Dynamic Buffer Capacity in Acid-Base Systems.

PubMed

Michałowska-Kaczmarczyk, Anna M; Michałowski, Tadeusz

The generalized concept of 'dynamic' buffer capacity β V 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.

First-principles calculations of lattice dynamics and thermal properties of polar solids

DOE PAGES

Wang, Yi; Shang, Shun -Li; Fang, Huazhi; ...

2016-05-13

Although the theory of lattice dynamics was established six decades ago, its accurate implementation for polar solids using the direct (or supercell, small displacement, frozen phonon) approach within the framework of density-function-theory-based first-principles calculations had been a challenge until recently. It arises from the fact that the vibration-induced polarization breaks the lattice periodicity, whereas periodic boundary conditions are required by typical first-principles calculations, leading to an artificial macroscopic electric field. In conclusion, the article reviews a mixed-space approach to treating the interactions between lattice vibration and polarization, its applications to accurately predicting the phonon and associated thermal properties, and itsmore » implementations in a number of existing phonon codes.« less

Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface.

PubMed

Li, Hongzhi; Yang, Wei

2007-03-21

An approach is developed in the replica exchange framework to enhance conformational sampling for the quantum mechanical (QM) potential based molecular dynamics simulations. Importantly, with our enhanced sampling treatment, a decent convergence for electronic structure self-consistent-field calculation is robustly guaranteed, which is made possible in our replica exchange design by avoiding direct structure exchanges between the QM-related replicas and the activated (scaled by low scaling parameters or treated with high "effective temperatures") molecular mechanical (MM) replicas. Although the present approach represents one of the early efforts in the enhanced sampling developments specifically for quantum mechanical potentials, the QM-based simulations treated with the present technique can possess the similar sampling efficiency to the MM based simulations treated with the Hamiltonian replica exchange method (HREM). In the present paper, by combining this sampling method with one of our recent developments (the dual-topology alchemical HREM approach), we also introduce a method for the sampling enhanced QM-based free energy calculations.

Investigation of oxygen self-diffusion in PuO 2 by combining molecular dynamics with thermodynamic calculations

DOE PAGES

Saltas, V.; Chroneos, A.; Cooper, Michael William D.; ...

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 anymore » 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.« less

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.

Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings.

PubMed

Cole, Casey A; Mukhopadhyay, Rishi; Omar, Hanin; Hennig, Mirko; Valafar, Homayoun

2016-04-12

Residual dipolar couplings (RDCs) acquired by nuclear magnetic resonance (NMR) spectroscopy are an indispensable source of information in investigation of molecular structures and dynamics. Here, we present a comprehensive strategy for structure calculation and reconstruction of discrete-state dynamics from RDC data that is based on the singular value decomposition (SVD) method of order tensor estimation. In addition to structure determination, we provide a mechanism of producing an ensemble of conformations for the dynamical regions of a protein from RDC data. The developed methodology has been tested on simulated RDC data with ±1 Hz of error from an 83 residue α protein (PDB ID 1A1Z ) and a 213 residue α/β protein DGCR8 (PDB ID 2YT4 ). In nearly all instances, our method reproduced the structure of the protein including the conformational ensemble to within less than 2 Å. On the basis of our investigations, arc motions with more than 30° of rotation are identified as internal dynamics and are reconstructed with sufficient accuracy. Furthermore, states with relative occupancies above 20% are consistently recognized and reconstructed successfully. Arc motions with a magnitude of 15° or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions within the context of ±1 Hz of error.

Structural, Electronic and Dynamical Properties of Curium Monopnictides: Density Functional Calculations

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.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

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.

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.

Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance

NASA Astrophysics Data System (ADS)

Wilson, Michael A.; Nguyen, Thuy Hien; Pohorille, Andrew

2014-12-01

Establishing the relation between the structures and functions of protein ion channels, which are protein assemblies that facilitate transmembrane ion transport through water-filled pores, is at the forefront of biological and medical sciences. A reliable way to determine whether our understanding of this relation is satisfactory is to reproduce the measured ionic conductance over a broad range of applied voltages. This can be done in molecular dynamics simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive we develop a markedly more efficient alternative in which molecular dynamics is combined with an electrodiffusion equation. This alternative approach applies if steady-state ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. The theory refers only to line densities of ions in the channel and, therefore, avoids ambiguities related to determining the surface area of the channel near its endpoints or other procedures connecting the line and bulk ion densities. We apply the theory to a simple, model system based on the trichotoxin channel. We test the assumptions of the electrodiffusion equation, and determine the precision and consistency of the calculated conductance. We demonstrate that it is possible to calculate current/voltage dependence and accurately reconstruct the underlying (equilibrium) free energy profile, all from molecular dynamics simulations at a single voltage. The approach developed here applies to other channels that satisfy the conditions of the electrodiffusion equation.

Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules

NASA Astrophysics Data System (ADS)

Huang, Jiayu; Liu, Shu; Zhang, Dong H.; Krems, Roman V.

2018-04-01

Because the de Broglie wavelength of ultracold molecules is very large, the cross sections for collisions of molecules at ultracold temperatures are always computed by the time-independent quantum scattering approach. Here, we report the first accurate time-dependent wave packet dynamics calculation for reactive scattering of ultracold molecules. Wave packet dynamics calculations can be applied to molecular systems with more dimensions and provide real-time information on the process of bond rearrangement and/or energy exchange in molecular collisions. Our work thus makes possible the extension of rigorous quantum calculations of ultracold reaction properties to polyatomic molecules and adds a new powerful tool for the study of ultracold chemistry.

Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules.

PubMed

Huang, Jiayu; Liu, Shu; Zhang, Dong H; Krems, Roman V

2018-04-06

Because the de Broglie wavelength of ultracold molecules is very large, the cross sections for collisions of molecules at ultracold temperatures are always computed by the time-independent quantum scattering approach. Here, we report the first accurate time-dependent wave packet dynamics calculation for reactive scattering of ultracold molecules. Wave packet dynamics calculations can be applied to molecular systems with more dimensions and provide real-time information on the process of bond rearrangement and/or energy exchange in molecular collisions. Our work thus makes possible the extension of rigorous quantum calculations of ultracold reaction properties to polyatomic molecules and adds a new powerful tool for the study of ultracold chemistry.

Calculation of Hugoniot properties for shocked nitromethane based on the improved Tsien's EOS

NASA Astrophysics Data System (ADS)

Zhao, Bo; Cui, Ji-Ping; Fan, Jing

2010-06-01

We have calculated the Hugoniot properties of shocked nitromethane based on the improved Tsien’s equation of state (EOS) that optimized by “exact” numerical molecular dynamic data at high temperatures and pressures. Comparison of the calculated results of the improved Tsien’s EOS with the existed experimental data and the direct simulations show that the behavior of the improved Tsien’s EOS is very good in many aspects. Because of its simple analytical form, the improved Tsien’s EOS can be prospectively used to study the condensed explosive detonation coupling with chemical reaction.

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.

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

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

Calculation and Analysis of Dynamic Characteristics of Multilink Permanent Magnetic Actuator in Vacuum Circuit Breaker

NASA Astrophysics Data System (ADS)

Liu, Yingyi; Yuan, Haiwen; Zhang, Qingjie; Chen, Degui; Yuan, Haibin

The dynamic characteristics are the key issues in the optimum design of a permanent magnetic actuator (PMA). A new approach to forecast the dynamic characteristics of the multilink PMA is proposed. By carrying out further developments of ADAMS and ANSOFT, a mathematic calculation model describing the coupling of mechanical movement, electric circuit and magnetic field considering eddy current effect, is constructed. With this model, the dynamic characteristics of the multilink PMA are calculated and compared with the experimental results. Factors that affect the opening time of the multilink PMA are analyzed with the model as well. The method is capable of providing a reference for the design of the PMA.

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.

Dynamic phase transitions and dynamic phase diagrams of the Blume-Emery-Griffiths model in an oscillating field: the effective-field theory based on the Glauber-type stochastic dynamics

NASA Astrophysics Data System (ADS)

Ertaş, Mehmet; Keskin, Mustafa

2015-06-01

Using the effective-field theory based on the Glauber-type stochastic dynamics (DEFT), we investigate dynamic phase transitions and dynamic phase diagrams of the Blume-Emery-Griffiths model under an oscillating magnetic field. We presented the dynamic phase diagrams in (T/J, h0/J), (D/J, T/J) and (K/J, T/J) planes, where T, h0, D, K and z are the temperature, magnetic field amplitude, crystal-field interaction, biquadratic interaction and the coordination number. The dynamic phase diagrams exhibit several ordered phases, coexistence phase regions and special critical points, as well as re-entrant behavior depending on interaction parameters. We also compare and discuss the results with the results of the same system within the mean-field theory based on the Glauber-type stochastic dynamics and find that some of the dynamic first-order phase lines and special dynamic critical points disappeared in the DEFT calculation.

Nonadiabatic nuclear dynamics of the ammonia cation studied by surface hopping classical trajectory calculations

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

Belyaev, Andrey K., E-mail: belyaev@herzen.spb.ru; Domcke, Wolfgang, E-mail: wolfgang.domcke@ch.tum.de; Lasser, Caroline, E-mail: classer@ma.tum.de

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 formore » 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.« less

An efficient quasi-3D particle tracking-based approach for transport through fractures with application to dynamic dispersion calculation.

PubMed

Wang, Lichun; Cardenas, M Bayani

2015-08-01

The quantitative study of transport through fractured media has continued for many decades, but has often been constrained by observational and computational challenges. Here, we developed an efficient quasi-3D random walk particle tracking (RWPT) algorithm to simulate solute transport through natural fractures based on a 2D flow field generated from the modified local cubic law (MLCL). As a reference, we also modeled the actual breakthrough curves (BTCs) through direct simulations with the 3D advection-diffusion equation (ADE) and Navier-Stokes equations. The RWPT algorithm along with the MLCL accurately reproduced the actual BTCs calculated with the 3D ADE. The BTCs exhibited non-Fickian behavior, including early arrival and long tails. Using the spatial information of particle trajectories, we further analyzed the dynamic dispersion process through moment analysis. From this, asymptotic time scales were determined for solute dispersion to distinguish non-Fickian from Fickian regimes. This analysis illustrates the advantage and benefit of using an efficient combination of flow modeling and RWPT. Copyright © 2015 Elsevier B.V. All rights reserved.

DynaMed Plus®: An Evidence-Based Clinical Reference Resource.

PubMed

Charbonneau, Deborah H; James, LaTeesa N

2018-01-01

DynaMed Plus ® from EBSCO Health is an evidence-based tool that health professionals can use to inform clinical care. DynaMed Plus content undergoes a review process, and the evidence is synthesized in detailed topic overviews. A unique three-level rating scale is used to assess the quality of available evidence. Topic overviews summarize current evidence and provide recommendations to support health providers at the point-of-care. Additionally, DynaMed Plus content can be accessed via a desktop computer or mobile platforms. Given this, DynaMed Plus can be a time-saving resource for health providers. Overall, DynaMed Plus provides evidence summaries using an easy-to-read bullet format, and the resource incorporates images, clinical calculators, patient handouts, and practice guidelines in one place.

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.

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines.

PubMed

Chen, Haochuan; Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng

2018-06-18

Extended adaptive biasing force (eABF), a collective variable (CV)-based importance-sampling algorithm, has proven to be very robust and efficient compared with the original ABF algorithm. Its implementation in Colvars, a software addition to molecular dynamics (MD) engines, is, however, currently limited to NAMD and LAMMPS. To broaden the scope of eABF and its variants, like its generalized form (egABF), and make them available to other MD engines, e.g., GROMACS, AMBER, CP2K, and openMM, we present a PLUMED-based implementation, called extended-Lagrangian free energy calculation (ELF). This implementation can be used as a stand-alone gradient estimator for other CV-based sampling algorithms, such as temperature-accelerated MD (TAMD) and extended-Lagrangian metadynamics (MtD). ELF provides the end user with a convenient framework to help select the best-suited importance-sampling algorithm for a given application without any commitment to a particular MD engine.

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...

Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

Raman Optical Activity Spectra from Density Functional Perturbation Theory and Density-Functional-Theory-Based Molecular Dynamics.

PubMed

Luber, Sandra

2017-03-14

We describe the calculation of Raman optical activity (ROA) tensors from density functional perturbation theory, which has been implemented into the CP2K software package. Using the mixed Gaussian and plane waves method, ROA spectra are evaluated in the double-harmonic approximation. Moreover, an approach for the calculation of ROA spectra by means of density functional theory-based molecular dynamics is derived and used to obtain an ROA spectrum via time correlation functions, which paves the way for the calculation of ROA spectra taking into account anharmonicities and dynamic effects at ambient conditions.

Lift calculations based on accepted wake models for animal flight are inconsistent and sensitive to vortex dynamics.

PubMed

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

Diffusion and viscosity of liquid tin: Green-Kubo relationship-based calculations from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mouas, Mohamed; Gasser, Jean-Georges; Hellal, Slimane; Grosdidier, Benoît; Makradi, Ahmed; Belouettar, Salim

2012-03-01

Molecular dynamics (MD) simulations of liquid tin between its melting point and 1600 °C have been performed in order to interpret and discuss the ionic structure. The interactions between ions are described by a new accurate pair potential built within the pseudopotential formalism and the linear response theory. The calculated structure factor that reflects the main information on the local atomic order in liquids is compared to diffraction measurements. Having some confidence in the ability of this pair potential to give a good representation of the atomic structure, we then focused our attention on the investigation of the atomic transport properties through the MD computations of the velocity autocorrelation function and stress autocorrelation function. Using the Green-Kubo formula (for the first time to our knowledge for liquid tin) we determine the macroscopic transport properties from the corresponding microscopic time autocorrelation functions. The selfdiffusion coefficient and the shear viscosity as functions of temperature are found to be in good agreement with the experimental data.

A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels.

PubMed

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.

Quasiparticle properties of DNA bases from GW calculations in a Wannier basis

NASA Astrophysics Data System (ADS)

Qian, Xiaofeng; Marzari, Nicola; Umari, Paolo

2009-03-01

The quasiparticle GW-Wannier (GWW) approach [1] has been recently developed to overcome the size limitations of conventional planewave GW calculations. By taking advantage of the localization properties of the maximally-localized Wannier functions and choosing a small set of polarization basis we reduce the number of Bloch wavefunctions products required for the evaluation of dynamical polarizabilities, and in turn greatly reduce memory requirements and computational efficiency. We apply GWW to study quasiparticle properties of different DNA bases and base-pairs, and solvation effects on the energy gap, demonstrating in the process the key advantages of this approach. [1] P. Umari,G. Stenuit, and S. Baroni, cond-mat/0811.1453

Dynamic Obstacle Avoidance for Unmanned Underwater Vehicles Based on an Improved Velocity Obstacle Method

PubMed Central

Zhang, Wei; Wei, Shilin; Teng, Yanbin; Zhang, Jianku; Wang, Xiufang; Yan, Zheping

2017-01-01

In view of a dynamic obstacle environment with motion uncertainty, we present a dynamic collision avoidance method based on the collision risk assessment and improved velocity obstacle method. First, through the fusion optimization of forward-looking sonar data, the redundancy of the data is reduced and the position, size and velocity information of the obstacles are obtained, which can provide an accurate decision-making basis for next-step collision avoidance. Second, according to minimum meeting time and the minimum distance between the obstacle and unmanned underwater vehicle (UUV), this paper establishes the collision risk assessment model, and screens key obstacles to avoid collision. Finally, the optimization objective function is established based on the improved velocity obstacle method, and a UUV motion characteristic is used to calculate the reachable velocity sets. The optimal collision speed of UUV is searched in velocity space. The corresponding heading and speed commands are calculated, and outputted to the motion control module. The above is the complete dynamic obstacle avoidance process. The simulation results show that the proposed method can obtain a better collision avoidance effect in the dynamic environment, and has good adaptability to the unknown dynamic environment. PMID:29186878

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Optimizing legacy molecular dynamics software with directive-based offload

DOE PAGES

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

Conformational analysis of a condensed macrocyclic β-lactam by NMR and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Keserű, György M.; Vásárhelyi, Helga; Makara, Gergely

1994-09-01

The conformation of the new macrocyclic β-lactam ( 1) was investigated by NMR and molecular dynamics (MD) calculations. Restraints obtained from NOESY and ROESY experiments were introduced into MD simulations which led to well-defined conformations. The preference for the calculated minimum energy conformation was confirmed by the analysis of vicinal coupling constants. Experimental coupling constants agreed with computed values.

Calculation of Individual Tree Water Use in a Bornean Tropical Rain Forest Using Individual-Based Dynamic Vegetation Model SEIB-DGVM

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.

Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations.

PubMed

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.

Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

NASA Astrophysics Data System (ADS)

Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

2018-04-01

Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

Calculating Nozzle Side Loads using Acceleration Measurements of Test-Based Models

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; Ruf, Joe

2007-01-01

As part of a NASA/MSFC research program to evaluate the effect of different nozzle contours on the well-known but poorly characterized "side load" phenomena, we attempt to back out the net force on a sub-scale nozzle during cold-flow testing using acceleration measurements. Because modeling the test facility dynamics is problematic, new techniques for creating a "pseudo-model" of the facility and nozzle directly from modal test results are applied. Extensive verification procedures were undertaken, resulting in a loading scale factor necessary for agreement between test and model based frequency response functions. Side loads are then obtained by applying a wide-band random load onto the system model, obtaining nozzle response PSD's, and iterating both the amplitude and frequency of the input until a good comparison of the response with the measured response PSD for a specific time point is obtained. The final calculated loading can be used to compare different nozzle profiles for assessment during rocket engine nozzle development and as a basis for accurate design of the nozzle and engine structure to withstand these loads. The techniques applied within this procedure have extensive applicability to timely and accurate characterization of all test fixtures used for modal test.A viewgraph presentation on a model-test based pseudo-model used to calculate side loads on rocket engine nozzles is included. The topics include: 1) Side Loads in Rocket Nozzles; 2) Present Side Loads Research at NASA/MSFC; 3) Structural Dynamic Model Generation; 4) Pseudo-Model Generation; 5) Implementation; 6) Calibration of Pseudo-Model Response; 7) Pseudo-Model Response Verification; 8) Inverse Force Determination; 9) Results; and 10) Recent Work.

