N.; Boris, A. V.; Capogna, L.; Gavartin, J. L.; Popovich, P.; Yordanov, P.; Maljuk, A.; Stoneham, A. M.; Keimer, B.
2009-01-01
The anisotropic complex dielectric response was accurately extracted from spectroscopic ellipsometry measurements at phonon frequencies for the three principal crystallographic directions of an orthorhombic (Pbnm) YTiO3 single crystal. We identify all 25 infrared-active phonon modes allowed by symmetry 7B1u , 9B2u , and 9B3u polarized along the c , b , and a axes, respectively. From a classical dispersion analysis of the complex dielectric functions γ˜(ω) and their inverses -1/γ˜(ω) , we define the resonant frequencies, widths, and oscillator strengths of the transverse-optical (TO) and longitudinal-optical phonon modes. We calculate eigenfrequencies and eigenvectors of B1u , B2u , and B3u normal modes and suggest assignments of the TO phonon modes observed in our ellipsometry spectra by comparing their frequencies and oscillator strengths with those resulting from the present lattice-dynamics study. Based on these assignments, we estimate dynamical effective charges of the atoms in the YTiO3 lattice. We find that in general, the dynamical effective charges in YTiO3 lattice are typical for a family of perovskite oxides. By contrast to a ferroelectric BaTiO3 , the dynamical effective charge of oxygen related to a displacement along the c axis does not show the anomalously large value. At the same time, the dynamical effective charges of Y and ab plane oxygen exhibit anisotropy, indicating a strong hybridization along the a axis.
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.
Czader, Arkadiusz; Bittner, Eric R
2008-01-21
Excited states of the double-stranded DNA model (A)12.(T)12 were calculated in the framework of the Frenkel exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal dipole approximation associated with the lowest energy pipi* excitations of the individual nucleobases as obtained from time-dependent density functional theory calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal dipole approximation (IDA) methods were found to be significantly different for the small interchromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of structural fluctuations of the DNA chain on the magnitude of dipolar coupling were also found to be very significant. The difference between the maximum and minimum values was as large as 1000 and 300 cm(-1) for the IDA and TDC methods, respectively. To account for these effects, the properties of the excited states were averaged over a large number of conformations obtained from the molecular dynamics simulations. Our calculations using the TDC method indicate that the absorption of the UV light creates exciton states carrying the majority of the oscillator strength that are delocalized over at least six DNA bases. Upon relaxation, the excitation states localize over at least four contiguous bases.
The accuracy of calculated base excess in blood.
Lang, Werner; Zander, Rolf
2002-04-01
Most equations used for calculation of the base excess (BE, mmol/l) in human blood are based on the fundamental equation derived by Siggaard-Andersen and called the Van Slyke equation: BE = Z x [[cHCO3-(P) - C7.4 HCO3-(P)] + beta x (pH -7.4)]. In simple approximation, where Z is a constant which depends only on total hemoglobin concentration (cHb, g/dl) in blood, three equations were tested: the ones proposed by Siggaard-Andersen (SA), the National Committee for Clinical Laboratory Standards (NCCLS) or Zander (ZA). They differ only slightly in the solubility factor for carbon dioxide (alphaCO2, mmol/l x mmHg) and in the apparent pK(pK'), but more significantly in the plasma bicarbonate concentration at reference pH (C7.4HCO3-(P), mmol/l) and in beta, the slope of the CO2-buffer line (mmol/l) for whole blood. Furthermore, the approximation was improved either by variation in Z (r(c)), or in the apparent pK (pK) with changing pH. Thus, from a total of seven equations and from a reference set for pH, pCO2 and BE taken from the literature (n=148), the base excess was calculated. Over the whole range of base excess (-30 to +30 mmol/l) and PCO2 (12 to 96 mmHg), mean accuracy (deltaBE, mmol/l) was greatest in the simple equation according to Zander and decreased in the following order: +/-0.86 (ZA); +/-0.94 (ZA, r(c)); +/-0.96 (SA, r(c)); +/-1.03 (NCCLS, r(c)); +/-1.40 (NCCLS); +/-1.48 (SA); and +/-1.50 (pK'). For all clinical purposes, the Van Slyke equation according to Zander is the best choice and can be recommended in the following form: BE= (1 -0.0143 x cHb) x [[0.0304 x PCO2 x 10pH-6.1-24.26] + (9.5+1.63 x cHb) x (pH -7.4)] - 0.2 x cHb x (1-sO2), where the last term is a correction for oxygen saturation (sO2). Hence, base excess can be obtained with high accuracy (<1 mmol/l) from the measured quantities of pH, pCO2, cHb, and SO2 in any sample, irrespective of whether venous or arterial blood is used.
Children Base Their Investment on Calculated Pay-Off
Steelandt, Sophie; Dufour, Valérie; Broihanne, Marie-Hélène; Thierry, Bernard
2012-01-01
To investigate the rise of economic abilities during development we studied children aged between 3 and 10 in an exchange situation requiring them to calculate their investment based on different offers. One experimenter gave back a reward twice the amount given by the children, and a second always gave back the same quantity regardless of the amount received. To maximize pay-offs children had to invest a maximal amount with the first, and a minimal amount with the second. About one third of the 5-year-olds and most 7- and 10-year-olds were able to adjust their investment according to the partner, while all 3-year-olds failed. Such performances should be related to the rise of cognitive and social skills after 4 years. PMID:22413006
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.
Distance-based classification of keystroke dynamics
NASA Astrophysics Data System (ADS)
Tran Nguyen, Ngoc
2016-07-01
This paper uses the keystroke dynamics in user authentication. The relationship between the distance metrics and the data template, for the first time, was analyzed and new distance based algorithm for keystroke dynamics classification was proposed. The results of the experiments on the CMU keystroke dynamics benchmark dataset1 were evaluated with an equal error rate of 0.0614. The classifiers using the proposed distance metric outperform existing top performing keystroke dynamics classifiers which use traditional distance metrics.
Effective binding force calculation in a dimeric protein by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Sergi, Alessandro; Ciccotti, Giovanni; Falconi, Mattia; Desideri, Alessandro; Ferrario, Mauro
2002-04-01
A good example of macromolecular recognition is found in the interaction of the two monomers of the dimeric superoxide dismutase protein found in Photobacterium leiognathi. We have produced, by molecular dynamics simulation techniques, a specific path for the rupture of the dimer and calculated the effective force involved in the process by extending a well established free energy calculation scheme, the molecular dynamics blue moon approach to rare events. Within this picture we have generalized the approach to a vectorial reaction coordinate and performed a number of different simulations in function of the monomer-momomer separation, at fixed relative orientation. We find a deep minimum and we compute the height of the free energy barrier to break the dimer. As for the system characterization we have found that, when the separation distance increases, the protein structure is stable and the monomer-monomer interface is uniformly hydrated. Moreover, identifying the crucial contacts for the stabilization of the dimer, we have found the sequence of the different microscopic events in the monomer-monomer recognition and we have developed a view of the process which requires a merging of standard explanations, in agreement with the recent picture of recognition as a dynamical process mixing the various mechanisms previously considered [Kimura et al., Biophys. J. 80 635 (2001)].
Han, Weiwei; Zhu, Jingxuan; Wang, Song; Xu, Dong
2017-04-20
Phosphorylation is one of the most frequent post-translational modifications on proteins. It regulates many cellular processes by modulation of phosphorylation on protein structure and dynamics. However, the mechanism of phosphorylation-induced conformational changes of proteins is still poorly understood. Here, we report a computational study of three representative groups of tyrosine in ADP-ribosylhydrolase 1, serine in BTG2, and serine in Sp100C by using six molecular dynamics (MD) simulations and quantum chemical calculations. Added phosphorylation was found to disrupt hydrogen bond, and increase new weak interactions (hydrogen bond and hydrophobic interaction) during MD simulations, leading to conformational changes. Quantum chemical calculations further indicate that the phosphorylation on tyrosine, threonine, and serine could decrease the optical band gap energy (Egap), which can trigger electronic transitions to form or disrupt interactions easily. Our results provide an atomic and electronic description of how phosphorylation facilitates conformational and dynamic changes in proteins, which may be useful for studying protein function and protein design.
NASA Astrophysics Data System (ADS)
Souliotis, G. A.; Shetty, D. V.; Galanopoulos, S.; Yennello, S. J.
2008-04-01
A systematic study of heavy residues formed in peripheral collisions below the Fermi energy has been undertaken at Texas A&M aiming at obtaining information on the mechanism of nucleon exchange and the course towards N/Z equilibration [1,2]. We expect to get insight on the dynamics and the nuclear equation of state by comparing our heavy residue data to detailed calculations using microscopic models of quantum molecular dynamics (QMD) type. We are performing calculations using two codes: the CoMD code of M. Papa, A. Bonasera [3] and the CHIMERA-QMD code of J. Lukasik [4]. Both codes implement an effective interaction with a nuclear-matter compressibility of K=200 (soft EOS) with several forms of the density dependence of the nucleon-nucleon symmetry potential. CoMD imposes a constraint in the phase space occupation for each nucleon restoring the Pauli principle at each time step of the collision. CHIMERA-QMD uses a Pauli potential term to mimic the Pauli principle. Results of the calculations and comparisons with our residue data will be presented. [1] G.A. Souliotis et al., Phys. Rev. Lett. 91, 022701 (2003). [2] G.A. Souliotis et al., Phys. Lett. B 588, 35 (2004). [3] M. Papa et al., Phys. Rev. C 64, 024612 (2001). [4] J. Lukasik, Z. Majka, Acta Phys. Pol. B 24, 1959 (1993).
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.
Saltas, V.; Chroneos, A.; Cooper, Michael William D.; ...
2016-01-01
In the present work, the defect properties of oxygen self-diffusion in PuO2 are investigated over a wide temperature (300–1900 K) and pressure (0–10 GPa) range, by combining molecular dynamics simulations and thermodynamic calculations. Based on the well-established cBΩ thermodynamic model which connects the activation Gibbs free energy of diffusion with the bulk elastic and expansion properties, various point defect parameters such as activation enthalpy, activation entropy, and activation volume were calculated as a function of T and P. Molecular dynamics calculations provided the necessary bulk properties for the proper implementation of the thermodynamic model, in the lack of any relevantmore » experimental data. The estimated compressibility and the thermal expansion coefficient of activation volume are found to be more than one order of magnitude greater than the corresponding values of the bulk plutonia. As a result, the diffusion mechanism is discussed in the context of the temperature and pressure dependence of the activation volume.« less
Saltas, V.; Chroneos, A.; Cooper, Michael William D.; Fitzpatrick, M. E.; Vallianatos, F.
2016-01-01
In the present work, the defect properties of oxygen self-diffusion in PuO_{2} are investigated over a wide temperature (300–1900 K) and pressure (0–10 GPa) range, by combining molecular dynamics simulations and thermodynamic calculations. Based on the well-established cBΩ thermodynamic model which connects the activation Gibbs free energy of diffusion with the bulk elastic and expansion properties, various point defect parameters such as activation enthalpy, activation entropy, and activation volume were calculated as a function of T and P. Molecular dynamics calculations provided the necessary bulk properties for the proper implementation of the thermodynamic model, in the lack of any relevant experimental data. The estimated compressibility and the thermal expansion coefficient of activation volume are found to be more than one order of magnitude greater than the corresponding values of the bulk plutonia. As a result, the diffusion mechanism is discussed in the context of the temperature and pressure dependence of the activation volume.
Lazar, Petr; Zhang, Shuai; Safářová, Klára; Li, Qiang; Froning, Jens Peter; Granatier, Jaroslav; Hobza, Pavel; Zbořil, Radek; Besenbacher, Flemming; Dong, Mingdong; Otyepka, Michal
2013-02-26
The two-dimensional material graphene has numerous potential applications in nano(opto)electronics, which inevitably involve metal graphene interfaces.Theoretical approaches have been employed to examine metal graphene interfaces, but experimental evidence is currently lacking. Here, we combine atomic force microscopy (AFM) based dynamic force measurements and density functional theory calculations to quantify the interaction between metal-coated AFM tips and graphene under ambient conditions. The results show that copper has the strongest affinity to graphene among the studied metals (Cu, Ag, Au, Pt, Si), which has important implications for the construction of a new generation of electronic devices. Observed differences in the nature of the metal-graphene bonding are well reproduced by the calculations, which included nonlocal Hartree-Fock exchange and van der Waals effects.
Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations.
Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei
2017-02-14
Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young's modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young's modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.
Validation of GPU based TomoTherapy dose calculation engine.
Chen, Quan; Lu, Weiguo; Chen, Yu; Chen, Mingli; Henderson, Douglas; Sterpin, Edmond
2012-04-01
The graphic processing unit (GPU) based TomoTherapy convolution/superposition(C/S) dose engine (GPU dose engine) achieves a dramatic performance improvement over the traditional CPU-cluster based TomoTherapy dose engine (CPU dose engine). Besides the architecture difference between the GPU and CPU, there are several algorithm changes from the CPU dose engine to the GPU dose engine. These changes made the GPU dose slightly different from the CPU-cluster dose. In order for the commercial release of the GPU dose engine, its accuracy has to be validated. Thirty eight TomoTherapy phantom plans and 19 patient plans were calculated with both dose engines to evaluate the equivalency between the two dose engines. Gamma indices (Γ) were used for the equivalency evaluation. The GPU dose was further verified with the absolute point dose measurement with ion chamber and film measurements for phantom plans. Monte Carlo calculation was used as a reference for both dose engines in the accuracy evaluation in heterogeneous phantom and actual patients. The GPU dose engine showed excellent agreement with the current CPU dose engine. The majority of cases had over 99.99% of voxels with Γ(1%, 1 mm) < 1. The worst case observed in the phantom had 0.22% voxels violating the criterion. In patient cases, the worst percentage of voxels violating the criterion was 0.57%. For absolute point dose verification, all cases agreed with measurement to within ±3% with average error magnitude within 1%. All cases passed the acceptance criterion that more than 95% of the pixels have Γ(3%, 3 mm) < 1 in film measurement, and the average passing pixel percentage is 98.5%-99%. The GPU dose engine also showed similar degree of accuracy in heterogeneous media as the current TomoTherapy dose engine. It is verified and validated that the ultrafast TomoTherapy GPU dose engine can safely replace the existing TomoTherapy cluster based dose engine without degradation in dose accuracy.
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.
Liu, Lihong; Xia, Shuhua; Fang, Wei-Hai
2014-10-02
In this article, structures and energies of cyclopropenone in the low-lying electronic states have been determined by the CASSCF and MS-CASPT2 calculations with different basis sets. Two minimum-energy conical intersections (CI-1 and CI-2) between S0 and S1 were obtained and their topographic characters were characterized by the SA4-CAS(10,9) calculated energy gradients and nonadiabatic coupling vectors. The AIMS method was used to carry out nonadiabatic dynamics simulation with ab initio calculation performed at the SA4-CAS(10,9) level. On the basis of time evolution of wave functions simulated here, the S1 lifetime is fitted to be 125 fs with a pure exponential decay for the S1 electronic population. The CI-1 intersection is mainly responsible for ultrafast S1→S0 nonadiabatic transition and the photoinduced decarbonylation is a sequential process, where the first C-C bond is broken in the S1 state and fission of the second C-C bond occurs in the S0 state as a result of the S1→S0 internal conversion via the CI-1 region. As a minor channel through the CI-2 region, the decarbonylation proceeds in an asynchronous concerted way. Effects of the S1 excess energies and the S1-S0 energy gap on the nonadiabatic dynamics were examined, which reveals that the S1→S0 nonadiabatic transition occurs within a small energy gap and high-energy conical intersection regions can play an important role. The present study provides new insights into mechanistic photochemistry of cyclopropenones and reveals that the AIMS dynamics simulation at a high-accuracy ab initio level is a powerful tool for exploring a mechanism of an ultrafast photochemical reaction.
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.
Why Dynamic Simulations are Needed to Calculate Thermally Averaged Spin Hamiltonians
NASA Astrophysics Data System (ADS)
Weitekamp, Daniel P.; Mueller, Leonard J.
1998-03-01
The spin Hamiltonian needed to describe nearly all magnetic resonance experiments is an average over rapidly relaxing spatial degrees of freedom. This has previously been taken to be a Boltzmann average of quantities calculable from the time-independent Hamiltonian describing the system. We show why this approach is conceptually flawed and describe the physics of previously unsuspected, intrinsically dynamic, contributions to the spin Hamiltonian for this ubiquitous situation. Numerical estimates indicate that these new terms are required in order to simulate nuclear magnetic resonance spectra at the resolution with which they are routinely measured. An approach is outlined in which ab initio electronic structures may be combined with a tractable semi-classical description of rovibrational relaxation to give the necessary dynamic corrections, which are described by an average Liouvillian born as the result of spatial susceptibility (ALBATROSS).
Time-reversed particle dynamics calculation with field line tracing at Titan - an update
NASA Astrophysics Data System (ADS)
Bebesi, Zsofia; Erdos, Geza; Szego, Karoly; Juhasz, Antal; Lukacs, Katalin
2014-05-01
We use CAPS-IMS Singles data of Cassini measured between 2004 and 2010 to investigate the pickup process and dynamics of ions originating from Titan's atmosphere. A 4th order Runge-Kutta method was applied to calculate the test particle trajectories in a time reversed scenario, in the curved magnetic environment. We evaluated the minimum variance directions along the S/C trajectory for all Cassini flybys during which the CAPS instrument was in operation, and assumed that the field was homogeneous perpendicular to the minimum variance direction. We calculated the magnetic field lines with this method along the flyby orbits and we could determine those observational intervals when Cassini and the upper atmosphere of Titan could be magnetically connected. We used three ion species (1, 2 and 16 amu ions) for time reversed tracking, and also considered the categorization of Rymer et al. (2009) and Nemeth et al. (2011) for further features studies.
van der Spoel, D; Berendsen, H J
1996-01-01
In this work we give an overview of the methodologies required to compute the rate of proton transfer in hydrogen bonded systems in solution. Using ab initio or density functional methods we determine proton potentials of a truncated system as a function of proton-donor proton-acceptor distance as well as nonbonding parameters. By classical molecular dynamics we evaluate a swarm of proton potentials with the proton fixed in the reactant well. The rate of proton transfer is calculated perturbatively using the Density Matrix Evolution (DME) method, going beyond the Born Oppenheimer approximation. The method is illustrated by two examples: hydrogen malonate and the active center of HIV-1 protease.
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.
First-principles molecular dynamics calculations of the equation of state for tantalum.
Ono, Shigeaki
2009-11-20
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.
The electronic nonadiabatic coupling term: can it be ignored in dynamic calculations?
Halász, G J; Vibók, A; Suhai, S; Baer, M
2007-12-28
Whereas the search for the degeneracy points which are better known as conical intersections (or ci-points) is usually carried out with a lot of devotion, the nonadiabatic coupling terms (NACTs) which together with the adiabatic potential energy surfaces appear in the nuclear Born-Oppenheimer-Schrodinger equation are ignored in most dynamical calculations. In the present article we consider two well known frameworks, namely, the semiclassical surface hopping method and the vibrational coupling model Hamiltonian that avoid the NACTs and examine to what extent, this procedure is justified.
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
A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity
NASA Astrophysics Data System (ADS)
Müller-Plathe, Florian
1997-04-01
A nonequilibrium molecular dynamics method for calculating the thermal conductivity is presented. It reverses the usual cause and effect picture. The "effect," the heat flux, is imposed on the system and the "cause," the temperature gradient is obtained from the simulation. Besides being very simple to implement, the scheme offers several advantages such as compatibility with periodic boundary conditions, conservation of total energy and total linear momentum, and the sampling of a rapidly converging quantity (temperature gradient) rather than a slowly converging one (heat flux). The scheme is tested on the Lennard-Jones fluid.
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.
Lill, Markus A.; Thompson, Jared J.
2011-01-01
End-point methods such as Linear Interaction Energy (LIE) analysis, Molecular Mechanics Generalized Born Solvent Accessible Surface (MM/GBSA) and Solvent Interaction Energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computationally expensive. In an attempt to reduce the high computational cost associated with end-point methods, we study several methods by which frames may be intelligently selected from the MD simulation including clustering and address the question how the number of selected frames influences the accuracy of the SIE calculations. PMID:21870864
Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package
Pierce, Levi T.; Walker, Ross C.; McCammont, J. Andrew
2013-01-01
Alchemical transformations are widely used methods to calculate free energies. Amber has traditionally included support for alchemical transformations as part of the sander molecular dynamics (MD) engine. Here we describe the implementation of a more efficient approach to alchemical transformations in the Amber MD package. Specifically we have implemented this new approach within the more computational efficient and scalable pmemd MD engine that is included with the Amber MD package. The majority of the gain in efficiency comes from the improved design of the calculation, which includes better parallel scaling and reduction in the calculation of redundant terms. This new implementation is able to reproduce results from equivalent simulations run with the existing functionality, but at 2.5 times greater computational efficiency. This new implementation is also able to run softcore simulations at the λ end states making direct calculation of free energies more accurate, compared to the extrapolation required in the existing implementation. The updated alchemical transformation functionality will be included in the next major release of Amber (scheduled for release in Q1 2014) and will be available at http://ambermd.org, under the Amber license. PMID:24185531
Philips, Adam; Marchenko, Alex; Truflandier, Lionel A; Autschbach, Jochen
2017-09-12
Quadrupolar NMR relaxation rates are computed for (17)O and (2)H nuclei of liquid water, and of (23)Na(+), and (35)Cl(-) in aqueous solution via Kohn-Sham (KS) density functional theory ab initio molecular dynamics (aiMD) and subsequent KS electric field gradient (EFG) calculations along the trajectories. The calculated relaxation rates are within about a factor of 2 of experimental results and improved over previous aiMD simulations. The relaxation rates are assessed with regard to the lengths of the simulations as well as configurational sampling. The latter is found to be the more limiting factor in obtaining good statistical sampling and is improved by averaging over many equivalent nuclei of a system or over several independent trajectories. Further, full periodic plane-wave basis calculations of the EFGs are compared with molecular-cluster atomic-orbital basis calculations. The two methods deliver comparable results with nonhybrid functionals. With the molecular-cluster approach, a larger variety of electronic structure methods is available. For chloride, the EFG computations benefit from using a hybrid KS functional.
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.
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.
Perišić, Ognjen; Lu, Hui
2014-01-01
The potential of mean force (PMF) calculation in single molecule manipulation experiments performed via the steered molecular dynamics (SMD) technique is a computationally very demanding task because the analyzed system has to be perturbed very slowly to be kept close to equilibrium. Faster perturbations, far from equilibrium, increase dissipation and move the average work away from the underlying free energy profile, and thus introduce a bias into the PMF estimate. The Jarzynski equality offers a way to overcome the bias problem by being able to produce an exact estimate of the free energy difference, regardless of the perturbation regime. However, with a limited number of samples and high dissipation the Jarzynski equality also introduces a bias. In our previous work, based on the Brownian motion formalism, we introduced three stochastic perturbation protocols aimed at improving the PMF calculation with the Jarzynski equality in single molecule manipulation experiments and analogous computer simulations. This paper describes the PMF reconstruction results based on full-atom molecular dynamics simulations, obtained with those three protocols. We also want to show that the protocols are applicable with the second-order cumulant expansion formula. Our protocols offer a very noticeable improvement over the simple constant velocity pulling. They are able to produce an acceptable estimate of PMF with a significantly reduced bias, even with very fast perturbation regimes. Therefore, the protocols can be adopted as practical and efficient tools for the analysis of mechanical properties of biological molecules. PMID:25232859
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.
NASA Astrophysics Data System (ADS)
Dyachenko, Leonid K.; Benin, Andrey V.
2017-06-01
When the high-speed railway traffic is being organized, it becomes necessary to elaborate bridge design standards for high-speed railways (HSR). Methodology of studying the issues of HSR bridge design is based on the comprehensive analysis of domestic research as well as international experience in design, construction and operation of high-speed railways. Serious requirements are imposed on the HSR artificial structures, which raise a number of scientific tasks associated mainly with the issues of the dynamic interaction of the rolling stock and the bridge elements. To ensure safety of traffic and reliability of bridges during the whole period of operation one needs to resolve the dynamic problems of various types of high-speed trains moving along the structures. The article analyses dependences of the magnitude of inertial response on the external stress parameters and proposes a simplified method of determination of the dynamic live load factor caused by the passage of high-speed trains. The usefulness of the given research arises from the reduction of complexity of the complicated dynamic calculations needed to describe a high-speed train travelling along the artificial structures.
Ice flood velocity calculating approach based on single view metrology
NASA Astrophysics Data System (ADS)
Wu, X.; Xu, L.
2017-02-01
Yellow River is the river in which the ice flood occurs most frequently in China, hence, the Ice flood forecasting has great significance for the river flood prevention work. In various ice flood forecast models, the flow velocity is one of the most important parameters. In spite of the great significance of the flow velocity, its acquisition heavily relies on manual observation or deriving from empirical formula. In recent years, with the high development of video surveillance technology and wireless transmission network, the Yellow River Conservancy Commission set up the ice situation monitoring system, in which live videos can be transmitted to the monitoring center through 3G mobile networks. In this paper, an approach to get the ice velocity based on single view metrology and motion tracking technique using monitoring videos as input data is proposed. First of all, River way can be approximated as a plane. On this condition, we analyze the geometry relevance between the object side and the image side. Besides, we present the principle to measure length in object side from image. Secondly, we use LK optical flow which support pyramid data to track the ice in motion. Combining the result of camera calibration and single view metrology, we propose a flow to calculate the real velocity of ice flood. At last we realize a prototype system by programming and use it to test the reliability and rationality of the whole solution.
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.
Calculation and Study of Graphene Conductivity Based on Terahertz Spectroscopy
NASA Astrophysics Data System (ADS)
Feng, Xiaodong; Hu, Min; Zhou, Jun; Liu, Shenggang
2017-07-01
Based on terahertz time-domain spectroscopy system and two-dimensional scanning control system, terahertz transmission and reflection intensity mapping images on a graphene film are obtained, respectively. Then, graphene conductivity mapping images in the frequency range 0.5 to 2.5 THz are acquired according to the calculation formula. The conductivity of graphene at some typical regions is fitted by Drude-Smith formula to quantitatively compare the transmission and reflection measurements. The results show that terahertz reflection spectroscopy has a higher signal-to-noise ratio with less interference of impurities on the back of substrates. The effect of a red laser excitation on the graphene conductivity by terahertz time-domain transmission spectroscopy is also studied. The results show that the graphene conductivity in the excitation region is enhanced while that in the adjacent area is weakened which indicates carriers transport in graphene under laser excitation. This paper can make great contribution to the study on graphene electrical and optical properties in the terahertz regime and help design graphene terahertz devices.
NASA Astrophysics Data System (ADS)
Todd, B.; Stackhouse, S.; Walker, A.; Mound, J. E.