A Dynamic Attitude Measurement System Based on LINS

PubMed Central

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

Calculational investigation of impact cratering dynamics - Material motions during the crater growth period

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

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.

Molecular dynamics simulation of polymer electrolytes based on poly(ethylene oxide) and ionic liquids. II. Dynamical properties.

PubMed

Costa, Luciano T; Ribeiro, Mauro C C

2007-10-28

Dynamical properties of polymer electrolytes based on poly(ethylene oxide) (PEO) and ionic liquids of 1-alkyl-3-methylimidazolium cations were calculated by molecular dynamics simulations with previously proposed models [L. T. Costa and M. C. Ribeiro, J. Chem. Phys. 124, 184902 (2006)]. The effect of changing the ionic liquid concentration, temperature, and the 1-alkyl-chain lengths, [1,3-dimethylimidazolium]PF(6) and [1-butyl-3-methylimidazolium]PF(6) ([dmim]PF(6) and [bmim]PF(6)), was investigated. Cation diffusion coefficient is higher than those of anion and oxygen atoms of PEO chains. Ionic mobility in PEO[bmim]PF(6) is higher than in PEO[dmim]PF(6), so that the ionic conductivity kappa of the former is approximately ten times larger than the latter. The ratio between kappa and its estimate from the Nernst-Einstein equation kappa/kappa(NE), which is inversely proportional to the strength of ion pairs, is higher in ionic liquid polymer electrolytes than in polymer electrolytes based on inorganic salts with Li(+) cations. Calculated time correlation functions corroborate previous evidence from the analysis of equilibrium structure that the ion pairs in ionic liquid polymer electrolytes are relatively weak. Structural relaxation at distinct spatial scales is revealed by the calculation of the intermediate scattering function at different wavevectors. These data are reproduced with stretched exponential functions, so that temperature and wavevector dependences of best fit parameters can be compared with corresponding results for polymer electrolytes containing simpler ions.

Carbonic anhydrase inhibition of Schiff base derivative of imino-methyl-naphthalen-2-ol: Synthesis, structure elucidation, molecular docking, dynamic simulation and density functional theory calculations

NASA Astrophysics Data System (ADS)

Abbas, Saghir; Nasir, Hafiza Huma; Zaib, Sumera; Ali, Saqib; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz; Iqbal, Jamshed

2018-03-01

In the present study, we have designed and synthesized a Schiff base derivative 3 and characterized by FT-IR, 1H and 13C NMR spectroscopy. Single crystal X-ray diffraction and NMR studies were also performed. The synthetic compound was screened for its inhibitory potential against carbonic anhydrase II. The experimental results were validated by molecular docking and dynamic simulations of compound 3 in the active pocket of enzyme. Important binding interactions with the key residues in the active site of the carbonic anhydrase enzyme were revealed. Moreover, supramolecular assembly of the title compound was analyzed by density functional theory (DFT) calculations. These studies rendered a more clear understanding for the demonstration of novel molecular mechanism involved in CA II inhibition by the synthesized compound.

Large scale exact quantum dynamics calculations: Ten thousand quantum states of acetonitrile

NASA Astrophysics Data System (ADS)

Halverson, Thomas; Poirier, Bill

2015-03-01

'Exact' quantum dynamics (EQD) calculations of the vibrational spectrum of acetonitrile (CH3CN) are performed, using two different methods: (1) phase-space-truncated momentum-symmetrized Gaussian basis and (2) correlated truncated harmonic oscillator basis. In both cases, a simple classical phase space picture is used to optimize the selection of individual basis functions-leading to drastic reductions in basis size, in comparison with existing methods. Massive parallelization is also employed. Together, these tools-implemented into a single, easy-to-use computer code-enable a calculation of tens of thousands of vibrational states of CH3CN to an accuracy of 0.001-10 cm-1.

Regulation of the Dynamic Live Load Factor for Calculation of Bridge Structures on High-Speed Railway Mainlines

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.

Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

PubMed

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

Methods for Calculating Frequency of Maintenance of Complex Information Security System Based on Dynamics of Its Reliability

NASA Astrophysics Data System (ADS)

Varlataya, S. K.; Evdokimov, V. E.; Urzov, A. Y.

2017-11-01

This article describes a process of calculating a certain complex information security system (CISS) reliability using the example of the technospheric security management model as well as ability to determine the frequency of its maintenance using the system reliability parameter which allows one to assess man-made risks and to forecast natural and man-made emergencies. The relevance of this article is explained by the fact the CISS reliability is closely related to information security (IS) risks. Since reliability (or resiliency) is a probabilistic characteristic of the system showing the possibility of its failure (and as a consequence - threats to the protected information assets emergence), it is seen as a component of the overall IS risk in the system. As it is known, there is a certain acceptable level of IS risk assigned by experts for a particular information system; in case of reliability being a risk-forming factor maintaining an acceptable risk level should be carried out by the routine analysis of the condition of CISS and its elements and their timely service. The article presents a reliability parameter calculation for the CISS with a mixed type of element connection, a formula of the dynamics of such system reliability is written. The chart of CISS reliability change is a S-shaped curve which can be divided into 3 periods: almost invariable high level of reliability, uniform reliability reduction, almost invariable low level of reliability. Setting the minimum acceptable level of reliability, the graph (or formula) can be used to determine the period of time during which the system would meet requirements. Ideally, this period should not be longer than the first period of the graph. Thus, the proposed method of calculating the CISS maintenance frequency helps to solve a voluminous and critical task of the information assets risk management.

A highly accurate dynamic contact angle algorithm for drops on inclined surface based on ellipse-fitting.

PubMed

Xu, Z N; Wang, S Y

2015-02-01

To improve the accuracy in the calculation of dynamic contact angle for drops on the inclined surface, a significant number of numerical drop profiles on the inclined surface with different inclination angles, drop volumes, and contact angles are generated based on the finite difference method, a least-squares ellipse-fitting algorithm is used to calculate the dynamic contact angle. The influences of the above three factors are systematically investigated. The results reveal that the dynamic contact angle errors, including the errors of the left and right contact angles, evaluated by the ellipse-fitting algorithm tend to increase with inclination angle/drop volume/contact angle. If the drop volume and the solid substrate are fixed, the errors of the left and right contact angles increase with inclination angle. After performing a tremendous amount of computation, the critical dimensionless drop volumes corresponding to the critical contact angle error are obtained. Based on the values of the critical volumes, a highly accurate dynamic contact angle algorithm is proposed and fully validated. Within nearly the whole hydrophobicity range, it can decrease the dynamic contact angle error in the inclined plane method to less than a certain value even for different types of liquids.

Reference voltage calculation method based on zero-sequence component optimisation for a regional compensation DVR

NASA Astrophysics Data System (ADS)

Jian, Le; Cao, Wang; Jintao, Yang; Yinge, Wang

2018-04-01

This paper describes the design of a dynamic voltage restorer (DVR) that can simultaneously protect several sensitive loads from voltage sags in a region of an MV distribution network. A novel reference voltage calculation method based on zero-sequence voltage optimisation is proposed for this DVR to optimise cost-effectiveness in compensation of voltage sags with different characteristics in an ungrounded neutral system. Based on a detailed analysis of the characteristics of voltage sags caused by different types of faults and the effect of the wiring mode of the transformer on these characteristics, the optimisation target of the reference voltage calculation is presented with several constraints. The reference voltages under all types of voltage sags are calculated by optimising the zero-sequence component, which can reduce the degree of swell in the phase-to-ground voltage after compensation to the maximum extent and can improve the symmetry degree of the output voltages of the DVR, thereby effectively increasing the compensation ability. The validity and effectiveness of the proposed method are verified by simulation and experimental results.

A Component-Based FPGA Design Framework for Neuronal Ion Channel Dynamics Simulations

PubMed Central

Mak, Terrence S. T.; Rachmuth, Guy; Lam, Kai-Pui; Poon, Chi-Sang

2008-01-01

Neuron-machine interfaces such as dynamic clamp and brain-implantable neuroprosthetic devices require real-time simulations of neuronal ion channel dynamics. Field Programmable Gate Array (FPGA) has emerged as a high-speed digital platform ideal for such application-specific computations. We propose an efficient and flexible component-based FPGA design framework for neuronal ion channel dynamics simulations, which overcomes certain limitations of the recently proposed memory-based approach. A parallel processing strategy is used to minimize computational delay, and a hardware-efficient factoring approach for calculating exponential and division functions in neuronal ion channel models is used to conserve resource consumption. Performances of the various FPGA design approaches are compared theoretically and experimentally in corresponding implementations of the AMPA and NMDA synaptic ion channel models. Our results suggest that the component-based design framework provides a more memory economic solution as well as more efficient logic utilization for large word lengths, whereas the memory-based approach may be suitable for time-critical applications where a higher throughput rate is desired. PMID:17190033

Pressure calculation in hybrid particle-field simulations

NASA Astrophysics Data System (ADS)

Milano, Giuseppe; Kawakatsu, Toshihiro

2010-12-01

In the framework of a recently developed scheme for a hybrid particle-field simulation techniques where self-consistent field (SCF) theory and particle models (molecular dynamics) are combined [J. Chem. Phys. 130, 214106 (2009)], we developed a general formulation for the calculation of instantaneous pressure and stress tensor. The expressions have been derived from statistical mechanical definition of the pressure starting from the expression for the free energy functional in the SCF theory. An implementation of the derived formulation suitable for hybrid particle-field molecular dynamics-self-consistent field simulations is described. A series of test simulations on model systems are reported comparing the calculated pressure with those obtained from standard molecular dynamics simulations based on pair potentials.

Calculation of left ventricular volumes and ejection fraction from dynamic cardiac-gated 15O-water PET/CT: 5D-PET.

PubMed

Nordström, Jonny; Kero, Tanja; Harms, Hendrik Johannes; Widström, Charles; Flachskampf, Frank A; Sörensen, Jens; Lubberink, Mark

2017-11-14

Quantitative measurement of myocardial blood flow (MBF) is of increasing interest in the clinical assessment of patients with suspected coronary artery disease (CAD). 15 O-water positron emission tomography (PET) is considered the gold standard for non-invasive MBF measurements. However, calculation of left ventricular (LV) volumes and ejection fraction (EF) is not possible from standard 15 O-water uptake images. The purpose of the present work was to investigate the possibility of calculating LV volumes and LVEF from cardiac-gated parametric blood volume (V B ) 15 O-water images and from first pass (FP) images. Sixteen patients with mitral or aortic regurgitation underwent an eight-gate dynamic cardiac-gated 15 O-water PET/CT scan and cardiac MRI. V B and FP images were generated for each gate. Calculations of end-systolic volume (ESV), end-diastolic volume (EDV), stroke volume (SV) and LVEF were performed with automatic segmentation of V B and FP images, using commercially available software. LV volumes and LVEF were calculated with surface-, count-, and volume-based methods, and the results were compared with gold standard MRI. Using V B images, high correlations between PET and MRI ESV (r = 0.89, p < 0.001), EDV (r = 0.85, p < 0.001), SV (r = 0.74, p = 0.006) and LVEF (r = 0.72, p = 0.008) were found for the volume-based method. Correlations for FP images were slightly, but not significantly, lower than those for V B images when compared to MRI. Surface- and count-based methods showed no significant difference compared with the volume-based correlations with MRI. The volume-based method showed the best agreement with MRI with no significant difference on average for EDV and LVEF but with an overestimation of values for ESV (14%, p = 0.005) and SV (18%, p = 0.004) when using V B images. Using FP images, none of the parameters showed a significant difference from MRI. Inter-operator repeatability was excellent for all

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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.

Structure, thermodynamic and transport properties of imidazolium-based bis(trifluoromethylsulfonyl)imide ionic liquids from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Androulaki, Eleni; Vergadou, Niki; Ramos, Javier; Economou, Ioannis G.

2012-06-01

Molecular dynamics (MD) simulations have been performed in order to investigate the properties of [C n mim+][Tf2N-] (n = 4, 8, 12) ionic liquids (ILs) in a wide temperature range (298.15-498.15 K) and at atmospheric pressure (1 bar). A previously developed methodology for the calculation of the charge distribution that incorporates ab initio quantum mechanical calculations based on density functional theory (DFT) was used to calculate the partial charges for the classical molecular simulations. The wide range of time scales that characterize the segmental dynamics of these ILs, especially at low temperatures, required very long MD simulations, on the order of several tens of nanoseconds, to calculate the thermodynamic (density, thermal expansion, isothermal compressibility), structural (radial distribution functions between the centers of mass of ions and between individual sites, radial-angular distribution functions) and dynamic (relaxation times of the reorientation of the bonds and the torsion angles, self-diffusion coefficients, shear viscosity) properties. The influence of the temperature and the cation's alkyl chain length on the above-mentioned properties was thoroughly investigated. The calculated thermodynamic (primary and derivative) and structural properties are in good agreement with the experimental data, while the extremely sluggish dynamics of the ILs under study renders the calculation of their transport properties a very complicated and challenging task, especially at low temperatures.

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

PubMed

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.

PubMed

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 ≤20 k B T) 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 (∼2-3 k B T). Finally, reweighting using cumulant expansion to the second order is able to recover the most accurate free energy profiles within statistical errors of ∼ k B T, 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/.

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

PubMed Central

2015-01-01

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/. PMID:25061441

Data base to compare calculations and observations

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

Tichler, J.L.

Meteorological and climatological data bases were compared with known tritium release points and diffusion calculations to determine if calculated concentrations could replace measure concentrations at the monitoring stations. Daily tritium concentrations were monitored at 8 stations and 16 possible receptors. Automated data retrieval strategies are listed. (PSB)

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations.

PubMed

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 SiC x O 6/5 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.

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.

A Calculation Method of Electric Distance and Subarea Division Application Based on Transmission Impedance

NASA Astrophysics Data System (ADS)

Fang, G. J.; Bao, H.

2017-12-01

The widely used method of calculating electric distances is sensitivity method. The sensitivity matrix is the result of linearization and based on the hypothesis that the active power and reactive power are decoupled, so it is inaccurate. In addition, it calculates the ratio of two partial derivatives as the relationship of two dependent variables, so there is no physical meaning. This paper presents a new method for calculating electrical distance, namely transmission impedance method. It forms power supply paths based on power flow tracing, then establishes generalized branches to calculate transmission impedances. In this paper, the target of power flow tracing is S instead of Q. Q itself has no direction and the grid delivers complex power so that S contains more electrical information than Q. By describing the power transmission relationship of the branch and drawing block diagrams in both forward and reverse directions, it can be found that the numerators of feedback parts of two block diagrams are all the transmission impedances. To ensure the distance is scalar, the absolute value of transmission impedance is defined as electrical distance. Dividing network according to the electric distances and comparing with the results of sensitivity method, it proves that the transmission impedance method can adapt to the dynamic change of system better and reach a reasonable subarea division scheme.

Implementing a GPU-based numerical algorithm for modelling dynamics of a high-speed train

NASA Astrophysics Data System (ADS)

Sytov, E. S.; Bratus, A. S.; Yurchenko, D.

2018-04-01

This paper discusses the initiative of implementing a GPU-based numerical algorithm for studying various phenomena associated with dynamics of a high-speed railway transport. The proposed numerical algorithm for calculating a critical speed of the bogie is based on the first Lyapunov number. Numerical algorithm is validated by analytical results, derived for a simple model. A dynamic model of a carriage connected to a new dual-wheelset flexible bogie is studied for linear and dry friction damping. Numerical results obtained by CPU, MPU and GPU approaches are compared and appropriateness of these methods is discussed.

Interactions between Nanoparticles and Polymer Brushes: Molecular Dynamics Simulations and Self-consistent Field Theory Calculations

NASA Astrophysics Data System (ADS)

Cheng, Shengfeng; Wen, Chengyuan; Egorov, Sergei

2015-03-01

Molecular dynamics simulations and self-consistent field theory calculations are employed to study the interactions between a nanoparticle and a polymer brush at various densities of chains grafted to a plane. Simulations with both implicit and explicit solvent are performed. In either case the nanoparticle is loaded to the brush at a constant velocity. Then a series of simulations are performed to compute the force exerted on the nanoparticle that is fixed at various distances from the grafting plane. The potential of mean force is calculated and compared to the prediction based on a self-consistent field theory. Our simulations show that the explicit solvent leads to effects that are not captured in simulations with implicit solvent, indicating the importance of including explicit solvent in molecular simulations of such systems. Our results also demonstrate an interesting correlation between the force on the nanoparticle and the density profile of the brush. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Tesla K40 GPU used for this research.

First principles calculations of thermal conductivity with out of equilibrium molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Puligheddu, Marcello; Gygi, Francois; Galli, Giulia

The prediction of the thermal properties of solids and liquids is central to numerous problems in condensed matter physics and materials science, including the study of thermal management of opto-electronic and energy conversion devices. We present a method to compute the thermal conductivity of solids by performing ab initio molecular dynamics at non equilibrium conditions. Our formulation is based on a generalization of the approach to equilibrium technique, using sinusoidal temperature gradients, and it only requires calculations of first principles trajectories and atomic forces. We discuss results and computational requirements for a representative, simple oxide, MgO, and compare with experiments and data obtained with classical potentials. This work was supported by MICCoM as part of the Computational Materials Science Program funded by the U.S. Department of Energy (DOE), Office of Science , Basic Energy Sciences (BES), Materials Sciences and Engineering Division under Grant DOE/BES 5J-30.