2016-12-01
Thermal conductivity is a key parameter for Earth models involving heat flow across the core-mantle boundary. It is not currently possible to measure the thermal conductivity of minerals at lower mantle temperatures, meaning that lower temperature experimental values must be extrapolated, introducing considerable uncertainty. Furthermore, the effect of impurities, such as Fe and Al, is poorly constrained. In view of this, we use two complementary theoretical methods to determine the lattice thermal conductivity of (Fe,Mg)SiO3 bridgmanite, with varying concentration and distribution of Fe impurities. First, we utilise the direct method (non-equilibrium molecular dynamics), which allows thermal conductivity to be calculated, via Fourier's law, from the ratio of an imposed heat-flux and induced thermal gradient. Second, equilibrium molecular dynamics is employed to measure the time-dependence of instantaneous heat-flux variations, which are related to thermal conductivity via the Green-Kubo equation. We find that both methods have finite-size effects, which must be resolved before considering the important issue of impurity content. These effects are assessed using interatomic potentials, in order to reach the requisite large simulation sizes (up to approximately 60,000 atoms) on a reasonable timescale. Our work provides a systematic study of the effects to consider when calculating the thermal conductivity of minerals at lower mantle conditions.
NASA Astrophysics Data System (ADS)
Feng, Chi; Li, Dong; Gao, Shan; Daniel, Ketui
2016-11-01
This paper presents a CFD (Computation Fluid Dynamic) simulation and experimental results for the reflected radiation error from turbine vanes when measuring turbine blade's temperature using a pyrometer. In the paper, an accurate reflection model based on discrete irregular surfaces is established. Double contour integral method is used to calculate view factor between the irregular surfaces. Calculated reflected radiation error was found to change with relative position between blades and vanes as temperature distribution of vanes and blades was simulated using CFD. Simulation results indicated that when the vanes suction surface temperature ranged from 860 K to 1060 K and the blades pressure surface average temperature is 805 K, pyrometer measurement error can reach up to 6.35%. Experimental results show that the maximum pyrometer absolute error of three different targets on the blade decreases from 6.52%, 4.15% and 1.35% to 0.89%, 0.82% and 0.69% respectively after error correction.
Lee, Kyungmin; Cho, Soohyun
2017-01-26
Mathematics anxiety (MA) refers to the experience of negative affect when engaging in mathematical activity. According to Ashcraft and Kirk (2001), MA selectively affects calculation with high working memory (WM) demand. On the other hand, Maloney, Ansari, and Fugelsang (2011) claim that MA affects all mathematical activities, including even the most basic ones such as magnitude comparison. The two theories make opposing predictions on the negative effect of MA on magnitude processing and simple calculation that make minimal demands on WM. We propose that MA has a selective impact on mathematical problem solving that likely involves processing of magnitude representations. Based on our hypothesis, MA will impinge upon magnitude processing even though it makes minimal demand on WM, but will spare retrieval-based, simple calculation, because it does not require magnitude processing. Our hypothesis can reconcile opposing predictions on the negative effect of MA on magnitude processing and simple calculation. In the present study, we observed a negative relationship between MA and performance on magnitude comparison and calculation with high but not low WM demand. These results demonstrate that MA has an impact on a wide range of mathematical performance, which depends on one's sense of magnitude, but spares over-practiced, retrieval-based calculation.
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.
Multiple pH Regime Molecular Dynamics Simulation for pK Calculations
Nilsson, Lennart; Karshikoff, Andrey
2011-01-01
Ionisation equilibria in proteins are influenced by conformational flexibility, which can in principle be accounted for by molecular dynamics simulation. One problem in this method is the bias arising from the fixed protonation state during the simulation. Its effect is mostly exhibited when the ionisation behaviour of the titratable groups is extrapolated to pH regions where the predetermined protonation state of the protein may not be statistically relevant, leading to conformational sampling that is not representative of the true state. In this work we consider a simple approach which can essentially reduce this problem. Three molecular dynamics structure sets are generated, each with a different protonation state of the protein molecule expected to be relevant at three pH regions, and pK calculations from the three sets are combined to predict pK over the entire pH range of interest. This multiple pH molecular dynamics approach was tested on the GCN4 leucine zipper, a protein for which a full data set of experimental data is available. The pK values were predicted with a mean deviation from the experimental data of 0.29 pH units, and with a precision of 0.13 pH units, evaluated on the basis of equivalent sites in the dimeric GCN4 leucine zipper. PMID:21647418
Oikawa, Masataka; Yonetani, Yoshiteru
2010-01-01
Abstract Are protein nonpolar cavities filled with water molecules? Although many experimental and theoretical investigations have been done, particularly for the nonpolar cavity of IL-1β, the results are still conflicting. To study this problem from the thermodynamic point of view, we calculated hydration free energies of four protein nonpolar cavities by means of the molecular dynamics thermodynamic integration method. In addition to the IL-1β cavity (69 Å3), we selected the three largest nonpolar cavities of AvrPphB (81 Å3), Trp repressor (87 Å3), and hemoglobin (108 Å3) from the structural database, in view of the simulation result from another study that showed larger nonpolar cavities are more likely to be hydrated. The calculations were performed with flexible and rigid protein models. The calculated free energy changes were all positive; hydration of the nonpolar cavities was energetically unfavorable for all four cases. Because hydration of smaller cavities should happen more rarely, we conclude that existing protein nonpolar cavities are not likely to be hydrated. Although a possibility remains for much larger nonpolar cavities, such cases are not found experimentally. We present a hypothesis to explain this: hydrated nonpolar cavities are quite unstable and the conformation could not be maintained. PMID:20550910
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 thermophysical properties for a highly reactive liquid.
Wang, H P; Luo, B C; Wei, B
2008-10-01
In order to further understand the physical characteristics of liquid silicon, the thermophysical properties are required over a broad temperature range. However, its high reactivity brings about great difficulties in the experimental measurement. Here we report the thermophysical properties by molecular dynamics calculation, including density, specific heat, diffusion coefficient, and surface tension. The calculation is performed with a system consisting of 64,000 atoms, and employing the Stillinger-Weber (SW) potential model and the modified embedded atom method (MEAM) potential model. The results show that the density increases as a quadratic function of undercooling, and the value calculated by SW potential model is only 2-4 % smaller than the reported experimental data. The specific heat is obtained to be 30.95 J mol;{-1}K;{-1} by SW potential model and 32.50 J mol;{-1}K;{-1} by MEAM potential model, both of which are constants in the corresponding ranges of temperature. The self-diffusion coefficient is exponentially dependent on the temperature and consistent with the Arrhenius equation. The surface tension increases linearly with the rise of undercooling and agrees well with the reported experimental results. This work provides reasonable data in much wider temperature range, especially for the undercooled metastable state.
Bhatnagar, Navendu; Kamath, Ganesh; Chelst, Issac; Potoff, Jeffrey J
2012-07-07
The 1-octanol-water partition coefficient log K(ow) of a solute is a key parameter used in the prediction of a wide variety of complex phenomena such as drug availability and bioaccumulation potential of trace contaminants. In this work, adaptive biasing force molecular dynamics simulations are used to determine absolute free energies of hydration, solvation, and 1-octanol-water partition coefficients for n-alkanes from methane to octane. Two approaches are evaluated; the direct transfer of the solute from 1-octanol to water phase, and separate transfers of the solute from the water or 1-octanol phase to vacuum, with both methods yielding statistically indistinguishable results. Calculations performed with the TIP4P and SPC∕E water models and the TraPPE united-atom force field for n-alkanes show that the choice of water model has a negligible effect on predicted free energies of transfer and partition coefficients for n-alkanes. A comparison of calculations using wet and dry octanol phases shows that the predictions for log K(ow) using wet octanol are 0.2-0.4 log units lower than for dry octanol, although this is within the statistical uncertainty of the calculation.
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.
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.
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.
Prévost, Martine
2004-10-05
Molecular dynamics (MD) simulations of several nanoseconds each were used to monitor the dynamic behavior of the five crystal water molecules buried in the interior of the N-terminal domain of apolipoprotein E. These crystal water molecules are fairly well conserved in several apolipoprotein E structures, suggesting that they are not an artifact of the crystal and that they may have a structural and/or functional role for the protein. All five buried crystal water molecules leave the protein interior in the course of the longest simulations and exchange with water molecules from the bulk. The free energies of binding evaluated from the electrostatic binding free energy computed using a continuum model and estimates of the binding entropy changes represent shallow minima. The corresponding calculated residence times of the buried water molecules range from tens of picoseconds to hundreds of nanoseconds, which denote rather short times as for buried water molecules. Several water exchanges monitored in the simulations show that water molecules along the exit/entrance pathway use a relay of H bonds primarily formed with charged residues which helps either the exit or the entrance from or into the buried site. The exit/entrance of water molecules from/into the sites is permitted essentially by local motions of, at most, two side chains, indicating that, in these cases, complex correlated atomic motions are not needed to open the buried site toward the surface of the protein. This provides a possible explanation for the short residence times.
[CUDA-based fast dose calculation in radiotherapy].
Wang, Xianliang; Liu, Cao; Hou, Qing
2011-10-01
Dose calculation plays a key role in treatment planning of radiotherapy. Algorithms for dose calculation require high accuracy and computational efficiency. Finite size pencil beam (FSPB) algorithm is a method commonly adopted in the treatment planning system for radiotherapy. However, improvement on its computational efficiency is still desirable for such purpose as real time treatment planning. In this paper, we present an implementation of the FSPB, by which the most time-consuming parts in the algorithm are parallelized and ported on graphic processing unit (GPU). Compared with the FSPB completely running on central processing unit (CPU), the GPU-implemented FSPB can speed up the dose calculation for 25-35 times on a low price GPU (Geforce GT320) and for 55-100 times on a Tesla C1060, indicating that the GPU-implemented FSPB can provide fast enough dose calculations for real-time treatment planning.
NASA Astrophysics Data System (ADS)
Crawford, Ben; Grimmond, Sue; Kent, Christoph; Gabey, Andrew; Ward, Helen; Sun, Ting; Morrison, William
2017-04-01
Remotely sensed data from satellites have potential to enable high-resolution, automated calculation of urban surface energy balance terms and inform decisions about urban adaptations to environmental change. However, aerodynamic resistance methods to estimate sensible heat flux (QH) in cities using satellite-derived observations of surface temperature are difficult in part due to spatial and temporal variability of the thermal aerodynamic resistance term (rah). In this work, we extend an empirical function to estimate rah using observational data from several cities with a broad range of surface vegetation land cover properties. We then use this function to calculate spatially and temporally variable rah in London based on high-resolution (100 m) land cover datasets and in situ meteorological observations. In order to calculate high-resolution QH based on satellite-observed land surface temperatures, we also develop and employ novel methods to i) apply source area-weighted averaging of surface and meteorological variables across the study spatial domain, ii) calculate spatially variable, high-resolution meteorological variables (wind speed, friction velocity, and Obukhov length), iii) incorporate spatially interpolated urban air temperatures from a distributed sensor network, and iv) apply a modified Monte Carlo approach to assess uncertainties with our results, methods, and input variables. Modeled QH using the aerodynamic resistance method is then compared to in situ observations in central London from a unique network of scintillometers and eddy-covariance measurements.
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies.
Fowler, Philip W; Jha, Shantenu; Coveney, Peter V
2005-08-15
The calculation of binding free energies is important in many condensed matter problems. Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming. We describe a Grid-based approach for the calculation of relative binding free energies, which we call Steered Thermodynamic Integration calculations using Molecular Dynamics (STIMD), and its application to Src homology 2 (SH2) protein cell signalling domains. We show that the time taken to compute free energy differences using thermodynamic integration can be significantly reduced: potentially from weeks or months to days of wall-clock time. To be able to perform such accelerated calculations requires the ability to both run concurrently and control in realtime several parallel simulations on a computational Grid. We describe how the RealityGrid computational steering system, in conjunction with a scalable classical MD code, can be used to dramatically reduce the time to achieve a result. This is necessary to improve the adoption of this technique and further allows more detailed investigations into the accuracy and precision of thermodynamic integration. Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach.
Opinion dynamics model based on quantum formalism
Artawan, I. Nengah; Trisnawati, N. L. P.
2016-03-11
Opinion dynamics model based on quantum formalism is proposed. The core of the quantum formalism is on the half spin dynamics system. In this research the implicit time evolution operators are derived. The analogy between the model with Deffuant dan Sznajd models is discussed.
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.
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.
Thermal transmission at Si/Ge interface: ab initio lattice dynamics calculation
NASA Astrophysics Data System (ADS)
Alkurdi, A.; Merabia, S.
2017-01-01
We perform lattice dynamics calculations (LD) on silicon/germanium interfaces using ab initio interatomic force constants to predict the interfacial phonon transmission as a function of both phonon frequency and the transmission angle. We carry out a spectral and angular analysis to quantify the contribution of each phonon mode in a given scattering direction. The effect of the interaction range was studied at this interface by taking account of more or less atom layers across the interface. Moreover, we were able to predict the thermal boundary conductance (TBC) as a function of the transmission angle and temperature as well. Our results show that, the thermal energy transmission is highly anisotropic while thermal energy reflection is almost isotropic. In addition, we found that it seems there is a global critical angle of transmission beyond which almost no thermal energy is transmitted. This can be used to device high pass phonon filter via changing the orientation of the interface.
Calculation of two-particle quantities in the typical medium dynamical cluster approximation
NASA Astrophysics Data System (ADS)
Zhang, Y.; Zhang, Y. F.; Yang, S. X.; Tam, K.-M.; Vidhyadhiraja, N. S.; Jarrell, M.
2017-04-01
The mean-field theory for disordered electron systems without interaction is widely and successfully used to describe equilibrium properties of materials over the whole range of disorder strengths. However, it fails to take into account the effects of quantum coherence and information of localization. Vertex corrections due to multiple backscatterings may drive the electrical conductivity to zero and make expansions around the mean field in strong disorder problematic. Here, we present a method for the calculation of two-particle quantities which enables us to characterize the metal-insulator transitions in disordered electron systems by using the typical medium dynamical cluster approximation. We show how to include vertex corrections and information about the mobility edge in the typical mean-field theory. We successfully demonstrate the application of the developed method by showing that the conductivity formulated in this way properly characterizes the metal-insulator transition in disordered systems.
NASA Astrophysics Data System (ADS)
Zang, Yan; Hatch, Michael R.
We describe a numerical method for the analysis of dynamic characteristics of coupled herringbone-type journal and thrust hydrodynamic bearings. The non-dimensional generalized Reynolds equation is discretized on a non-orthogonal grid which is mapped into a square. The computational domain conforms to the herringbone grooves to improve the accuracy of the solution. The journal and thrust regions are mapped separately and connected through internal flux boundary conditions. The discretized pressure field is solved iteratively using the rapidly convergent ADI method. The stiffness and damping coefficients are obtained by perturbing the equilibrium solution of the Reynolds equation and solving the perturbation equations. The accuracy of the present calculation is confirmed by comparing with previously existing data. Analyses are performed for self-contained coupled hydrodynamic bearing systems which can be used to support the spindle motor of a magnetic hard-disk drive.
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.
Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A
2015-10-26
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.
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.
Aguilella-Arzo, M; Aguilella, V M
2010-04-01
We have computed the pK(a)'s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin alpha-hemolysin, by using two types of input structures, namely the crystal structure of the heptameric alpha-hemolysin and a set of over four hundred snapshots from a 4.38 ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pK(a) of a given residue to small changes in the local structure. The calculated pK(a) are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements.
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
Ruiz, B C; Tucker, W K; Kirby, R R
1975-01-01
With a desk-top, programmable calculator, it is now possible to do complex, previously time-consuming computations in the blood-gas laboratory. The authors have developed a program with the necessary algorithms for temperature correction of blood gases and calculation of acid-base variables and intrapulmonary shunt. It was necessary to develop formulas for the Po2 temperature-correction coefficient, the oxyhemoglobin-dissociation curve for adults (withe necessary adjustments for fetal blood), and changes in water vapor pressure due to variation in body temperature. Using this program in conjuction with a Monroe 1860-21 statistical programmable calculator, it is possible to temperature-correct pH,Pco2, and Po2. The machine will compute alveolar-arterial oxygen tension gradient, oxygen saturation (So2), oxygen content (Co2), actual HCO minus 3 and a modified base excess. If arterial blood and mixed venous blood are obtained, the calculator will print out intrapulmonary shunt data (Qs/Qt) and arteriovenous oxygen differences (a minus vDo2). There also is a formula to compute P50 if pH,Pco2,Po2, and measured So2 from two samples of tonometered blood (one above 50 per cent and one below 50 per cent saturation) are put into the calculator.
Ji, Changge; Mei, Ye; Zhang, John Z H
2008-08-01
Ab initio quantum mechanical calculation of protein in solution is carried out to generate polarized protein-specific charge(s) (PPC) for molecular dynamics (MD) stimulation of protein. The quantum calculation of protein is made possible by developing a fragment-based quantum chemistry approach in combination with the implicit continuum solvent model. The computed electron density of protein is utilized to derive PPCs that represent the polarized electrostatic state of protein near the native structure. These PPCs are atom-centered like those in the standard force fields and are thus computationally attractive for molecular dynamics simulation of protein. Extensive MD simulations have been carried out to investigate the effect of electronic polarization on the structure and dynamics of thioredoxin. Our study shows that the dynamics of thioredoxin is stabilized by electronic polarization through explicit comparison between MD results using PPC and AMBER charges. In particular, MD free-energy calculation using PPCs accurately reproduced the experimental value of pK(a) shift for ionizable residue Asp(26) buried inside thioredoxin, whereas previous calculations using standard force fields overestimated pK(a) shift by twice as much. Accurate prediction of pK(a) shifts by rigorous MD free energy simulation for ionizable residues buried inside protein has been a significant challenge in computational biology for decades. This study presented strong evidence that electronic polarization of protein plays an important role in protein dynamics.
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.
Huang, Baoling L.; Kaviany, Massoud
2010-05-25
The phonon conductivities of CoSb_{3} and its Ba-filled structure Ba_{x}(CoSb_{3})_{4} are investigated using first-principle calculations and molecular dynamics (MD) simulations, along with the Green–Kubo theory. The effects of fillers on the reduction of the phonon conductivity of filled skutterudites are then explored. It is found that the coupling between filler and host is strong, with minor anharmonicity. The phonon density of states and its dispersion are significantly influenced by filler-induced softening of the host bonds (especially the short Sb–Sb bonds). Lattice dynamics and MD simulations show that, without a change in the host interatomic potentials, the filler–host bonding alone cannot lead to significant alteration of acoustic phonons or lowering of phonon conductivity. The observed smaller phonon conductivity of partially filled skutterudites is explained by treating it as a solid solution of the empty and fully filled structures.
Photodissociation dynamics of the pyridinyl radical: Time-dependent quantum wave-packet calculations
NASA Astrophysics Data System (ADS)
Ehrmaier, Johannes; Picconi, David; Karsili, Tolga N. V.; Domcke, Wolfgang
2017-03-01
The H-atom photodissociation reaction from the pyridinyl radical (C5H5NH ) via the low-lying π σ* excited electronic state is investigated by nonadiabatic time-dependent quantum wave-packet dynamics calculations. A model comprising three electronic states and three nuclear coordinates has been constructed using ab initio multi-configurational self-consistent-field and multi-reference perturbation theory methods. Two conical intersections among the three lowest electronic states have been characterized in the framework of the linear vibronic-coupling model. Time-dependent wave-packet simulations have been performed using the multi-configuration time-dependent Hartree method. The population dynamics of the diabatic and adiabatic electronic states and the time-dependent dissociation behavior are analyzed for various vibrational initial conditions. The results provide detailed mechanistic insight into the photoinduced H-atom dissociation process from a hypervalent aromatic radical and show that an efficient dissociation reaction through two conical intersections is possible.
Formaldehyde roaming dynamics: Comparison of quasi-classical trajectory calculations and experiments
NASA Astrophysics Data System (ADS)
Houston, Paul L.; Wang, Xiaohong; Ghosh, Aryya; Bowman, Joel M.; Quinn, Mitchell S.; Kable, Scott H.
2017-07-01
The photodissociation dynamics of roaming in formaldehyde are studied by comparing quasi-classical trajectory calculations performed on a new potential energy surface (PES) to new and detailed experimental results detailing the CO + H2 product state distributions and their correlations. The new PES proves to be a significant improvement over the past one, now more than a decade old. The new experiments probe both the CO and H2 products of the formaldehyde dissociation. The experimental and trajectory data offer unprecedented detail about the correlations between internal states of the CO and H2 dissociation products as well as information on how these distributions are different for the roaming and transition-state pathways. The data investigated include, for dissociation on the formaldehyde 2143 band, (a) the speed distributions for individual vibrational/rotational states of the CO products, providing information about the correlated internal energy distributions of the H2 product, and (b) the rotational and vibrational distributions for the CO and H2 products as well as the contributions to each from both the transition state and roaming channels. The agreement between the trajectory and experimental data is quite satisfactory, although minor differences are noted. The general agreement provides support for future use of the experimental techniques and the new PES in understanding the dynamics of photodissociative processes.
Collier, Bradley B.; McShane, Michael J.
2014-01-01
With advances to chemical sensing, methods for compensation of errors introduced by interfering analytes are needed. In this work, a dual lifetime calculation technique was developed to enable simultaneous monitoring of two luminescence decays. Utilizing a windowed time-domain luminescence approach, the response of two luminophores is separated temporally. The ability of the dual dynamic rapid lifetime determination (DDRLD) approach to determine the response of two luminophores simultaneously was investigated through mathematical modeling and experimental testing. Modeling results indicated that lifetime predictions will be most accurate when the ratio of the lifetimes from each luminophore is at least three and the ratio of intensities is near unity. In vitro experiments were performed using a porphyrin that is sensitive to both oxygen and temperature, combined with a temperature-sensitive inorganic phosphor used for compensation of the porphyrin response. In static experiments, the dual measurements were found to be highly accurate when compared to single-luminophore measurements—statistically equivalent for the long lifetime emission and an average difference of 2% for the short lifetimes. Real-time testing with dynamic windowing was successful in demonstrating dual lifetime measurements and temperature compensation of the oxygen sensitive dye. When comparing the actual oxygen and temperature values with predictions made using a dual calibration approach, an overall difference of less than 1% was obtained. Thus, this method enables rapid, accurate extraction of multiple lifetimes without requiring computationally intense curve fitting, providing a significant advancement toward multi-analyte sensing and imaging techniques. PMID:26566384
Accurate and fast narcissus calculation based on sequential ray trace.
Liu, Yang; Zhong, Xiaobing; Zhong, Ning; Zheng, Changsheng; Wen, Lizhan
2013-11-20
A narcissus calculating method for cryogenic infrared imaging systems is proposed in this paper. The accuracy is largely improved compared to the traditional paraxial analysis, as ray blocking of the optical opertures is taken into account and real ray data are used during the calculation. The narcissus distribution on the full focal plane can be obtained via analyzing field by field. Meanwhile, it can be implemented simply and fast as sequential ray tracing is utilized and rays only pass through three surfaces during the cold return statistics for every retro-reflecting surface. According to this method, a general narcissus calculation package was realized using the macro language of optical design software Code V. The performance of the new method was tested by calculating an example system using this package and comparing it with traditional methods. The results showed that the new method produced the same result accuracy and information quantity as the nonsequential ray trace, while the whole analysis took only 5 s, which was significantly shortened compared with the nonsequential ray trace, which took about 30 min.
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).
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).
Open Quantum Dynamics Calculations with the Hierarchy Equations of Motion on Parallel Computers.
Strümpfer, Johan; Schulten, Klaus
2012-08-14
Calculating the evolution of an open quantum system, i.e., a system in contact with a thermal environment, has presented a theoretical and computational challenge for many years. With the advent of supercomputers containing large amounts of memory and many processors, the computational challenge posed by the previously intractable theoretical models can now be addressed. The hierarchy equations of motion present one such model and offer a powerful method that remained under-utilized so far due to its considerable computational expense. By exploiting concurrent processing on parallel computers the hierarchy equations of motion can be applied to biological-scale systems. Herein we introduce the quantum dynamics software PHI, that solves the hierarchical equations of motion. We describe the integrator employed by PHI and demonstrate PHI's scaling and efficiency running on large parallel computers by applying the software to the calculation of inter-complex excitation transfer between the light harvesting complexes 1 and 2 of purple photosynthetic bacteria, a 50 pigment system.
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.
The cost of different types of lameness in dairy cows calculated by dynamic programming.
Cha, E; Hertl, J A; Bar, D; Gröhn, Y T
2010-10-01
Traditionally, studies which placed a monetary value on the effect of lameness have calculated the costs at the herd level and rarely have they been specific to different types of lameness. These costs which have been calculated from former studies are not particularly useful for farmers in making economically optimal decisions depending on individual cow characteristics. The objective of this study was to calculate the cost of different types of lameness at the individual cow level and thereby identify the optimal management decision for each of three representative lameness diagnoses. This model would provide a more informed decision making process in lameness management for maximal economic profitability. We made modifications to an existing dynamic optimization and simulation model, studying the effects of various factors (incidence of lameness, milk loss, pregnancy rate and treatment cost) on the cost of different types of lameness. The average cost per case (US$) of sole ulcer, digital dermatitis and foot rot were 216.07, 132.96 and 120.70, respectively. It was recommended that 97.3% of foot rot cases, 95.5% of digital dermatitis cases and 92.3% of sole ulcer cases be treated. The main contributor to the total cost per case of sole ulcer was milk loss (38%), treatment cost for digital dermatitis (42%) and the effect of decreased fertility for foot rot (50%). This model affords versatility as it allows for parameters such as production costs, economic values and disease frequencies to be altered. Therefore, cost estimates are the direct outcome of the farm specific parameters entered into the model. Thus, this model can provide farmers economically optimal guidelines specific to their individual cows suffering from different types of lameness.
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.
Straka, Michal; Lantto, Perttu; Vaara, Juha
2008-03-27
We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized
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.
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.
Diffraction Grating Efficiency Calculations Based on Real Groove Profiles
NASA Technical Reports Server (NTRS)
Content, David; Sroda, Tom; Palmer, Christopher; Kuznetsov, Ivan
2000-01-01
The program we are attempting to bring about combines 3 difficult features, in order to demonstrate accuracy of efficiency predictions: (1) Accurate groove metrology methods on surface relief gratings; (2) Rigorous and usable electromagnetic efficiency calculation codes; (3) Accurate efficiency measurements in polarized light The benefit would be an increase in yield for high-performance gratings. Many such applications suffer long lead time or serious performance loss when new gratings are made which do not meet requirements or expectations.
Tang, Xiaoli; Dong, Jianjun
2009-06-01
We report a recent first-principles calculation of harmonic and anharmonic lattice dynamics of MgO. The 2nd order harmonic and 3rd order anharmonic interatomic interaction terms are computed explicitly, and their pressure dependences are discussed. The phonon mode Grueneisen parameters derived based on our calculated 3rd order lattice anharmonicity are in good agreement with those estimated using the finite difference method. The implications for lattice thermal conductivity at high pressure are discussed based on a simple kinetic transport theory.
Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations.
Lange, Adrian W; Voth, Gregory A
2013-09-10
We introduce a multistate framework for Fragment Molecular Orbital (FMO) quantum mechanical calculations and implement it in the context of protonated water clusters. The purpose of the framework is to address issues of nonuniqueness and dynamic fragmentation in FMO as well as other related fragment methods. We demonstrate that our new approach, Fragment Molecular Orbital Multistate Reactive Molecular Dynamics (FMO-MS-RMD), can improve energetic accuracy and yield stable molecular dynamics for small protonated water clusters undergoing proton transfer reactions.
Shen, Mingyun; Zhou, Shunye; Li, Youyong; Pan, Peichen; Zhang, Liling; Hou, Tingjun
2013-03-01
Rho-associated protein kinases (ROCK1 and ROCK2) are promising targets for a number of diseases, including cardiovascular disorders, nervous system diseases, cancers, etc. Recently, we have successfully identified a ROCK1 inhibitor (1) with the triazine core. In order to gain a deeper insight into the microscopic binding of this inhibitor with ROCK1 and design derivatives with improved potency, the interactions between ROCK1 and a series of triazine/pyrimidine-based inhibitors were studied by using an integrated computational protocol that combines molecular docking, molecular dynamics (MD) simulations, binding free energy calculations, and binding energy decomposition analysis. First, three docking protocols, rigid receptor docking, induced fit docking, QM-polarized ligand docking, were used to determine the binding modes of the studied inhibitors in the active site of ROCK1. The results illustrate that rigid receptor docking achieves the best performance to rank the binding affinities of the studied inhibitors. Then, based on the predicted structures from molecular docking, MD simulations and MM/GBSA free energy calculations were employed to determine the dynamic binding process and compare the binding modes of the inhibitors with different activities. The binding free energies predicted by MM/GBSA are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. In addition, the residue-inhibitor interaction spectra were obtained by the MM/GBSA free energy decomposition analysis, and the important residues for achieving strong binding were highlighted, which affords important guidance for the rational design of novel ROCK inhibitors. Finally, a variety of derivatives of inhibitor 1 were designed and four of them showed promising potency according to the predictions. We expect that our study can provide significant insight into the
NASA Astrophysics Data System (ADS)
Micha, David A.
This contribution deals with two approaches for localized phenomena in excited many-atom systems. The first approach develops a quantum quasi-classical treatment for the density operator, including all atoms. It is based on a partial Wigner representation and is illustrated with applications to photodissociation of NaI, and to light emission of excited Li interacting with a He cluster. This second application describes the direct dynamics with a time-dependent electronic density matrix, expanded in a basis set of atomic functions. It shows that such an approach can deal with electronically excited many-atom systems involving tens of quantum states and hundreds of classical variables. The second approach makes use of the reduced density operator description for a system in a medium. This allows for dissipative dynamics, which can be instantaneous or delayed. An application is presented for femtosecond photodesorption using a Markovian dissipation and construction of the density operator from density amplitudes, for CO/Cu(001). A second application of a reduced density operator has been made to vibrational relaxation of adsorbates, solving integrodifferential equations to compare delayed, instantaneous, and Markovian dissipation. It is concluded that delayed dissipation is needed at short times and that a Markovian treatment is suitable for the interpretation of cross-sectional measurements that involve long-term dynamics.
Direct grid-based quantum dynamics on propagated diabatic potential energy surfaces
NASA Astrophysics Data System (ADS)
Richings, Gareth W.; Habershon, Scott
2017-09-01
We present a method for performing non-adiabatic, grid-based nuclear quantum dynamics calculations using diabatic potential energy surfaces (PESs) generated ;on-the-fly;. Gaussian process regression is used to interpolate PESs by using electronic structure energies, calculated at points in configuration space determined by the nuclear dynamics, and diabatising the results using the propagation diabatisation method reported recently (Richings and Worth, 2015). Our new method is successfully demonstrated using a grid-based approach to model the non-adiabatic dynamics of the butatriene cation. Overall, our scheme offers a route towards accurate quantum dynamics on diabatic PESs learnt on-the-fly.
An inviscid-viscous interaction approach to the calculation of dynamic stall initiation on airfoils
Cebeci, T. . Aerospace Engineering Dept.); Platzer, M.F. . Dept. of Aeronautics and Astronautics); Jang, H.M.; Chen, H.H. . Aerospace Engineering Dept.)
1993-10-01
An interactive boundary-layer method is described for computing unsteady incompressible flow over airfoils, including the initiation of dynamic stall. The inviscid unsteady panel method developed by Platzer and Teng is extended to include viscous effects. The solutions of the boundary-layer equations are obtained with an inverse finite-difference method employing an interaction law based on the Hilbert integral, and the algebraic eddy-viscosity formulation of Cebeci and Smith. The method is applied to airfoils subject to periodic and ramp-type motions and its abilities are examined for a range of angles of attack, reduced frequency, and pitch rate.
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.
Waegeneers, Nadia; Ruttens, Ann; De Temmerman, Ludwig
2011-06-15
A chain model was developed to calculate the flow of cadmium from soil, drinking water and feed towards bovine tissues. The data used for model development were tissue Cd concentrations of 57 bovines and Cd concentrations in soil, feed and drinking water, sampled at the farms were the bovines were reared. Validation of the model occurred with a second set of measured tissue Cd concentrations of 93 bovines of which age and farm location were known. The exposure part of the chain model consists of two parts: (1) a soil-plant transfer model, deriving cadmium concentrations in feed from basic soil characteristics (pH and organic matter content) and soil Cd concentrations, and (2) bovine intake calculations, based on typical feed and water consumption patterns for cattle and Cd concentrations in feed and drinking water. The output of the exposure model is an animal-specific average daily Cd intake, which is then taken forward to a kinetic uptake model in which time-dependent Cd concentrations in bovine tissues are calculated. The chain model was able to account for 65%, 42% and 32% of the variation in observed kidney, liver and meat Cd concentrations in the validation study.
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
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.
NASA Astrophysics Data System (ADS)
Caro, Miguel A.; Laurila, Tomi; Lopez-Acevedo, Olga
2016-12-01
We explore different schemes for improved accuracy of entropy calculations in aqueous liquid mixtures from molecular dynamics (MD) simulations. We build upon the two-phase thermodynamic (2PT) model of Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and explore new ways to obtain the partition between the gas-like and solid-like parts of the density of states, as well as the effect of the chosen ideal "combinatorial" entropy of mixing, both of which have a large impact on the results. We also propose a first-order correction to the issue of kinetic energy transfer between degrees of freedom (DoF). This problem arises when the effective temperatures of translational, rotational, and vibrational DoF are not equal, either due to poor equilibration or reduced system size/time sampling, which are typical problems for ab initio MD. The new scheme enables improved convergence of the results with respect to configurational sampling, by up to one order of magnitude, for short MD runs. To ensure a meaningful assessment, we perform MD simulations of liquid mixtures of water with several other molecules of varying sizes: methanol, acetonitrile, N, N-dimethylformamide, and n-butanol. Our analysis shows that results in excellent agreement with experiment can be obtained with little computational effort for some systems. However, the ability of the 2PT method to succeed in these calculations is strongly influenced by the choice of force field, the fluidicity (hard-sphere) formalism employed to obtain the solid/gas partition, and the assumed combinatorial entropy of mixing. We tested two popular force fields, GAFF and OPLS with SPC/E water. For the mixtures studied, the GAFF force field seems to perform as a slightly better "all-around" force field when compared to OPLS+SPC/E.
Caro, Miguel A; Laurila, Tomi; Lopez-Acevedo, Olga
2016-12-28
We explore different schemes for improved accuracy of entropy calculations in aqueous liquid mixtures from molecular dynamics (MD) simulations. We build upon the two-phase thermodynamic (2PT) model of Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and explore new ways to obtain the partition between the gas-like and solid-like parts of the density of states, as well as the effect of the chosen ideal "combinatorial" entropy of mixing, both of which have a large impact on the results. We also propose a first-order correction to the issue of kinetic energy transfer between degrees of freedom (DoF). This problem arises when the effective temperatures of translational, rotational, and vibrational DoF are not equal, either due to poor equilibration or reduced system size/time sampling, which are typical problems for ab initio MD. The new scheme enables improved convergence of the results with respect to configurational sampling, by up to one order of magnitude, for short MD runs. To ensure a meaningful assessment, we perform MD simulations of liquid mixtures of water with several other molecules of varying sizes: methanol, acetonitrile, N, N-dimethylformamide, and n-butanol. Our analysis shows that results in excellent agreement with experiment can be obtained with little computational effort for some systems. However, the ability of the 2PT method to succeed in these calculations is strongly influenced by the choice of force field, the fluidicity (hard-sphere) formalism employed to obtain the solid/gas partition, and the assumed combinatorial entropy of mixing. We tested two popular force fields, GAFF and OPLS with SPC/E water. For the mixtures studied, the GAFF force field seems to perform as a slightly better "all-around" force field when compared to OPLS+SPC/E.
A comparison of methods for melting point calculation using molecular dynamics simulations.
Zhang, Yong; Maginn, Edward J
2012-04-14
Accurate and efficient prediction of melting points for complex molecules is still a challenging task for molecular simulation, although many methods have been developed. Four melting point computational methods, including one free energy-based method (the pseudo-supercritical path (PSCP) method) and three direct methods (two interface-based methods and the voids method) were applied to argon and a widely studied ionic liquid 1-n-butyl-3-methylimidazolium chloride ([BMIM][Cl]). The performance of each method was compared systematically. All the methods under study reproduce the argon experimental melting point with reasonable accuracy. For [BMIM][Cl], the melting point was computed to be 320 K using a revised PSCP procedure, which agrees with the experimental value 337-339 K very well. However, large errors were observed in the computed results using the direct methods, suggesting that these methods are inappropriate for large molecules with sluggish dynamics. The strengths and weaknesses of each method are discussed.
NASA Astrophysics Data System (ADS)
Borkar, Aditi N.; De Simone, Alfonso; Montalvao, Rinaldo W.; Vendruscolo, Michele
2013-06-01
We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. In this approach, the alignment tensor required to calculate the RDCs corresponding to a given conformation is estimated from its shape, and multiple replicas of the RNA molecule are simulated simultaneously to reproduce in silico the ensemble-averaging procedure performed in the NMR measurements. We provide initial evidence that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.
Wang, Guo-Xiang; Dong, Shuai; Hou, Jing-Min
2016-03-31
The lattice structures and topological properties of X8 (X = C, Si, Ge, Sn, Pb) under hydrostatic strain have been investigated based on first-principle calculations. Among the materials, 8, Si8, Ge8 and Sn8 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 C8 and Si8, while for Ge8 and Sn8 the tensile strain can play a unique role in tuning the band topology, which will lead to a topological nontrivial state with Z2 invariants (1;111). Although the topological transition occurs above the Fermi level, the Fermi level can be tuned by applying electrostatic gating voltage.
NASA Technical Reports Server (NTRS)
Vinokur, M.
1983-01-01
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 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. Previously announced in STAR as N80-25055
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.
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
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.
Konecny, Lukas; Kadek, Marius; Komorovsky, Stanislav; Malkina, Olga L; Ruud, Kenneth; Repisky, Michal
2016-12-13
The Liouville-von Neumann equation based on the four-component matrix Dirac-Kohn-Sham Hamiltonian is transformed to a quasirelativistic exact two-component (X2C) form and then used to solve the time evolution of the electronic states only. By this means, a significant acceleration by a factor of 7 or more has been achieved. The transformation of the original four-component equation of motion is formulated entirely in matrix algebra, following closely the X2C decoupling procedure of Ilias and Saue [ J. Chem. Phys. 2007 , 126 , 064102 ] proposed earlier for a static (time-independent) case. In a dynamic (time-dependent) regime, however, an adiabatic approximation must in addition be introduced in order to preserve the block-diagonal form of the time-dependent Dirac-Fock operator during the time evolution. The resulting X2C Liouville-von Neumann electron dynamics (X2C-LvNED) is easy to implement as it does not require an explicit form of the picture-change transformed operators responsible for the (higher-order) relativistic corrections and/or interactions with external fields. To illustrate the accuracy and performance of the method, numerical results and computational timings for nonlinear optical properties are presented. All of the time domain X2C-LvNED results show excellent agreement with the reference four-component calculations as well as with the results obtained from frequency domain response theory.
Hong, Gongyi; Pachter, Ruth
2012-07-20
Designing O(2)-tolerant hydrogenases is a major challenge in applying [Fe-Fe]H(2)ases for H(2) production. The inhibition involves transport of oxygen through the enzyme to the H-cluster, followed by binding and subsequent deactivation of the active site. To explore the nature of the oxygen diffusion channel for the hydrogenases from Desulfovibrio desulfuricans (Dd) and Clostridium pasteurianum (Cp), empirical molecular dynamics simulations were performed. The dynamic nature of the oxygen pathways in Dd and Cp was elucidated, and insight is provided, in part, into the experimental observation on the difference of oxygen inhibition in Dd and the hydrogenase from Clostridium acetobutylicum (Ca, assumed homologous to Cp). Further, to gain an understanding of the mechanism of oxygen inhibition of the [Fe-Fe]H(2)ase, density functional theory calculations of model compounds composed of the H-cluster and proximate amino acids are reported. Confirmation of the experimentally based suppositions on inactivation by oxygen at the [2Fe](H) domain is provided, validating the model compounds used and oxidation state assumptions, further explaining the mode of damage. This unified approach provides insight into oxygen diffusion in the enzyme, followed by deactivation at the H-cluster.
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.
Wu, D; He, X T; Yu, W; Fritzsche, S
2017-02-01
A physical model based on a Monte Carlo approach is proposed to calculate the ionization dynamics of hot-solid-density plasmas within particle-in-cell (PIC) simulations, and where the impact (collision) ionization (CI), electron-ion recombination (RE), and ionization potential depression (IPD) by surrounding plasmas are taken into consideration self-consistently. When compared with other models, which are applied in the literature for plasmas near thermal equilibrium, the temporal relaxation of ionization dynamics can also be simulated by the proposed model. Besides, this model is general and can be applied for both single elements and alloys with quite different compositions. The proposed model is implemented into a PIC code, with (final) ionization equilibriums sustained by competitions between CI and its inverse process (i.e., RE). Comparisons between the full model and model without IPD or RE are performed. Our results indicate that for bulk aluminium at temperature of 1 to 1000 eV, (i) the averaged ionization degree increases by including IPD; while (ii) the averaged ionization degree is significantly over estimated when the RE is neglected. A direct comparison from the PIC code is made with the existing models for the dependence of averaged ionization degree on thermal equilibrium temperatures and shows good agreements with that generated from Saha-Boltzmann model and/or FLYCHK code.
Caro, Miguel A; Lopez-Acevedo, Olga; Laurila, Tomi
2017-08-08
We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr(2+/3+), V(2+/3+), Ru(NH3)6(2+/3+), Sn(2+/4+), Cu(1+/2+), FcMeOH(0/1+), and Fe(2+/3+) (in aqueous solution) and Fc(0/1+) (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations.
NASA Astrophysics Data System (ADS)
Wu, D.; He, X. T.; Yu, W.; Fritzsche, S.
2017-02-01
A physical model based on a Monte Carlo approach is proposed to calculate the ionization dynamics of hot-solid-density plasmas within particle-in-cell (PIC) simulations, and where the impact (collision) ionization (CI), electron-ion recombination (RE), and ionization potential depression (IPD) by surrounding plasmas are taken into consideration self-consistently. When compared with other models, which are applied in the literature for plasmas near thermal equilibrium, the temporal relaxation of ionization dynamics can also be simulated by the proposed model. Besides, this model is general and can be applied for both single elements and alloys with quite different compositions. The proposed model is implemented into a PIC code, with (final) ionization equilibriums sustained by competitions between CI and its inverse process (i.e., RE). Comparisons between the full model and model without IPD or RE are performed. Our results indicate that for bulk aluminium at temperature of 1 to 1000 eV, (i) the averaged ionization degree increases by including IPD; while (ii) the averaged ionization degree is significantly over estimated when the RE is neglected. A direct comparison from the PIC code is made with the existing models for the dependence of averaged ionization degree on thermal equilibrium temperatures and shows good agreements with that generated from Saha-Boltzmann model and/or FLYCHK code.
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 (CA) and word problems (WP) development, while controlling for the role of traditional assessments. Among 184 1st graders, predictors (DA, Quantity Discrimination, Test of Mathematics Ability, language, and reasoning) were assessed near the start of 1st grade. CA and WP were assessed near the end of 1st grade. Planned regression and commonality analyses indicated that for forecasting CA development, Quantity Discrimination, which accounted for 8.84% of explained variance, was the single most powerful predictor, followed by Test of Mathematics Ability and DA; language and reasoning were not uniquely predictive. By contrast, for predicting WP development, DA was the single most powerful predictor, which accounted for 12.01% of explained variance, with Test of Mathematics Ability, Quantity Discrimination, and language also uniquely predictive. Results suggest that different constellations of cognitive resources are required for CA versus WP development and that DA may be useful in predicting 1st-grade mathematics development, especially WP. PMID:22347725
NASA Astrophysics Data System (ADS)
Mirsakiyeva, Amina; Hugosson, Håkan W.; Crispin, Xavier; Delin, Anna
2016-12-01
We present simulation results, computed with the Car-Parrinello molecular dynamics method, at zero and ambient temperature (300 K) for poly(3,4-ethylenedioxythiophene) [PEDOT] and its selenium and tellurium derivatives PEDOS and PEDOTe, represented as 12-oligomer chains. In particular, we focus on structural parameters such as the dihedral rotation angle distribution, as well as how the charge distribution is affected by temperature. We find that for PEDOT, the dihedral angle distribution shows two distinct local maxima whereas for PEDOS and PEDOTe, the distributions only have one clear maximum. The twisting stiffness at ambient temperature appears to be larger the lighter the heteroatom (S, Se, Te) is, in contrast to the case at 0 K. As regards point charge distributions, they suggest that aromaticity increases with temperature, and also that aromaticity becomes more pronounced the lighter the heteroatom is, both at 0 K and ambient temperature. Our results agree well with previous results, where available. The bond lengths are consistent with substantial aromatic character both at 0 K and at ambient temperature. Our calculations also reproduce the expected trend of diminishing gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital with increasing atomic number of the heteroatom.
Heyd-Scuseria-Ernzerhof hybrid functional for calculating the lattice dynamics of semiconductors
NASA Astrophysics Data System (ADS)
Hummer, Kerstin; Harl, Judith; Kresse, Georg
2009-09-01
We present an ab initio study of the lattice dynamics of group-IV elemental semiconductors and insulators using a finite differences approach. The investigated solids include cubic diamond (C), silicon (Si), germanium (Ge), and the zero-gap semiconductor gray tin (α-Sn) . The main objective of this work is to examine the performance of the screened hybrid functional (HSE) proposed by Heyd, Scuseria, and Ernzerhof [J. Chem. Phys. 118, 8207 (2003); J. Chem. Phys. 124, 219906(E) (2006)] for calculating phonon-dispersion relations. We find that all local and semilocal functionals tend to underestimate the phonon frequencies, with the errors increasing with increasing atomic mass. For α-Sn , semilocal functionals even qualitatively fail to describe the dispersion of the highest optical phonon mode. We show that this is related to semilocal functionals predicting α-Sn to be a metal, whereas experimentally it is a zero-gap semiconductor. The HSE functional yields the correct electronic band structure resulting in qualitatively correct phonon-dispersion relations for all four solids. Quantitatively, the phonon frequencies are slightly overestimated using HSE, in particular for the lighter elements C and Si. Our results are compared to previously reported theoretical findings.
Force calculation on walls and embedded particles in multiparticle-collision-dynamics simulations.
Imperio, A; Padding, J T; Briels, W
2011-04-01
Colloidal solutions posses a wide range of time and length scales so that it is unfeasible to keep track of all of them within a single simulation. As a consequence, some form of coarse graining must be applied. In this work we use the multiparticle collision dynamics scheme. We describe a particular implementation of no-slip boundary conditions upon a solid surface, capable of providing correct forces on the solid bypassing the calculation of the velocity profile or the stress tensor in the fluid near the surface. As an application we measure the friction on a spherical particle when it is placed in a bulk fluid and when it is confined in a slit. We show that the implementation of the no-slip boundary conditions leads to an enhanced Enskog friction, which can be understood analytically. Because of the long-range nature of hydrodynamic interactions, the Stokes friction obtained from the simulations is sensitive of the simulation box size. We address this topic for the slit geometry, showing that the dependence on the system size differs very much from what is expected in a three-dimensional system where periodic boundary conditions are used in all directions.
NASA Astrophysics Data System (ADS)
Weinstein, Oleg; Brandon, Simon
2005-10-01
The modeling of partially faceted melt-crystal interfaces in bulk melt growth systems has been addressed in a number of recent publications. In particular, in Weinstein and Brandon [J. Crystal Growth 268(1-2) (2004) 299], a method for self-consistent two-dimensional dynamic analysis of such systems while accounting for both macro- and nano-scale phenomena, which result from the coupling between competing kinetic mechanisms and associated thermal fields, was presented. In this manuscript, we report on an extension of this approach to three-dimensional systems. The method is first described in detail after which it is applied to model processes involving the vertical gradient freeze growth both of silicon and of yttrium aluminum garnet. In axisymmetric situations, results are shown to successfully reproduce calculations obtained using the previous two-dimensional modeling approach. Additional results demonstrate a number of important three-dimensional nano- and macro-scale features of the melt-crystal interface. These include observations of the dominant role of the coldest dislocation step source in the case where more than one such dislocation line intersects an advancing facet, a demonstration of the effect of growth rate on the morphology of a multi-faceted interface, and a simple explicit analysis of step flow on an evolving facet.
NASA Astrophysics Data System (ADS)
Kitao, Akio; Harada, Ryuhei; Nishihara, Yasutaka; Tran, Duy Phuoc
2016-12-01
Parallel Cascade Selection Molecular Dynamics (PaCS-MD) was proposed as an efficient conformational sampling method to investigate conformational transition pathway of proteins. In PaCS-MD, cycles of (i) selection of initial structures for multiple independent MD simulations and (ii) conformational sampling by independent MD simulations are repeated until the convergence of the sampling. The selection is conducted so that protein conformation gradually approaches a target. The selection of snapshots is a key to enhance conformational changes by increasing the probability of rare event occurrence. Since the procedure of PaCS-MD is simple, no modification of MD programs is required; the selections of initial structures and the restart of the next cycle in the MD simulations can be handled with relatively simple scripts with straightforward implementation. Trajectories generated by PaCS-MD were further analyzed by the Markov state model (MSM), which enables calculation of free energy landscape. The combination of PaCS-MD and MSM is reported in this work.
Sarangapani, Radhakrishnan; Reddy, Sreekantha T; Sikder, Arun K
2015-04-01
Molecular dynamics simulations studies are carried out on hydroxyl terminated polyethers that are useful in energetic polymeric binder applications. Energetic polymers derived from oxetanes with heterocyclic side chains with different energetic substituents are designed and simulated under the ensembles of constant particle number, pressure, temperature (NPT) and constant particle number, volume, temperature (NVT). Specific volume of different amorphous polymeric models is predicted using NPT-MD simulations as a function of temperature. Plots of specific volume versus temperature exhibited a characteristic change in slope when amorphous systems change from glassy to rubbery state. Several material properties such as Young's, shear, and bulk modulus, Poisson's ratio, etc. are predicted from equilibrated structures and established the structure-property relations among designed polymers. Energetic performance parameters of these polymers are calculated and results reveal that the performance of the designed polymers is comparable to the benchmark energetic polymers like polyNIMMO, polyAMMO and polyBAMO. Overall, it is worthy remark that this molecular simulations study on novel energetic polyethers provides a good guidance on mastering the design principles and allows us to design novel polymers of tailored properties.
NASA Astrophysics Data System (ADS)
Yu, Hua-Gen
2009-08-01
An exact variational algorithm is presented for calculating vibrational energy levels of pentaatomic molecules without any dynamical approximation. The quantum mechanical Hamiltonian of the system is expressed in a set of orthogonal coordinates defined by four scattering vectors in the body-fixed frame. The eigenvalue problem is solved using a two-layer Lanczos iterative diagonalization method in a mixed grid/basis set. A direct product potential-optimized discrete variable representation (PO-DVR) basis is used for the radial coordinates while a non-direct product finite basis representation (FBR) is employed for the angular variables. The two-layer Lanczos method requires only the actions of the Hamiltonian operator on the Lanczos vectors, where the potential-vector products are accomplished via a pseudo-spectral transform technique. By using Jacobi, Radau and orthogonal satellite vectors, we have proposed 21 types of orthogonal coordinate systems so that the algorithm is capable of describing most five-atom systems with small and/or large amplitude vibrational motions. Finally, an universal program ( PetroVib) has been developed. Its applications to the molecules CH and HO2-, and the van der Waals cluster HeCl are also discussed.
NASA Astrophysics Data System (ADS)
Dilthey, Stefan; Hahn, Susanne; Stock, Gerhard
2000-03-01
An approximate theory of femtosecond spectroscopy of nonadiabatically coupled electronic states is developed. Neglecting the commutators of vibrational Hamiltonians pertaining to different diabatic electronic states, the formulation represents a generalization of the semiclassical Franck-Condon approximation to the case of nonadiabatic dynamics. Explicit expressions for various time- and frequency-resolved spectra are derived which allow for a simple interpretation of femtosecond spectroscopy of vibronically coupled molecular systems. Employing multidimensional model problems describing (i) the nonadiabatic cis-trans isomerization of an electronic two-state system, and (ii) the S2→S1 internal conversion of pyrazine, exact reference data are compared to approximate calculations of transient absorbance and emission as well as time-resolved photoelectron spectra. In all cases considered, the approximation is shown to be appropriate for probe-pulse durations that are shorter than the period of the fastest relevant vibrational mode of the molecular system. Reducing the numerical costs of pump-probe simulations to the costs of a standard time-dependent wave-packet propagation, the approximate theory leads to substantial computational savings.
NASA Astrophysics Data System (ADS)
Mirsakiyeva, Amina; Hugosson, Håkan W.; Crispin, Xavier; Delin, Anna
2017-05-01
We present simulation results, computed with the Car-Parrinello molecular dynamics method, at zero and ambient temperature (300 K) for poly(3,4-ethylenedioxythiophene) [PEDOT] and its selenium and tellurium derivatives PEDOS and PEDOTe, represented as 12-oligomer chains. In particular, we focus on structural parameters such as the dihedral rotation angle distribution, as well as how the charge distribution is affected by temperature. We find that for PEDOT, the dihedral angle distribution shows two distinct local maxima whereas for PEDOS and PEDOTe, the distributions only have one clear maximum. The twisting stiffness at ambient temperature appears to be larger the lighter the heteroatom (S, Se, Te) is, in contrast to the case at 0 K. As regards point charge distributions, they suggest that aromaticity increases with temperature, and also that aromaticity becomes more pronounced the lighter the heteroatom is, both at 0 K and ambient temperature. Our results agree well with previous results, where available. The bond lengths are consistent with substantial aromatic character both at 0 K and at ambient temperature. Our calculations also reproduce the expected trend of diminishing gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital with increasing atomic number of the heteroatom.
Thermal conductivity of the Lennard-Jones liquid by molecular dynamics calculations
NASA Astrophysics Data System (ADS)
Vogelsang, R.; Hoheisel, C.; Ciccotti, G.
1987-06-01
Precise results for the thermal conductivity of the Lennard-Jones liquid obtained by equilibrium molecular dynamics (MD) are presented. These are compared in detail with previous nonequilibrium MD results. Effects due to the truncation of the potential and the particle number dependence are considered. The contributions of the partial correlation functions to the total one were separately calculated. Main results are: (i) in contrast to the viscosity, the thermal conductivity is rather insensitive to the MD conditions, even for the state corresponding virtually to the triple point of argon. The reason for this originates from the simple short ranged time decay of the correlation function. (ii) For the states considered, the partial correlation function involving the ``potential-potential'' term governs the transport coefficient. (iii) Nonequilibrium MD and MD give consistent values, except for the nonequilibrium method devised by Heyes which generates data far off the range permitted by the error bars. (iv) The computed thermal conductivities fall well in line with experimental data for argon.
NASA Astrophysics Data System (ADS)
Urbina-Villalba, German; García-Sucre, Máximo; Toro-Mendoza, Jhoan
2003-12-01
In order to account for the hydrodynamic interaction (HI) between suspended particles in an average way, Honig et al. [J. Colloid Interface Sci. 36, 97 (1971)] and more recently Heyes [Mol. Phys. 87, 287 (1996)] proposed different analytical forms for the diffusion constant. While the formalism of Honig et al. strictly applies to a binary collision, the one from Heyes accounts for the dependence of the diffusion constant on the local concentration of particles. However, the analytical expression of the latter approach is more complex and depends on the particular characteristics of each system. Here we report a combined methodology, which incorporates the formula of Honig et al. at very short distances and a simple local volume-fraction correction at longer separations. As will be shown, the flocculation behavior calculated from Brownian dynamics simulations employing the present technique, is found to be similar to that of Batchelor’s tensor [J. Fluid. Mech. 74, 1 (1976); 119, 379 (1982)]. However, it corrects the anomalous coalescence found in concentrated systems as a result of the overestimation of many-body HI.
Ibarra, Ignacio L; Melo, Francisco
2010-07-01
Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm version and the gap opening/extension penalties. We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications. The software is freely available at: http:/melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX. All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl.
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.
NASA Astrophysics Data System (ADS)
He, Yang; Chen, Changfeng; Yu, Haobo; Lu, Guiwu
2017-01-01
Formation of the double-layer electric field and capacitance of the water-metal interface is of significant interest in physicochemical processes. In this study, we perform first- principles molecular dynamics simulations on the water/Pt(111) interface to investigate the temperature dependence of the compact layer electric field and capacitance based on the calculated charge densities. On the Pt (111) surface, water molecules form ice-like structures that exhibit more disorder along the height direction with increasing temperature. The Osbnd H bonds of more water molecules point toward the Pt surface to form Ptsbnd H covalent bonds with increasing temperature, which weaken the corresponding Osbnd H bonds. In addition, our calculated capacitance at 300 K is 15.2 mF/cm2, which is in good agreement with the experimental results. As the temperature increases from 10 to 450 K, the field strength and capacitance of the compact layer on Pt (111) first increase and then decrease slightly, which is significant for understanding the water/Pt interface from atomic level.
Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations
Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei
2017-01-01
Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions. PMID:28195190
NASA Astrophysics Data System (ADS)
Machado, Kelly; Zanghi, Didier; Sarou-Kanian, Vincent; Cadars, Sylvian; Burbano, Mario; Salanne, Mathieu; Bessada, Catherine
In aluminum production, the electrolyte is a molten fluorides mixture typically around 1000°C. In order to have a better understanding of the industrial process, it is necessary to have a model which will describe the molten salts on a wide range of compositions and temperatures, to accurately cover all the combinations that may be encountered in an operating electrolysis vessel. The aim of this study is to describe the speciation in the electrolyte in terms of anionic species in the bulk materials far from electrodes. To determine the speciation in situ at high temperature in the absence of an electrical field, we develop an original approach combining experimental methods such as Nuclear Magnetic Resonance spectroscopy (NMR) at high temperature with Molecular Dynamics (MD) simulation coupled with first principle calculations based on Density Functional Theory (DFT). This approach allows the calculation of NMR parameters and the comparison with the experimental ones. It will be provide an additional validation and constraint of the model used for MD. We test this approach on the model NaF-AlF3 system.
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.
Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations
NASA Astrophysics Data System (ADS)
Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei
2017-02-01
Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.
NASA Astrophysics Data System (ADS)
Dongre, B.; Wang, T.; Madsen, G. K. H.
2017-07-01
Different molecular dynamics methods like the direct method, the Green-Kubo (GK) method and homogeneous non-equilibrium molecular dynamics (HNEMD) method have been widely used to calculate lattice thermal conductivity ({κ }{\\ell }). While the first two methods have been used and compared quite extensively, there is a lack of comparison of these methods with the HNEMD method. Focusing on the underlying computational parameters, we present a detailed comparison of the GK and HNEMD methods for both bulk and vacancy Si using the Stillinger-Weber potential. For the bulk calculations, we find both methods to perform well and yield {κ }{\\ell } within acceptable uncertainties. In case of the vacancy calculations, HNEMD method has a slight advantage over the GK method as it becomes computationally cheaper for lower {κ }{\\ell } values. This study could promote the application of HNEMD method in {κ }{\\ell } calculations involving other lattice defects like nanovoids, dislocations, interfaces.
NASA Astrophysics Data System (ADS)
Kim, D. Y.; Scheicher, R. H.; Ahuja, R.
2008-09-01
We have characterized the high-pressure cubic phase of AlH3 from ab initio using density functional theory to determine mechanical as well as electronic properties and lattice dynamics (phonon-dispersion relations) from the response function method. Our zero-temperature phonon calculations show the softening of a particular mode with decreasing pressure, indicating the onset of a dynamic instability that continues to persist at ambient conditions. This instability can, however, be removed when finite electronic temperature effects are considered in the calculations. We furthermore identify a particular momentum transfer in the phonon-dispersion relation, matching a corresponding momentum transfer in the electronic band structure.
QED Based Calculation of the Fine Structure Constant
Lestone, John Paul
2016-10-13
Quantum electrodynamics is complex and its associated mathematics can appear overwhelming for those not trained in this field. Here, semi-classical approaches are used to obtain a more intuitive feel for what causes electrostatics, and the anomalous magnetic moment of the electron. These intuitive arguments lead to a possible answer to the question of the nature of charge. Virtual photons, with a reduced wavelength of λ, are assumed to interact with isolated electrons with a cross section of πλ^{2}. This interaction is assumed to generate time-reversed virtual photons that are capable of seeking out and interacting with other electrons. This exchange of virtual photons between particles is assumed to generate and define the strength of electromagnetism. With the inclusion of near-field effects the model presented here gives a fine structure constant of ~1/137 and an anomalous magnetic moment of the electron of ~0.00116. These calculations support the possibility that near-field corrections are the key to understanding the numerical value of the dimensionless fine structure constant.
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.
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
Analytic calculation of physiological acid-base parameters in plasma.
Wooten, E W
1999-01-01
Analytic expressions for plasma total titratable base, base excess (DeltaCB), strong-ion difference, change in strong-ion difference (DeltaSID), change in Van Slyke standard bicarbonate (DeltaVSSB), anion gap, and change in anion gap are derived as a function of pH, total buffer ion concentration, and conditional molar equilibrium constants. The behavior of these various parameters under respiratory and metabolic acid-base disturbances for constant and variable buffer ion concentrations is considered. For constant noncarbonate buffer concentrations, DeltaSID = DeltaCB = DeltaVSSB, whereas these equalities no longer hold under changes in noncarbonate buffer concentration. The equivalence is restored if the reference state is changed to include the new buffer concentrations.
NASA Astrophysics Data System (ADS)
Gündüç, Semra; Dilaver, Mehmet; Aydın, Meral; Gündüç, Yiğit
2005-02-01
In this work we have studied the dynamic scaling behavior of two scaling functions and we have shown that scaling functions obey the dynamic finite size scaling rules. Dynamic finite size scaling of scaling functions opens possibilities for a wide range of applications. As an application we have calculated the dynamic critical exponent (z) of Wolff's cluster algorithm for 2-, 3- and 4-dimensional Ising models. Configurations with vanishing initial magnetization are chosen in order to avoid complications due to initial magnetization. The observed dynamic finite size scaling behavior during early stages of the Monte Carlo simulation yields z for Wolff's cluster algorithm for 2-, 3- and 4-dimensional Ising models with vanishing values which are consistent with the values obtained from the autocorrelations. Especially, the vanishing dynamic critical exponent we obtained for d=3 implies that the Wolff algorithm is more efficient in eliminating critical slowing down in Monte Carlo simulations than previously reported.
Application of ab initio calculations and molecular dynamics to collagen and brome mosaic virus
NASA Astrophysics Data System (ADS)
Eifler, Jay Quinson
In bio-related research, large proteins are of important interest. We study two such proteins. Collagen is one such protein which forms part of the structural matrix for animals, such as in their bones and teeth. 1JS9 is another protein that is a component of the protein shell of the brome mosaic virus (BMV). And BMV is important for drug delivery and imaging. To better understand the properties of these proteins, quantum mechanically (QM) based results are needed, however computationally feasible methods are also necessary. The Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) method is well-suited for application to such large proteins. However, a new approach to reduce the computational cost is required and this extension to the method we call the Amino-Acid Based Method (AAPM) of OLCAO. The AAPM roughly calculates electronic, self-consistent field (scf) potentials for individual amino-acids with their neighboring amino-acids included as a boundary condition. This allows the costly scf part of the calculation to be skipped out. Additionally, the number of potentials used to describe the how protein i s also minimized. Results for effective charge and bond order are obtained and analyzed for Collagen and preliminary effective charge results are obtained for 1JS9. The effective charge results reproduce those already obtained with other QM based methods but without reduced cost and preserved accuracy that are characteristically different than the formal charges mostly still in use to describe the charge properties of proteins. The bond order results for Collagen nicely reproduce the observed experimentally-derived hydrogen bonding between the individual chains of the collagen triple-helix as well as the observed hydrogen bonding network.
NASA Astrophysics Data System (ADS)
Epa, V. C.; Thorson, W. R.
1990-09-01
This paper concludes a theoretical study of vibrational dynamics in the bifluoride ion FHF-, which exhibits strongly anharmonic and coupled motions. Two previous papers have described an extended model potential surface for the system, developed a scheme for analysis based on a zero-order adiabatic separation of the proton bending and stretching motions (ν2,ν3) from the slower F-F symmetric-stretch motion (ν1), and presented results of accurate calculations of the adiabatic protonic eigenstates. Here the ν1 motion has been treated, in adiabatic approximation and also including nonadiabatic couplings in close-coupled calculations with up to three protonic states (channels). States of the system involving more than one quantum of protonic excitation (e.g., 2ν2, 2ν3 σg states; 3ν2, ν2+2ν3 πu states; ν3+2ν2, 3ν3 σu states) exhibit strong mixing at avoided crossings of protonic levels, and these effects are discussed in detail. Dipole matrix elements and relative intensities for vibrational transitions have been computed with an electronic dipole moment function based on ab initio calculations for an extended range of geometries. Frequencies, relative IR intensities and other properties of interest are compared with high resolution spectroscopic data for the gas-phase free ion and with the IR absorption spectra of KHF2(s) and NaHF2(s). Errors in the ab initio potential surface yield fundamental frequencies ν2 and ν3 100-250 cm-1 higher than those observed in either the free ion or the crystalline solids, but these differences are consistent and an unambiguous assignment of essentially all transitions in the IR spectrum of KHF2 is made. Calculated relative intensities for stretching mode (ν3, σu symmetry) transitions agree well with those observed in both KHF2 [e.g., bands (ν3+nν1), (ν3+2ν2), (3ν3), etc.] and the free ion (ν3,ν3+ν1). Calculated intensities for bending mode (ν2, πu symmetry) transitions agree well with experiment for the ν2
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.
Grid-based electronic structure calculations: The tensor decomposition approach
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. 8192{sup 3} 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.
Coupled cluster calculations for static and dynamic polarizabilities of C60
NASA Astrophysics Data System (ADS)
Kowalski, Karol; Hammond, Jeff R.; de Jong, Wibe A.; Sadlej, Andrzej J.
2008-12-01
New theoretical predictions for the static and frequency dependent polarizabilities of C60 are reported. Using the linear response coupled cluster approach with singles and doubles and a basis set especially designed to treat the molecular properties in external electric field, we obtained 82.20 and 83.62 Å3 for static and dynamic (λ =1064 nm) polarizabilities. These numbers are in a good agreement with experimentally inferred data of 76.5±8 and 79±4 Å3 [R. Antoine et al., J. Chem. Phys.110, 9771 (1999); A. Ballard et al., J. Chem. Phys.113, 5732 (2000)]. The reported results were obtained with the highest wave function-based level of theory ever applied to the C60 system.
NASA Astrophysics Data System (ADS)
Zhou, Q.; Joseph, P. F.
2005-05-01
An approach combining finite element with boundary element methods is proposed to calculate the elastic vibration and acoustic field radiated from an underwater structure. The FEM software NASTRAN is employed for computation of the structural vibration. An uncoupled boundary element method, based on the potential decomposition technique, is described to determine the acoustic added mass and damping coefficients that result due to fluid loading effects. The acoustic matrices of added mass and damping coefficients are then added to the structural mass and damping matrices, respectively, by the DMAP modules of NASTRAN. Numerical results are shown to be in good agreement with experimental data. The complex eigenvalue analyses of underwater structure are obtained by NASTRAN solution sequence SOL107. Results obtained from this study suggest that the natural frequencies of underwater structures are only weakly dependent on the acoustic frequency if the acoustic wavelength is roughly twice as large as the maximum structural dimension.
Attosecond-resolution quantum dynamics calculations for atoms and molecules in strong laser fields.
Lu, Rui-Feng; Zhang, Pei-Yu; Han, Ke-Li
2008-06-01
A parallel quantum electron and nuclei wave packet computer code, LZH-DICP, has been developed to study laser-atom-molecule interaction in the nonperturbative regime with attosecond resolution. The nonlinear phenomena occurring in that regime can be studied with the code in a rigorous way by numerically solving the time-dependent Schrödinger equation of electrons and nuclei. Time propagation of the wave functions is performed using a split-operator approach, and based on a sine discrete variable representation. Photoelectron spectra for hydrogen and kinetic-energy spectra for molecular hydrogen ion in linearly polarized laser fields are calculated using a flux operator scheme, which testifies to the validity and the high efficiency of LZH-DICP.
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
A method for calculating the acid-base equilibria in aqueous and nonaqueous electrolyte solutions
NASA Astrophysics Data System (ADS)
Tanganov, B. B.; Alekseeva, I. A.
2017-06-01
Concentrations of particles in acid-base equilibria in aqueous and nonaqueous solutions of electrolytes are calculated on the basis of logarithmic charts, activity coefficients, and equilibrium constants.
A calculable and correlation-based magnetic field fluctuation thermometer
NASA Astrophysics Data System (ADS)
Kirste, A.; Regin, M.; Engert, J.; Drung, D.; Schurig, T.
2014-12-01
We have developed a new Magnetic Field Fluctuation Thermometer (MFFT) specifically designed for operation in primary mode, which requires the determination of the relation between thermal flux noise density and thermodynamic temperature. The noise thermometer combines a correlation-based SQUID readout and an integrated conductivity measurement on the metallic temperature sensor with an in situ flux calibration. The operation of the MFFT is modelled theoretically. First temperature measurements in secondary mode between 9 mK and 4.2 K showed excellent agreement with a copy of the PLTS-2000 within 0.5%.
Zhang, Yong; Otani, Akihito; Maginn, Edward J
2015-08-11
Equilibrium molecular dynamics is often used in conjunction with a Green-Kubo integral of the pressure tensor autocorrelation function to compute the shear viscosity of fluids. This approach is computationally expensive and is subject to a large amount of variability because the plateau region of the Green-Kubo integral is difficult to identify unambiguously. Here, we propose a time decomposition approach for computing the shear viscosity using the Green-Kubo formalism. Instead of one long trajectory, multiple independent trajectories are run and the Green-Kubo relation is applied to each trajectory. The averaged running integral as a function of time is fit to a double-exponential function with a weighting function derived from the standard deviation of the running integrals. Such a weighting function minimizes the uncertainty of the estimated shear viscosity and provides an objective means of estimating the viscosity. While the formal Green-Kubo integral requires an integration to infinite time, we suggest an integration cutoff time tcut, which can be determined by the relative values of the running integral and the corresponding standard deviation. This approach for computing the shear viscosity can be easily automated and used in computational screening studies where human judgment and intervention in the data analysis are impractical. The method has been applied to the calculation of the shear viscosity of a relatively low-viscosity liquid, ethanol, and relatively high-viscosity ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([BMIM][Tf2N]), over a range of temperatures. These test cases show that the method is robust and yields reproducible and reliable shear viscosity values.
Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation.
Hu, Guodong; Zhang, Qinggang; Chen, L Y
2011-08-01
Molecular dynamics simulations and free energy calculation have been performed to study how the single-chain variable fragment (scFv) binds methamphetamine (METH) and amphetamine (AMP). The structures of the scFv:METH and the scFv:AMP complexes are analyzed by examining the time-dependence of their RMSDs, by analyzing the distance between some key atoms of the selected residues, and by comparing the averaged structures with their corresponding crystallographic structures. It is observed that binding an AMP to the scFv does not cause significant changes to the binding pocket of the scFv:ligand complex. The binding free energy of scFv:AMP without introducing an extra water into the binding pocket is much stronger than scFv:METH. This is against the first of the two scenarios postulated in the experimental work of Celikel et al. (Protein Science 18, 2336 (2009)). However, adding a water to the AMP (at the position of the methyl group of METH), the binding free energy of the scFv:AMP-H2O complex, is found to be significantly weaker than scFv:METH. This is consistent with the second of the two scenarios given by Celikel et al. Decomposition of the binding energy into ligand-residue pair interactions shows that two residues (Tyr175 and Tyr177) have nearly-zero interactions with AMP in the scFv:AMP-H2O complex, whereas their interactions with METH in the scFv:METH complex are as large as -0.8 and -0.74 kcal mol(-1). The insights gained from this study may be helpful in designing more potent antibodies in treating METH abuse.
Optimization-based Dynamic Human Lifting Prediction
2008-06-01
Anith Mathai, Steve Beck,Timothy Marler , Jingzhou Yang, Jasbir S. Arora, Karim Abdel-Malek Virtual Soldier Research Program, Center for Computer Aided...Rahmatalla, S., Kim, J., Marler , T., Beck, S., Yang, J., busek, J., Arora, J.S., and Abdel-Malek, K. Optimization-based dynamic human walking prediction
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.
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.
Calculation of thermomechanical fatigue life based on isothermal behavior
NASA Technical Reports Server (NTRS)
Halford, G. R.; Saltsman, J. 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.
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.
A comparison of methods for melting point calculation using molecular dynamics simulations
Zhang, Y; Maginn, EJ
2012-04-14
Accurate and efficient prediction of melting points for complex molecules is still a challenging task for molecular simulation, although many methods have been developed. Four melting point computational methods, including one free energy-based method (the pseudo-supercritical path (PSCP) method) and three direct methods (two interface-based methods and the voids method) were applied to argon and a widely studied ionic liquid 1-n-butyl-3-methylimidazolium chloride ([BMIM][Cl]). The performance of each method was compared systematically. All the methods under study reproduce the argon experimental melting point with reasonable accuracy. For [BMIM][Cl], the melting point was computed to be 320 K using a revised PSCP procedure, which agrees with the experimental value 337-339 K very well. However, large errors were observed in the computed results using the direct methods, suggesting that these methods are inappropriate for large molecules with sluggish dynamics. The strengths and weaknesses of each method are discussed. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3702587
Aeroelastic Calculations Based on Three-Dimensional Euler Analysis
NASA Technical Reports Server (NTRS)
Bakhle, Milind A.; Srivastava, Rakesh; Keith, Theo G., Jr.; Stefko, George L.
1998-01-01
This paper presents representative results from an aeroelastic code (TURBO-AE) based on an Euler/Navier-Stokes unsteady aerodynamic code (TURBO). Unsteady pressure, lift, and moment distributions are presented for a helical fan test configuration which is used to verify the code by comparison to two-dimensional linear potential (flat plate) theory. The results are for pitching and plunging motions over a range of phase angles, Good agreement with linear theory is seen for all phase angles except those near acoustic resonances. The agreement is better for pitching motions than for plunging motions. The reason for this difference is not understood at present. Numerical checks have been performed to ensure that solutions are independent of time step, converged to periodicity, and linearly dependent on amplitude of blade motion. The paper concludes with an evaluation of the current state of development of the TURBO-AE code and presents some plans for further development and validation of the TURBO-AE code.
Evidence-Based Current Surgical Practice: Calculous Gallbladder Disease
Duncan, Casey B.; Riall, Taylor S.
2012-01-01
Gallbladder disease is common and, if managed incorrectly, can lead to high rates of morbidity, mortality, and extraneous costs. The most common complications of gallstones include biliary colic, acute cholecystitis, common bile duct stones, and gallstone pancreatitis. Ultrasound is the initial imaging modality of choice. Additional diagnostic and therapeutic studies including computed tomography (CT), magnetic resonance imaging (MRI), magnetic resonance cholangiopancreatography (MRCP), endoscopic ultrasound (EUS), and endoscopic retrograde cholangiopancreatography (ERCP) are not routinely required but may play a role in specific situations. Biliary colic and acute cholecystitis are best treated with early laparoscopic cholecystectomy. Patients with common bile duct stones should be managed with cholecystectomy, either after or concurrent with endoscopic or surgical relief of obstruction and clearance of stones from the bile duct. Mild gallstone pancreatitis should be treated with cholecystectomy during the initial hospitalization to prevent recurrence. Emerging techniques for cholecystectomy include single-incision laparoscopic surgery (SILS) and natural orifice transluminal endoscopic surgery (NOTES). Early results in highly selected patients demonstrate the safety of these techniques. The management of complications of the gallbladder should be timely and evidence-based, and choice of procedures, particularly for common bile duct stones, is largely influenced by facility and surgeon factors. PMID:22986769
Pan, Yongping; Priyakumar, U Deva; MacKerell, Alexander D
2005-02-08
Structure and energetic properties of base pair mismatches in duplex RNA have been the focus of numerous investigations due to their role in many important biological functions. Such efforts have contributed to the development of models for secondary structure prediction of RNA, including the nearest-neighbor model. In RNA duplexes containing GU mismatches, 5'-GU-3' tandem mismatches have a different thermodynamic stability than 5'-UG-3' mismatches. In addition, 5'-GU-3' mismatches in some sequence contexts do not follow the nearest-neighbor model for stability. To characterize the underlying atomic forces that determine the structural and thermodynamic properties of GU tandem mismatches, molecular dynamics (MD) simulations were performed on a series of 5'-GU-3' and 5'-UG-3' duplexes in different sequence contexts. Overall, the MD-derived structural models agree well with experimental data, including local deviations in base step helicoidal parameters in the region of the GU mismatches and the model where duplex stability is associated with the pattern of GU hydrogen bonding. Further analysis of the simulations, validated by data from quantum mechanical calculations, suggests that the experimentally observed differences in thermodynamic stability are dominated by GG interstrand followed by GU intrastrand base stacking interactions that dictate the one versus two hydrogen bonding scenarios for the GU pairs. In addition, the inability of 5'-GU-3' mismatches in different sequence contexts to all fit into the nearest-neighbor model is indicated to be associated with interactions of the central four base pairs with the surrounding base pairs. The results emphasize the role of GG and GU stacking interactions on the structure and thermodynamics of GU mismatches in RNA.
Edirisinghe, Y; Troupis, J M; Patel, M; Smith, J; Crossett, M
2014-05-01
We used a dynamic three-dimensional (3D) mapping method to model the wrist in dynamic unrestricted dart throwers motion in three men and four women. With the aid of precision landmark identification, a 3D coordinate system was applied to the distal radius and the movement of the carpus was described. Subsequently, with dynamic 3D reconstructions and freedom to position the camera viewpoint anywhere in space, we observed the motion pathways of all carpal bones in dart throwers motion and calculated its axis of rotation. This was calculated to lie in 27° of anteversion from the coronal plane and 44° of varus angulation relative to the transverse plane. This technique is a safe and a feasible carpal imaging method to gain key information for decision making in future hand surgical and rehabilitative practices.
Environment-based pin-power reconstruction method for homogeneous core calculations
Leroyer, H.; Brosselard, C.; Girardi, E.
2012-07-01
Core calculation schemes are usually based on a classical two-step approach associated with assembly and core calculations. During the first step, infinite lattice assemblies calculations relying on a fundamental mode approach are used to generate cross-sections libraries for PWRs core calculations. This fundamental mode hypothesis may be questioned when dealing with loading patterns involving several types of assemblies (UOX, MOX), burnable poisons, control rods and burn-up gradients. This paper proposes a calculation method able to take into account the heterogeneous environment of the assemblies when using homogeneous core calculations and an appropriate pin-power reconstruction. This methodology is applied to MOX assemblies, computed within an environment of UOX assemblies. The new environment-based pin-power reconstruction is then used on various clusters of 3x3 assemblies showing burn-up gradients and UOX/MOX interfaces, and compared to reference calculations performed with APOLLO-2. The results show that UOX/MOX interfaces are much better calculated with the environment-based calculation scheme when compared to the usual pin-power reconstruction method. The power peak is always better located and calculated with the environment-based pin-power reconstruction method on every cluster configuration studied. This study shows that taking into account the environment in transport calculations can significantly improve the pin-power reconstruction so far as it is consistent with the core loading pattern. (authors)
Model-based calculations of fiber output fields for fiber-based spectroscopy
NASA Astrophysics Data System (ADS)
Hernandez, Eloy; Bodenmüller, Daniel; Roth, Martin M.; Kelz, Andreas
2016-08-01
The accurate characterization of the field at the output of the optical fibres is of relevance for precision spectroscopy in astronomy. The modal effects of the fibre translate to the illumination of the pupil in the spectrograph and impact on the resulting point spread function (PSF). A Model is presented that is based on the Eigenmode Expansion Method (EEM) that calculates the output field from a given fibre for different manipulations of the input field. The fibre design and modes calculation are done via the commercially available Rsoft-FemSIM software. We developed a Python script to apply the EEM. Results are shown for different configuration parameters, such as spatial and angular displacements of the input field, spot size and propagation length variations, different transverse fibre geometries and different wavelengths. This work is part of the phase A study of the fibre system for MOSAIC, a proposed multi-object spectrograph for the European Extremely Large Telescope (ELT-MOS).