Calculation of broadband time histories of ground motion, Part II: Kinematic and dynamic modeling using theoretical Green's functions and comparison with the 1994 northridge earthquake

USGS Publications Warehouse

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.

Nascent energy distribution of the Criegee intermediate CH2OO from direct dynamics calculations of primary ozonide dissociation.

PubMed

Pfeifle, Mark; Ma, Yong-Tao; Jasper, Ahren W; Harding, Lawrence B; Hase, William L; Klippenstein, Stephen J

2018-05-07

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c-C 2 H 4 O 3 , the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H 2 COO) and formaldehyde (H 2 CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on new high-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 ± 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (∼30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum.

Nascent energy distribution of the Criegee intermediate CH2OO from direct dynamics calculations of primary ozonide dissociation

NASA Astrophysics Data System (ADS)

Pfeifle, Mark; Ma, Yong-Tao; Jasper, Ahren W.; Harding, Lawrence B.; Hase, William L.; Klippenstein, Stephen J.

2018-05-01

Ozonolysis produces chemically activated carbonyl oxides (Criegee intermediates, CIs) that are either stabilized or decompose directly. This branching has an important impact on atmospheric chemistry. Prior theoretical studies have employed statistical models for energy partitioning to the CI arising from dissociation of the initially formed primary ozonide (POZ). Here, we used direct dynamics simulations to explore this partitioning for decomposition of c-C2H4O3, the POZ in ethylene ozonolysis. A priori estimates for the overall stabilization probability were then obtained by coupling the direct dynamics results with master equation simulations. Trajectories were initiated at the concerted cycloreversion transition state, as well as the second transition state of a stepwise dissociation pathway, both leading to a CI (H2COO) and formaldehyde (H2CO). The resulting CI energy distributions were incorporated in master equation simulations of CI decomposition to obtain channel-specific stabilized CI (sCI) yields. Master equation simulations of POZ formation and decomposition, based on new high-level electronic structure calculations, were used to predict yields for the different POZ decomposition channels. A non-negligible contribution of stepwise POZ dissociation was found, and new mechanistic aspects of this pathway were elucidated. By combining the trajectory-based channel-specific sCI yields with the channel branching fractions, an overall sCI yield of (48 ± 5)% was obtained. Non-statistical energy release was shown to measurably affect sCI formation, with statistical models predicting significantly lower overall sCI yields (˜30%). Within the range of experimental literature values (35%-54%), our trajectory-based calculations favor those clustered at the upper end of the spectrum.

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

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. 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 H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

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 H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

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 H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Semantic Edge Based Disparity Estimation Using Adaptive Dynamic Programming for Binocular Sensors

PubMed Central

Zhu, Dongchen; Li, Jiamao; Wang, Xianshun; Peng, Jingquan; Shi, Wenjun; Zhang, Xiaolin

2018-01-01

Disparity calculation is crucial for binocular sensor ranging. The disparity estimation based on edges is an important branch in the research of sparse stereo matching and plays an important role in visual navigation. In this paper, we propose a robust sparse stereo matching method based on the semantic edges. Some simple matching costs are used first, and then a novel adaptive dynamic programming algorithm is proposed to obtain optimal solutions. This algorithm makes use of the disparity or semantic consistency constraint between the stereo images to adaptively search parameters, which can improve the robustness of our method. The proposed method is compared quantitatively and qualitatively with the traditional dynamic programming method, some dense stereo matching methods, and the advanced edge-based method respectively. Experiments show that our method can provide superior performance on the above comparison. PMID:29614028

Semantic Edge Based Disparity Estimation Using Adaptive Dynamic Programming for Binocular Sensors.

PubMed

Zhu, Dongchen; Li, Jiamao; Wang, Xianshun; Peng, Jingquan; Shi, Wenjun; Zhang, Xiaolin

2018-04-03

Disparity calculation is crucial for binocular sensor ranging. The disparity estimation based on edges is an important branch in the research of sparse stereo matching and plays an important role in visual navigation. In this paper, we propose a robust sparse stereo matching method based on the semantic edges. Some simple matching costs are used first, and then a novel adaptive dynamic programming algorithm is proposed to obtain optimal solutions. This algorithm makes use of the disparity or semantic consistency constraint between the stereo images to adaptively search parameters, which can improve the robustness of our method. The proposed method is compared quantitatively and qualitatively with the traditional dynamic programming method, some dense stereo matching methods, and the advanced edge-based method respectively. Experiments show that our method can provide superior performance on the above comparison.

Environment-based pin-power reconstruction method for homogeneous core calculations

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

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 MOXmore » 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)« less

Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog

PubMed Central

Spring-Connell, Alexander M.; Evich, Marina G.; Debelak, Harald; Seela, Frank; Germann, Markus W.

2016-01-01

A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2′deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. PMID:27566150

Dynamic Magnification Factor in a Box-Shape Steel Girder

NASA Astrophysics Data System (ADS)

Rahbar-Ranji, A.

2014-01-01

The dynamic effect of moving loads on structures is treated as a dynamic magnification factor when resonant is not imminent. Studies have shown that the calculated magnification factors from field measurements could be higher than the values specified in design codes. It is the main aim of present paper to investigate the applicability and accuracy of a rule-based expression for calculation of dynamic magnification factor for lifting appliances used in marine industry. A steel box shape girder of a crane is considered and transient dynamic analysis using computer code ANSYS is implemented. Dynamic magnification factor is calculated for different loading conditions and compared with rule-based equation. The effects of lifting speeds, acceleration, damping ratio and position of cargo are examined. It is found that rule-based expression underestimate dynamic magnification factor.

Free energy calculations of short peptide chains using Adaptively Biased Molecular Dynamics

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-10-01

We performed a computational study of monomer peptides composed of methionine, alanine, leucine, glutamate, lysine (all amino acids with a helix-forming propensities); and proline, glycine tyrosine, serine, arginine (which all have poor helix-forming propensities). The free energy landscapes as a function of the handedness and radius of gyration have been calculated using the recently introduced Adaptively Biased Molecular Dynamics (ABMD) method, combined with replica exchange, multiple walkers, and post-processing Umbrella Correction (UC). Minima that correspond to some of the left- and right-handed 310-, α- and π-helixes were identified by secondary structure assignment methods (DSSP, Stride). The resulting free energy surface (FES) and the subsequent steered molecular dynamics (SMD) simulation results are in agreement with the empirical evidence of preferred secondary structures for the peptide chains considered.

Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations

PubMed Central

Peter, Christine; Hummer, Gerhard

2005-01-01

Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic membrane pores by molecular dynamics simulation of model membranes formed of hexagonally packed carbon nanotubes. We focus on the factors that determine the energetics of ion translocation through such nonpolar nanopores and compare the resulting free-energy barriers for pores with different diameters corresponding to the gating regions in closed and open forms of potassium channels. Our model system also allows us to compare the results from molecular dynamics simulations directly to continuum electrostatics calculations. Both simulations and continuum calculations show that subnanometer wide pores pose a huge free-energy barrier for ions, but a small increase in the pore diameter to ∼1 nm nearly eliminates that barrier. We also find that in those wider channels the ion mobility is comparable to that in the bulk phase. By calculating local electrostatic potentials, we show that the long range Coulomb interactions of ions are strongly screened in the wide water-filled channels. Whereas continuum calculations capture the overall energetics reasonably well, the local water structure, which is not accounted for in this model, leads to interesting effects such as the preference of hydrated ions to move along the pore wall rather than through the center of the pore. PMID:16006629

Nonlinear dynamics based digital logic and circuits.

PubMed

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.

Dynamics and Structure of Point Defects in Forsterite: ab initio calculations

NASA Astrophysics Data System (ADS)

Churakov, S.; Khisina, N.; Urusov, V.; Wirth, R.

2001-12-01

OH-bearing fluid inclusions in Fo92 forsterite samples from peridotite nodule 9206 (Udachnaja kimberlite pipe)[1] were documented recently based on TEM and IR studies. The Fourier transform of diffraction pattern from the inclusions exhibited a pattern, which is interpreted as ordered planar (2H)xMg defects. In this study the structure and dynamics of protons associated with Mg(1), Mg(2) vacancies and interstitial polyhedrons ordered in a (100) plane corresponding to double unite cell periodicity of the forsterite lattice has been investigated by ab initio quantum mechanic calculations. Static structure optimizations and ab-initio molecular dynamics (MD) simulations have been performed using the CPMD density functional code[2]. The calculations were accomplished with the BLYP-functional utilizing the generalized gradient approximation. Non-local Goedecker-type pseudopotentials[3] have been applied to account for core electrons. Valence electron orbitals were approximated by plane wave expansion up to 70 Ry energy cutoff. The energy of static structures was sampled on 2x2x2 Monkhorst-Pack mesh[4]. During the structure relaxation parameters of an orthorhombic 2x1x2 supercell contaning 116 atoms corresponding to Mg28Si16O64H8 hydrous olivine was fixed at experimental values of a=9.524Å b=10.225Å and c=11.988Å relative to the Pbnm space group. Series of NVT-MD calculations were performed at 1000 K on 2x1x1 supercell with 58 atoms using four chain Nose thermostat. Randomly disturbed optimized structures were used as initial configuration for MD runs. The 1ps system equilibration is followed by trajectory production over 5 ps interval. A point energy sampling was applied in all MD calculations. A series of geometry optimizations, starting with various initial position of protons in Mg(1), Mg(2) and interstitial sites were carried out to obtain a structure with the lowest lattice energy. It was found that structures with protons completely located within the M1

Theoretical calculations and experimental verification for the pumping effect caused by the dynamic micro-tapered angle

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.

SU-E-T-100: Designing a QA Tool for Enhance Dynamic Wedges Based On Dynalog Files

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

Yousuf, A; Hussain, A

2014-06-01

Purpose: A robust quality assurance (QA) program for computer controlled enhanced dynamic wedge (EDW) has been designed and tested. Calculations to perform such QA test is based upon the EDW dynamic log files generated during dose delivery. Methods: Varian record and verify system generates dynamic log (dynalog) files during dynamic dose delivery. The system generated dynalog files contain information such as date and time of treatment, energy, monitor units, wedge orientation, and type of treatment. It also contains the expected calculated segmented treatment tables (STT) and the actual delivered STT for the treatment delivery as a verification record. These filesmore » can be used to assess the integrity and precision of the treatment plan delivery. The plans were delivered with a 6 MV beam from a Varian linear accelerator. For available EDW angles (10°, 15°, 20°, 25°, 30°, 45°, and 60°) Varian STT values were used to manually calculate monitor units for each segment. It can also be used to calculate the EDW factors. Independent verification of fractional MUs per segment was performed against those generated from dynalog files. The EDW factors used to calculate MUs in TPS were dosimetrically verified in solid water phantom with semiflex chamber on central axis. Results: EDW factors were generated from the STT provided by Varian and verified against practical measurements. The measurements were in agreement of the order of 1 % to the calculated EDW data. Variation between the MUs per segment obtained from dynalog files and those manually calculated was found to be less than 2%. Conclusion: An efficient and easy tool to perform routine QA procedure of EDW is suggested. The method can be easily implemented in any institution without a need for expensive QA equipment. An error of the order of ≥2% can be easily detected.« less

SU-E-T-465: Dose Calculation Method for Dynamic Tumor Tracking Using a Gimbal-Mounted Linac

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

Sugimoto, S; Inoue, T; Kurokawa, C

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 gimbalmore » 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.« less

Self-diffusion and conductivity in an ultracold strongly coupled plasma: Calculation by the method of molecular dynamics

NASA Astrophysics Data System (ADS)

Zelener, B. B.; Zelener, B. V.; Manykin, E. A.; Bronin, S. Ya; Bobrov, A. A.; Khikhlukha, D. R.

2018-01-01

We present results of calculations by the method of molecular dynamics of self-diffusion and conductivity of electron and ion components of ultracold plasma in a comparison with available theoretical and experimental data. For the ion self-diffusion coefficient, good agreement was obtained with experiments on ultracold plasma. The results of the calculation of self-diffusion also agree well with other calculations performed for the same values of the coupling parameter, but at high temperatures. The difference in the results of the conductivity calculations on the basis of the current autocorrelation function and on the basis of the diffusion coefficient is discussed.

Dynamic motion analysis of dart throwers motion visualized through computerized tomography and calculation of the axis of rotation.

PubMed

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.

Molecular dynamics calculation of rotational diffusion coefficient of a carbon nanotube in fluid.

PubMed

Cao, Bing-Yang; Dong, Ruo-Yu

2014-01-21

Rotational diffusion processes are correlated with nanoparticle visualization and manipulation techniques, widely used in nanocomposites, nanofluids, bioscience, and so on. However, a systematical methodology of deriving this diffusivity is still lacking. In the current work, three molecular dynamics (MD) schemes, including equilibrium (Green-Kubo formula and Einstein relation) and nonequilibrium (Einstein-Smoluchowski relation) methods, are developed to calculate the rotational diffusion coefficient, taking a single rigid carbon nanotube in fluid argon as a case. We can conclude that the three methods produce same results on the basis of plenty of data with variation of the calculation parameters (tube length, diameter, fluid temperature, density, and viscosity), indicative of the validity and accuracy of the MD simulations. However, these results have a non-negligible deviation from the theoretical predictions of Tirado et al. [J. Chem. Phys. 81, 2047 (1984)], which may come from several unrevealed factors of the theory. The three MD methods proposed in this paper can also be applied to other situations of calculating rotational diffusion coefficient.

CL-20/DNB co-crystal based PBX with PEG: molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Gao, Pei; Xiao, Ji Jun; Zhao, Feng; Xiao, He Ming

2016-12-01

Molecular dynamics simulation was carried out for CL-20/DNB co-crystal based PBX (polymer-bonded explosive) blended with polymer PEG (polyethylene glycol). In this paper, the miscibility of the PBX models is investigated through the calculated binding energy. Pair correlation function (PCF) analysis is applied to study the interaction of the interface structures in the PBX models. The mechanical properties of PBXs are also discussed to understand the change of the mechanical properties after adding the polymer. Moreover, the calculated diffusion coefficients of the interfacial explosive molecules are used to discuss the dispersal ability of CL-20 and DNB molecules in the interface layer.

129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: essential role of the relativity, dynamics, and explicit solvent.

PubMed

Standara, Stanislav; Kulhánek, Petr; Marek, Radek; Straka, Michal

2013-08-15

The isotropic (129)Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C60 dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the (129)Xe NMR CS. The (129)Xe shielding constant was obtained by averaging the (129)Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C60 system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit-Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C60 system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated (129)Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental (129)Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of (129)Xe NMR parameters in different Xe atom guest-host systems. Copyright © 2013 Wiley Periodicals, Inc.

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package.

PubMed

Kaus, Joseph W; Pierce, Levi T; Walker, Ross C; McCammont, J Andrew

2013-09-10

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.

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

PubMed Central

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

Predicting First Graders' Development of Calculation versus Word-Problem Performance: The Role of Dynamic Assessment

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…

Gas flow calculation method of a ramjet engine

NASA Astrophysics Data System (ADS)

Kostyushin, Kirill; Kagenov, Anuar; Eremin, Ivan; Zhiltsov, Konstantin; Shuvarikov, Vladimir

2017-11-01

At the present study calculation methodology of gas dynamics equations in ramjet engine is presented. The algorithm is based on Godunov`s scheme. For realization of calculation algorithm, the system of data storage is offered, the system does not depend on mesh topology, and it allows using the computational meshes with arbitrary number of cell faces. The algorithm of building a block-structured grid is given. Calculation algorithm in the software package "FlashFlow" is implemented. Software package is verified on the calculations of simple configurations of air intakes and scramjet models.

Summary of methods for calculating dynamic lateral stability and response and for estimating aerodynamic stability derivatives

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.

MEAM interatomic force calculation subroutine for LAMMPS

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

Stukowski, A.

2010-10-25

Interatomic force and energy calculation subroutine tobe used with the molecular dynamics simulation code LAMMPS (Ref a.). The code evaluates the total energy and atomic forces (energy gradient) according to cubic spine-based variant (Ref b.) of the Modified Embedded Atom Method (MEAM).

Long Dynamics Simulations of Proteins Using Atomistic Force Fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties

PubMed Central

Li, Xianfeng; Hassan, Sergio A.; Mehler, Ernest L.

2006-01-01

Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP–ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding Cα root mean square deviations (RMSD) of about 1.0 and 0.8 Å respectively along the entire simulation time, compared to 0.8 Å for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a Cα RMSD of ≈ 1.4 Å, while the PAR22/LD trajectory became unstable

Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation.

PubMed

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. Graphical Abstract ᅟ.

Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

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.

The algorithm of numerical calculation of constraints reactions in a dynamic system of transport machine

NASA Astrophysics Data System (ADS)

Akhtulov, A. L.

2018-01-01

The questions of construction and practical application of the automation system for the design of components and aggregates for the construction of transport vehicles are considered, taking into account their dynamic characteristics. Based on the results of the studies, a unified method for determining the reactions of bonds of a complex spatial structure is proposed. The technique, based on the method of substructures, allows us to determine the values of the transfer functions taking into account the reactions of the bonds. After the carried out researches it is necessary to note, that such approach gives the most satisfactory results and can be used for calculations of complex mechanical systems of machines and units of different purposes. The directions of increasing the degree of validity of technical decisions are shown, especially in the early stages of design, when the cost of errors is high, with careful thorough working out of all the elements of the design, which is really feasible only on the basis of automation of design and technological work.

Method of calculating gas dynamics and heat transfer in single stage refrigeration units

NASA Technical Reports Server (NTRS)

Zhitomirskiy, I. S.; Popolskiy, A. B.