Baxa, Michael C.; Haddadian, Esmael J.; Jumper, John M.; Freed, Karl F.; Sosnick, Tobin R.
2014-01-01
The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity has proven challenging. We calculate this loss using molecular dynamic simulations of both the native protein and a realistic denatured state ensemble. For ubiquitin, the total change in entropy is TΔSTotal = 1.4 kcal⋅mol−1 per residue at 300 K with only 20% from the loss of side-chain entropy. Our analysis exhibits mixed agreement with prior studies because of the use of more accurate ensembles and contributions from correlated motions. Buried side chains lose only a factor of 1.4 in the number of conformations available per rotamer upon folding (ΩU/ΩN). The entropy loss for helical and sheet residues differs due to the smaller motions of helical residues (TΔShelix−sheet = 0.5 kcal⋅mol−1), a property not fully reflected in the amide N-H and carbonyl C=O bond NMR order parameters. The results have implications for the thermodynamics of folding and binding, including estimates of solvent ordering and microscopic entropies obtained from NMR. PMID:25313044
Molar conductivity calculation of Li-ion battery electrolyte based on mode coupling theory
NASA Astrophysics Data System (ADS)
Pu, Weihua; He, Xiangming; Lu, Jiufang; Jiang, Changyin; Wan, Chunrong
2005-12-01
A method is proposed to calculate molar conductivity based on mode coupling theory in which the ion transference number is introduced into the theory. The molar conductivities of LiPF6, LiClO4, LiBF4, LiAsF6 in PC (propylene carbonate) are calculated based on this method. The results fit well to the literature data. This presents a potential way to calculate the conductivities of Li-ion battery electrolytes.
Molar conductivity calculation of Li-ion battery electrolyte based on mode coupling theory.
Pu, Weihua; He, Xiangming; Lu, Jiufang; Jiang, Changyin; Wan, Chunrong
2005-12-15
A method is proposed to calculate molar conductivity based on mode coupling theory in which the ion transference number is introduced into the theory. The molar conductivities of LiPF6, LiClO4, LiBF4, LiAsF6 in PC (propylene carbonate) are calculated based on this method. The results fit well to the literature data. This presents a potential way to calculate the conductivities of Li-ion battery electrolytes.
Bai, Shuming; Xie, Weiwei; Zhu, Lili; Shi, Qiang
2014-02-28
We investigate the calculation of absorption spectra based on the mixed quantum classical Liouville equation (MQCL) methods. It has been shown previously that, for a single excited state, the averaged classical dynamics approach to calculate the linear and nonlinear spectroscopy can be derived using the MQCL formalism. This work focuses on problems involving multiple coupled excited state surfaces, such as in molecular aggregates and in the cases of coupled electronic states. A new equation of motion to calculate the dipole-dipole correlation functions within the MQCL formalism is first presented. Two approximate methods are then proposed to solve the resulted equations of motion. The first approximation results in a mean field approach, where the nuclear dynamics is governed by averaged forces depending on the instantaneous electronic states. A modification to the mean field approach based on first order moment expansion is also proposed. Numerical examples including calculation of the absorption spectra of Frenkel exciton models of molecular aggregates, and the pyrazine molecule are presented.
Bai, Shuming; Xie, Weiwei; Zhu, Lili; Shi, Qiang
2014-02-28
We investigate the calculation of absorption spectra based on the mixed quantum classical Liouville equation (MQCL) methods. It has been shown previously that, for a single excited state, the averaged classical dynamics approach to calculate the linear and nonlinear spectroscopy can be derived using the MQCL formalism. This work focuses on problems involving multiple coupled excited state surfaces, such as in molecular aggregates and in the cases of coupled electronic states. A new equation of motion to calculate the dipole-dipole correlation functions within the MQCL formalism is first presented. Two approximate methods are then proposed to solve the resulted equations of motion. The first approximation results in a mean field approach, where the nuclear dynamics is governed by averaged forces depending on the instantaneous electronic states. A modification to the mean field approach based on first order moment expansion is also proposed. Numerical examples including calculation of the absorption spectra of Frenkel exciton models of molecular aggregates, and the pyrazine molecule are presented.
Zhang, Gaigong; Lin, Lin; Hu, Wei; ...
2017-01-27
Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less
NASA Astrophysics Data System (ADS)
Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.
2017-04-01
Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.
NASA Astrophysics Data System (ADS)
Çiftci, Yasemin Ö.; Çoban, Cansu
2016-02-01
The structural, mechanical, electronic, dynamic, and optical properties of the ZrPdSn compound crystallising into the MgAgAs structure are investigated by the ab initio calculations based on the density functional theory. The lattice constant, bulk modulus, and first derivative of bulk modulus were obtained by fitting the calculated total energy-atomic volume results to the Murnaghan equation of state. These results were compared to the previous data. The band structure and corresponding density of states (DOS) were also calculated and discussed. The elastic properties were calculated by using the stress-strain method, which shows that the MgAgAs phase of this compound is mechanically stable. The presented phonon dispersion curves and one-phonon DOS confirms that this compound is dynamically stable. In addition, the heat capacity, entropy, and free energy of ZrPdSn were calculated by using the phonon frequencies. Finally, the optical properties, such as dielectric function, reflectivity function, extinction coefficient, refractive index, and energy loss spectrum, were obtained under different pressures.
NASA Astrophysics Data System (ADS)
Strehmel, Alexander; Erzgräber, Beate; Gottesbüren, Bernhard
2016-04-01
The exposure assessment for the EU registration procedure of plant protection products (PPP), which is based on the 'Forum for the co-ordination of pesticide fate models and their use' (FOCUS), currently considers only periods of 12-16 months for the exposure assessment in surface water bodies. However, in a recent scientific opinion of the European Food Safety Authority (EFSA) it is argued that in a multi-year exposure assessment, the accumulation of PPP substances in river sediment may be a relevant process. Therefore, the EFSA proposed to introduce a sediment accumulation factor in order to account for enrichment of PPP substances over several years in the sediment. The calculation of this accumulation factor, however, would consider degradation in sediment as the only dissipation path, and does not take into account riverine sediment dynamics. In order to assess the influence of deposition and the possible extent of substance accumulation in the sediment phase, the hydraulic model HEC-RAS was employed for an assessment of in-stream sediment dynamics of the FOCUS stream scenarios. The model was parameterized according to the stream characteristics of the FOCUS scenarios and was run over a period of 20 years. The results show that with the distribution of grain sizes and the ranges of flow velocity in the FOCUS streams the main sediment process in the streams is transport. First modeling results suggest that about 80% of the eroded sediment mass from the adjacent field are transported to the downstream end of the stream and out of the system, while only about 20% are deposited in the river bed. At the same time, only about 30% of in-stream sediment mass stems from the adjacent field and is associated with PPP substance, while the remaining sediment consists of the substance-free base sediment concentration regarded in the scenarios. With this, the hydraulic modelling approach is able to support the development of a meaningful sediment accumulation factor by
Trotter-based simulation of quantum-classical dynamics.
Kernan, Dónal Mac; Ciccotti, Giovanni; Kapral, Raymond
2008-01-17
Quantum rate processes in condensed phase systems are often computed by combining quantum and classical descriptions of the dynamics. An algorithm for simulating the quantum-classical Liouville equation, which describes the dynamics of a quantum subsystem coupled to a classical bath, is presented in this paper. The algorithm is based on a Trotter decomposition of the quantum-classical propagator, in conjunction with Monte Carlo sampling of quantum transitions, to yield a surface-hopping representation of the dynamics. An expression for the nonadiabatic propagator that is responsible for quantum transitions and associated bath momentum changes is derived in a form that is convenient for Monte Carlo sampling and exactly conserves the total energy of the system in individual trajectories. The expectation values of operators or quantum correlation functions can be evaluated by initial sampling of quantum states and use of quantum-classical Liouville dynamics for the time evolution. The algorithm is tested by calculations on the spin-boson model, for which exact quantum results are available, and is shown to reproduce the exact results for stronger nonadiabatic coupling and much longer times using fewer trajectories than other schemes for simulating quantum-classical Liouville dynamics.
First principle calculation of structure and lattice dynamics of Lu2Si2O7
NASA Astrophysics Data System (ADS)
Nazipov, D. V.; Nikiforov, A. E.
2016-12-01
Ab initio calculations of crystal structure and Raman spectra has been performed for single crystal of lutetium pyrosilicate Lu2Si2O7. The types of fundamental vibrations, their frequencies and intensities in the Raman spectrum has been obtained for two polarizations. Calculations were made in the framework of density functional theory (DFT) with hybrid functionals. The isotopic substitution was calculated for all inequivalent ions in cell. The results in a good agreement with experimental data.
Dynamics and Thermodynamics of Artificial Muscles Based on Nematic Gels
NASA Astrophysics Data System (ADS)
Hébert, M.; Kant, R.; de Gennes, P.-G.
1997-07-01
A scheme based on nemato-mechanical conversion has been proposed for potential artificial muscle applications (de Gennes P.-G., Hébert M. and Kant R., to appear in Macromol. Symp. (1996)). As the temperature in a nematic gel is reduced through the transition temperature, strong uniaxial deformation is encountered. We briefly expose the dynamics of contraction/elongation in this system. Work and dissipative losses are calculated for an operating cycle to get an approximative expression of the ratio work/losses, which can then be compared with real muscular efficiencies.
HP-9825A calculator programs for plotting orbiter RCS jet dynamic pressure contours
NASA Technical Reports Server (NTRS)
Wilson, S. W.
1977-01-01
Computer programs which generate displays of the dynamic pressure fields generated by orbiter RCS thruster firings are described. The programs can be used to generate dynamic contours for an isolated RCS jet and to superimpose the plume contours for specific jets or jet clusters on front and side views of the orbiter profile.
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; ...
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
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.
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.
Calculation of the Dynamic Characteristics of an Electric Arc Subjected to Forced Extinction
NASA Astrophysics Data System (ADS)
Nekrasov, S. A.
2016-11-01
Models and methods of calculating the currents in a free-burning arc and in an arc in an arc chute with magnetic blow and the voltages across them in the process of their extinction are considered. A comparison of calculation and experimental data has been performed.
ERIC Educational Resources Information Center
Schumann, Heinz; Green, David
2000-01-01
Discusses software for geometric construction, measurement, and calculation, and software for numerical calculation and symbolic analysis that allows for new approaches to the solution of geometric problems. Illustrates these computer-aided graphical, numerical, and algebraic methods of solution and discusses examples using the appropriate choice…
ERIC Educational Resources Information Center
Schumann, Heinz; Green, David
2000-01-01
Discusses software for geometric construction, measurement, and calculation, and software for numerical calculation and symbolic analysis that allows for new approaches to the solution of geometric problems. Illustrates these computer-aided graphical, numerical, and algebraic methods of solution and discusses examples using the appropriate choice…
SU-E-T-465: Dose Calculation Method for Dynamic Tumor Tracking Using a Gimbal-Mounted Linac
Sugimoto, S; Inoue, T; Kurokawa, C; Usui, K; Sasai, K; Utsunomiya, S; Ebe, K
2014-06-01
Purpose: Dynamic tumor tracking using the gimbal-mounted linac (Vero4DRT, Mitsubishi Heavy Industries, Ltd., Japan) has been available when respiratory motion is significant. The irradiation accuracy of the dynamic tumor tracking has been reported to be excellent. In addition to the irradiation accuracy, a fast and accurate dose calculation algorithm is needed to validate the dose distribution in the presence of respiratory motion because the multiple phases of it have to be considered. A modification of dose calculation algorithm is necessary for the gimbal-mounted linac due to the degrees of freedom of gimbal swing. The dose calculation algorithm for the gimbal motion was implemented using the linear transformation between coordinate systems. Methods: The linear transformation matrices between the coordinate systems with and without gimbal swings were constructed using the combination of translation and rotation matrices. The coordinate system where the radiation source is at the origin and the beam axis along the z axis was adopted. The transformation can be divided into the translation from the radiation source to the gimbal rotation center, the two rotations around the center relating to the gimbal swings, and the translation from the gimbal center to the radiation source. After operating the transformation matrix to the phantom or patient image, the dose calculation can be performed as the no gimbal swing. The algorithm was implemented in the treatment planning system, PlanUNC (University of North Carolina, NC). The convolution/superposition algorithm was used. The dose calculations with and without gimbal swings were performed for the 3 × 3 cm{sup 2} field with the grid size of 5 mm. Results: The calculation time was about 3 minutes per beam. No significant additional time due to the gimbal swing was observed. Conclusions: The dose calculation algorithm for the finite gimbal swing was implemented. The calculation time was moderate.
Nattino, Francesco; Ueta, Hirokazu; Chadwick, Helen; van Reijzen, Maarten E; Beck, Rainer D; Jackson, Bret; van Hemert, Marc C; Kroes, Geert-Jan
2014-04-17
The dissociative chemisorption of methane on metal surfaces is of fundamental and practical interest, being a rate-limiting step in the steam reforming process. The reaction is best modeled with quantum dynamics calculations, but these are currently not guaranteed to produce accurate results because they rely on potential energy surfaces based on untested density functionals and on untested dynamical approximations. To help overcome these limitations, here we present for the first time statistically accurate reaction probabilities obtained with ab initio molecular dynamics (AIMD) for a polyatomic gas-phase molecule reacting with a metal surface. Using a general purpose density functional, the AIMD reaction probabilities are in semiquantitative agreement with new quantum-state-resolved experiments on CHD3 + Pt(111). The comparison suggests the use of the sudden approximation for treating the rotations even though CHD3 has large rotational constants and yields an estimated reaction barrier of 0.9 eV for CH4 + Pt(111).
Sofronov, I.D.; Voronin, B.L.; Butnev, O.I.
1997-12-31
The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle. The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.
Pimenta, A C; Martins, J M; Fernandes, R; Moreira, I S
2013-10-28
The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM-1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70-Oγ and Lys73-Nζ, Lys73-Nζ and Ser130-Oγ, and Ser70-Oγ-Ser130-Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.
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
NASA Astrophysics Data System (ADS)
Nakai, Hiromi; Yoshikawa, Takeshi
2017-03-01
In this study, we developed an excited-state calculation method for large systems using dynamical polarizabilities at the time-dependent density functional theory level. Three equivalent theories, namely, coupled-perturbed self-consistent field (CPSCF), random phase approximation (RPA), and Green function (GF), were extended to linear-scaling methods using the divide-and-conquer (DC) technique. The implementations of the standard and DC-based CPSCF, RPA, and GF methods are described. Numerical applications of these methods to polyene chains, single-wall carbon nanotubes, and water clusters confirmed the accuracy and efficiency of the DC-based methods, especially DC-GF.
Welsch, Ralph; Manthe, Uwe
2014-08-07
The mode-selective chemistry of the title reaction is studied by full-dimensional quantum dynamics simulation on an accurate ab initio potential energy surface for vanishing total angular momentum. Using a rigorous transition state based approach and multi-configurational time-dependent Hartree wave packet propagation, initial state-selected reaction probabilities for many ro-vibrational states of methane are calculated. The theoretical results are compared with experimental trends seen in reactions of methane. An intuitive interpretation of the ro-vibrational control of the chemical reactivity provided by a sudden model based on the quantum transition state concept is discussed.
Oh, Suk Yung; Bae, Young Chan
2010-07-15
The method presented in this paper was developed to predict liquid-liquid equilibria in ternary liquid mixtures by using a combination of a thermodynamic model and molecular dynamics simulations. In general, common classical thermodynamic models have many parameters which are determined by fitting a model with experimental data. This proposed method, however, provides a simple procedure for calculating liquid-liquid equilibria utilizing binary interaction parameters and molecular size parameters determined from molecular dynamics simulations. This method was applied to mixtures containing water, hydrocarbons, alcohols, chlorides, ketones, acids, and other organic liquids over various temperature ranges. The predicted results agree well with the experimental data without the use of adjustable parameters.
Hartzell, S.; Guatteri, Mariagiovanna; Mai, P.M.; Liu, P.-C.; Fisk, M. R.
2005-01-01
In the evolution of methods for calculating synthetic time histories of ground motion for postulated earthquakes, kinematic source models have dominated to date because of their ease of application. Dynamic models, however, which incorporate a physical relationship between important faulting parameters of stress drop, slip, rupture velocity, and rise time, are becoming more accessible. This article compares a class of kinematic models based on the summation of a fractal distribution of subevent sizes with a dynamic model based on the slip-weakening friction law. Kinematic modeling is done for the frequency band 0.2 to 10.0. Hz, dynamic models are calculated from 0.2 to 2.0. Hz. The strong motion data set for the 1994 Northridge earthquake is used to evaluate and compare the synthetic time histories. Source models are propagated to the far field by convolution with 1D and 3D theoretical Green’s functions. In addition, the kinematic model is used to evaluate the importance of propagation path effects: velocity structure, scattering, and nonlinearity. At present, the kinematic model gives a better broadband fit to the Northridge ground motion than the simple slip-weakening dynamic model. In general, the dynamic model overpredicts rise times and produces insufficient shorter-period energy. Within the context of the slip-weakening model, the Northridge ground motion requires a short slip-weakening distance, on the order of 0.15 m or less. A more complex dynamic model including rate weakening or one that allows shorter rise times near the hypocenter may fit the data better.
Fast calculation with point-based method to make CGHs of the polygon model
NASA Astrophysics Data System (ADS)
Ogihara, Yuki; Ichikawa, Tsubasa; Sakamoto, Yuji
2014-02-01
Holography is one of the three-dimensional technology. Light waves from an object are recorded and reconstructed by using a hologram. Computer generated holograms (CGHs), which are made by simulating light propagation using a computer, are able to represent virtual object. However, an enormous amount of computation time is required to make CGHs. There are two primary methods of calculating CGHs: the polygon-based method and the point-based method. In the polygon-based method with Fourier transforms, CGHs are calculated using a fast Fourier transform (FFT). The calculation of complex objects composed of multiple polygons requires as many FFTs, so unfortunately the calculation time become enormous. In contrast, in the point-based method, it is easy to express complex objects, an enormous calculation time is still required. Graphics processing units (GPUs) have been used to speed up the calculations of point-based method. Because a GPU is specialized for parallel computation and CGH calculation can be calculated independently for each pixel. However, expressing a planar object by the point-based method requires a signi cant increase in the density of points and consequently in the number of point light sources. In this paper, we propose a fast calculation algorithm to express planar objects by the point-based method with a GPU. The proposed method accelerate calculation by obtaining the distance between a pixel and the point light source from the adjacent point light source by a difference method. Under certain speci ed conditions, the difference between adjacent object points becomes constant, so the distance is obtained by only an additions. Experimental results showed that the proposed method is more effective than the polygon-based method with FFT when the number of polygons composing an objects are high.
Structure and dynamics of the Lu2Si2O7 lattice: Ab initio calculation
NASA Astrophysics Data System (ADS)
Nazipov, D. V.; Nikiforov, A. E.
2017-01-01
The ab initio calculations have been carried out for the crystal structure and Raman spectrum of a single crystal of lutetium pyrosilicate Lu2Si2O7. The types of fundamental vibrations and their frequencies and intensities in the Raman spectrum for two polarizations of the crystal have been determined. The calculations have been performed within the framework of the density functional theory (DFT) using the hybrid functionals. The ions involved in the vibrations have been identified using the method of isotopic substitution. The results of the calculations are in good agreement with the experiment.
NASA Astrophysics Data System (ADS)
Pankoke, S.; Buck, B.; Woelfel, H. P.
1998-08-01
Long-term whole-body vibrations can cause degeneration of the lumbar spine. Therefore existing degeneration has to be assessed as well as industrial working places to prevent further damage. Hence, the mechanical stress in the lumbar spine—especially in the three lower vertebrae—has to be known. This stress can be expressed as internal forces. These internal forces cannot be evaluated experimentally, because force transducers cannot be implementated in the force lines because of ethical reasons. Thus it is necessary to calculate the internal forces with a dynamic mathematical model of sitting man.A two dimensional dynamic Finite Element model of sitting man is presented which allows calculation of these unknown internal forces. The model is based on an anatomic representation of the lower lumbar spine (L3-L5). This lumber spine model is incorporated into a dynamic model of the upper torso with neck, head and arms as well as a model of the body caudal to the lumbar spine with pelvis and legs. Additionally a simple dynamic representation of the viscera is used. All these parts are modelled as rigid bodies connected by linear stiffnesses. Energy dissipation is modelled by assigning modal damping ratio to the calculated undamped eigenvalues. Geometry and inertial properties of the model are determined according to human anatomy. Stiffnesses of the spine model are derived from static in-vitro experiments in references [1] and [2]. Remaining stiffness parameters and parameters for energy dissipation are determined by using parameter identification to fit measurements in reference [3]. The model, which is available in 3 different postures, allows one to adjust its parameters for body height and body mass to the values of the person for which internal forces have to be calculated.
Severin, Jonathan; Jund, Philippe
2017-02-07
In this work, we aim to study the thermal properties of materials using classical molecular dynamics simulations and specialized numerical methods. We focus primarily on the thermal conductivity κ using non-equilibrium molecular dynamics (NEMD) to study the response of a crystalline solid, namely hematite (α-Fe2O3), to an imposed heat flux as is the case in real life applications. We present a methodology for the calculation of κ as well as an adapted potential for hematite. Taking into account the size of the simulation box, we show that not only the longitudinal size (in the direction of the heat flux) but also the transverse size plays a role in the determination of κ and should be converged properly in order to have reliable results. Moreover we propose a comparison of thermal conductivity calculations in two different crystallographic directions to highlight the spatial anisotropy and we investigate the non-linear temperature behavior typically observed in NEMD methods.
NASA Astrophysics Data System (ADS)
Severin, Jonathan; Jund, Philippe
2017-02-01
In this work, we aim to study the thermal properties of materials using classical molecular dynamics simulations and specialized numerical methods. We focus primarily on the thermal conductivity κ using non-equilibrium molecular dynamics (NEMD) to study the response of a crystalline solid, namely hematite (α -Fe2O3 ), to an imposed heat flux as is the case in real life applications. We present a methodology for the calculation of κ as well as an adapted potential for hematite. Taking into account the size of the simulation box, we show that not only the longitudinal size (in the direction of the heat flux) but also the transverse size plays a role in the determination of κ and should be converged properly in order to have reliable results. Moreover we propose a comparison of thermal conductivity calculations in two different crystallographic directions to highlight the spatial anisotropy and we investigate the non-linear temperature behavior typically observed in NEMD methods.
Koski, J.A.; Wix, S.D.; Cole, J.K.
1997-09-01
Shipboard fires both in the same ship hold and in an adjacent hold aboard a break-bulk cargo ship are simulated with a commercial finite-volume computational fluid mechanics code. The fire models and modeling techniques are described and discussed. Temperatures and heat fluxes to a simulated materials package are calculated and compared to experimental values. The overall accuracy of the calculations is assessed.
BEM performance in calculation of pressure distribution in spline based segmented medical images.
Pashaee, A; Fatouraee, N
2007-01-01
Conventional methods for non-invasively estimation of pressure distribution in the cardiovascular flow domain use the differential form of governing equations. This study evaluates the advantages of using integral form of governing equations. The concepts provided with the Boundary Element Method (BEM) together with the boundary based image segmentation tools are used to develop a fast calculation algorithm. Boundary based segmentation provides facility for BEM with domain pixel extraction, boundary meshing, wall normal vector calculation and accurate calculation of boundary element length. The integral form of governing equation reviewed in detail. Both the differential and integral based formulations are evaluated using mathematical test flow image.
NASA Astrophysics Data System (ADS)
Paranin, Y.; Burmistrov, A.; Salikeev, S.; Fomina, M.
2015-08-01
Basic propositions of calculation procedures for oil free scroll compressors characteristics are presented. It is shown that mathematical modelling of working process in a scroll compressor makes it possible to take into account such factors influencing the working process as heat and mass exchange, mechanical interaction in working chambers, leakage through slots, etc. The basic mathematical model may be supplemented by taking into account external heat exchange, elastic deformation of scrolls, inlet and outlet losses, etc. To evaluate the influence of procedure on scroll compressor characteristics calculations accuracy different calculations were carried out. Internal adiabatic efficiency was chosen as a comparative parameter which evaluates the perfection of internal thermodynamic and gas-dynamic compressor processes. Calculated characteristics are compared with experimental values obtained for the compressor pilot sample.
NASA Astrophysics Data System (ADS)
Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J. Valentine, Stephen
2017-05-01
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.
NASA Astrophysics Data System (ADS)
Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J. Valentine, Stephen
2017-02-01
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.
Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J Valentine, Stephen
2017-02-16
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.
Creative Uses for Calculator-based Laboratory (CBL) Technology in Chemistry.
ERIC Educational Resources Information Center
Sales, Cynthia L.; Ragan, Nicole M.; Murphy, Maureen Kendrick
1999-01-01
Reviews three projects that use a graphing calculator linked to a calculator-based laboratory device as a portable data-collection system for students in chemistry classes. Projects include Isolation, Purification and Quantification of Buckminsterfullerene from Woodstove Ashes; Determination of the Activation Energy Associated with the…
19 CFR 351.405 - Calculation of normal value based on constructed value.
Code of Federal Regulations, 2013 CFR
2013-04-01
... 19 Customs Duties 3 2013-04-01 2013-04-01 false Calculation of normal value based on constructed value. 351.405 Section 351.405 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE ANTIDUMPING AND COUNTERVAILING DUTIES Calculation of Export Price, Constructed Export Price, Fair Value,...
19 CFR 351.405 - Calculation of normal value based on constructed value.
Code of Federal Regulations, 2012 CFR
2012-04-01
... 19 Customs Duties 3 2012-04-01 2012-04-01 false Calculation of normal value based on constructed value. 351.405 Section 351.405 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE ANTIDUMPING AND COUNTERVAILING DUTIES Calculation of Export Price, Constructed Export Price, Fair Value,...
19 CFR 351.405 - Calculation of normal value based on constructed value.
Code of Federal Regulations, 2014 CFR
2014-04-01
... 19 Customs Duties 3 2014-04-01 2014-04-01 false Calculation of normal value based on constructed value. 351.405 Section 351.405 Customs Duties INTERNATIONAL TRADE ADMINISTRATION, DEPARTMENT OF COMMERCE ANTIDUMPING AND COUNTERVAILING DUTIES Calculation of Export Price, Constructed Export Price, Fair Value,...
Creative Uses for Calculator-based Laboratory (CBL) Technology in Chemistry.