1974-01-01

A generalized mathematical model of gas-dynamic and heat transfer processes in single-stage regenerative installations operating in Stirling, MacMahon, Gifford-MacMahon, and pulsating tube cycles is proposed. A numerical method os solving initial equations on a digital computer is given. This makes it possible to calculate the change in the thermodynamic parameters in the working cycle in different machine components, as well as the dependence of cold productivity on the temperature level in the steady regime.

Effect of temperature on compact layer of Pt electrode in PEMFCs by first-principles molecular dynamics calculations

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.

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.

Microscopic calculations of dynamics and N/Z equilibration in peripheral collisions below the Fermi energy.

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).

Experimental Verification of Buffet Calculation Procedure Using Unsteady PSP

NASA Technical Reports Server (NTRS)

Panda, Jayanta

2016-01-01

Typically a limited number of dynamic pressure sensors are employed to determine the unsteady aerodynamic forces on large, slender aerospace structures. The estimated forces are known to be very sensitive to the number of the dynamic pressure sensors and the details of the integration scheme. This report describes a robust calculation procedure, based on frequency-specific correlation lengths, that is found to produce good estimation of fluctuating forces from a few dynamic pressure sensors. The validation test was conducted on a flat panel, placed on the floor of a wind tunnel, and was subjected to vortex shedding from a rectangular bluff-body. The panel was coated with fast response Pressure Sensitive Paint (PSP), which allowed time-resolved measurements of unsteady pressure fluctuations on a dense grid of spatial points. The first part of the report describes the detail procedure used to analyze the high-speed, PSP camera images. The procedure includes steps to reduce contamination by electronic shot noise, correction for spatial non-uniformities, and lamp brightness variation, and finally conversion of fluctuating light intensity to fluctuating pressure. The latter involved applying calibration constants from a few dynamic pressure sensors placed at selective points on the plate. Excellent comparison in the spectra, coherence and phase, calculated via PSP and dynamic pressure sensors validated the PSP processing steps. The second part of the report describes the buffet validation process, for which the first step was to use pressure histories from all PSP points to determine the "true" force fluctuations. In the next step only a selected number of pixels were chosen as "virtual sensors" and a correlation-length based buffet calculation procedure was applied to determine "modeled" force fluctuations. By progressively decreasing the number of virtual sensors it was observed that the present calculation procedure was able to make a close estimate of the "true

CoMoDo: identifying dynamic protein domains based on covariances of motion.

PubMed

Wieninger, Silke A; Ullmann, G Matthias

2015-06-09

Most large proteins are built of several domains, compact units which enable functional protein motions. Different domain assignment approaches exist, which mostly rely on concepts of stability, folding, and evolution. We describe the automatic assignment method CoMoDo, which identifies domains based on protein dynamics. Covariances of atomic fluctuations, here calculated by an Elastic Network Model, are used to group residues into domains of different hierarchical levels. The so-called dynamic domains facilitate the study of functional protein motions involved in biological processes like ligand binding and signal transduction. By applying CoMoDo to a large number of proteins, we demonstrate that dynamic domains exhibit features absent in the commonly assigned structural domains, which can deliver insight into the interactions between domains and between subunits of multimeric proteins. CoMoDo is distributed as free open source software at www.bisb.uni-bayreuth.de/CoMoDo.html .

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.

PubMed

Miao, Yinglong; Feher, Victoria A; McCammon, J Andrew

2015-08-11

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding, and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low-energy states of the biomolecules and characterize the protein-folding and ligand-binding pathways quantitatively.

One-dimensional thermal evolution calculation based on a mixing length theory: Application to Saturnian icy satellites

NASA Astrophysics Data System (ADS)

Kamata, S.

2017-12-01

Solid-state thermal convection plays a major role in the thermal evolution of solid planetary bodies. Solving the equation system for thermal evolution considering convection requires 2-D or 3-D modeling, resulting in large calculation costs. A 1-D calculation scheme based on mixing length theory (MLT) requires a much lower calculation cost and is suitable for parameter studies. A major concern for the MLT scheme is its accuracy due to a lack of detailed comparisons with higher dimensional schemes. In this study, I quantify its accuracy via comparisons of thermal profiles obtained by 1-D MLT and 3-D numerical schemes. To improve the accuracy, I propose a new definition of the mixing length (l), which is a parameter controlling the efficiency of heat transportation due to convection. Adopting this new definition of l, I investigate the thermal evolution of Dione and Enceladus under a wide variety of parameter conditions. Calculation results indicate that each satellite requires several tens of GW of heat to possess a 30-km-thick global subsurface ocean. Dynamical tides may be able to account for such an amount of heat, though their ices need to be highly viscous.

Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations.

PubMed

Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala

2018-06-01

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 (∆G binding  = -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

Estimation of static parameters based on dynamical and physical properties in limestone rocks

NASA Astrophysics Data System (ADS)

Ghafoori, Mohammad; Rastegarnia, Ahmad; Lashkaripour, Gholam Reza

2018-01-01

Due to the importance of uniaxial compressive strength (UCS), static Young's modulus (ES) and shear wave velocity, it is always worth to predict these parameters from empirical relations that suggested for other formations with same lithology. This paper studies the physical, mechanical and dynamical properties of limestone rocks using the results of laboratory tests which carried out on 60 the Jahrum and the Asmari formations core specimens. The core specimens were obtained from the Bazoft dam site, hydroelectric supply and double-curvature arch dam in Iran. The Dynamic Young's modulus (Ed) and dynamic Poisson ratio were calculated using the existing relations. Some empirical relations were presented to estimate uniaxial compressive strength, as well as static Young's modulus and shear wave velocity (Vs). Results showed the static parameters such as uniaxial compressive strength and static Young's modulus represented low correlation with water absorption. It is also found that the uniaxial compressive strength and static Young's modulus had high correlation with compressional wave velocity and dynamic Young's modulus, respectively. Dynamic Young's modulus was 5 times larger than static Young's modulus. Further, the dynamic Poisson ratio was 1.3 times larger than static Poisson ratio. The relationship between shear wave velocity (Vs) and compressional wave velocity (Vp) was power and positive with high correlation coefficient. Prediction of uniaxial compressive strength based on Vp was better than that based on Vs . Generally, both UCS and static Young's modulus (ES) had good correlation with Ed.

Linked-List-Based Multibody Dynamics (MBDyn) Engine

NASA Technical Reports Server (NTRS)

MacLean, John; Brain, Thomas; Wuiocho, Leslie; Huynh, An; Ghosh, Tushar

2012-01-01

This new release of MBDyn is a software engine that calculates the dynamics states of kinematic, rigid, or flexible multibody systems. An MBDyn multibody system may consist of multiple groups of articulated chains, trees, or closed-loop topologies. Transient topologies are handled through conservation of energy and momentum. The solution for rigid-body systems is exact, and several configurable levels of nonlinear term fidelity are available for flexible dynamics systems. The algorithms have been optimized for efficiency and can be used for both non-real-time (NRT) and real-time (RT) simulations. Interfaces are currently compatible with NASA's Trick Simulation Environment. This new release represents a significant advance in capability and ease of use. The two most significant new additions are an application programming interface (API) that clarifies and simplifies use of MBDyn, and a link-list infrastructure that allows a single MBDyn instance to propagate an arbitrary number of interacting groups of multibody top ologies. MBDyn calculates state and state derivative vectors for integration using an external integration routine. A Trickcompatible interface is provided for initialization, data logging, integration, and input/output.

Calculating lattice thermal conductivity: a synopsis

NASA Astrophysics Data System (ADS)

Fugallo, Giorgia; Colombo, Luciano

2018-04-01

We provide a tutorial introduction to the modern theoretical and computational schemes available to calculate the lattice thermal conductivity in a crystalline dielectric material. While some important topics in thermal transport will not be covered (including thermal boundary resistance, electronic thermal conduction, and thermal rectification), we aim at: (i) framing the calculation of thermal conductivity within the general non-equilibrium thermodynamics theory of transport coefficients, (ii) presenting the microscopic theory of thermal conduction based on the phonon picture and the Boltzmann transport equation, and (iii) outlining the molecular dynamics schemes to calculate heat transport. A comparative and critical addressing of the merits and drawbacks of each approach will be discussed as well.

Auxiliary-field-based trial wave functions in quantum Monte Carlo calculations

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

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

Calculation of phase diagrams for the FeCl2, PbCl2, and ZnCl2 binary systems by using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Seo, Won-Gap; Matsuura, Hiroyuki; Tsukihashi, Fumitaka

2006-04-01

Recently, molecular dynamics (MD) simulation has been widely employed as a very useful method for the calculation of various physicochemical properties in the molten slags and fluxes. In this study, MD simulation has been applied to calculate the structural, transport, and thermodynamic properties for the FeCl2, PbCl2, and ZnCl2 systems using the Born—Mayer—Huggins type pairwise potential with partial ionic charges. The interatomic potential parameters were determined by fitting the physicochemical properties of iron chloride, lead chloride, and zinc chloride systems with experimentally measured results. The calculated structural, transport, and thermodynamic properties of pure FeCl2, PbCl2, and ZnCl2 showed the same tendency with observed results. Especially, the calculated structural properties of molten ZnCl2 and FeCl2 show the possibility of formation of polymeric network structures based on the ionic complexes of ZnCl{4/2-}, ZnCl{3/-}, FeCl{4/2-}, and FeCl{3/-}, and these calculations have successfully reproduced the measured results. The enthalpy, entropy, and Gibbs energy of mixing for the PbCl2-ZnCl2, FeCl2-PbCl2, and FeCl2-ZnCl2 systems were calculated based on the thermodynamic and structural parameters of each binary system obtained from MD simulation. The phase diagrams of the PbCl2-ZnCl2, FeCl2-PbCl2, and FeCl2-ZnCl2 systems estimated by using the calculated Gibbs energy of mixing reproduced the experimentally measured ones reasonably well.

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

PubMed Central

2016-01-01

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding, and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low-energy states of the biomolecules and characterize the protein-folding and ligand-binding pathways quantitatively. PMID:26300708

Approach of the Molten Salt Chemistry for Aluminium Production: High Temperature NMR Measurements, Molecular Dynamics and DFT Calculations

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.

DNA-Based Dynamic Reaction Networks.

PubMed

Fu, Ting; Lyu, Yifan; Liu, Hui; Peng, Ruizi; Zhang, Xiaobing; Ye, Mao; Tan, Weihong

2018-05-21

Deriving from logical and mechanical interactions between DNA strands and complexes, DNA-based artificial reaction networks (RNs) are attractive for their high programmability, as well as cascading and fan-out ability, which are similar to the basic principles of electronic logic gates. Arising from the dream of creating novel computing mechanisms, researchers have placed high hopes on the development of DNA-based dynamic RNs and have strived to establish the basic theories and operative strategies of these networks. This review starts by looking back on the evolution of DNA dynamic RNs; in particular' the most significant applications in biochemistry occurring in recent years. Finally, we discuss the perspectives of DNA dynamic RNs and give a possible direction for the development of DNA circuits. Copyright © 2018. Published by Elsevier Ltd.

Proline-based chiral stationary phases: a molecular dynamics study of the interfacial structure.

PubMed

Ashtari, M; Cann, N M

2011-09-16

Proline chains have generated considerable interest as a possible basis for new selectors in chiral chromatography. In this article, we employ molecular dynamics simulations to examine the interfacial structure of two diproline chiral selectors, one with a terminal trimethylacetyl group and one with a terminal t-butyl carbamate group. The solvents consist of a relatively apolar n-hexane/2-propanol and a polar water/methanol mixture. We begin with electronic structure calculations for the two chiral selectors to assess the energetics of conformational changes, particularly along the backbone where the amide bonds can alternate between cis and trans conformations. Force fields have been developed for the two selectors, based on these ab initio calculations. Molecular dynamics simulations of the selective interfaces are performed to examine the preferred backbone conformations, as a function of end-group and solvent. The full chiral surface includes the diproline selectors, trimethylsilyl end-caps, and silanol groups. Connection is made with selectivity measurements on these interfaces, where significant differences are observed between these two very similar selectors. Copyright © 2011 Elsevier B.V. All rights reserved.

Rotorcraft Dynamics 1984

NASA Technical Reports Server (NTRS)

1985-01-01

In the conference proceedings are 24 presented papers, their discussions, and material given in two panels. The presented papers address the general areas of the dynamics of rotorcraft or helicopters. Specific topics include the stability of rotors in hover and forward flight, the stability of coupled rotor-fuselage systems in hover, the loads on a rotor in forward flight including new developments in rotor loads calculations, and the calculation of rotorcraft vibration and means for its control or suppression. Material in the first panel deals with the successful application of dynamics technology to engineering development of flight vehicles. Material in the second panel is concerned with large data bases in the area of rotorocraft dynamics and how they are developed, managed, and used.

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

Effects of vacancies on atom displacement threshold energy calculations through Molecular Dynamics Methods in BaTiO3

NASA Astrophysics Data System (ADS)

Gonzalez Lazo, Eduardo; Cruz Inclán, Carlos M.; Rodríguez Rodríguez, Arturo; Guzmán Martínez, Fernando; Abreu Alfonso, Yamiel; Piñera Hernández, Ibrahin; Leyva Fabelo, Antonio

2017-09-01

A primary approach for evaluating the influence of point defects like vacancies on atom displacement threshold energies values Td in BaTiO3 is attempted. For this purpose Molecular Dynamics Methods, MD, were applied based on previous Td calculations on an ideal tetragonal crystalline structure. It is an important issue in achieving more realistic simulations of radiation damage effects in BaTiO3 ceramic materials. It also involves irradiated samples under severe radiation damage effects due to high fluency expositions. In addition to the above mentioned atom displacement events supported by a single primary knock-on atom, PKA, a new mechanism was introduced. It corresponds to the simultaneous excitation of two close primary knock-on atoms in BaTiO3, which might take place under a high flux irradiation. Therefore, two different BaTiO3 Td MD calculation trials were accomplished. Firstly, single PKA excitations in a defective BaTiO3 tetragonal crystalline structure, consisting in a 2×2×2 BaTiO3 perovskite like super cell, were considered. It contains vacancies on Ba and O atomic positions under the requirements of electrical charge balance. Alternatively, double PKA excitations in a perfect BaTiO3 tetragonal unit cell were also simulated. On this basis, the corresponding primary knock-on atom (PKA) defect formation probability functions were calculated at principal crystal directions, and compared with the previous one we calculated and reported at an ideal BaTiO3 tetrahedral crystal structure. As a general result, a diminution of Td values arises in present calculations in comparison with those calculated for single PKA excitation in an ideal BaTiO3 crystal structure.

DYGABCD: A program for calculating linear A, B, C, and D matrices from a nonlinear dynamic engine simulation

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.

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.

Calculations of kaonic nuclei based on chiral meson-baryon amplitudes

NASA Astrophysics Data System (ADS)

Gazda, Daniel; Mareš, Jiří

2013-09-01

In-medium KbarN scattering amplitudes developed within a chirally motivated coupled-channel model are used to construct K- nuclear potentials for calculations of K- nuclear quasi-bound states. Self-consistent evaluations yield K- potential depths -Re VK(ρ0) of order 100 MeV. Dynamical polarization effects and two-nucleon KbarNN→YN absorption modes are discussed. The widths ΓK of allK- nuclear quasi-bound states are comparable or even larger than the corresponding binding energies BK, exceeding considerably the energy level spacing.

Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory.

PubMed

Qi, Shuanhu; Schmid, Friederike

2017-11-08

We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense such that particles can switch their level of resolution on the fly. The switching of resolution is controlled by a tuning function which can be chosen at will according to the geometry of the system. As an application, the hybrid scheme is used to study the kinetics of interfacial broadening of a polymer blend, and is validated by comparing the results to the predictions from pure Brownian dynamics and pure local dynamics calculations.

Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations.

PubMed

Chen, Jianzhong; Yang, Maoyou; Hu, Guodong; Shi, Shuhua; Yi, Changhong; Zhang, Qinggang

2009-10-01

The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with molecular dynamics (MD) simulations were used to investigate the functional role of protonation in human immunodeficiency virus type 1 (HIV-1) protease complexed with the inhibitor BEA369. Our results demonstrate that protonation of two aspartic acids (Asp25/Asp25') has a strong influence on the dynamics behavior of the complex, the binding free energy of BEA369, and inhibitor-residue interactions. Relative binding free energies calculated using the MM-PBSA method show that protonation of Asp25 results in the strongest binding of BEA369 to HIV-1 protease. Inhibitor-residue interactions computed by the theory of free energy decomposition also indicate that protonation of Asp25 has the most favorable effect on binding of BEA369. In addition, hydrogen-bond analysis based on the trajectories of the MD simulations shows that protonation of Asp25 strongly influences the water-mediated link of a conserved water molecule, Wat301. We expect that the results of this study will contribute significantly to binding calculations for BEA369, and to the design of high affinity inhibitors.

Adaptations in Electronic Structure Calculations in Heterogeneous Environments

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

Talamudupula, Sai

Modern quantum chemistry deals with electronic structure calculations of unprecedented complexity and accuracy. They demand full power of high-performance computing and must be in tune with the given architecture for superior e ciency. To make such applications resourceaware, it is desirable to enable their static and dynamic adaptations using some external software (middleware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application. The present work investigates scienti c application interlinking with middleware based on the example of the computational chemistry package GAMESS and middleware NICAN. The existing synchronous model ismore » limited by the possible delays due to the middleware processing time under the sustainable runtime system conditions. Proposed asynchronous and hybrid models aim at overcoming this limitation. When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting statically and dynamically its fragment scheduling policy based on the computing platform conditions. Signi cant execution time and throughput gains have been obtained due to such static adaptations when the compute nodes have very di erent core counts. Dynamic adaptations are based on the main memory availability at run time. NICAN prompts FMO to postpone scheduling certain fragments, if there is not enough memory for their immediate execution. Hence, FMO may be able to complete the calculations whereas without such adaptations it aborts.« less

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.