ERIC Educational Resources Information Center
Sales, Cynthia L.; Ragan, Nicole M.; Murphy, Maureen Kendrick
1999-01-01
Reviews three projects that use a graphing calculator linked to a calculator-based laboratory device as a portable data-collection system for students in chemistry classes. Projects include Isolation, Purification and Quantification of Buckminsterfullerene from Woodstove Ashes; Determination of the Activation Energy Associated with the…
GPAW - massively parallel electronic structure calculations with Python-based software.
Enkovaara, J.; Romero, N.; Shende, S.; Mortensen, J.
2011-01-01
Electronic structure calculations are a widely used tool in materials science and large consumer of supercomputing resources. Traditionally, the software packages for these kind of simulations have been implemented in compiled languages, where Fortran in its different versions has been the most popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most of the productivity enhancing features together with a good numerical performance. We have used this approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges it is possible to obtain good numerical performance and good parallel scalability with Python based software.
Auxiliary-field-based trial wave functions in quantum Monte Carlo calculations
NASA Astrophysics Data System (ADS)
Chang, Chia-Chen; Rubenstein, Brenda M.; Morales, Miguel A.
2016-12-01
Quantum Monte Carlo (QMC) algorithms have long relied on Jastrow factors to incorporate dynamic correlation into trial wave functions. While Jastrow-type wave functions have been widely employed in real-space algorithms, they have seen limited use in second-quantized QMC methods, particularly in projection methods that involve a stochastic evolution of the wave function in imaginary time. Here we propose a scheme for generating Jastrow-type correlated trial wave functions for auxiliary-field QMC methods. The method is based on decoupling the two-body Jastrow into one-body projectors coupled to auxiliary fields, which then operate on a single determinant to produce a multideterminant trial wave function. We demonstrate that intelligent sampling of the most significant determinants in this expansion can produce compact trial wave functions that reduce errors in the calculated energies. Our technique may be readily generalized to accommodate a wide range of two-body Jastrow factors and applied to a variety of model and chemical systems.
Auxiliary-field-based trial wave functions in quantum Monte Carlo calculations
Chang, Chia -Chen; Rubenstein, Brenda M.; Morales, Miguel A.
2016-12-19
Quantum Monte Carlo (QMC) algorithms have long relied on Jastrow factors to incorporate dynamic correlation into trial wave functions. While Jastrow-type wave functions have been widely employed in real-space algorithms, they have seen limited use in second-quantized QMC methods, particularly in projection methods that involve a stochastic evolution of the wave function in imaginary time. Here we propose a scheme for generating Jastrow-type correlated trial wave functions for auxiliary-field QMC methods. The method is based on decoupling the two-body Jastrow into one-body projectors coupled to auxiliary fields, which then operate on a single determinant to produce a multideterminant trial wave function. We demonstrate that intelligent sampling of the most significant determinants in this expansion can produce compact trial wave functions that reduce errors in the calculated energies. Lastly, our technique may be readily generalized to accommodate a wide range of two-body Jastrow factors and applied to a variety of model and chemical systems.
Auxiliary-field-based trial wave functions in quantum Monte Carlo calculations
Chang, Chia -Chen; Rubenstein, Brenda M.; Morales, Miguel A.
2016-12-19
Quantum Monte Carlo (QMC) algorithms have long relied on Jastrow factors to incorporate dynamic correlation into trial wave functions. While Jastrow-type wave functions have been widely employed in real-space algorithms, they have seen limited use in second-quantized QMC methods, particularly in projection methods that involve a stochastic evolution of the wave function in imaginary time. Here we propose a scheme for generating Jastrow-type correlated trial wave functions for auxiliary-field QMC methods. The method is based on decoupling the two-body Jastrow into one-body projectors coupled to auxiliary fields, which then operate on a single determinant to produce a multideterminant trial wavemore » function. We demonstrate that intelligent sampling of the most significant determinants in this expansion can produce compact trial wave functions that reduce errors in the calculated energies. Lastly, our technique may be readily generalized to accommodate a wide range of two-body Jastrow factors and applied to a variety of model and chemical systems.« less
NASA Astrophysics Data System (ADS)
Çiftci, Yasemin Ö.; Evecen, Meryem; Aldırmaz, Emine
2017-01-01
First-principles calculations for the structural, elastic, electronic and vibrational properties of BeGeAs2 with chalcopyrite structure have been reported in the frame work of the density functional theory. The calculated ground state properties are in good agreement with the available data. By considering the electronic band structure and electronic density of states calculation, it is found that this compound is a semiconductor which confirmed the previous work. Single-crystal elastic constants and related properties such as Young's modulus, Poisson ratio, shear modulus and bulk modulus have been predicted using the stress-finite strain technique. It can be seen from the calculated elastic constants that this compound is mechanically stable in the chalcopyrite structure. Pressure dependences of elastic constants and band gap are also reported. Finally, the phonon dispersion curves and total and partial density of states were calculated and discussed. The calculated phonon frequencies BeGeAs2 are positive, indicating the dynamical stability of the studied compound.
Li, Yongle; Suleimanov, Yury V; Guo, Hua
2014-02-20
The thermal rate constants of two prototypical insertion-type reactions, namely, N/O + H2 → NH/OH + H, are investigated with ring polymer molecular dynamics (RPMD) on full-dimensional potential energy surfaces using recently developed RPMDrate code. It is shown that the unique ability of the RPMD approach among the existing theoretical methods to capture the quantum effects, e.g., tunneling and zero-point energy, as well as recrossing dynamics quantum mechanically with ring-polymer trajectories leads to excellent agreement with rigorous quantum dynamics calculations. The present result is encouraging for future applications of the RPMD method and the RPMDrate code to complex-forming chemical reactions involving polyatomic reactants.
NASA Astrophysics Data System (ADS)
Mebrouki, M.; Ouahrani, T.; Çiftci, Y. Öztekin
2016-07-01
Using a toolkit of theoretical techniques comprising ab initio density functional theory calculations and quasiharmonic approximation, we investigate temperature dependence of dynamical properties of BaVO_3 perovskite. This interest is triggered by the fact that, recently, it was possible to synthesize a BaVO_3 perovskite, in a cubic phase, at high pressure and temperature. First-principle calculations are achieved thanks to recent development in numerical facilities, especially phonon dispersion curves which are then fully obtained. Elastic constants of the compound are dependent on temperature due to the inevitable anharmonic effects in solids. We show that at low temperature, the full account of the thermal effects incorporating the phonon densities and Sommerfeld model is more appropriate to calculate the thermal properties of a metal.
Lakel, S.; Okbi, F.; Ibrir, M.; Almi, K.
2015-03-30
We have performed first-principles calculations to investigate the behavior under hydrostatic pressure of the structural, elastic and lattice dynamics properties of aluminum phosphide crystal (AlP), in both zinc-blende (B3) and nickel arsenide (B8) phases. Our calculated structural and electronic properties are in good agreement with previous theoretical and experimental results. The elastic constants, bulk modulus (B), shear modulus (G), and Young's modulus (E), Born effective charge and static dielectric constant ε{sub 0}, were calculated with the generalized gradient approximations and the density functional perturbation theory (DFPT). Our results in the pressure behavior of the elastic and dielectric properties of both phases are compared and contrasted with the common III–V materials. The Born effective charge ZB decreases linearly with pressure increasing, while the static dielectric constant decreases quadratically with the increase of pressure.
NASA Astrophysics Data System (ADS)
Khare, Ankur; Himmetoglu, Burak; Johnson, Melissa; Norris, David J.; Cococcioni, Matteo; Aydil, Eray S.
2012-04-01
The electronic structure, lattice dynamics, and Raman spectra of the kesterite, stannite, and pre-mixed Cu-Au (PMCA) structures of Cu2ZnSnS4 (CZTS) and Cu2ZnSnSe4 (CZTSe) were calculated using density functional theory (DFT). Differences in longitudinal and transverse optical (LO-TO) splitting in kesterite, stannite, and PMCA structures can be used to differentiate them. The Γ-point phonon frequencies, which give rise to Raman scattering, exhibit small but measurable shifts, for these three structures. Experimentally measured Raman scattering from CZTS and CZTSe thin films were examined in light of DFT calculations and deconvoluted to explain subtle shifts and asymmetric line shapes often observed in CZTS and CZTSe Raman spectra. Raman spectroscopy in conjunction with ab initio calculations can be used to differentiate between kesterite, stannite, and PMCA structures of CZTS and CZTSe.
Fairbank, Michael; Alonso, Eduardo; Prokhorov, Danil
2012-10-01
We derive an algorithm to exactly calculate the mixed second-order derivatives of a neural network's output with respect to its input vector and weight vector. This is necessary for the adaptive dynamic programming (ADP) algorithms globalized dual heuristic programming (GDHP) and value-gradient learning. The algorithm calculates the inner product of this second-order matrix with a given fixed vector in a time that is linear in the number of weights in the neural network. We use a "forward accumulation" of the derivative calculations which produces a much more elegant and easy-to-implement solution than has previously been published for this task. In doing so, the algorithm makes GDHP simple to implement and efficient, bridging the gap between the widely used DHP and GDHP ADP methods.
Czakó, Gábor; Kaledin, Alexey L; Bowman, Joel M
2010-04-28
We report the implementation of a previously suggested method to constrain a molecular system to have mode-specific vibrational energy greater than or equal to the zero-point energy in quasiclassical trajectory calculations [J. M. Bowman et al., J. Chem. Phys. 91, 2859 (1989); W. H. Miller et al., J. Chem. Phys. 91, 2863 (1989)]. The implementation is made practical by using a technique described recently [G. Czako and J. M. Bowman, J. Chem. Phys. 131, 244302 (2009)], where a normal-mode analysis is performed during the course of a trajectory and which gives only real-valued frequencies. The method is applied to the water dimer, where its effectiveness is shown by computing mode energies as a function of integration time. Radial distribution functions are also calculated using constrained quasiclassical and standard classical molecular dynamics at low temperature and at 300 K and compared to rigorous quantum path integral calculations.
Balcan, D; Erzan, A
2005-02-01
We have defined a type of clustering scheme preserving the connectivity of the nodes in a network, ignored by the conventional Migdal-Kadanoff bond moving process. In high dimensions, our clustering scheme performs better for correlation length and dynamical critical exponents than the conventional Migdal-Kadanoff bond moving scheme. In two and three dimensions we find the dynamical critical exponents for the kinetic Ising model to be z=2.13 and z=2.09 , respectively, at the pure Ising fixed point. These values are in very good agreement with recent Monte Carlo results. We investigate the phase diagram and the critical behavior of randomly bond diluted lattices in d=2 and 3 in the light of this transformation. We also provide exact correlation exponent and dynamical critical exponent values on hierarchical lattices with power-law and Poissonian degree distributions.
[Design of high performance DSP-based gradient calculation module for MRI].
Pan, Wenyu; Zhang, Fu; Luo, Hai; Zhou, Heqin
2011-05-01
A gradient calculation module based on high performance DSP was designed to meet the needs of digital MRI spectrometer. According to the requirements of users, this apparatus can achieve rotation transformation, pre-emphasis, shimming and other gradient calculation functions in a single chip of DSP. It then outputs gradient waveform data of channel X, Y, Z and shimming data of channel B0. Experiments show that the design has good versatility and can satisfy the functional, speed and accuracy requirements of MRI gradient calculation. It provides a practical gradient calculation solution for the development of digital spectrometer.
Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes
NASA Astrophysics Data System (ADS)
Kondratyuk, Nikolay D.; Norman, Genri E.; Stegailov, Vladimir V.
2016-11-01
Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description.
Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory
NASA Technical Reports Server (NTRS)
Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.
1990-01-01
New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.
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.
Martins, Murillo L; Eckert, Juergen; Jacobsen, Henrik; Dos Santos, Éverton C; Ignazzi, Rosanna; de Araujo, Daniele Ribeiro; Bellissent-Funel, Marie-Claire; Natali, Francesca; Koza, Michael Marek; Matic, Aleksander; de Paula, Eneida; Bordallo, Heloisa N
2017-05-30
Since potential changes in the dynamics and mobility of drugs upon complexation for delivery may affect their ultimate efficacy, we have investigated the dynamics of two local anesthetic molecules, bupivacaine (BVC, C18H28N2O) and ropivacaine (RVC, C17H26N2O), in both their crystalline forms and complexed with water-soluble oligosaccharide 2-hydroxypropyl-β-cyclodextrin (HP-β-CD). The study was carried out by neutron scattering spectroscopy, along with thermal analysis, and density functional theory computation. Mean square displacements suggest that RVC may be less flexible in crystalline form than BVC, but both molecules exhibit very similar dynamics when confined in HP-β-CD. The use of vibrational analysis by density functional theory (DFT) made possible the identification of molecular modes that are most affected in both molecules by insertion into HP-β-CD, namely those of the piperidine rings and methyl groups. Nonetheless, the somewhat greater structure in the vibrational spectrum at room temperature of complexed RVC than that of BVC, suggests that the effects of complexation are more severe for the latter. This unique approach to the molecular level study of encapsulated drugs should lead to deeper understanding of their mobility and the respective release dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.
On a class of TVD schemes for gas dynamic calculations. [Total Variation Diminishing
NASA Technical Reports Server (NTRS)
Yee, H. C.; Warming, R. F.; Harten, A.
1985-01-01
The purpose of this paper is to review a class of explicit and implicit second-order accurate Total Variation Diminishing (TVD) schemes and to show by numerical experiments, the performance of these schemes to the Euler equations of gas dynamics. The method of constructing these second-order accurate TVD schemes is sometimes known as the modified flux approach.
Dynamic Load Balancing for Finite Element Calculations on Parallel Computers. Chapter 1
NASA Technical Reports Server (NTRS)
Pramono, Eddy; Simon, Horst D.; Sohn, Andrew; Lasinski, T. A. (Technical Monitor)
1994-01-01
Computational requirements of full scale computational fluid dynamics change as computation progresses on a parallel machine. The change in computational intensity causes workload imbalance of processors, which in turn requires a large amount of data movement at runtime. If parallel CFD is to be successful on a parallel or massively parallel machine, balancing of the runtime load is indispensable. Here a frame work is presented for dynamic load balancing for CFD applications, called Jove. One processor is designated as a decision maker Jove while others are assigned to computational fluid dynamics. Processors running CFD send flags to Jove in a predetermined number of iterations to initiate load balancing. Jove starts working on load balancing while other processors continue working with the current data and load distribution. Jove goes through several steps to decide if the new data should be taken, including preliminary evaluate, partition, processor reassignment, cost evaluation, and decision. Jove running on a single SP2 node has been completely implemented. Preliminary experimental results show that the Jove approach to dynamic load balancing can be effective for full scale grid partitioning on the target machine SP2.
Dynamic Load Balancing for Finite Element Calculations on Parallel Computers. Chapter 1
NASA Technical Reports Server (NTRS)
Pramono, Eddy; Simon, Horst D.; Sohn, Andrew; Lasinski, T. A. (Technical Monitor)
1994-01-01
Computational requirements of full scale computational fluid dynamics change as computation progresses on a parallel machine. The change in computational intensity causes workload imbalance of processors, which in turn requires a large amount of data movement at runtime. If parallel CFD is to be successful on a parallel or massively parallel machine, balancing of the runtime load is indispensable. Here a frame work is presented for dynamic load balancing for CFD applications, called Jove. One processor is designated as a decision maker Jove while others are assigned to computational fluid dynamics. Processors running CFD send flags to Jove in a predetermined number of iterations to initiate load balancing. Jove starts working on load balancing while other processors continue working with the current data and load distribution. Jove goes through several steps to decide if the new data should be taken, including preliminary evaluate, partition, processor reassignment, cost evaluation, and decision. Jove running on a single SP2 node has been completely implemented. Preliminary experimental results show that the Jove approach to dynamic load balancing can be effective for full scale grid partitioning on the target machine SP2.
A Simple Molecular Dynamics Lab to Calculate Viscosity as a Function of Temperature
ERIC Educational Resources Information Center
Eckler, Logan H.; Nee, Matthew J.
2016-01-01
A simple molecular dynamics experiment is described to demonstrate transport properties for the undergraduate physical chemistry laboratory. The AMBER package is used to monitor self-diffusion in "n"-hexane. Scripts (available in the Supporting Information) make the process considerably easier for students, allowing them to focus on the…
A Simple Molecular Dynamics Lab to Calculate Viscosity as a Function of Temperature
ERIC Educational Resources Information Center
Eckler, Logan H.; Nee, Matthew J.
2016-01-01
A simple molecular dynamics experiment is described to demonstrate transport properties for the undergraduate physical chemistry laboratory. The AMBER package is used to monitor self-diffusion in "n"-hexane. Scripts (available in the Supporting Information) make the process considerably easier for students, allowing them to focus on the…
NASA Astrophysics Data System (ADS)
Kehlenbeck, Matthias; Breitner, Michael H.
Business users define calculated facts based on the dimensions and facts contained in a data warehouse. These business calculation definitions contain necessary knowledge regarding quantitative relations for deep analyses and for the production of meaningful reports. The business calculation definitions are implementation and widely organization independent. But no automated procedures facilitating their exchange across organization and implementation boundaries exist. Separately each organization currently has to map its own business calculations to analysis and reporting tools. This paper presents an innovative approach based on standard Semantic Web technologies. This approach facilitates the exchange of business calculation definitions and allows for their automatic linking to specific data warehouses through semantic reasoning. A novel standard proxy server which enables the immediate application of exchanged definitions is introduced. Benefits of the approach are shown in a comprehensive case study.
Er, Li; Xiangying, Zeng
2014-01-01
To simulate the variation of biochemical oxygen demand (BOD) in the tidal Foshan River, inverse calculations based on time domain are applied to the longitudinal dispersion coefficient (E(x)) and BOD decay rate (K(x)) in the BOD model for the tidal Foshan River. The derivatives of the inverse calculation have been respectively established on the basis of different flow directions in the tidal river. The results of this paper indicate that the calculated values of BOD based on the inverse calculation developed for the tidal Foshan River match the measured ones well. According to the calibration and verification of the inversely calculated BOD models, K(x) is more sensitive to the models than E(x) and different data sets of E(x) and K(x) hardly affect the precision of the models.
ERIC Educational Resources Information Center
Cutchins, M. A.
1982-01-01
Presents programmable calculator solutions to selected problems, including area moments of inertia and principal values, the 2-D principal stress problem, C.G. and pitch inertia computations, 3-D eigenvalue problems, 3 DOF vibrations, and a complex flutter determinant. (SK)
ERIC Educational Resources Information Center
Cutchins, M. A.
1982-01-01
Presents programmable calculator solutions to selected problems, including area moments of inertia and principal values, the 2-D principal stress problem, C.G. and pitch inertia computations, 3-D eigenvalue problems, 3 DOF vibrations, and a complex flutter determinant. (SK)
Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine.
Suzuki, Masayo; Kino, Katsuhito; Morikawa, Masayuki; Kobayashi, Takanobu; Komori, Rie; Miyazawa, Hiroshi
2012-06-01
DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H)-oxazolone (Oz), guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiro-imino-dihydantoin (Sp) are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.
NASA Astrophysics Data System (ADS)
Feng, Xuan-Kai; Shi, Siqi; Shen, Jian-Yun; Shang, Shun-Li; Yao, Mei-Yi; Liu, Zi-Kui
2016-10-01
Since Zr-Fe-Sn is one of the key ternary systems for cladding and structural materials in nuclear industry, it is of significant importance to understand physicochemical properties related to Zr-Fe-Sn system. In order to design the new Zr alloys with advanced performance by CALPHAD method, the thermodynamic model for the lower order systems is required. In the present work, first-principles calculations are employed to obtain phonon, thermodynamic and elastic properties of Zr6FeSn2 with C22 structure and the end-members (C22-Zr6FeFe2, C22-Zr6SnSn2 and C22-Zr6SnFe2) in the model of (Zr)6(Fe, Sn)2(Fe, Sn)1. It is found that the imaginary phonon modes are absent for C22-Zr6FeSn2 and C22-Zr6SnSn2, indicating they are dynamically stable, while the other two end-members are unstable. Gibbs energies of C22-Zr6FeSn2 and C22-Zr6SnSn2 are obtained from the quasiharmonic phonon approach and can be added in the thermodynamic database: Nuclearbase. The C22-Zr6FeSn2's single-crystal elasticity tensor components along with polycrystalline bulk, shear and Young's moduli are computed with a least-squares approach based upon the stress tensor computed from first-principles method. The results indicate that distortion is more difficult in the directions normal the c-axis than along to it.
Robert, T; Chèze, L; Dumas, R; Verriest, J-P
2007-01-01
The joint forces and moments driving the motion of a human subject are classically computed by an inverse dynamic calculation. However, even if this process is theoretically simple, many sources of errors may lead to huge inaccuracies in the results. Moreover, a direct comparison with in vivo measured loads or with "gold standard" values from literature is only possible for very specific studies. Therefore, assessing the inaccuracy of inverse dynamic results is not a trivial problem and a simple method is still required. This paper presents a simple method to evaluate both: (1) the consistency of the results obtained by inverse dynamics; (2) the influence of possible modifications in the inverse dynamic hypotheses. This technique concerns recursive calculation performed on full kinematic chains, and consists in evaluating the loads obtained by two different recursive strategies. It has been applied to complex 3D whole body movements of balance recovery. A recursive Newton-Euler procedure was used to compute the net joint loads. Two models were used to represent the subject bodies, considering or not the upper body as a unique rigid segment. The inertial parameters of the body segments were estimated from two different sets of scaling equations [De Leva, P., 1996. Adjustments to Zatsiorsky-Suleyanov's segment inertia parameters. Journal of Biomechanics 29, 1223-1230; Dumas, R., Chèze, L., Verriest, J.-P., 2006b. Adjustments to McConville et al. and Young et al. Body Segment Inertial Parameters. Journal of Biomechanics, in press]. Using this comparison technique, it has been shown that, for the balance recovery motions investigated: (1) the use of the scaling equations proposed by Dumas et al., instead of those proposed by De Leva, improves the consistency of the results (average relative influence up to 30% for the transversal moment); (2) the arm motions dynamically influence the recovery motion in a non negligible way (average relative influence up to 15% and 30
Zhang, Zhao; Liu, Juan; Jia, Jia; Li, Xin; Han, Jian; Hu, Bin; Wang, Yongtian
2013-08-01
Heavy computational load of computer-generated hologram (CGH) and imprecise intensity modulation of 3D images are crucial problems in dynamic holographic display. The nonuniform sampling method is proposed to speed up CGH generation and precisely modulate the reconstructed intensities of phase-only CGH. The proposed method can eliminate the redundant information properly, where 70% reduction in the storage amount can be reached when it is combined with the novel lookup table method. Multigrayscale modulation of reconstructed 3D images can be achieved successfully. Numerical simulations and optical experiments are performed, and both are in good agreement. It is believed that the proposed method can be used in 3D dynamic holographic display.
NASA Astrophysics Data System (ADS)
Borg, Michael; Melchior Hansen, Anders; Bredmose, Henrik
2016-09-01
Designing floating substructures for the next generation of 10MW and larger wind turbines has introduced new challenges in capturing relevant physical effects in dynamic simulation tools. In achieving technically and economically optimal floating substructures, structural flexibility may increase to the extent that it becomes relevant to include in addition to the standard rigid body substructure modes which are typically described through linear radiation-diffraction theory. This paper describes a method for the inclusion of substructural flexibility in aero-hydro-servo-elastic dynamic simulations for large-volume substructures, including wave-structure interactions, to form the basis of deriving sectional loads and stresses within the substructure. The method is applied to a case study to illustrate the implementation and relevance. It is found that the flexible mode is significantly excited in an extreme event, indicating an increase in predicted substructure internal loads.
Dynamic plasmapause model based on THEMIS measurements
NASA Astrophysics Data System (ADS)
Liu, W.; Liu, X.
2015-12-01
We will present a dynamic plasmapause location model established based on five years of THEMIS measurements from 2009 to 2013. In total, 5878 plasmapause crossing events are identified, sufficiently covering all 24 Magnetic Local Time (MLT) sectors. Based on this plasmapause crossing database, we investigate the correlations between plasmapause locations with solar wind parameters and geomagnetic indices. Input parameters for the best fits are obtained for different MLT sectors and finally we choose five input parameters to build a plasmapause location model, including five-minute-averaged SYM-H, AL and AU indices as well as hourly-averaged AE and Kp indices. An out-of-sample comparison on the evolution of the plasmapause is shown during April 2001 magnetic storm, demonstrating good agreement between model results and observations. Two major advantages are achieved by this model. First, this model provides plasmapause locations at 24 MLT sectors, still providing good consistency with observations. Second, this model is able to reproduce dynamic variations of plasmapause in the time scale as short as five minutes.
Motion detection based on recurrent network dynamics
Joukes, Jeroen; Hartmann, Till S.; Krekelberg, Bart
2014-01-01
The detection of visual motion requires temporal delays to compare current with earlier visual input. Models of motion detection assume that these delays reside in separate classes of slow and fast thalamic cells, or slow and fast synaptic transmission. We used a data-driven modeling approach to generate a model that instead uses recurrent network dynamics with a single, fixed temporal integration window to implement the velocity computation. This model successfully reproduced the temporal response dynamics of a population of motion sensitive neurons in macaque middle temporal area (MT) and its constituent parts matched many of the properties found in the motion processing pathway (e.g., Gabor-like receptive fields (RFs), simple and complex cells, spatially asymmetric excitation and inhibition). Reverse correlation analysis revealed that a simplified network based on first and second order space-time correlations of the recurrent model behaved much like a feedforward motion energy (ME) model. The feedforward model, however, failed to capture the full speed tuning and direction selectivity properties based on higher than second order space-time correlations typically found in MT. These findings support the idea that recurrent network connectivity can create temporal delays to compute velocity. Moreover, the model explains why the motion detection system often behaves like a feedforward ME network, even though the anatomical evidence strongly suggests that this network should be dominated by recurrent feedback. PMID:25565992
Dynamic graph cut based segmentation of mammogram.
Angayarkanni, S Pitchumani; Kamal, Nadira Banu; Thangaiya, Ranjit Jeba
2015-01-01
This work presents the dynamic graph cut based Otsu's method to segment the masses in mammogram images. Major concern that threatens human life is cancer. Breast cancer is the most common type of disease among women in India and abroad. Breast cancer increases the mortality rate in India especially in women since it is considered to be the second largest form of disease which leads to death. Mammography is the best method for diagnosing early stage of cancer. The computer aided diagnosis lacks accuracy and it is time consuming. The main approach which makes the detection of cancerous masses accurate is segmentation process. This paper is a presentation of the dynamic graph cut based approach for effective segmentation of region of interest (ROI). The sensitivity, the specificity, the positive prediction value and the negative prediction value of the proposed algorithm are determined and compared with the existing algorithms. Both qualitative and quantitative methods are used to detect the accuracy of the proposed system. The sensitivity, the specificity, the positive prediction value and the negative prediction value of the proposed algorithm accounts to 98.88, 98.89, 93 and 97.5% which rates very high when compared to the existing algorithms.