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Multi-attribute Regret-Based Dynamic Pricing

NASA Astrophysics Data System (ADS)

Jumadinova, Janyl; Dasgupta, Prithviraj

In this paper, we consider the problem of dynamic pricing by a set of competing sellers in an information economy where buyers differentiate products along multiple attributes, and buyer preferences can change temporally. Previous research in this area has either focused on dynamic pricing along a limited number of (e.g. binary) attributes, or, assumes that each seller has access to private information such as preference distribution of buyers, and profit/price information of other sellers. However, in real information markets, private information about buyers and sellers cannot be assumed to be available a priori. Moreover, due to the competition between sellers, each seller faces a tradeoff between accuracy and rapidity of the pricing mechanism. In this paper, we describe a multi-attribute dynamic pricing algorithm based on minimax regret that can be used by a seller's agent called a pricebot, to maximize the seller's utility. Our simulation results show that the minimax regret based dynamic pricing algorithm performs significantly better than other algorithms for rapidly and dynamically tracking consumer attributes without using any private information from either buyers or sellers.

Quantum Tunneling in Testosterone 6β-Hydroxylation by Cytochrome P450: Reaction Dynamics Calculations Employing Multiconfiguration Molecular-Mechanical Potential Energy Surfaces

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.

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.

The effects of calculator-based laboratories on standardized test scores

NASA Astrophysics Data System (ADS)

Stevens, Charlotte Bethany Rains

Nationwide, the goal of providing a productive science and math education to our youth in today's educational institutions is centering itself around the technology being utilized in these classrooms. In this age of digital technology, educational software and calculator-based laboratories (CBL) have become significant devices in the teaching of science and math for many states across the United States. Among the technology, the Texas Instruments graphing calculator and Vernier Labpro interface, are among some of the calculator-based laboratories becoming increasingly popular among middle and high school science and math teachers in many school districts across this country. In Tennessee, however, it is reported that this type of technology is not regularly utilized at the student level in most high school science classrooms, especially in the area of Physical Science (Vernier, 2006). This research explored the effect of calculator based laboratory instruction on standardized test scores. The purpose of this study was to determine the effect of traditional teaching methods versus graphing calculator teaching methods on the state mandated End-of-Course (EOC) Physical Science exam based on ability, gender, and ethnicity. The sample included 187 total tenth and eleventh grade physical science students, 101 of which belonged to a control group and 87 of which belonged to the experimental group. Physical Science End-of-Course scores obtained from the Tennessee Department of Education during the spring of 2005 and the spring of 2006 were used to examine the hypotheses. The findings of this research study suggested the type of teaching method, traditional or calculator based, did not have an effect on standardized test scores. However, the students' ability level, as demonstrated on the End-of-Course test, had a significant effect on End-of-Course test scores. This study focused on a limited population of high school physical science students in the middle Tennessee

Dynamic current susceptibility as a probe of Majorana bound states in nanowire-based Josephson junctions

NASA Astrophysics Data System (ADS)

Trif, Mircea; Dmytruk, Olesia; Bouchiat, Hélène; Aguado, Ramón; Simon, Pascal

2018-02-01

We theoretically study a Josephson junction based on a semiconducting nanowire subject to a time-dependent flux bias. We establish a general density-matrix approach for the dynamical response of the Majorana junction and calculate the resulting flux-dependent susceptibility using both microscopic and effective low-energy descriptions for the nanowire. We find that the diagonal component of the susceptibility, associated with the dynamics of the Majorana state populations, dominates over the standard Kubo contribution for a wide range of experimentally relevant parameters. The diagonal term, explored, in this Rapid Communication, in the context of Majorana physics, allows probing accurately the presence of Majorana bound states in the junction.

A program for calculation of intrapulmonary shunts, blood-gas and acid-base values with a programmable calculator.

PubMed

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.

Electronic Structure, Mechanical and Dynamical Stability of Hexagonal Subcarbides M2C (M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt): Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Suetin, D. V.; Shein, I. R.

2018-02-01

Ab initio calculations were used to study the properties of a series of hexagonal (Fe2N-like) subcarbides M2C, where M = Tc, Ru, Rh, Pd, Re, Os, Ir, and Pt, and to calculate their equilibrium structural parameters, electronic properties, phase stability, elastic constants, compression modulus, shear modulus, Young's modulus, compressibility, Pugh's indicator, Poisson ratio, elastic anisotropy indices, and also hardness, Debye temperature, sound velocity, and low-temperature heat capacity. It is found based on these results that all the subcarbides are mechanically stable; however, their formation energies E form are positive with respect to a mixture of d-metal and graphite. In addition, the calculation of the phonon spectra of these subcarbides shows the existence of negative modes, which indicates their dynamical instability. Thus, a successful synthesis of these subcarbides at normal conditions is highly improbable.

GPAW - massively parallel electronic structure calculations with Python-based software.

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

Enkovaara, J.; Romero, N.; Shende, S.

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 thismore » 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.« less

Formaldehyde roaming dynamics: Comparison of quasi-classical trajectory calculations and experiments.

PubMed

Houston, Paul L; Wang, Xiaohong; Ghosh, Aryya; Bowman, Joel M; Quinn, Mitchell S; Kable, Scott H

2017-07-07

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 + H 2 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 H 2 products of the formaldehyde dissociation. The experimental and trajectory data offer unprecedented detail about the correlations between internal states of the CO and H 2 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 2 1 4 3 band, (a) the speed distributions for individual vibrational/rotational states of the CO products, providing information about the correlated internal energy distributions of the H 2 product, and (b) the rotational and vibrational distributions for the CO and H 2 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.

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

NASA Astrophysics Data System (ADS)

Kumar, Rohit; Puri, Rajeev K.

2018-03-01

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

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…

Testing the Efficacy of OurSpace, a Brief, Group Dynamics-Based Physical Activity Intervention: A Randomized Controlled Trial.

PubMed

Irwin, Brandon; Kurz, Daniel; Chalin, Patrice; Thompson, Nicholas

2016-05-06

Emerging technologies (ie, mobile phones, Internet) may be effective tools for promoting physical activity (PA). However, few interventions have provided effective means to enhance social support through these platforms. Face-to-face programs that use group dynamics-based principles of behavior change have been shown to be highly effective in enhancing social support through promoting group cohesion and PA, but to date, no studies have examined their effects in Web-based programs. The aim was to explore proof of concept and test the efficacy of a brief, online group dynamics-based intervention on PA in a controlled experiment. We expected that the impact of the intervention on PA would be moderated by perceptions of cohesion and the partner's degree of presence in the online media. Participants (n=135) were randomized into same-sex dyads and randomly assigned to one of four experimental conditions: standard social support (standard), group dynamics-based-high presence, group dynamics-based-low presence, or individual control. Participants performed two sets of planking exercises (pre-post). Between sets, participants in partnered conditions interacted with a virtual partner using either a standard social support app or a group dynamics-based app (group dynamics-based-low presence and group dynamics-based-high presence), the latter of which they participated in a series of online team-building exercises. Individual participants were given an equivalent rest period between sets. To increase presence during the second set, participants in the group dynamics-based-high presence group saw a live video stream of their partner exercising. Perceptions of cohesion were measured using a modified PA Group Environment Questionnaire. Physical activity was calculated as the time persisted during set 2 after controlling for persistence in set 1. Perceptions of cohesion were higher in the group dynamics-based-low presence (overall mean 5.81, SD 1.04) condition compared to the

Ultrafast Electronic Relaxation through a Conical Intersection: Nonadiabatic Dynamics Disentangled through an Oscillator Strength-Based Diabatization Framework

DOE PAGES

Medders, Gregory R.; Alguire, Ethan C.; Jain, Amber; ...

2017-01-18

Here, we employ surface hopping trajectories to model the short-time dynamics of gas-phase and partially solvated 4-(N,N-dimethylamino)benzonitrile (DMABN), a dual fluorescent molecule that is known to undergo a nonadiabatic transition through a conical intersection. To compare theory vs time-resolved fluorescence measurements, we calculate the mixed quantum–classical density matrix and the ensemble averaged transition dipole moment. We introduce a diabatization scheme based on the oscillator strength to convert the TDDFT adiabatic states into diabatic states of L a and L b character. Somewhat surprisingly, we find that the rate of relaxation reported by emission to the ground state is almost 50%more » slower than the adiabatic population relaxation. Although our calculated adiabatic rates are largely consistent with previous theoretical calculations and no obvious effects of decoherence are seen, the diabatization procedure introduced here enables an explicit picture of dynamics in the branching plane, raising tantalizing questions about geometric phase effects in systems with dozens of atoms.« less

Time Analysis of Building Dynamic Response Under Seismic Action. Part 2: Example of Calculation

NASA Astrophysics Data System (ADS)

Ufimtcev, E. M.

2017-11-01

The second part of the article illustrates the use of the time analysis method (TAM) by the example of the calculation of a 3-storey building, the design dynamic model (DDM) of which is adopted in the form of a flat vertical cantilever rod with 3 horizontal degrees of freedom associated with floor and coverage levels. The parameters of natural oscillations (frequencies and modes) and the results of the calculation of the elastic forced oscillations of the building’s DDM - oscillograms of the reaction parameters on the time interval t ∈ [0; 131,25] sec. The obtained results are analyzed on the basis of the computed values of the discrepancy of the DDS motion equation and the comparison of the results calculated on the basis of the numerical approach (FEM) and the normative method set out in SP 14.13330.2014 “Construction in Seismic Regions”. The data of the analysis testify to the accuracy of the construction of the computational model as well as the high accuracy of the results obtained. In conclusion, it is revealed that the use of the TAM will improve the strength of buildings and structures subject to seismic influences when designing them.

High dynamic range image acquisition based on multiplex cameras

NASA Astrophysics Data System (ADS)

Zeng, Hairui; Sun, Huayan; Zhang, Tinghua

2018-03-01

High dynamic image is an important technology of photoelectric information acquisition, providing higher dynamic range and more image details, and it can better reflect the real environment, light and color information. Currently, the method of high dynamic range image synthesis based on different exposure image sequences cannot adapt to the dynamic scene. It fails to overcome the effects of moving targets, resulting in the phenomenon of ghost. Therefore, a new high dynamic range image acquisition method based on multiplex cameras system was proposed. Firstly, different exposure images sequences were captured with the camera array, using the method of derivative optical flow based on color gradient to get the deviation between images, and aligned the images. Then, the high dynamic range image fusion weighting function was established by combination of inverse camera response function and deviation between images, and was applied to generated a high dynamic range image. The experiments show that the proposed method can effectively obtain high dynamic images in dynamic scene, and achieves good results.

Dopamine and Caffeine Encapsulation within Boron Nitride (14,0) Nanotubes: Classical Molecular Dynamics and First Principles Calculations.

PubMed

García-Toral, Dolores; González-Melchor, Minerva; Rivas-Silva, Juan F; Meneses-Juárez, Efraín; Cano-Ordaz, José; H Cocoletzi, Gregorio

2018-06-07

Classical molecular dynamics (MD) and density functional theory (DFT) calculations are developed to investigate the dopamine and caffeine encapsulation within boron nitride (BN) nanotubes (NT) with (14,0) chirality. Classical MD studies are done at canonical and isobaric-isothermal conditions at 298 K and 1 bar in explicit water. Results reveal that both molecules are attracted by the nanotube; however, only dopamine is able to enter the nanotube, whereas caffeine moves in its vicinity, suggesting that both species can be transported: the first by encapsulation and the second by drag. Findings are analyzed using the dielectric behavior, pair correlation functions, diffusion of the species, and energy contributions. The DFT calculations are performed according to the BLYP approach and applying the atomic base of the divided valence 6-31g(d) orbitals. The geometry optimization uses the minimum-energy criterion, accounting for the total charge neutrality and multiplicity of 1. Adsorption energies in the dopamine encapsulation indicate physisorption, which induces the highly occupied molecular orbital-lower unoccupied molecular orbital gap reduction yielding a semiconductor behavior. The charge redistribution polarizes the BNNT/dopamine and BNNT/caffeine structures. The work function decrease and the chemical potential values suggest the proper transport properties in these systems, which may allow their use in nanobiomedicine.

Manipulating the magnetic anisotropy and magnetization dynamics by stress: Numerical calculation and experiment

NASA Astrophysics Data System (ADS)

Correa, M. A.; Bohn, F.

2018-05-01

We perform a theoretical and experimental investigation of the magnetic properties and magnetization dynamics of a ferromagnetic magnetostrictive multilayer grown onto a flexible substrate and submitted to external stress. We calculate the magnetic behavior and magnetoimpedance effect for a trilayered system from an approach that considers a magnetic permeability model for planar geometry and a magnetic free energy density which takes into account induced uniaxial and magnetoelastic anisotropy contributions. We verify remarkable modifications of the magnetic anisotropy with external stress, as well as we show that the dynamic magnetic response is strongly affected by these changes. We discuss the magnetic features that lead to modifications of the frequency limits where distinct mechanisms are responsible by the magnetoimpedance variations, enabling us to manipulate the resonance fields. To test the robustness of the approach, we directly compare theoretical results with experimental data. Thus, we provide experimental evidence to confirm the validity of the theoretical approach, as well as to manipulate the resonance fields to tune the MI response according to real applications in devices.

An Adaptive Nonlinear Basal-Bolus Calculator for Patients With Type 1 Diabetes

PubMed Central

Boiroux, Dimitri; Aradóttir, Tinna Björk; Nørgaard, Kirsten; Poulsen, Niels Kjølstad; Madsen, Henrik; Jørgensen, John Bagterp

2016-01-01

Background: Bolus calculators help patients with type 1 diabetes to mitigate the effect of meals on their blood glucose by administering a large amount of insulin at mealtime. Intraindividual changes in patients physiology and nonlinearity in insulin-glucose dynamics pose a challenge to the accuracy of such calculators. Method: We propose a method based on a continuous-discrete unscented Kalman filter to continuously track the postprandial glucose dynamics and the insulin sensitivity. We augment the Medtronic Virtual Patient (MVP) model to simulate noise-corrupted data from a continuous glucose monitor (CGM). The basal rate is determined by calculating the steady state of the model and is adjusted once a day before breakfast. The bolus size is determined by optimizing the postprandial glucose values based on an estimate of the insulin sensitivity and states, as well as the announced meal size. Following meal announcements, the meal compartment and the meal time constant are estimated, otherwise insulin sensitivity is estimated. Results: We compare the performance of a conventional linear bolus calculator with the proposed bolus calculator. The proposed basal-bolus calculator significantly improves the time spent in glucose target (P < .01) compared to the conventional bolus calculator. Conclusion: An adaptive nonlinear basal-bolus calculator can efficiently compensate for physiological changes. Further clinical studies will be needed to validate the results. PMID:27613658

Development of a web-based CT dose calculator: WAZA-ARI.

PubMed

Ban, N; Takahashi, F; Sato, K; Endo, A; Ono, K; Hasegawa, T; Yoshitake, T; Katsunuma, Y; Kai, M

2011-09-01

A web-based computed tomography (CT) dose calculation system (WAZA-ARI) is being developed based on the modern techniques for the radiation transport simulation and for software implementation. Dose coefficients were calculated in a voxel-type Japanese adult male phantom (JM phantom), using the Particle and Heavy Ion Transport code System. In the Monte Carlo simulation, the phantom was irradiated with a 5-mm-thick, fan-shaped photon beam rotating in a plane normal to the body axis. The dose coefficients were integrated into the system, which runs as Java servlets within Apache Tomcat. Output of WAZA-ARI for GE LightSpeed 16 was compared with the dose values calculated similarly using MIRD and ICRP Adult Male phantoms. There are some differences due to the phantom configuration, demonstrating the significance of the dose calculation with appropriate phantoms. While the dose coefficients are currently available only for limited CT scanner models and scanning options, WAZA-ARI will be a useful tool in clinical practice when development is finalised.

Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

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

Kimminau, G; Nagler, B; Higginbotham, A

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.

Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations.

PubMed

Venken, Tom; Daelemans, Dirk; De Maeyer, Marc; Voet, Arnout

2012-06-01

The HIV Rev protein mediates the nuclear export of viral mRNA, and is thereby essential for the production of late viral proteins in the replication cycle. Rev forms a large organized multimeric protein-protein complex for proper functioning. Recently, the three-dimensional structures of a Rev dimer and tetramer have been resolved and provide the basis for a thorough structural analysis of the binding interaction. Here, molecular dynamics (MD) and binding free energy calculations were performed to elucidate the forces thriving dimerization and higher order multimerization of the Rev protein. It is found that despite the structural differences between each crystal structure, both display a similar behavior according to our calculations. Our analysis based on a molecular mechanics-generalized Born surface area (MM/GBSA) and a configurational entropy approach demonstrates that the higher order multimerization site is much weaker than the dimerization site. In addition, a quantitative hot spot analysis combined with a mutational analysis reveals the most contributing amino acid residues for protein interactions in agreement with experimental results. Additional residues were found in each interface, which are important for the protein interaction. The investigation of the thermodynamics of the Rev multimerization interactions performed here could be a further step in the development of novel antiretrovirals using structure based drug design. Moreover, the variability of the angle between each Rev monomer as measured during the MD simulations suggests a role of the Rev protein in allowing flexibility of the arginine rich domain (ARM) to accommodate RNA binding. Copyright © 2012 Wiley Periodicals, Inc.

A framework for standardized calculation of weather indices in Germany

NASA Astrophysics Data System (ADS)

Möller, Markus; Doms, Juliane; Gerstmann, Henning; Feike, Til

2018-05-01

Climate change has been recognized as a main driver in the increasing occurrence of extreme weather. Weather indices (WIs) are used to assess extreme weather conditions regarding its impact on crop yields. Designing WIs is challenging, since complex and dynamic crop-climate relationships have to be considered. As a consequence, geodata for WI calculations have to represent both the spatio-temporal dynamic of crop development and corresponding weather conditions. In this study, we introduce a WI design framework for Germany, which is based on public and open raster data of long-term spatio-temporal availability. The operational process chain enables the dynamic and automatic definition of relevant phenological phases for the main cultivated crops in Germany. Within the temporal bounds, WIs can be calculated for any year and test site in Germany in a reproducible and transparent manner. The workflow is demonstrated on the example of a simple cumulative rainfall index for the phenological phase shooting of winter wheat using 16 test sites and the period between 1994 and 2014. Compared to station-based approaches, the major advantage of our approach is the possibility to design spatial WIs based on raster data characterized by accuracy metrics. Raster data and WIs, which fulfill data quality standards, can contribute to an increased acceptance and farmers' trust in WI products for crop yield modeling or weather index-based insurances (WIIs).

Vicinage effect in the energy loss of H2 dimers: Experiment and calculations based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Koval, N. E.; Borisov, A. G.; Rosa, L. F. S.; Stori, E. M.; Dias, J. F.; Grande, P. L.; Sánchez-Portal, D.; Muiño, R. Díez

2017-06-01

We present a combined theoretical and experimental study of the energy loss of H2+ molecular ions interacting with thin oxide and carbon films. As a result of quantum mechanical interference of the target electrons, the energy loss of a molecular projectile differs from the sum of the energy losses of individual atomic projectiles. This difference is known as the vicinage effect. Calculations based on the time-dependent density functional theory allow the first-principles description of the dynamics of target excitations produced by the correlated motion of the nucleons forming the molecule. We investigate in detail the dependence of the vicinage effect on the speed and charge state of the projectile and find an excellent agreement between calculated and measured data.

Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics.

PubMed

Meirovitch, Hagai

2010-01-01

The commonly used simulation techniques, Metropolis Monte Carlo (MC) and molecular dynamics (MD) are of a dynamical type which enables one to sample system configurations i correctly with the Boltzmann probability, P(i)(B), while the value of P(i)(B) is not provided directly; therefore, it is difficult to obtain the absolute entropy, S approximately -ln P(i)(B), and the Helmholtz free energy, F. With a different simulation approach developed in polymer physics, a chain is grown step-by-step with transition probabilities (TPs), and thus their product is the value of the construction probability; therefore, the entropy is known. Because all exact simulation methods are equivalent, i.e. they lead to the same averages and fluctuations of physical properties, one can treat an MC or MD sample as if its members have rather been generated step-by-step. Thus, each configuration i of the sample can be reconstructed (from nothing) by calculating the TPs with which it could have been constructed. This idea applies also to bulk systems such as fluids or magnets. This approach has led earlier to the "local states" (LS) and the "hypothetical scanning" (HS) methods, which are approximate in nature. A recent development is the hypothetical scanning Monte Carlo (HSMC) (or molecular dynamics, HSMD) method which is based on stochastic TPs where all interactions are taken into account. In this respect, HSMC(D) can be viewed as exact and the only approximation involved is due to insufficient MC(MD) sampling for calculating the TPs. The validity of HSMC has been established by applying it first to liquid argon, TIP3P water, self-avoiding walks (SAW), and polyglycine models, where the results for F were found to agree with those obtained by other methods. Subsequently, HSMD was applied to mobile loops of the enzymes porcine pancreatic alpha-amylase and acetylcholinesterase in explicit water, where the difference in F between the bound and free states of the loop was calculated. Currently

Toward extending photosynthetic biosignatures: quantum dynamics calculation of light harvesting complexes

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.

Haptics-based dynamic implicit solid modeling.

PubMed

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.

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations.

PubMed

Hou, Tingjun; Wang, Junmei; Li, Youyong; Wang, Wei

2011-01-24

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) on the binding free energies predicted by MM/PBSA. The following three important conclusions could be observed: (1) MD simulation length has an obvious impact on the predictions, and longer MD simulation is not always necessary to achieve better predictions. (2) The predictions are quite sensitive to the solute dielectric constant, and this parameter should be carefully determined according to the characteristics of the protein/ligand binding interface. (3) Conformational entropy often show 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.

Dynamic Inversion based Control of a Docking Mechanism

NASA Technical Reports Server (NTRS)

Kulkarni, Nilesh V.; Ippolito, Corey; Krishnakumar, Kalmanje

2006-01-01

The problem of position and attitude control of the Stewart platform based docking mechanism is considered motivated by its future application in space missions requiring the autonomous docking capability. The control design is initiated based on the framework of the intelligent flight control architecture being developed at NASA Ames Research Center. In this paper, the baseline position and attitude control system is designed using dynamic inversion with proportional-integral augmentation. The inverse dynamics uses a Newton-Euler formulation that includes the platform dynamics, the dynamics of the individual legs along with viscous friction in the joints. Simulation results are presented using forward dynamics simulated by a commercial physics engine that builds the system as individual elements with appropriate joints and uses constrained numerical integration,

Variation Among Internet Based Calculators in Predicting Spontaneous Resolution of Vesicoureteral Reflux

PubMed Central

Routh, Jonathan C.; Gong, Edward M.; Cannon, Glenn M.; Yu, Richard N.; Gargollo, Patricio C.; Nelson, Caleb P.

2010-01-01

Purpose An increasing number of parents and practitioners use the Internet for health related purposes, and an increasing number of models are available on the Internet for predicting spontaneous resolution rates for children with vesi-coureteral reflux. We sought to determine whether currently available Internet based calculators for vesicoureteral reflux resolution produce systematically different results. Materials and Methods Following a systematic Internet search we identified 3 Internet based calculators of spontaneous resolution rates for children with vesicoureteral reflux, of which 2 were academic affiliated and 1 was industry affiliated. We generated a random cohort of 100 hypothetical patients with a wide range of clinical characteristics and entered the data on each patient into each calculator. We then compared the results from the calculators in terms of mean predicted resolution probability and number of cases deemed likely to resolve at various cutoff probabilities. Results Mean predicted resolution probabilities were 41% and 36% (range 31% to 41%) for the 2 academic affiliated calculators and 33% for the industry affiliated calculator (p = 0.02). For some patients the calculators produced markedly different probabilities of spontaneous resolution, in some instances ranging from 24% to 89% for the same patient. At thresholds greater than 5%, 10% and 25% probability of spontaneous resolution the calculators differed significantly regarding whether cases would resolve (all p < 0.0001). Conclusions Predicted probabilities of spontaneous resolution of vesicoureteral reflux differ significantly among Internet based calculators. For certain patients, particularly those with a lower probability of spontaneous resolution, these differences can significantly influence clinical decision making. PMID:20172550

Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations.

PubMed

Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M; Zhan, Chang-Guo

2014-04-01

Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Exploring the dynamics of reaction N((2)D)+C2H4 with crossed molecular-beam experiments and quantum-chemical calculations.

PubMed

Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun

2011-05-14

We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.

Dynamic Price Vector Formation Model-Based Automatic Demand Response Strategy for PV-Assisted EV Charging Stations

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

Chen, Qifang; Wang, Fei; Hodge, Bri-Mathias

A real-time price (RTP)-based automatic demand response (ADR) strategy for PV-assisted electric vehicle (EV) Charging Station (PVCS) without vehicle to grid is proposed. The charging process is modeled as a dynamic linear program instead of the normal day-ahead and real-time regulation strategy, to capture the advantages of both global and real-time optimization. Different from conventional price forecasting algorithms, a dynamic price vector formation model is proposed based on a clustering algorithm to form an RTP vector for a particular day. A dynamic feasible energy demand region (DFEDR) model considering grid voltage profiles is designed to calculate the lower and uppermore » bounds. A deduction method is proposed to deal with the unknown information of future intervals, such as the actual stochastic arrival and departure times of EVs, which make the DFEDR model suitable for global optimization. Finally, both the comparative cases articulate the advantages of the developed methods and the validity in reducing electricity costs, mitigating peak charging demand, and improving PV self-consumption of the proposed strategy are verified through simulation scenarios.« less

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

PubMed

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Validation of a dynamic linked segment model to calculate joint moments in lifting.

PubMed

de Looze, M P; Kingma, I; Bussmann, J B; Toussaint, H M

1992-08-01

A two-dimensional dynamic linked segment model was constructed and applied to a lifting activity. Reactive forces and moments were calculated by an instantaneous approach involving the application of Newtonian mechanics to individual adjacent rigid segments in succession. The analysis started once at the feet and once at a hands/load segment. The model was validated by comparing predicted external forces and moments at the feet or at a hands/load segment to actual values, which were simultaneously measured (ground reaction force at the feet) or assumed to be zero (external moments at feet and hands/load and external forces, beside gravitation, at hands/load). In addition, results of both procedures, in terms of joint moments, including the moment at the intervertebral disc between the fifth lumbar and first sacral vertebra (L5-S1), were compared. A correlation of r = 0.88 between calculated and measured vertical ground reaction forces was found. The calculated external forces and moments at the hands showed only minor deviations from the expected zero level. The moments at L5-S1, calculated starting from feet compared to starting from hands/load, yielded a coefficient of correlation of r = 0.99. However, moments calculated from hands/load were 3.6% (averaged values) and 10.9% (peak values) higher. This difference is assumed to be due mainly to erroneous estimations of the positions of centres of gravity and joint rotation centres. The estimation of the location of L5-S1 rotation axis can affect the results significantly. Despite the numerous studies estimating the load on the low back during lifting on the basis of linked segment models, only a few attempts to validate these models have been made. This study is concerned with the validity of the presented linked segment model. The results support the model's validity. Effects of several sources of error threatening the validity are discussed. Copyright © 1992. Published by Elsevier Ltd.

A practical method to avoid zero-point leak in molecular dynamics calculations: application to the water dimer.

PubMed

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.

Vibrational dynamics of rutile-type GeO2 from micro-Raman spectroscopy experiments and first-principles calculations

NASA Astrophysics Data System (ADS)

Sanson, A.; Pokrovski, G. S.; Giarola, M.; Mariotto, G.

2015-01-01

The vibrational dynamics of germanium dioxide in the rutile structure has been investigated by using polarized micro-Raman scattering spectroscopy coupled with first-principles calculations. Raman spectra were carried out in backscattering geometry at room temperature from micro-crystalline samples either unoriented or oriented by means of a micromanipulator, which enabled successful detection and identification of all the Raman active modes expected on the basis of the group theory. In particular, the Eg mode, incorrectly assigned or not detected in the literature, has been definitively observed by us and unambiguously identified at 525 \\text{cm}-1 under excitation by certain laser lines, thus revealing an unusual resonance phenomenon. First-principles calculations within the framework of the density functional theory allow quantifying both wave number and intensity of the Raman vibrational spectra. The excellent agreement between calculated and experimental data corroborates the reliability of our findings.

Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations.

PubMed

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.

Simulation and analysis of main steam control system based on heat transfer calculation

NASA Astrophysics Data System (ADS)

Huang, Zhenqun; Li, Ruyan; Feng, Zhongbao; Wang, Songhan; Li, Wenbo; Cheng, Jiwei; Jin, Yingai

2018-05-01

In this paper, after thermal power plant 300MW boiler was studied, mat lab was used to write calculation program about heat transfer process between the main steam and boiler flue gas and amount of water was calculated to ensure the main steam temperature keeping in target temperature. Then heat transfer calculation program was introduced into Simulink simulation platform based on control system multiple models switching and heat transfer calculation. The results show that multiple models switching control system based on heat transfer calculation not only overcome the large inertia of main stream temperature, a large hysteresis characteristic of main stream temperature, but also adapted to the boiler load changing.

THE AB INITIO CALCULATION OF THE DYNAMICAL AND THE THERMODYNAMIC PROPERTIES OF THE ZINC-BLENDE GaX (X=N, P, As AND Sb)

NASA Astrophysics Data System (ADS)

Bouhadda, Y.; Bentabet, A.; Fenineche, N. E.; Boudouma, Y.

2012-12-01

By this work, we aim to study the dynamical and the thermodynamic properties of the zinc-blende GaX (X = N, P, As and Sb) using the Ab initio simulation method. Indeed, we studied the lattice dynamics, the constant-volume specific heat (Cv), the internal energy (U), the entropy (S) and the free energy (F). The observed differences between the properties of GaX elements were discussed. Our results and the available literature data (theoretical and experimental) seems to be in good agreement. Moreover, Cv, U, F and S were calculated by using the harmonic approximation in the calculation of the dynamic lattice vibration. The good agreement between our results of both the phonon frequency, the constant-volume specific heat and the experimental data allows us to conclude that our results of S, U and F of GaX were well predicted.

Beyond Problem-Based Learning: Using Dynamic PBL in Chemistry

ERIC Educational Resources Information Center

Overton, Tina L.; Randles, Christopher A.

2015-01-01

This paper describes the development and implementation of a novel pedagogy, dynamic problem-based learning. The pedagogy utilises real-world problems that evolve throughout the problem-based learning activity and provide students with choice and different data sets. This new dynamic problem-based learning approach was utilised to teach…

Trust-based access control model from sociological approach in dynamic online social network environment.

PubMed

Baek, Seungsoo; Kim, Seungjoo

2014-01-01

There has been an explosive increase in the population of the OSN (online social network) in recent years. The OSN provides users with many opportunities to communicate among friends and family. Further, it facilitates developing new relationships with previously unknown people having similar beliefs or interests. However, the OSN can expose users to adverse effects such as privacy breaches, the disclosing of uncontrolled material, and the disseminating of false information. Traditional access control models such as MAC, DAC, and RBAC are applied to the OSN to address these problems. However, these models are not suitable for the dynamic OSN environment because user behavior in the OSN is unpredictable and static access control imposes a burden on the users to change the access control rules individually. We propose a dynamic trust-based access control for the OSN to address the problems of the traditional static access control. Moreover, we provide novel criteria to evaluate trust factors such as sociological approach and evaluate a method to calculate the dynamic trust values. The proposed method can monitor negative behavior and modify access permission levels dynamically to prevent the indiscriminate disclosure of information.

Trust-Based Access Control Model from Sociological Approach in Dynamic Online Social Network Environment

PubMed Central

Kim, Seungjoo

2014-01-01

There has been an explosive increase in the population of the OSN (online social network) in recent years. The OSN provides users with many opportunities to communicate among friends and family. Further, it facilitates developing new relationships with previously unknown people having similar beliefs or interests. However, the OSN can expose users to adverse effects such as privacy breaches, the disclosing of uncontrolled material, and the disseminating of false information. Traditional access control models such as MAC, DAC, and RBAC are applied to the OSN to address these problems. However, these models are not suitable for the dynamic OSN environment because user behavior in the OSN is unpredictable and static access control imposes a burden on the users to change the access control rules individually. We propose a dynamic trust-based access control for the OSN to address the problems of the traditional static access control. Moreover, we provide novel criteria to evaluate trust factors such as sociological approach and evaluate a method to calculate the dynamic trust values. The proposed method can monitor negative behavior and modify access permission levels dynamically to prevent the indiscriminate disclosure of information. PMID:25374943

Independent Monte-Carlo dose calculation for MLC based CyberKnife radiotherapy

NASA Astrophysics Data System (ADS)

Mackeprang, P.-H.; Vuong, D.; Volken, W.; Henzen, D.; Schmidhalter, D.; Malthaner, M.; Mueller, S.; Frei, D.; Stampanoni, M. F. M.; Dal Pra, A.; Aebersold, D. M.; Fix, M. K.; Manser, P.

2018-01-01

This work aims to develop, implement and validate a Monte Carlo (MC)-based independent dose calculation (IDC) framework to perform patient-specific quality assurance (QA) for multi-leaf collimator (MLC)-based CyberKnife® (Accuray Inc., Sunnyvale, CA) treatment plans. The IDC framework uses an XML-format treatment plan as exported from the treatment planning system (TPS) and DICOM format patient CT data, an MC beam model using phase spaces, CyberKnife MLC beam modifier transport using the EGS++ class library, a beam sampling and coordinate transformation engine and dose scoring using DOSXYZnrc. The framework is validated against dose profiles and depth dose curves of single beams with varying field sizes in a water tank in units of cGy/Monitor Unit and against a 2D dose distribution of a full prostate treatment plan measured with Gafchromic EBT3 (Ashland Advanced Materials, Bridgewater, NJ) film in a homogeneous water-equivalent slab phantom. The film measurement is compared to IDC results by gamma analysis using 2% (global)/2 mm criteria. Further, the dose distribution of the clinical treatment plan in the patient CT is compared to TPS calculation by gamma analysis using the same criteria. Dose profiles from IDC calculation in a homogeneous water phantom agree within 2.3% of the global max dose or 1 mm distance to agreement to measurements for all except the smallest field size. Comparing the film measurement to calculated dose, 99.9% of all voxels pass gamma analysis, comparing dose calculated by the IDC framework to TPS calculated dose for the clinical prostate plan shows 99.0% passing rate. IDC calculated dose is found to be up to 5.6% lower than dose calculated by the TPS in this case near metal fiducial markers. An MC-based modular IDC framework was successfully developed, implemented and validated against measurements and is now available to perform patient-specific QA by IDC.

Dynamic reasoning in a knowledge-based system

NASA Technical Reports Server (NTRS)

Rao, Anand S.; Foo, Norman Y.

1988-01-01

Any space based system, whether it is a robot arm assembling parts in space or an onboard system monitoring the space station, has to react to changes which cannot be foreseen. As a result, apart from having domain-specific knowledge as in current expert systems, a space based AI system should also have general principles of change. This paper presents a modal logic which can not only represent change but also reason with it. Three primitive operations, expansion, contraction and revision are introduced and axioms which specify how the knowledge base should change when the external world changes are also specified. Accordingly the notion of dynamic reasoning is introduced, which unlike the existing forms of reasoning, provide general principles of change. Dynamic reasoning is based on two main principles, namely minimize change and maximize coherence. A possible-world semantics which incorporates the above two principles is also discussed. The paper concludes by discussing how the dynamic reasoning system can be used to specify actions and hence form an integral part of an autonomous reasoning and planning system.