Molecular-dynamics calculations of the velocity autocorrelation function: Hard-sphere results
NASA Astrophysics Data System (ADS)
Erpenbeck, Jerome J.; Wood, Wiilliam W.
1985-07-01
The velocity autocorrelation function for the hard-sphere fluid is computed for ten values of the volume ranging from 25 to 1.6 times the close-packed volume V0 for systems of from 108 to 4000 hard spheres, using a Monte Carlo, molecular-dynamics technique. The results are compared with the theoretical predictions of the mode-coupling theory, modified to take into account the finite size of the system and the periodic boundary conditions. The data are found to be in good agreement with the theory, evaluated using Enskog values for the transport coefficients, for values of the time greater than roughly 15 to 30 mean free times (depending on density), for volumes as small as 2V0. The higher-density results do not agree with the theory, unless the actual transport coefficients (evaluated using molecular dynamics) are used in the theory. The latter version of the theory, however, fails to fit the data at lower densities, except at very long times. To answer the recent critique by Fox, the data are further compared with the theory over time intervals for which the molecular-dynamics trajectories retain some measure of accuracy. The agreement between the data and the theory is largely unaffected, except at a volume 1.8V0 for which there is a marginally significant difference at very long times only.
Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?
Hele, Timothy J. H.; Suleimanov, Yury V.
2015-08-21
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H{sub 2}, D + MuH, and F + H{sub 2}, and the prototypical polyatomic reaction H + CH{sub 4}. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.
NASA Astrophysics Data System (ADS)
Dattani, Nikesh S.
2013-12-01
This MATLAB program calculates the dynamics of the reduced density matrix of an open quantum system modeled either by the Feynman-Vernon model or the Caldeira-Leggett model. The user gives the program a Hamiltonian matrix that describes the open quantum system as if it were in isolation, a matrix of the same size that describes how that system couples to its environment, and a spectral distribution function and temperature describing the environment’s influence on it, in addition to the open quantum system’s initial density matrix and a grid of times. With this, the program returns the reduced density matrix of the open quantum system at all moments specified by that grid of times (or just the last moment specified by the grid of times if the user makes this choice). This overall calculation can be divided into two stages: the setup of the Feynman integral, and the actual calculation of the Feynman integral for time propagation of the density matrix. When this program calculates this propagation on a multi-core CPU, it is this propagation that is usually the rate-limiting step of the calculation, but when it is calculated on a GPU, the propagation is calculated so quickly that the setup of the Feynman integral can actually become the rate-limiting step. The overhead of transferring information from the CPU to the GPU and back seems to have a negligible effect on the overall runtime of the program. When the required information cannot fit on the GPU, the user can choose to run the entire program on a CPU. Catalogue identifier: AEPX_v1_0. Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPX_v1_0.html. Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html. No. of lines in distributed program, including test data, etc.: 703. No. of bytes in distributed program, including test data, etc.: 11026. Distribution format: tar.gz. Programming
Lattice dynamics of diamond-like crystals from a tight-binding calculation of valence bands
NASA Astrophysics Data System (ADS)
Roman, R.; Pascual, J.
1988-11-01
We report on the results of calculations of the TA(X) phonon energy in the series of C, Si, Ge, Sn homopolar crystals. The starting point is the tight-binding model for the electronic Hamiltonian where Es and Ep are taken to be the free atomic energies while the interatomic matrix elements are described by a universal d-2 Harrison's scaling law. The change of the total energy with the atomic distortion is given in terms of changes in the valence band energy and changes in the overlap energy. The numerical calculations for Si gives U1 = -21.77eV and U2 = 60.44eV, close to the values predicted by Harrison U1 = -17.76eV and U2 = 53.28eV. The calculations of the TA(X) phonon energy gives (in the case the interatomic distances are held constant): 26.09 THz (C), 6.46 THz (Si), 3.37THz (Ge) and 1.91 THz (Sn), in reasonably good agreement with the experimental results 24.1 THz (C), 4.49 THz (Si), 2.39 THz (Ge) and 1.26 THz (Sn).
Lattice dynamics and thermodynamics of molybdenum from first-principles calculations.
Zeng, Zhao-Yi; Hu, Cui-E; Cai, Ling-Cang; Chen, Xiang-Rong; Jing, Fu-Qian
2010-01-14
We calculated the phase transition, elastic constants, full phonon dispersion curves, and thermal properties of molybdenum (Mo) for a wide range of pressures using density functional theory. Mo is stable in the body-centered-cubic (bcc) structure up to 703 +/- 19 GPa and then transforms to the face-centered close-packed (fcc) structure at zero temperature. Under high temperature and pressure, the fcc phase of Mo is more stable than the bcc phase. The calculated phonon dispersion curves accord excellently with experiments. Under pressure, we captured a large softening along H-P in the TA branches. When the volume is compressed to 7.69 A(3), the frequencies along H-P in the TA branches soften to imaginary frequencies, indicating a structural instability. When the pressure increases, the phonon calculations on the fcc Mo predict the stability by promoting the frequencies along Gamma to X and Gamma to L symmetry lines from imaginary to real. The thermal equation of state was also investigated. From the thermal expansion coefficient and the heat capacity, we found that the quasiharmonic approximation was valid only up to about melting point at zero pressure. However, under pressure, the validity can be extended to a much higher temperature.
Particle-dynamics calculations of gravity flow of inelastic, frictional spheres
Walton, O.R.; Braun, R.L.; Mallon, R.G.; Cervelli, D.M.
1987-11-17
Three-dimensional discrete-particle computer models that calculate the motion of each individual grain in assemblies of hundreds of particles in steady shearing flows with either periodic or real boundaries have been modified to simulate gravity flow of particles through arrays of cylindrical horizontal rods and down inclined chutes. The particle interaction models reproduce experimentally measured recoil trajectories for colliding frictional particles, including rotation effects. Laboratory measurements of the flow of glass beads cascading down through an array of horizontal cylindrical rods correlate well with gravity flow calculations of inelastic, frictional spheres falling through a similar rod array. Less elastic particles are found to cascade through the array faster than nearly elastic particles. Likewise, smaller particles are found to flow faster than large ones. Model simulations of nearly two-dimensional inclined chute flow tests of 6mm diameter cellulose-acetate spheres flowing over a rough surface between parallel vertical glass plates, result in particle velocities that are considerably higher than values measured in similar laboratory tests at UCLA; however, inclusion of approximate air drag effects in the calculational model eliminates most of the discrepancy producing both density and velocity profiles that are close to the measured values. 15 refs., 5 figs.
Dynamics of hospital-based plastic surgery.
Chandawarkar, Rajiv Y; Dutta, Satyajit
2007-02-01
Legislative regulations, decreasing reimbursements for office procedures, and malpractice premiums have transformed plastic surgery from an office-based specialty into a hospital-based one. Simultaneously, hospital economics has altered, wherein the "business model" has all but subsumed the old "medical care" model. Integration between plastic surgeons and the new hospital structure has been difficult for both. Limited understanding of the financial dynamics of hospital-based practices, unfamiliarity with the administrative processes, and resistance to accept and assimilate changes by both sides pose hurdles, in some situations even forcing plastic surgeons out of hospital settings. Using well-defined financial terminology, changing national development in health care policy, and hospital-based administrative strategies as a backdrop, this study finds common ground for the plastic surgery specialty to coapt with the hospital. Key missing elements in the interaction between plastic surgeons and hospital administrations and ways of integrating these components are identified. To do so effectively, plastic surgeons must first understand the basic tenets of management that drive hospital administrators, participate at every level they can in guiding these processes, and assume leadership roles that will ultimately dictate the way they work and conduct their professional lives. It is critical that plastic surgeons engage in important processes that govern the economics of hospital-based health care delivery. This commitment will also ensure that all three groups (the patients, physicians, and hospital administrators) achieve a degree of satisfaction. The message to plastic surgeons is clear: be proactive and lead a campaign of change.
Giovannelli, Edoardo; Cardini, Gianni; Chelli, Riccardo
2016-03-08
An important issue concerning computer simulations addressed to free energy estimates via nonequilibrium work theorems, such as the Jarzynski equality [Phys. Rev. Lett. 1997, 78, 2690], is the computational effort required to achieve results with acceptable accuracy. In this respect, the dynamical freezing approach [Phys. Rev. E 2009, 80, 041124] has been shown to improve the efficiency of this kind of simulations, by blocking the dynamics of particles located outside an established mobility region. In this report, we show that dynamical freezing produces a systematic spurious decrease of the particle density inside the mobility region. As a consequence, the requirements to apply nonequilibrium work theorems are only approximately met. Starting from these considerations, we have developed a simulation scheme, called "elastic barrier dynamical freezing", according to which a stiff potential-energy barrier is enforced at the boundaries of the mobility region, preventing the particles from leaving this region of space during the nonequilibrium trajectories. The method, tested on the calculation of the distance-dependent free energy of a dimer immersed into a Lennard-Jones fluid, provides an accuracy comparable to the conventional steered molecular dynamics, with a computational speedup exceeding a few orders of magnitude.
Karabag Aydin, Arzu; Dinç, Leyla
2016-12-29
Drug dosage calculation skill is critical for all nursing students to ensure patient safety, particularly during clinical practice. The study purpose was to evaluate the effectiveness of Web-based instruction on improving nursing students' arithmetical and drug dosage calculation skills using a pretest-posttest design. A total of 63 nursing students participated. Data were collected through the Demographic Information Form, and the Arithmetic Skill Test and Drug Dosage Calculation Skill Test were used as pre and posttests. The pretest was conducted in the classroom. A Web site was then constructed, which included audio presentations of lectures, quizzes, and online posttests. Students had Web-based training for 8 weeks and then they completed the posttest. Pretest and posttest scores were compared using the Wilcoxon test and correlation coefficients were used to identify the relationship between arithmetic and calculation skills scores. The results demonstrated that Web-based teaching improves students' arithmetic and drug dosage calculation skills. There was a positive correlation between the arithmetic skill and drug dosage calculation skill scores of students. Web-based teaching programs can be used to improve knowledge and skills at a cognitive level in nursing students.
Molecular-Dynamic Calculation of Effects Appearing in Removing a Lead Film from Graphene
NASA Astrophysics Data System (ADS)
Galashev, A. E.; Rakhmanova, O. R.
2017-07-01
By the molecular-dynamics technique, the authors have investigated the bombardment of a thin lead film on graphene by a beam of Xe clusters in the range of energies 5-30 eV at an angle of incidence of 45o. Visual observation and the density profile of the Pb film point to a complete separation of the film from graphene followed by the formation of a lead cluster during the bombardment with a cluster energy of 20 eV. Such bombardment leads to maximum horizontal and minimum vertical mobilities of C atoms in graphene and also generates a minimum stress in the film's plane due to vertical forces.
NASA Astrophysics Data System (ADS)
Nikiforov, Ilia; Tang, Dai-Ming; Wei, Xianlong; Dumitricǎ, Traian; Golberg, Dmitri
2012-07-01
By combining experiments performed on nanoribbons in situ within a high-resolution TEM with objective molecular dynamics simulations, we reveal common mechanisms in the bending response of few-layer-thick hexagonal boron nitride and graphene nanoribbons. Both materials are observed forming localized kinks in the fully reversible bending experiments. Microscopic simulations and theoretical analysis indicate platelike bending behavior prior to kinking, in spite of the possibility of interlayer sliding, and give the critical curvature for the kinking onset. This behavior is distinct from the rippling and kinking of multi- and single-wall nanotubes under bending. Our findings have implications for future study of nanoscale layered materials, including nanomechanical device design.
NASA Technical Reports Server (NTRS)
Levin, D.
1981-01-01
A nonsteady vortex-lattice method is introduced for predicting the dynamic stability derivatives of a delta wing undergoing an oscillatory motion. The analysis is applied to several types of small oscillations in pitch. The angle of attack varied between + or - 1 deg, with the mean held at 0 deg when the flow was assumed to be attached and between + or - 1 deg and the mean held at 15 deg when both leading-edge separation and wake roll-up were included. The computed results for damping in pitch are compared with several other methods and with experiments, and are found to be consistent and in good agreement.
NASA Astrophysics Data System (ADS)
Zhang, Yan; Lin, Hai
2009-05-01
Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.
Implicit Total Variation Diminishing (TVD) schemes for steady-state calculations. [in gas dynamics
NASA Technical Reports Server (NTRS)
Yee, H. C.; Warming, R. F.; Harten, A.
1985-01-01
The novel implicit and unconditionally stable, high resolution Total Variation Diminishing (TVD) scheme whose application to steady state calculations is presently examined is a member of a one-parameter family of implicit, second-order accurate systems developed by Harten (1983) for the computation of weak solutions for one-dimensional hyperbolic conservation laws. The scheme will not generate spurious oscillations for a nonlinear scalar equation and a constant coefficient system. Numerical experiments for a quasi-one-dimensional nozzle problem show that the experimentally determined stability limit correlates exactly with the theoretical stability limit for the nonlinear scalar hyberbolic conservation laws.
Reif, Maria M; Oostenbrink, Chris
2014-01-01
The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker–Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry
Reif, Maria M; Oostenbrink, Chris
2014-01-30
The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved. © The Authors Journal of Computational Chemistry
Micoulaut, Matthieu; Le Roux, Sébastien; Massobrio, Carlo
2012-06-14
The structural properties of liquid GeSe(2) have been calculated by first-principles molecular dynamics by using a periodic simulation box containing N = 480 atoms. This has allowed a comparison with previous results obtained on a smaller system size (N = 120) [M. Micoulaut, R. Vuilleumier, and C. Massobrio, Phys. Rev. B 79, 214205 (2009)]. In the domain of first-principles molecular dynamics, we obtain an assessment of system size effects of unprecedented quality. Overall, no drastic differences are found between the two sets of results, confirming that N = 120 is a suitable size to achieve a realistic description of this prototypical disordered network. However, for N = 480, short range properties are characterized by an increase of chemical order, the number of Ge tetrahedra coordinated to four Se atoms being larger. At the intermediate range order level, size effect mostly modify the low wavevector region (k ~1 Å(-1)) in the concentration-concentration partial structure factor.
Fang, Liang; Wang, Xiaojian; Xi, Meiyang; Liu, Tianqi; Yin, Dali
2016-04-01
The dynamic balance of sphingolipids plays a crucial role in diverse biological processes such as mitogenesis, cell migration and angiogenesis. Sphingosine kinases (SKs) including SK1 and SK2 phosphorylate sphingosine to sphingosine 1-phosphate (S1P), and control the critical balance. SK1 overexpression was reported to increase cell survival and proliferation. Although several SK1 selective inhibitors have been reported, detailed analysis toward their selectivity to understand the molecular mechanism has not been performed to our knowledge. Herein, the crystal structure of SK1 and a homology model of SK2 were used to dock five inhibitors (1, 2, 3, 4 and 5). Protein-ligand complexes were then subjected to a molecular dynamics study and MM-PBSA binding free energy calculations. By analyzing the binding model of these inhibitors, we found that residues ILE170, PHE188 and THR192 in SK1 significantly contribute a favorable binding energy to the selectivity.
Wang, Ya-Ting; Gao, Yuan-Jun; Wang, Qian; Cui, Ganglong
2017-02-02
Intramolecularly bridged diarylethenes exhibit improved photocyclization quantum yields because the anti-syn isomerization that originally suppresses photocyclization in classical diarylethenes is blocked. Experimentally, three possible channels have been proposed to interpret experimental observation, but many details of photochromic mechanism remain ambiguous. In this work we have employed a series of electronic structure methods (OM2/MRCI, DFT, TDDFT, RI-CC2, DFT/MRCI, and CASPT2) to comprehensively study excited state properties, photocyclization, and photoreversion dynamics of 1,2-dicyano[2,2]metacyclophan-1-ene. On the basis of optimized stationary points and minimum-energy conical intersections, we have refined experimentally proposed photochromic mechanism. Only an S1/S0 minimum-energy conical intersection is located; thus, we can exclude the third channel experimentally proposed. In addition, we find that both photocyclization and photoreversion processes use the same S1/S0 conical intersection to decay the S1 system to the S0 state, so we can unify the remaining two channels into one. These new insights are verified by our OM2/MRCI nonadiabatic dynamics simulations. The S1 excited-state lifetimes of photocyclization and photoreversion are estimated to be 349 and 453 fs, respectively, which are close to experimentally measured values: 240 ± 60 and 250 fs in acetonitrile solution. The present study not only interprets experimental observations and refines previously proposed mechanism but also provides new physical insights that are valuable for future experiments.
ERIC Educational Resources Information Center
Hagedorn, Linda Serra
1998-01-01
A study explored two distinct methods of calculating a precise measure of gender-based wage differentials among college faculty. The first estimation considered wage differences using a formula based on human capital; the second included compensation for past discriminatory practices. Both measures were used to predict three specific aspects of…
Spatiotemporal-atlas-based dynamic speech imaging
NASA Astrophysics Data System (ADS)
Fu, Maojing; Woo, Jonghye; Liang, Zhi-Pei; Sutton, Bradley P.
2016-03-01
Dynamic magnetic resonance imaging (DS-MRI) has been recognized as a promising method for visualizing articulatory motion of speech in scientific research and clinical applications. However, characterization of the gestural and acoustical properties of the vocal tract remains a challenging task for DS-MRI because it requires: 1) reconstructing high-quality spatiotemporal images by incorporating stronger prior knowledge; and 2) quantitatively interpreting the reconstructed images that contain great motion variability. This work presents a novel imaging method that simultaneously meets both requirements by integrating a spatiotemporal atlas into a Partial Separability (PS) model-based imaging framework. Through the use of an atlas-driven sparsity constraint, this method is capable of capturing high-quality articulatory dynamics at an imaging speed of 102 frames per second and a spatial resolution of 2.2 × 2.2 mm2. Moreover, the proposed method enables quantitative characterization of variability of speech motion, compared to the generic motion pattern across all subjects, through the spatial residual components.
Lattice dynamics and electron-phonon coupling calculations using nondiagonal supercells
NASA Astrophysics Data System (ADS)
Lloyd-Williams, Jonathan; Monserrat, Bartomeu
Quantities derived from electron-phonon coupling matrix elements require a fine sampling of the vibrational Brillouin zone. Converged results are typically not obtainable using the direct method, in which a perturbation is frozen into the system and the total energy derivatives are calculated using a finite difference approach, because the size of simulation cell needed is prohibitively large. 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. This is accomplished by utilizing supercell matrices containing nonzero off-diagonal elements. We present the results of electron-phonon coupling calculations using the direct method to sample the vibrational Brillouin zone with grids of unprecedented size for a range of systems, including the canonical example of diamond. We also demonstrate that the use of nondiagonal supercells reduces by over an order of magnitude the computational cost of obtaining converged vibrational densities of states and phonon dispersion curves. J.L.-W. is supported by the Engineering and Physical Sciences Research Council (EPSRC). B.M. is supported by Robinson College, Cambridge, and the Cambridge Philosophical Society. This work was supported by EPSRC Grants EP/J017639/1 and EP/K013564/1.
Rapo, Mark A; Jiang, Houshuo; Grosenbaugh, Mark A; Coombs, Sheryl
2009-05-01
This paper presents the first computational fluid dynamics (CFD) simulations of viscous flow due to a small sphere vibrating near a fish, a configuration that is frequently used for experiments on dipole source localization by the lateral line. Both two-dimensional (2-D) and three-dimensional (3-D) meshes were constructed, reproducing a previously published account of a mottled sculpin approaching an artificial prey. Both the fish-body geometry and the sphere vibration were explicitly included in the simulations. For comparison purposes, calculations using potential flow theory (PFT) of a 3-D dipole without a fish body being present were also performed. Comparisons between the 2-D and 3-D CFD simulations showed that the 2-D calculations did not accurately represent the 3-D flow and therefore did not produce realistic results. The 3-D CFD simulations showed that the presence of the fish body perturbed the dipole source pressure field near the fish body, an effect that was obviously absent in the PFT calculations of the dipole alone. In spite of this discrepancy, the pressure-gradient patterns to the lateral line system calculated from 3-D CFD simulations and PFT were similar. Conversely, the velocity field, which acted on the superficial neuromasts (SNs), was altered by the oscillatory boundary layer that formed at the fish's skin due to the flow produced by the vibrating sphere (accounted for in CFD but not PFT). An analytical solution of an oscillatory boundary layer above a flat plate, which was validated with CFD, was used to represent the flow near the fish's skin and to calculate the detection thresholds of the SNs in terms of flow velocity and strain rate. These calculations show that the boundary layer effects can be important, especially when the height of the cupula is less than the oscillatory boundary layer's Stokes viscous length scale.
A transport based one-dimensional perturbation code for reactivity calculations in metal systems
Wenz, Tracy Renee
1995-02-01
A one-dimensional reactivity calculation code is developed using first order perturbation theory. The reactivity equation is based on the multi-group transport equation using the discrete ordinates method for angular dependence. In addition to the first order perturbation approximations, the reactivity code uses only the isotropic scattering data, but cross section libraries with higher order scattering data can still be used with this code. The reactivity code obtains all the flux, cross section, and geometry data from the standard interface files created by ONEDANT, a discrete ordinates transport code. Comparisons between calculated and experimental reactivities were done with the central reactivity worth data for Lady Godiva, a bare uranium metal assembly. Good agreement is found for isotopes that do not violate the assumptions in the first order approximation. In general for cases where there are large discrepancies, the discretized cross section data is not accurately representing certain resonance regions that coincide with dominant flux groups in the Godiva assembly. Comparing reactivities calculated with first order perturbation theory and a straight Δk/k calculation shows agreement within 10% indicating the perturbation of the calculated fluxes is small enough for first order perturbation theory to be applicable in the modeled system. Computation time comparisons between reactivities calculated with first order perturbation theory and straight {Delta}k/k calculations indicate considerable time can be saved performing a calculation with a perturbation code particularly as the complexity of the modeled problems increase.
Jakobsson, E; Chiu, S W
1988-01-01
This paper shows how Brownian motion theory can be used to analyze features of individual ion trajectories in channels as calculated by molecular dynamics, and that its use permits more precise determinations of diffusion coefficients than would otherwise be possible. We also show how a consideration of trajectories of single particles can distinguish between effects due to the magnitude of the diffusion coefficient and effects due to barriers and wells in the potential profile, effects which can not be distinguished by consideration of average fluxes. PMID:2465032
NASA Astrophysics Data System (ADS)
Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki
2007-11-01
Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.
A simple method for calculating the financial balance of a hospital, based on proportional dividing.
Makie, Toshio; Miyazaki, Miho; Kobayashi, Shinji; Yamanaka, Takeharu; Kinukawa, Naoko; Hanada, Eisuke; Nose, Yoshiaki
2002-04-01
It is necessary to estimate financial status to determine hospital management policy. The costs and revenues (financial balance) of each hospital division are one good index. However, it is difficult to calculate the financial balance for each division, since clinics and central services are intricately involved with each other There are no reports on a pragmatic method for calculating the financial balance. We devised a simple method based on proportional dividing. Consequently, one individual was able to complete the calculation for our hospital, which consists of 1300 beds and 23 clinics, without using the central hospital computer system.
Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala
2017-03-09
Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆Gbinding = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation
NASA Astrophysics Data System (ADS)
Tsuchiya, Yooko; Yoshii, Noriyuki; Iwatsubo, Tetsushiro
2004-08-01
Since heat storage technology contributes greatly to the effective use of energy, we are attempting to develop latent heat storage materials. If computer simulations enable the estimation of material properties prior to experiments, they will provide us with very effective tools for the development of new materials. We use molecular dynamics calculations to predict the melting points and latent heats of fusion, which are crucial thermal properties for evaluating the suitability of heat-storage materials. As the object of calculation, poly(vinyl alcohol) (PVA) was chosen, because polymer materials are effective in that they can be made to cover all temperature ranges by changing the molecular weight. The melting points were determined from the volume change, and the latent heats of fusion were determined from the internal energy. As for these calculations, it was ascertained that these thermal properties were suitable values in comparison with the results of actual calorimetry. From the comparative calculation of the polymer consistent force field (PCFF) and optimized potentials for liquid simulations (OPLS) force field, it was shown that the intermolecular potential could be simplified. Moreover, the stability of the structural isomer of PVA and the state of the hydrogen bond were evaluated, because a strong intermolecular bond leads to structural stability and a high melting temperature.
NASA Astrophysics Data System (ADS)
Knyazev, D. V.; Levashov, P. R.
2015-11-01
This work covers an ab initio calculation of transport and optical properties of plastics of the effective composition CH2 at density 0.954 g/cm3 in the temperature range from 5 kK up to 100 kK. The calculation is based on the quantum molecular dynamics, density functional theory and the Kubo-Greenwood formula. The temperature dependence of the static electrical conductivity σ1DC (T) has an unusual shape: σ1DC(T) grows rapidly for 5 kK ≤ T ≤ 10 kK and is almost constant for 20 kK ≤ T ≤ 60 kK. The additional analysis based on the investigation of the electron density of states (DOS) was performed. The rapid growth of σ1DC(T) at 5 kK ≤ T ≤ 10 kK is connected with the increase of DOS at the electron energy equal to the chemical potential ɛ = μ. The frequency dependence of the dynamic electrical conductivity σ1(ω) at 5 kK has the distinct non-Drude shape with the peak at ω ≈ 10 eV. This behavior of σ1(ω) was explained by the dip at the electron DOS.
Dynamic visual cryptography based on chaotic oscillations
NASA Astrophysics Data System (ADS)
Petrauskiene, Vilma; Palivonaite, Rita; Aleksa, Algiment; Ragulskis, Minvydas
2014-01-01
Dynamic visual cryptography scheme based on chaotic oscillations is proposed in this paper. Special computational algorithms are required for hiding the secret image in the cover moiré grating, but the decryption of the secret is completely visual. The secret image is leaked in the form of time-averaged geometric moiré fringes when the cover image is oscillated by a chaotic law. The relationship among the standard deviation of the stochastic time variable, the pitch of the moiré grating and the pixel size ensuring visual decryption of the secret is derived. The parameters of these chaotic oscillations must be carefully preselected before the secret image is leaked from the cover image. Several computational experiments are used to illustrate the functionality and the applicability of the proposed image hiding technique.
[Dynamic bimaxillary osteotomy: the new occlusal base].
Audion, M; Darmon, Y
1989-01-01
The authors present an ortho-surgical method which unites occlusion and aesthetic without compromise and without stopping orthodontic work during the immediate post-operative period. The occlusal preparation permits us a global and simultaneous mobilisation of the two maxillars which are ostesynthezed in posterior skeletal disclosing. This disposition allows a lingual replacement and gives more facility to an eventual immediate post-operative occlusal replacement. The stiff osteosynthesis with immovable plates realize a therapeutic dissociation between the skeletal stage and the basal alveolo-dental stage. The "proprioceptive amnesia" and the "muscular sideration" permit a proprioceptive reorganisation and a new neuro-muscular fonctionnement elaborated from a new occlusal base. The free movements of the T.M.J. facilitate these acquisitions and allow a perspective supervision of the occlusion in a dynamic perspective.
Calculating the dynamics of High Explosive Violent Response (HEVR) after ignition
Reaugh, J E
2008-10-15
. Such measures include damage to the confinement, the velocity and fragment size distributions from what was the confinement, and air blast. In the first phase (advisory) model described in [1], the surface to volume ratio and the ignition parameter are calibrated by comparison with experiments using the UK explosive. In order to achieve the second phase (interactive) model, and so calculate the pressure developed and the velocity imparted to the confinement, we need to calculate the spread of the ignition front, the subsequent burn behavior behind that front, and the response of unburned and partially burned explosive to pressurization. A preliminary model to do such calculations is described here.
NASA Astrophysics Data System (ADS)
Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan
2015-11-01
We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).
Applying dynamic wake models to induced power calculations for an optimum rotor
NASA Astrophysics Data System (ADS)
Garcia-Duffy, Cristina
Recent studies have pointed out that conventional lifting rotors in forward flight have efficiencies far lower than the optimum efficiencies predicted by theory. This dissertation explains how a closed-form optimization of induced power with finite-state models is expanded to successfully reproduce the results for the optimization of induced power given by classical theories for axial flow and for a rotor in forward flight. Results for induced power change in forward flight and for different conditions will help the determination of what produces the efficiency in real rotors to be inferior to the predicted values by theoretical calculations. Mainly three factors contribute to the decreased efficiency for real rotors: a finite number of blades, the effect of lift tilt and the lift distribution. The ultimate goals of the present research effort are to: (1) develop a complete and comprehensive inflow model, and (2) determine which of these contribute to the drastic increase in induced power.
A gas-dynamic calculation of type 2 shock propagation through the corona
NASA Technical Reports Server (NTRS)
Kopp, R. A.
1972-01-01
An approximate analytic theory of acoustic shock propagation in nonuniform media is used to determine the motion of a flare-generated shock wave in the corona. The shock is followed from the time it strikes the chromosphere-corona transition region (density interface) out to 5 solar radii under the assumption that the corona in this region is approximately in hydrostatic equilibrium. The strength of the shock incident on the transition region from below determines the ejection velocity of eruptive prominence material, as well as the initial velocity of the coronal shock. The calculation is applied to one well-documented case of a related flare spray, moving type 4 isolated source, and type 2 burst. It is shown that a chromospheric shock of the appropriate strength to produce the observed prominence and type 4 velocities strengthens as it moves out in the corona by an amount sufficient to account for the observed high velocity of the type 2 burst.
Payne, J.L.; Hassan, B.
1998-09-01
Massively parallel computers have enabled the analyst to solve complicated flow fields (turbulent, chemically reacting) that were previously intractable. Calculations are presented using a massively parallel CFD code called SACCARA (Sandia Advanced Code for Compressible Aerothermodynamics Research and Analysis) currently under development at Sandia National Laboratories as part of the Department of Energy (DOE) Accelerated Strategic Computing Initiative (ASCI). Computations were made on a generic reentry vehicle in a hypersonic flowfield utilizing three different distributed parallel computers to assess the parallel efficiency of the code with increasing numbers of processors. The parallel efficiencies for the SACCARA code will be presented for cases using 1, 150, 100 and 500 processors. Computations were also made on a subsonic/transonic vehicle using both 236 and 521 processors on a grid containing approximately 14.7 million grid points. Ongoing and future plans to implement a parallel overset grid capability and couple SACCARA with other mechanics codes in a massively parallel environment are discussed.
Density functional theory calculations of III-N based semiconductors with mBJLDA
NASA Astrophysics Data System (ADS)
Gürel, Hikmet Hakan; Akıncı, Özden; Ünlü, Hilmi
2017-02-01
In this work, we present first principles calculations based on a full potential linear augmented plane-wave method (FP-LAPW) to calculate structural and electronic properties of III-V based nitrides such as GaN, AlN, InN in a zinc-blende cubic structure. First principles calculation using the local density approximation (LDA) and generalized gradient approximation (GGA) underestimate the band gap. We proposed a new potential called modified Becke-Johnson local density approximation (MBJLDA) that combines modified Becke-Johnson exchange potential and the LDA correlation potential to get better band gap results compared to experiment. We compared various exchange-correlation potentials (LSDA, GGA, HSE, and MBJLDA) to determine band gaps and structural properties of semiconductors. We show that using MBJLDA density potential gives a better agreement with experimental data for band gaps III-V nitrides based semiconductors.
Poongavanam, Vasanthanathan; Steinmann, Casper; Kongsted, Jacob
2014-01-01
Quantum mechanical (QM) calculations have been used to predict the binding affinity of a set of ligands towards HIV-1 RT associated RNase H (RNH). The QM based chelation calculations show improved binding affinity prediction for the inhibitors compared to using an empirical scoring function. Furthermore, full protein fragment molecular orbital (FMO) calculations were conducted and subsequently analysed for individual residue stabilization/destabilization energy contributions to the overall binding affinity in order to better understand the true and false predictions. After a successful assessment of the methods based on the use of a training set of molecules, QM based chelation calculations were used as filter in virtual screening of compounds in the ZINC database. By this, we find, compared to regular docking, QM based chelation calculations to significantly reduce the large number of false positives. Thus, the computational models tested in this study could be useful as high throughput filters for searching HIV-1 RNase H active-site molecules in the virtual screening process. PMID:24897431
Indoor dynamic positioning system based on strapdown inertial navigation technology
NASA Astrophysics Data System (ADS)
Xing, YaDong; Wu, Hong
2011-11-01
Strapdown inertial navigation technology, which is widely used in aerospace, is a navigation technology in which the gyros sensor and accelerometers sensor are rigidly attached to the body of the object. This article describes an application of strapdown inertial navigation technology in indoor dynamic positioning system. The hardware design of the node include the master controller, data collection, sensors, antenna and related peripheral circuit. Positioning algorithm, data acquisition and transmission are done by software programming based on the hardware circuit. The strapdown inertial navigation composed of the hardware and the software could calculate the position of the object. Simulation software(matlab) is used to confirm the correctness of the positioning algorithm which is implemented by software programming in the system. The system uses the wireless sensor network to expand the range of the positioning. The system of which the information transmission is reliable and the mobility is strongly can satisfy the requirements of the emergency.
Multiple sequence alignment based on dynamic weighted guidance tree.
Nguyen, Ken D; Pan, Yi
2011-01-01
Aligning multiple DNA/RNA/protein sequences to identify common functionalities, structures, or relationships between species is a fundamental task in bioinformatics. In this study, we propose a new multiple sequence strategy that extracts sequence information, sequence global and local similarities to provide different weights for each input sequence. A weighted pair-wise distance matrix is calculated from these sequences to build a dynamic alignment guiding tree. The tree can reorder its higher-level branches based on corresponding alignment results from lower tree levels to guarantee the highest alignment scores at each level of the tree. This technique improves the alignment accuracy up to 10% on many benchmarks tested against alignment tools such as CLUSTALW (Thompson et al., 1994), DIALIGN (Morgenstern, 1999), T-COFFEE (Notredame et al., 2000), MUSCLE (Edgar, 2004), and PROBCONS (Do et al., 2005) of the multiple sequence alignment.
Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations
NASA Astrophysics Data System (ADS)
Polson, James M.; Montgomery, Logan G.
2014-10-01
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, λ, and examine the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity κ. For infinitely long cylinders, F is a maximum at λ = 0, and decreases with λ until the polymers are no longer in contact. For flexible chains (κ = 0), the polymers overlap along the cylinder for low λ, while above some critical value of λ they are longitudinally compressed and non-overlapping while still in contact. We find that the free energy barrier height, ΔF ≡ F(0) - F(∞), scales as ΔF/kBT ˜ ND-1.93 ± 0.01, for N ⩽ 200 and D ⩽ 9σ, where σ is the monomer diameter. In addition, the overlap free energy appears to scale as F/kBT = Nf(λ/N; D) for sufficiently large N, where f is a function parameterized by the cylinder diameter D. For channels of finite length, the free energy barrier height increases with increasing confinement aspect ratio L/D at fixed volume fraction ϕ, and it decreases with increasing ϕ at fixed L/D. Increasing the polymer bending rigidity κ monotonically reduces the overlap free energy. For strongly confined systems, where the chain persistence length P satisfies D ≪ P, F varies linearly with λ with a slope that scales as F'(λ) ˜ -kBTD-βP-α, where β ≈ 2 and α ≈ 0.37 for N = 200 chains. These exponent values deviate slightly from those predicted using a simple model, possibly due to insufficiently satisfying the conditions defining the Odijk regime. Finally, we use Monte Carlo dynamics simulations to examine polymer segregation dynamics for fully flexible chains and observe segregation rates that decrease with decreasing entropic force magnitude, f ≡ |dF/dλ|. For both
Polson, James M; Montgomery, Logan G
2014-10-28
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, λ, and examine the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity κ. For infinitely long cylinders, F is a maximum at λ = 0, and decreases with λ until the polymers are no longer in contact. For flexible chains (κ = 0), the polymers overlap along the cylinder for low λ, while above some critical value of λ they are longitudinally compressed and non-overlapping while still in contact. We find that the free energy barrier height, ΔF ≡ F(0) - F(∞), scales as ΔF/k(B)T ∼ ND(-1.93 ± 0.01), for N ⩽ 200 and D ⩽ 9σ, where σ is the monomer diameter. In addition, the overlap free energy appears to scale as F/k(B)T = Nf(λ/N; D) for sufficiently large N, where f is a function parameterized by the cylinder diameter D. For channels of finite length, the free energy barrier height increases with increasing confinement aspect ratio L/D at fixed volume fraction ϕ, and it decreases with increasing ϕ at fixed L/D. Increasing the polymer bending rigidity κ monotonically reduces the overlap free energy. For strongly confined systems, where the chain persistence length P satisfies D ≪ P, F varies linearly with λ with a slope that scales as F'(λ) ∼ -k(B)TD(-β)P(-α), where β ≈ 2 and α ≈ 0.37 for N = 200 chains. These exponent values deviate slightly from those predicted using a simple model, possibly due to insufficiently satisfying the conditions defining the Odijk regime. Finally, we use Monte Carlo dynamics simulations to examine polymer segregation dynamics for fully flexible chains and observe segregation rates that decrease with decreasing entropic force magnitude, f ≡ |d
Medical applications of model-based dynamic thermography
NASA Astrophysics Data System (ADS)
Nowakowski, Antoni; Kaczmarek, Mariusz; Ruminski, Jacek; Hryciuk, Marcin; Renkielska, Alicja; Grudzinski, Jacek; Siebert, Janusz; Jagielak, Dariusz; Rogowski, Jan; Roszak, Krzysztof; Stojek, Wojciech
2001-03-01
The proposal to use active thermography in medical diagnostics is promising in some applications concerning investigation of directly accessible parts of the human body. The combination of dynamic thermograms with thermal models of investigated structures gives attractive possibility to make internal structure reconstruction basing on different thermal properties of biological tissues. Measurements of temperature distribution synchronized with external light excitation allow registration of dynamic changes of local temperature dependent on heat exchange conditions. Preliminary results of active thermography applications in medicine are discussed. For skin and under- skin tissues an equivalent thermal model may be determined. For the assumed model its effective parameters may be reconstructed basing on the results of transient thermal processes. For known thermal diffusivity and conductivity of specific tissues the local thickness of a two or three layer structure may be calculated. Results of some medical cases as well as reference data of in vivo study on animals are presented. The method was also applied to evaluate the state of the human heart during the open chest cardio-surgical interventions. Reference studies of evoked heart infarct in pigs are referred, too. We see the proposed new in medical applications technique as a promising diagnostic tool. It is a fully non-invasive, clean, handy, fast and affordable method giving not only qualitative view of investigated surfaces but also an objective quantitative measurement result, accurate enough for many applications including fast screening of affected tissues.
Li, Ming-Juan; Liu, Ming-Xia; Zhao, Yan-Ying; Pei, Ke-Mei; Wang, Hui-Gang; Zheng, Xuming; Fang, Wei Hai
2013-10-03
The resonance Raman spectroscopic study of the excited state structural dynamics of 1,3-dimethyluracil (DMU), 5-bromo-1,3-dimethyluracil (5BrDMU), uracil, and thymine in water and acetonitrile were reported. Density functional theory calculations were carried out to help elucidate the ultraviolet electronic transitions associated with the A-, and B-band absorptions and the vibrational assignments of the resonance Raman spectra. The effect of the methylation at N1, N3 and C5 sites of pyrimidine ring on the structural dynamics of uracils in different solvents were explored on the basis of the resonance Raman intensity patterns. The relative resonance Raman intensities of DMU and 5BrDMU are computed at the B3LYP-TD level. Huge discrepancies between the experimental resonance Raman intensities and the B3LYP-TD predicted ones were observed. The underlying mechanism was briefly discussed. The decay channel through the S1((1)nπ*)/S2((1)ππ*) conical intersection and the S1((1)nπ*)/T1((3)ππ*) intersystem crossing were revealed by using the CASSCF(8,7)/6-31G(d) level of theory calculations.
Petty, Corey; Chen, Wenwu; Poirier, Bill
2013-08-15
In a previous article [J. Theor. Comput. Chem. 2010, 9, 435], all rovibrational bound states of HO2 were systematically computed, for all total angular momentum values J = 0-10. In this article, the high-J rovibrational states are computed for every multiple-of-ten J value up to J = 130, which is the point where the centrifugal barrier obliterates the potential well, and bound states no longer exist. The results are used to assess the importance of Coriolis coupling in this floppy system and to evaluate two different J-shifting schemes. Though not effective for multiply vibrationally excited bound states, vibrational-state-dependent J-shifting obtains modestly accurate predictions for the lowest-lying energies [J. Phys. Chem. A 2006, 110, 3246]. However, much better performance is obtained-especially for large J values, and despite substantial Coriolis coupling-using a second, rotational-state-dependent J-shifting scheme [J. Chem. Phys. 1998, 108, 5216], for which the rotational constants themselves depend on J and K. The latter formalism also yields important dynamical insight into the structure of the strongly Coriolis-coupled eigenstate wave functions. The calculations were performed using ScalIT, a suite of codes enabling quantum dynamics calculations on massively parallel computing architectures.
Wang, Feng; Stuart, Steven J.; Latour, Robert A.
2009-01-01
The adsorption behavior of a biomolecule, such as a peptide or protein, to a functionalized surface is of fundamental importance for a broad range of applications in biotechnology. The adsorption free energy for these types of interactions can be determined from a molecular dynamics simulation using the partitioning between adsorbed and nonadsorbed states, provided that sufficient sampling of both states is obtained. However, if interactions between the solute and the surface are strong, the solute will tend to be trapped near the surface during the simulation, thus preventing the adsorption free energy from being calculated by this method. This situation occurs even when using an advanced sampling algorithm such as replica-exchange molecular dynamics (REMD). In this paper, the authors demonstrate the fundamental basis of this problem using a model system consisting of one sodium ion (Na+) as the solute positioned over a surface functionalized with one negatively charged group (COO−) in explicit water. With this simple system, the authors show that sufficient sampling in the coordinate normal to the surface cannot be obtained by conventional REMD alone. The authors then present a method to overcome this problem through the use of an adaptive windowed-umbrella sampling technique to develop a biased-energy function that is combined with REMD. This approach provides an effective method for the calculation of adsorption free energy for solute-surface interactions. PMID:19768127
Kachmar, Ali; Floquet, Sébastien; Lemonnier, Jean-François; Cadot, Emmanuel; Rohmer, Marie-Madeleine; Bénard, Marc
2009-07-20
Variable temperature (1)H NMR studies of the host-guest complex [Mo(16)O(16)S(16)(OH)(16)(H(2)O)(4)(PDA)(2)](4-) (1 ; PDA(2-) = phenylenediacetate) previously carried out in D(2)O have revealed a complex behavior in solution, involving a gliding motion of both parallel phenyl rings of the PDA(2-) ligands. In the present work, we present new NMR spectra carried out in the aprotic solvent CD(3)CN, which allow the observation of the proton signals associated with the bridging hydroxo groups of the inorganic host. The new spectra provide detailed information about the concerted reorganization of the guest components, that is, PDA(2-) and water molecules. The existence of an equilibrium between two distinct isomers differing in the linking mode between the inorganic host and the two equivalent PDA(2-) ligands is evidenced. This equilibrium appears strongly dependent upon the temperature, leading to a complete inversion of the distribution between 300 and 226 K. The thermodynamic data related to the isomerization reaction have been determined (Delta(r)H = -50.5 kJ mol(-1) and Delta(r)S = -215 J mol(-1) K(-1)). Furthermore, at low temperature, one of the isomers exists in two conformations, only differing in the H-bond network involving the inner water molecules. Density functional theory calculations were carried out to push ahead the interpretations obtained from experiment, identify the isomers of 1, and specify the role and the positions of the guest water molecules. Among the various structures that have been calculated for 1, three fall in a narrow energy range and should correspond to the species characterized by variable-temperature (1)H NMR experiments in CD(3)CN. Finally, this study shows how the internal disposition of the ligands affects the ellipticity of the Mo(16) ring which varies from one isomer to the other in the 0.73-1 range and highlights solvation of the ring as one of the key parameters for the conformational design of these flexible host
Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra
2015-09-24
Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant.
[Terahertz Absorption Spectra Simulation of Glutamine Based on Quantum-Chemical Calculation].
Zhang, Tian-yao; Zhang, Zhao-hui; Zhao, Xiao-yan; Zhang, Han; Yan, Fang; Qian, Ping
2015-08-01
With simulation of absorption spectra in THz region based on quantum-chemical calculation, the THz absorption features of target materials can be assigned with theoretical normal vibration modes. This is necessary for deeply understanding the origin of THz absorption spectra. The reliabilities of simulation results mainly depend on the initial structures and theoretical methods used throughout the calculation. In our study, we utilized THz-TDS to obtain the THz absorption spectrum of solid-state L-glutamine. Then three quantum-chemical calculation schemes with different initial structures commonly used in previous studies were proposed to study the inter-molecular interactions' contribution to the THz absorption of glutamine, containing monomer structure, dimer structure and crystal unit cell structure. After structure optimization and vibration modes' calculation based on density functional theory, the calculation results were converted to absorption spectra by Lorentzian line shape function for visual comparison with experimental spectra. The result of dimmer structure is better than monomer structure in number of absorption features while worse than crystal unit cell structure in position of absorption peaks. With the most reliable simulation result from crystal unit cell calculation, we successfully assigned all three experimental absorption peaks of glutamine ranged from 0.3 to 2.6 THz with overall vibration modes. Our study reveals that the crystal unit cell should be used as initial structure during theoretical simulation of solid-state samples' THz absorption spectrum which comprehensively considers not only the intra-molecular interactions but also inter-molecular interactions.
Simulating the Dynamics of Earth's Core: Using NCCS Supercomputers Speeds Calculations
NASA Technical Reports Server (NTRS)
2002-01-01
If one wanted to study Earth's core directly, one would have to drill through about 1,800 miles of solid rock to reach liquid core-keeping the tunnel from collapsing under pressures that are more than 1 million atmospheres and then sink an instrument package to the bottom that could operate at 8,000 F with 10,000 tons of force crushing every square inch of its surface. Even then, several of these tunnels would probably be needed to obtain enough data. Faced with difficult or impossible tasks such as these, scientists use other available sources of information - such as seismology, mineralogy, geomagnetism, geodesy, and, above all, physical principles - to derive a model of the core and, study it by running computer simulations. One NASA researcher is doing just that on NCCS computers. Physicist and applied mathematician Weijia Kuang, of the Space Geodesy Branch, and his collaborators at Goddard have what he calls the,"second - ever" working, usable, self-consistent, fully dynamic, three-dimensional geodynamic model (see "The Geodynamic Theory"). Kuang runs his model simulations on the supercomputers at the NCCS. He and Jeremy Bloxham, of Harvard University, developed the original version, written in Fortran 77, in 1996.
Ger, Rachel B; Mohamed, Abdallah S R; Awan, Musaddiq J; Ding, Yao; Li, Kimberly; Fave, Xenia J; Beers, Andrew L; Driscoll, Brandon; Elhalawani, Hesham; Hormuth, David A; Houdt, Petra J van; He, Renjie; Zhou, Shouhao; Mathieu, Kelsey B; Li, Heng; Coolens, Catherine; Chung, Caroline; Bankson, James A; Huang, Wei; Wang, Jihong; Sandulache, Vlad C; Lai, Stephen Y; Howell, Rebecca M; Stafford, R Jason; Yankeelov, Thomas E; Heide, Uulke A van der; Frank, Steven J; Barboriak, Daniel P; Hazle, John D; Court, Laurence E; Kalpathy-Cramer, Jayashree; Fuller, Clifton D
2017-09-11
Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) provides quantitative metrics (e.g. K(trans), ve) via pharmacokinetic models. We tested inter-algorithm variability in these quantitative metrics with 11 published DCE-MRI algorithms, all implementing Tofts-Kermode or extended Tofts pharmacokinetic models. Digital reference objects (DROs) with known K(trans) and ve values were used to assess performance at varying noise levels. Additionally, DCE-MRI data from 15 head and neck squamous cell carcinoma patients over 3 time-points during chemoradiotherapy were used to ascertain K(trans) and ve kinetic trends across algorithms. Algorithms performed well (less than 3% average error) when no noise was present in the DRO. With noise, 87% of K(trans) and 84% of ve algorithm-DRO combinations were generally in the correct order. Low Krippendorff's alpha values showed that algorithms could not consistently classify patients as above or below the median for a given algorithm at each time point or for differences in values between time points. A majority of the algorithms produced a significant Spearman correlation in ve of the primary gross tumor volume with time. Algorithmic differences in K(trans) and ve values over time indicate limitations in combining/comparing data from distinct DCE-MRI model implementations. Careful cross-algorithm quality-assurance must be utilized as DCE-MRI results may not be interpretable using differing software.
Free energy calculation of mechanically unstable but dynamically stabilized bcc titanium
NASA Astrophysics Data System (ADS)
Kadkhodaei, Sara; Hong, Qi-Jun; van de Walle, Axel
2017-02-01
The phase diagram of numerous materials of technological importance features high-symmetry high-temperature phases that exhibit phonon instabilities. Leading examples include shape-memory alloys, as well as ferroelectric, refractory, and structural materials. The thermodynamics of these phases have proven challenging to handle by atomistic computational thermodynamic techniques due to the occurrence of constant anharmonicity-driven hopping between local low-symmetry distortions, while maintaining a high-symmetry time-averaged structure. To compute the free energy in such phases, we propose to explore the system's potential-energy surface by discrete sampling of local minima by means of a lattice gas Monte Carlo approach and by continuous sampling by means of a lattice dynamics approach in the vicinity of each local minimum. Given the proximity of the local minima, it is necessary to carefully partition phase space by using a Voronoi tessellation to constrain the domain of integration of the partition function in order to avoid double counting artifacts and enable an accurate harmonic treatment near each local minima. We consider the bcc phase of titanium as a prototypical example to illustrate our approach.
Cárdenas, F; Thormann, M; Feliz, M; Caba, J M; Lloyd-Williams, P; Giralt, E
2001-06-29
Dehydrodidemnin B (DDB or aplidine), a potent antitumoral natural product currently in phase II clinical trials, exists as an approximately 1:1 mixture of two slowly interconverting conformations. These are sufficiently long-lived so as to allow their resolution by HPLC. NMR spectroscopy shows that this phenomenon is a consequence of restricted rotation about the Pyr-Pro(8) terminal amide bond of the molecule's side chain. The same technique also indicates that the overall three-dimensional structures of both the cis and trans isomers of DDB are similar despite the conformational change. Molecular dynamics simulations with different implicit and explicit solvent models show that the ensembles of three-dimensional structures produced are indeed similar for both the cis and trans isomers. These studies also show that hydrogen bonding patterns in both isomers are alike and that each one is stabilized by a hydrogen bond between the pyruvyl unit at the terminus of the molecule's side chain and the Thr(6) residue situated at the junction betwen the macrocycle and the molecule's side chain. Nevertheless, each conformational isomer forms this hydrogen bond using a different pyruvyl carbonyl group: CO(2) in the case of the cis isomer and CO(1) in the case of the trans isomer.
Knops, André; Viarouge, Arnaud; Dehaene, Stanislas
2009-05-01
When we add or subtract, do the corresponding quantities "move" along a mental number line? Does this internal movement lead to spatial biases? A new method was designed to investigate the psychophysics of approximate arithmetic. Addition and subtraction problems were presented either with sets of dots or with Arabic numerals, and subjects selected, from among seven choices, the most plausible result. In two experiments, the subjects selected larger numbers for addition than for subtraction problems, as if moving too far along the number line. This operational momentum effect was present in both notations and increased with the size of the outcome. Furthermore, we observed a new effect of spatial-numerical congruence, related to but distinct from the spatial numerical association of response codes effect: During nonsymbolic addition, the subjects preferentially selected numbers at the upper right location, whereas during subtraction, they were biased toward the upper left location. These findings suggest that approximate mental arithmetic involves dynamic shifts on a spatially organized mental representation of numbers. Supplemental materials for this study may be downloaded from app.psychonomic-journals.org/content/supplemental.
Denning, Elizabeth J.; Woolf, Thomas B.
2009-01-01
The growing dataset of K+ channel x-ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage-dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply Dynamic Importance Sampling (DIMS) to a set of homology models for the molecular conformations of K+ channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the PVP region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra-subunit motions to influence the cooperative behavior of all four subunits of the K+ channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter- S5-S6 subunit motions, and lastly the large-scale domain rearrangements. PMID:19950367
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V
2013-09-05
Micelle formation in surfactant solutions is a self-assembly process governed by complex interplay of solvent-mediated interactions between hydrophilic and hydrophobic groups, which are commonly called heads and tails. However, the head-tail repulsion is not the only factor affecting the micelle formation. For the first time, we present a systematic study of the effect of chain rigidity on critical micelle concentration and micelle size, which is performed with the dissipative particle dynamics simulation method. Rigidity of the coarse-grained surfactant molecule was controlled by the harmonic bonds set between the second-neighbor beads. Compared to flexible molecules with the nearest-neighbor bonds being the only type of bonded interactions, rigid molecules exhibited a lower critical micelle concentration and formed larger and better-defined micelles. By varying the strength of head-tail repulsion and the chain rigidity, we constructed two-dimensional diagrams presenting how the critical micelle concentration and aggregation number depend on these parameters. We found that the solutions of flexible and rigid molecules that exhibited approximately the same critical micelle concentration could differ substantially in the micelle size and shape depending on the chain rigidity. With the increase of surfactant concentration, primary micelles of more rigid molecules were found less keen to agglomeration and formation of nonspherical aggregates characteristic of flexible molecules.