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

PubMed

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

2011-07-30

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

Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

NASA Astrophysics Data System (ADS)

Wu, Xiongwu; Brooks, Bernard R.

2011-11-01

The self-guided Langevin dynamics (SGLD) is a method to accelerate conformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on their frequency to accelerate conformational searching without modifying energy surfaces or raising temperatures. It has been applied to studies of many long time scale events, such as protein folding. Recent progress in the understanding of the conformational distribution in SGLD simulations makes SGLD also an accurate method for quantitative studies. The SGLD partition function provides a way to convert the SGLD conformational distribution to the canonical ensemble distribution and to calculate ensemble average properties through reweighting. Based on the SGLD partition function, this work presents a force-momentum-based self-guided Langevin dynamics (SGLDfp) simulation method to directly sample the canonical ensemble. This method includes interaction forces in its guiding force to compensate the perturbation caused by the momentum-based guiding force so that it can approximately sample the canonical ensemble. Using several example systems, we demonstrate that SGLDfp simulations can approximately maintain the canonical ensemble distribution and significantly accelerate conformational searching. With optimal parameters, SGLDfp and SGLD simulations can cross energy barriers of more than 15 kT and 20 kT, respectively, at similar rates for LD simulations to cross energy barriers of 10 kT. The SGLDfp method is size extensive and works well for large systems. For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space.

SU-E-T-226: Correction of a Standard Model-Based Dose Calculator Using Measurement Data

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

Chen, M; Jiang, S; Lu, W

Purpose: To propose a hybrid method that combines advantages of the model-based and measurement-based method for independent dose calculation. Modeled-based dose calculation, such as collapsed-cone-convolution/superposition (CCCS) or the Monte-Carlo method, models dose deposition in the patient body accurately; however, due to lack of detail knowledge about the linear accelerator (LINAC) head, commissioning for an arbitrary machine is tedious and challenging in case of hardware changes. On the contrary, the measurement-based method characterizes the beam property accurately but lacks the capability of dose disposition modeling in heterogeneous media. Methods: We used a standard CCCS calculator, which is commissioned by published data,more » as the standard model calculator. For a given machine, water phantom measurements were acquired. A set of dose distributions were also calculated using the CCCS for the same setup. The difference between the measurements and the CCCS results were tabulated and used as the commissioning data for a measurement based calculator. Here we used a direct-ray-tracing calculator (ΔDRT). The proposed independent dose calculation consists of the following steps: 1. calculate D-model using CCCS. 2. calculate D-ΔDRT using ΔDRT. 3. combine Results: D=D-model+D-ΔDRT. Results: The hybrid dose calculation was tested on digital phantoms and patient CT data for standard fields and IMRT plan. The results were compared to dose calculated by the treatment planning system (TPS). The agreement of the hybrid and the TPS was within 3%, 3 mm for over 98% of the volume for phantom studies and lung patients. Conclusion: The proposed hybrid method uses the same commissioning data as those for the measurement-based method and can be easily extended to any non-standard LINAC. The results met the accuracy, independence, and simple commissioning criteria for an independent dose calculator.« less

Calculation of noncontact forces between silica nanospheres.

PubMed

Sun, Weifu; Zeng, Qinghua; Yu, Aibing

2013-02-19

Quantification of the interactions between nanoparticles is important in understanding their dynamic behaviors and many related phenomena. In this study, molecular dynamics simulation is used to calculate the interaction potentials (i.e., van der Waals attraction, Born repulsion, and electrostatic interaction) between two silica nanospheres of equal radius in the range of 0.975 to 5.137 nm. The results are compared with those obtained from the conventional Hamaker approach, leading to the development of modified formulas to calculate the van der Waals attraction and Born repulsion between nanospheres, respectively. Moreover, Coulomb's law is found to be valid for calculating the electrostatic potential between nanospheres. The developed formulas should be useful in the study of the dynamic behaviors of nanoparticle systems under different conditions.

Kuznetsov-Ma Soliton Dynamics Based on the Mechanical Effect of Light

NASA Astrophysics Data System (ADS)

Xiong, Hao; Gan, Jinghui; Wu, Ying

2017-10-01

A Kuznetsov-Ma soliton that exhibits an unusual pulsating dynamics has attracted particular attention in hydrodynamics and plasma physics in the context of understanding nonlinear coherent phenomena. Here, we demonstrate theoretically the formation of a novel form of Kuznetsov-Ma soliton in a microfabricated optomechanical array, where both photonic and phononic evolutionary dynamics exhibit periodic structure and coherent localized behavior enabled by radiation-pressure coupling of optical fields and mechanical oscillations, which is a manifestation of the unique property of optomechanical systems. Numerical calculations of the optomechanical dynamics show an excellent agreement with this theory. In addition to providing insight into optomechanical nonlinearity, optomechanical Kuznetsov-Ma soliton dynamics fundamentally broadens the regime of cavity optomechanics and may find applications in on-chip manipulation of light propagation.

Multiphase Equation of State and Strength Properties of Beryllium from AB INITIO and Quantum Molecular Dynamics Calculations.

NASA Astrophysics Data System (ADS)

Robert, G.; Sollier, A.; Legrand, Ph.

2007-12-01

In the framework of density functional theory, static properties and phonon spectra of beryllium have been calculated under high compression (for pressures up to 4 Mbar) for two solid phases: hexagonal compact (hcp) and body-centered cubic (bcc). The melting curve and some isotherms in the liquid phase have been calculated using quantum molecular dynamics. The coupling of these theoretical data to a quasi-harmonic approach (phonon moments) allows us to suggest a new theoretical phase diagram and to build a multiphase equation of state (EOS) valid in a large range of pressure and temperature. The resulting Hugoniot curves as well as the evolution of the longitudinal sound speed with both pressure and temperature are in good agreement with available experimental data.

Calculation of the surface tension of liquid Ga-based alloys

NASA Astrophysics Data System (ADS)

Dogan, Ali; Arslan, Hüseyin

2018-05-01

As known, Eyring and his collaborators have applied the structure theory to the properties of binary liquid mixtures. In this work, the Eyring model has been extended to calculate the surface tension of liquid Ga-Bi, Ga-Sn and Ga-In binary alloys. It was found that the addition of Sn, In and Bi into Ga leads to significant decrease in the surface tension of the three Ga-based alloy systems, especially for that of Ga-Bi alloys. The calculated surface tension values of these alloys exhibit negative deviation from the corresponding ideal mixing isotherms. Moreover, a comparison between the calculated results and corresponding literature data indicates a good agreement.

Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations.

PubMed

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.

Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations

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.

Calculation of the lateral-dynamic stability of aircraft

NASA Technical Reports Server (NTRS)

Raikh, A

1952-01-01

Graphs and formulas are given with the aid of which all the aerodynamic coefficients required for computing the lateral dynamic stability can be determined. A number of numerical examples are given for obtaining the stability derivatives and solving the characteristic-stability equation. Approximate formulas are derived with the aid of which rapid preliminary computations may be made and the stability coefficients corrected for certain modifications of the airplane. A derivation of the lateral-dynamic-stability equations is included.

Method of calculating tsunami travel times in the Andaman Sea region

PubMed Central

Visuthismajarn, Parichart; Tanavud, Charlchai; Robson, Mark G.

2014-01-01

A new model to calculate tsunami travel times in the Andaman Sea region has been developed. The model specifically provides more accurate travel time estimates for tsunamis propagating to Patong Beach on the west coast of Phuket, Thailand. More generally, the model provides better understanding of the influence of the accuracy and resolution of bathymetry data on the accuracy of travel time calculations. The dynamic model is based on solitary wave theory, and a lookup function is used to perform bilinear interpolation of bathymetry along the ray trajectory. The model was calibrated and verified using data from an echosounder record, tsunami photographs, satellite altimetry records, and eyewitness accounts of the tsunami on 26 December 2004. Time differences for 12 representative targets in the Andaman Sea and the Indian Ocean regions were calculated. The model demonstrated satisfactory time differences (<2 min/h), despite the use of low resolution bathymetry (ETOPO2v2). To improve accuracy, the dynamics of wave elevation and a velocity correction term must be considered, particularly for calculations in the nearshore region. PMID:25741129

Method of calculating tsunami travel times in the Andaman Sea region.

PubMed

Kietpawpan, Monte; Visuthismajarn, Parichart; Tanavud, Charlchai; Robson, Mark G

2008-07-01

A new model to calculate tsunami travel times in the Andaman Sea region has been developed. The model specifically provides more accurate travel time estimates for tsunamis propagating to Patong Beach on the west coast of Phuket, Thailand. More generally, the model provides better understanding of the influence of the accuracy and resolution of bathymetry data on the accuracy of travel time calculations. The dynamic model is based on solitary wave theory, and a lookup function is used to perform bilinear interpolation of bathymetry along the ray trajectory. The model was calibrated and verified using data from an echosounder record, tsunami photographs, satellite altimetry records, and eyewitness accounts of the tsunami on 26 December 2004. Time differences for 12 representative targets in the Andaman Sea and the Indian Ocean regions were calculated. The model demonstrated satisfactory time differences (<2 min/h), despite the use of low resolution bathymetry (ETOPO2v2). To improve accuracy, the dynamics of wave elevation and a velocity correction term must be considered, particularly for calculations in the nearshore region.

Particle-based membrane model for mesoscopic simulation of cellular dynamics

NASA Astrophysics Data System (ADS)

Sadeghi, Mohsen; Weikl, Thomas R.; Noé, Frank

2018-01-01

We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.

In-Stream Sediment Dynamics for predicted environmental concentration calculations of plant protection products in the FOCUSSW Scenarios

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

Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations.

PubMed

Lin, Hai; Zhao, Yan; Tishchenko, Oksana; Truhlar, Donald G

2006-09-01

The multiconfiguration molecular mechanics (MCMM) method is a general algorithm for generating potential energy surfaces for chemical reactions by fitting high-level electronic structure data with the help of molecular mechanical (MM) potentials. It was previously developed as an extension of standard MM to reactive systems by inclusion of multidimensional resonance interactions between MM configurations corresponding to specific valence bonding patterns, with the resonance matrix element obtained from quantum mechanical (QM) electronic structure calculations. In particular, the resonance matrix element is obtained by multidimensional interpolation employing a finite number of geometries at which electronic-structure calculations of the energy, gradient, and Hessian are carried out. In this paper, we present a strategy for combining MCMM with hybrid quantum mechanical molecular mechanical (QM/MM) methods. In the new scheme, electronic-structure information for obtaining the resonance integral is obtained by means of hybrid QM/MM calculations instead of fully QM calculations. As such, the new strategy can be applied to the studies of very large reactive systems. The new MCMM scheme is tested for two hydrogen-transfer reactions. Very encouraging convergence is obtained for rate constants including tunneling, suggesting that the new MCMM method, called QM/MM-MCMM, is a very general, stable, and efficient procedure for generating potential energy surfaces for large reactive systems. The results are found to converge well with respect to the number of Hessians. The results are also compared to calculations in which the resonance integral data are obtained by pure QM, and this illustrates the sensitivity of reaction rate calculations to the treatment of the QM-MM border. For the smaller of the two systems, comparison is also made to direct dynamics calculations in which the potential energies are computed quantum mechanically on the fly.

Development of a potent 2-oxoamide inhibitor of secreted phospholipase A2 guided by molecular docking calculations and molecular dynamics simulations

PubMed Central

Vasilakaki, Sofia; Barbayianni, Efrosini; Leonis, Georgios; Papadopoulos, Manthos G.; Mavromoustakos, Thomas; Gelb, Michael H.; Kokotos, George

2016-01-01

Inhibition of group IIA secreted phospholipase A2 (GIIA sPLA2) has been an important objective for medicinal chemists. We have previously shown that inhibitors incorporating the 2-oxoamide functionality may inhibit human and mouse GIIA sPLA2s. Herein, the development of new potent inhibitors by molecular docking calculations using the structure of the known inhibitor 7 as scaffold, are described. Synthesis and biological evaluation of the new compounds revealed that the long chain 2-oxoamide based on (S)-valine GK241 led to improved activity (IC50 = 143 nM and 68 nM against human and mouse GIIA sPLA2, respectively). In addition, molecular dynamics simulations were employed to shed light on GK241 potent and selective inhibitory activity. PMID:26970660

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

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

Andoh, Y.; Yoshii, N.; Yamada, 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)more » 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.« less

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.

Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

NASA Astrophysics Data System (ADS)

Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

2018-04-01

A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

Lagrangian Transport Calculations Using UARS Data. Part 2; Ozone

NASA Technical Reports Server (NTRS)

Manney, Gloria L.; Zurek, R. W.; Froidevaux, L.; Waters, J. W.; ONeill, A.; Swinbank, R.

1995-01-01

Trajectory calculations are used to examine ozone transport in the polar winter stratosphere during periods of the Upper Atmosphere Research Satellite (UARS) observations. The value of these calculations for determining mass transport was demonstrated previously using UARS observations of long-lived tracers, In the middle stratosphere, the overall ozone behavior observed by the Microwave Limb Sounder in the polar vortex is reproduced by this purely dynamical model. Calculations show the evolution of ozone in the lower stratosphere during early winter to be dominated by dynamics in December 1992 in the Arctic. Calculations for June 1992 in the Antarctic show evidence of chemical ozone destruction and indicate that approx. 50% of the chemical destruction may be masked by dynamical effects, mainly diabatic descent, which bring higher ozone into the lower-stratospheric vortex. Estimating differences between calculated and observed fields suggests that dynamical changes masked approx. 20% - 35% of chemical ozone loss during late February and early March 1993 in the Arctic. In the Antarctic late winter, in late August and early September 1992, below approx. 520 K, the evolution of vortex-averaged ozone is entirely dominated by chemical effects; above this level, however, chemical ozone depletion can be partially or completely masked by dynamical effects. Our calculations for 1992 showed that chemical loss was nearly completely compensated by increases due to diabatic descent at 655 K.

Static and dynamic stress analyses of the prototype high head Francis runner based on site measurement

NASA Astrophysics Data System (ADS)

Huang, X.; Oram, C.; Sick, M.

2014-03-01

More efforts are put on hydro-power to balance voltage and frequency within seconds for primary control in modern smart grids. This requires hydraulic turbines to run at off-design conditions. especially at low load or speed-no load. Besides. the tendency of increasing power output and decreasing weight of the turbine runners has also led to the high level vibration problem of the runners. especially high head Francis runners. Therefore. it is important to carry out the static and dynamic stress analyses of prototype high head Francis runners. This paper investigates the static and dynamic stresses on the prototype high head Francis runner based on site measurements and numerical simulations. The site measurements are performed with pressure transducers and strain gauges. Based on the measured results. computational fluid dynamics (CFD) simulations for the flow channel from stay vane to draft tube cone are performed. Static pressure distributions and dynamic pressure pulsations caused by rotor-stator interaction (RSI) are obtained under various operating conditions. With the CFD results. static and dynamic stresses on the runner at different operating points are calculated by means of the finite element method (FEM). The agreement between simulation and measurement is analysed with linear regression method. which indicates that the numerical result agrees well with that of measurement. Furthermore. the maximum static and dynamic stresses on the runner blade are obtained at various operating points. The relations of the maximum stresses and the power output are discussed in detail. The influences of the boundary conditions on the structural behaviour of the runner are also discussed.

Sea ice type dynamics in the Arctic based on Sentinel-1 Data

NASA Astrophysics Data System (ADS)

Babiker, Mohamed; Korosov, Anton; Park, Jeong-Won

2017-04-01

Sea ice observation from satellites has been carried out for more than four decades and is one of the most important applications of EO data in operational monitoring as well as in climate change studies. Several sensors and retrieval methods have been developed and successfully utilized to measure sea ice area, concentration, drift, type, thickness, etc [e.g. Breivik et al., 2009]. Today operational sea ice monitoring and analysis is fully dependent on use of satellite data. However, new and improved satellite systems, such as multi-polarisation Synthetic Apperture Radar (SAR), require further studies to develop more advanced and automated sea ice monitoring methods. In addition, the unprecedented volume of data available from recently launched Sentinel missions provides both challenges and opportunities for studying sea ice dynamics. In this study we investigate sea ice type dynamics in the Fram strait based on Sentinel-1 A, B SAR data. Series of images for the winter season are classified into 4 ice types (young ice, first year ice, multiyear ice and leads) using the new algorithm developed by us for sea ice classification, which is based on segmentation, GLCM calculation, Haralick texture feature extraction, unsupervised and supervised classifications and Support Vector Machine (SVM) [Zakhvatkina et al., 2016; Korosov et al., 2016]. This algorithm is further improved by applying thermal and scalloping noise removal [Park et al. 2016]. Sea ice drift is retrieved from the same series of Sentinel-1 images using the newly developed algorithm based on combination of feature tracking and pattern matching [Mukenhuber et al., 2016]. Time series of these two products (sea ice type and sea ice drift) are combined in order to study sea ice deformation processes at small scales. Zones of sea ice convergence and divergence identified from sea ice drift are compared with ridges and leads identified from texture features. That allows more specific interpretation of SAR

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

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.

Dynamic Game Behavior of Retailers Considering the Quality of Substitute Products Based on Delay Decision

NASA Astrophysics Data System (ADS)

Bao, Binshuo; Ma, Junhai

2017-12-01

Motivated by the Silk Road Economic Belt and the 21st-Century Maritime Silk Road project, i.e. the Belt and Road (B&R), more goods will flow around the world. With this trading platform, people can buy products at relatively cheap prices, and it is easier for people to buy various goods. The quality and quantity of products thus attract more and more attention in the supply chains. This paper discusses the quantity decision by considering the product quality in parallel supply chains where two manufacturers produce substitute products and then sell them to their downstream retailers separately. In terms of the changing quantity, as well as the different quality, this paper establishes a dynamic game model to explore the dynamic behavior when the optimal profits of two retailers have been calculated. The dynamic behaviors of the system, such as stable region, bifurcation and chaos, strange attractors and the largest Lyapunov exponents (LLE) are analyzed. The effect of the quantity adjustment parameter on the stability of the supply chain system is investigated through numerical simulations. Furthermore, a dynamic game model is established based on the quality delay decision, to investigate the influence of the quality delay parameter on the dynamic game model and the profits. Finally, the optimal decisions are obtained and analyzed.

Developing ultrasensitive pressure sensor based on graphene nanoribbon: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Kwon, Oh Kuen; Lee, Jun Ha; Kim, Ki-Sub; Kang, Jeong Won

2013-01-01

We propose schematics for an ultra-sensitive pressure sensor based on graphene-nanoribbon (GNR) and investigate its electromechanical properties using classical molecular dynamics simulations and piezo-electricity theory. Since the top plate applied to the actual pressure is large whereas the contact area on the GNR is very small, both the sensitivity and the sensing range can be adjusted by controlling the aspect ratio between the top plate and the contact point areas. Our calculation shows that the electrical conductivity of GNRs can be tuned by the applied pressure and the electric conductance of the deflected GNR linearly increases with increasing applied pressure for the linear elastic region in low pressure below the cut-off point. In the curves for both the deflection and potential energy, the linear elastic regime in low pressure was explicitly separated with the non-linear elastic regime in high pressure. The proposed GNR-based nanoelectromechanical devices have great potential for application as electromechanical memory, relay or switching devices.

An agent-based approach for modeling dynamics of contagious disease spread

PubMed Central

Perez, Liliana; Dragicevic, Suzana

2009-01-01

Background The propagation of communicable diseases through a population is an inherent spatial and temporal process of great importance for modern society. For this reason a spatially explicit epidemiologic model of infectious disease is proposed for a greater understanding of the disease's spatial diffusion through a network of human contacts. Objective The objective of this study is to develop an agent-based modelling approach the integrates geographic information systems (GIS) to simulate the spread of a communicable disease in an urban environment, as a result of individuals' interactions in a geospatial context. Methods The methodology for simulating spatiotemporal dynamics of communicable disease propagation is presented and the model is implemented using measles outbreak in an urban environment as a case study. Individuals in a closed population are explicitly represented by agents associated to places where they interact with other agents. They are endowed with mobility, through a transportation network allowing them to move between places within the urban environment, in order to represent the spatial heterogeneity and the complexity involved in infectious diseases diffusion. The model is implemented on georeferenced land use dataset from Metro Vancouver and makes use of census data sets from Statistics Canada for the municipality of Burnaby, BC, Canada study site. Results The results provide insights into the application of the model to calculate ratios of susceptible/infected in specific time frames and urban environments, due to its ability to depict the disease progression based on individuals' interactions. It is demonstrated that the dynamic spatial interactions within the population lead to high numbers of exposed individuals who perform stationary activities in areas after they have finished commuting. As a result, the sick individuals are concentrated in geographical locations like schools and universities. Conclusion The GIS-agent based model

Parameterizing Coefficients of a POD-Based Dynamical System

NASA Technical Reports Server (NTRS)

Kalb, Virginia L.

2010-01-01

A method of parameterizing the coefficients of a dynamical system based of a proper orthogonal decomposition (POD) representing the flow dynamics of a viscous fluid has been introduced. (A brief description of POD is presented in the immediately preceding article.) The present parameterization method is intended to enable construction of the dynamical system to accurately represent the temporal evolution of the flow dynamics over a range of Reynolds numbers. The need for this or a similar method arises as follows: A procedure that includes direct numerical simulation followed by POD, followed by Galerkin projection to a dynamical system has been proven to enable representation of flow dynamics by a low-dimensional model at the Reynolds number of the simulation. However, a more difficult task is to obtain models that are valid over a range of Reynolds numbers. Extrapolation of low-dimensional models by use of straightforward Reynolds-number-based parameter continuation has proven to be inadequate for successful prediction of flows. A key part of the problem of constructing a dynamical system to accurately represent the temporal evolution of the flow dynamics over a range of Reynolds numbers is the problem of understanding and providing for the variation of the coefficients of the dynamical system with the Reynolds number. Prior methods do not enable capture of temporal dynamics over ranges of Reynolds numbers in low-dimensional models, and are not even satisfactory when large numbers of modes are used. The basic idea of the present method is to solve the problem through a suitable parameterization of the coefficients of the dynamical system. The parameterization computations involve utilization of the transfer of kinetic energy between modes as a function of Reynolds number. The thus-parameterized dynamical system accurately predicts the flow dynamics and is applicable to a range of flow problems in the dynamical regime around the Hopf bifurcation. Parameter

An Evaluation of the Scattering Law for Light and Heavy Water in ENDF-6 Format, Based on Experimental Data and Molecular Dynamics

NASA Astrophysics Data System (ADS)

Márquez Damián, J. I.; Granada, J. R.; Malaspina, D. C.

2014-04-01

In this work we present an evaluation in ENDF-6 format of the scattering law for light and heavy water computed using the LEAPR module of NJOY99. The models used in this evaluation are based on experimental data on light water dynamics measured by Novikov, partial structure factors obtained by Soper, and molecular dynamics calculations performed with GROMACS using a reparameterized version of the flexible SPC model by Toukan and Rahman. The models use the Egelstaff-Schofield diffusion equation for translational motion, and a continuous spectrum calculated from the velocity autocorrelation function computed with GROMACS. The scattering law for H in H2O is computed using the incoherent approximation, and the scattering law D and O in D2O are computed using the Sköld approximation for coherent scattering. The calculations show significant improvement over ENDF/B-VI and ENDF/B-VII when compared with measurements of the total cross section, differential scattering experiments and quasi-elastic neutron scattering experiments (QENS).

Double dynamic scaling in human communication dynamics

NASA Astrophysics Data System (ADS)

Wang, Shengfeng; Feng, Xin; Wu, Ye; Xiao, Jinhua

2017-05-01

In the last decades, human behavior has been deeply understanding owing to the huge quantities data of human behavior available for study. The main finding in human dynamics shows that temporal processes consist of high-activity bursty intervals alternating with long low-activity periods. A model, assuming the initiator of bursty follow a Poisson process, is widely used in the modeling of human behavior. Here, we provide further evidence for the hypothesis that different bursty intervals are independent. Furthermore, we introduce a special threshold to quantitatively distinguish the time scales of complex dynamics based on the hypothesis. Our results suggest that human communication behavior is a composite process of double dynamics with midrange memory length. The method for calculating memory length would enhance the performance of many sequence-dependent systems, such as server operation and topic identification.

A new 2D segmentation method based on dynamic programming applied to computer aided detection in mammography.

PubMed

Timp, Sheila; Karssemeijer, Nico

2004-05-01

Mass segmentation plays a crucial role in computer-aided diagnosis (CAD) systems for classification of suspicious regions as normal, benign, or malignant. In this article we present a robust and automated segmentation technique--based on dynamic programming--to segment mass lesions from surrounding tissue. In addition, we propose an efficient algorithm to guarantee resulting contours to be closed. The segmentation method based on dynamic programming was quantitatively compared with two other automated segmentation methods (region growing and the discrete contour model) on a dataset of 1210 masses. For each mass an overlap criterion was calculated to determine the similarity with manual segmentation. The mean overlap percentage for dynamic programming was 0.69, for the other two methods 0.60 and 0.59, respectively. The difference in overlap percentage was statistically significant. To study the influence of the segmentation method on the performance of a CAD system two additional experiments were carried out. The first experiment studied the detection performance of the CAD system for the different segmentation methods. Free-response receiver operating characteristics analysis showed that the detection performance was nearly identical for the three segmentation methods. In the second experiment the ability of the classifier to discriminate between malignant and benign lesions was studied. For region based evaluation the area Az under the receiver operating characteristics curve was 0.74 for dynamic programming, 0.72 for the discrete contour model, and 0.67 for region growing. The difference in Az values obtained by the dynamic programming method and region growing was statistically significant. The differences between other methods were not significant.

Dynamic Stark broadening as the Dicke narrowing effect

NASA Astrophysics Data System (ADS)

Calisti, A.; Mossé, C.; Ferri, S.; Talin, B.; Rosmej, F.; Bureyeva, L. A.; Lisitsa, V. S.

2010-01-01

A very fast method to account for charged particle dynamics effects in calculations of spectral line shape emitted by plasmas is presented. This method is based on a formulation of the frequency fluctuation model (FFM), which provides an expression of the dynamic line shape as a functional of the static distribution of frequencies. Thus, the main numerical work rests on the calculation of the quasistatic Stark profile. This method for taking into account ion dynamics allows a very fast and accurate calculation of Stark broadening of atomic hydrogen high- n series emission lines. It is not limited to hydrogen spectra. Results on helium- β and Lyman- α lines emitted by argon in microballoon implosion experiment conditions compared with experimental data and simulation results are also presented. The present approach reduces the computer time by more than 2 orders of magnitude as compared with the original FFM with an improvement of the calculation precision, and it opens broad possibilities for its application in spectral line-shape codes.

Large dynamic range pressure sensor based on two semicircle-holes microstructured fiber.

PubMed

Liu, Zhengyong; Htein, Lin; Lee, Kang-Kuen; Lau, Kin-Tak; Tam, Hwa-Yaw

2018-01-08

This paper presents a sensitive and large dynamic range pressure sensor based on a novel birefringence microstructured optical fiber (MOF) deployed in a Sagnac interferometer configuration. The MOF has two large semicircle holes in the cladding and a rectangular strut with germanium-doped core in the center. The fiber structure permits surrounding pressure to induce large effective index difference between the two polarized modes. The calculated and measured group birefringence of the fiber are 1.49 × 10 -4 , 1.23 × 10 -4 , respectively, at the wavelength of 1550 nm. Experimental results shown that the pressure sensitivity of the sensor varied from 45,000 pm/MPa to 50,000 pm/MPa, and minimum detectable pressure of 80 Pa and dynamic range of better than 116 dB could be achieved with the novel fiber sensor. The proposed sensor could be used in harsh environment and is an ideal candidate for downhole applications where high pressure measurement at elevated temperature up to 250 °C is needed.

Many-body calculations with deuteron based single-particle bases and their associated natural orbits

NASA Astrophysics Data System (ADS)

Puddu, G.

2018-06-01

We use the recently introduced single-particle states obtained from localized deuteron wave-functions as a basis for nuclear many-body calculations. We show that energies can be substantially lowered if the natural orbits (NOs) obtained from this basis are used. We use this modified basis for {}10{{B}}, {}16{{O}} and {}24{{Mg}} employing the bare NNLOopt nucleon–nucleon interaction. The lowering of the energies increases with the mass. Although in principle NOs require a full scale preliminary many-body calculation, we found that an approximate preliminary many-body calculation, with a marginal increase in the computational cost, is sufficient. The use of natural orbits based on an harmonic oscillator basis leads to a much smaller lowering of the energies for a comparable computational cost.

Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

NASA Astrophysics Data System (ADS)

Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

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

PubMed Central

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

1998-01-01

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

Model based control of dynamic atomic force microscope.

PubMed

Lee, Chibum; Salapaka, Srinivasa M

2015-04-01

A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

Density Functional O(N) Calculations

NASA Astrophysics Data System (ADS)

Ordejón, Pablo

1998-03-01

We have developed a scheme for performing Density Functional Theory calculations with O(N) scaling.(P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B, 53), 10441 (1996) The method uses arbitrarily flexible and complete Atomic Orbitals (AO) basis sets. This gives a wide range of choice, from extremely fast calculations with minimal basis sets, to greatly accurate calculations with complete sets. The size-efficiency of AO bases, together with the O(N) scaling of the algorithm, allow the application of the method to systems with many hundreds of atoms, in single processor workstations. I will present the SIESTA code,(D. Sanchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quantum Chem., 65), 453 (1997) in which the method is implemented, with several LDA, LSD and GGA functionals available, and using norm-conserving, non-local pseudopotentials (in the Kleinman-Bylander form) to eliminate the core electrons. The calculation of static properties such as energies, forces, pressure, stress and magnetic moments, as well as molecular dynamics (MD) simulations capabilities (including variable cell shape, constant temperature and constant pressure MD) are fully implemented. I will also show examples of the accuracy of the method, and applications to large-scale materials and biomolecular systems.

Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations.

PubMed

Steinbrecher, Thomas; Abel, Robert; Clark, Anthony; Friesner, Richard

2017-04-07

Protein side-chain mutation is fundamental both to natural evolutionary processes and to the engineering of protein therapeutics, which constitute an increasing fraction of important medications. Molecular simulation enables the prediction of the effects of mutation on properties such as binding affinity, secondary and tertiary structure, conformational dynamics, and thermal stability. A number of widely differing approaches have been applied to these predictions, including sequence-based algorithms, knowledge-based potential functions, and all-atom molecular mechanics calculations. Free energy perturbation theory, employing all-atom and explicit-solvent molecular dynamics simulations, is a rigorous physics-based approach for calculating thermodynamic effects of, for example, protein side-chain mutations. Over the past several years, we have initiated an investigation of the ability of our most recent free energy perturbation methodology to model the thermodynamics of protein mutation for two specific problems: protein-protein binding affinities and protein thermal stability. We highlight recent advances in the field and outline current and future challenges. Copyright © 2017 Elsevier Ltd. All rights reserved.

Innovative methods for calculation of freeway travel time using limited data : executive summary report.

DOT National Transportation Integrated Search

2008-08-01

ODOTs policy for Dynamic Message Sign : utilization requires travel time(s) to be displayed as : a default message. The current method of : calculating travel time involves a workstation : operator estimating the travel time based upon : observati...

Guidelines for the analysis of free energy calculations.

PubMed

Klimovich, Pavel V; Shirts, Michael R; Mobley, David L

2015-05-01

Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.

Guidelines for the analysis of free energy calculations

PubMed Central

Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.

2015-01-01

Free energy calculations based on molecular dynamics (MD) simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical–analysis.py, freely available on GitHub at https://github.com/choderalab/pymbar–examples, that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope these tools and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134

Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations

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

Cao, Jun, E-mail: caojunbnu@mail.bnu.edu.cn

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 intomore » 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.« less

Scale-invariant entropy-based theory for dynamic ordering

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

Mahulikar, Shripad P., E-mail: spm@iitmandi.ac.in, E-mail: spm@aero.iitb.ac.in; Department of Aerospace Engineering, Indian Institute of Technology Bombay, Mumbai 400076; Kumari, Priti

2014-09-01

Dynamically Ordered self-organized dissipative structure exists in various forms and at different scales. This investigation first introduces the concept of an isolated embedding system, which embeds an open system, e.g., dissipative structure and its mass and/or energy exchange with its surroundings. Thereafter, scale-invariant theoretical analysis is presented using thermodynamic principles for Order creation, existence, and destruction. The sustainability criterion for Order existence based on its structured mass and/or energy interactions with the surroundings is mathematically defined. This criterion forms the basis for the interrelationship of physical parameters during sustained existence of dynamic Order. It is shown that the sufficient conditionmore » for dynamic Order existence is approached if its sustainability criterion is met, i.e., its destruction path is blocked. This scale-invariant approach has the potential to unify the physical understanding of universal dynamic ordering based on entropy considerations.« less

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

NASA Astrophysics Data System (ADS)

Hudson, Brian D.; George, Ashley R.; Ford, Martyn G.; Livingstone, David J.

1992-04-01

Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

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

2016-07-14

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

In Vivo Patellofemoral Contact Mechanics During Active Extension Using a Novel Dynamic MRI-based Methodology

PubMed Central

Borotikar, Bhushan S.; Sheehan, Frances T.

2017-01-01

Objectives To establish an in vivo, normative patellofemoral cartilage contact mechanics database acquired during voluntary muscle control using a novel dynamic magnetic resonance (MR) imaging-based computational methodology and validate the contact mechanics sensitivity to the known sub-millimeter methodological inaccuracies. Design Dynamic cine phase-contrast and multi-plane cine images were acquired while female subjects (n=20, sample of convenience) performed an open kinetic chain (knee flexion-extension) exercise inside a 3-Tesla MR scanner. Static cartilage models were created from high resolution three-dimensional static MR data and accurately placed in their dynamic pose at each time frame based on the cine-PC data. Cartilage contact parameters were calculated based on the surface overlap. Statistical analysis was performed using paired t-test and a one-sample repeated measures ANOVA. The sensitivity of the contact parameters to the known errors in the patellofemoral kinematics was determined. Results Peak mean patellofemoral contact area was 228.7±173.6mm2 at 40° knee angle. During extension, contact centroid and peak strain locations tracked medially on the femoral and patellar cartilage and were not significantly different from each other. At 30°, 35°, and 40° of knee extension, contact area was significantly different. Contact area and centroid locations were insensitive to rotational and translational perturbations. Conclusion This study is a first step towards unfolding the biomechanical pathways to anterior patellofemoral pain and OA using dynamic, in vivo, and accurate methodologies. The database provides crucial data for future studies and for validation of, or as an input to, computational models. PMID:24012620

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Computational model for calculating the dynamical behaviour of generators caused by unbalanced magnetic pull and experimental validation

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.

Calculation of thermal expansion coefficient of glasses based on topological constraint theory

NASA Astrophysics Data System (ADS)

Zeng, Huidan; Ye, Feng; Li, Xiang; Wang, Ling; Yang, Bin; Chen, Jianding; Zhang, Xianghua; Sun, Luyi

2016-10-01

In this work, the thermal expansion behavior and the structure configuration evolution of glasses were studied. Degree of freedom based on the topological constraint theory is correlated with configuration evolution; considering the chemical composition and the configuration change, the analytical equation for calculating the thermal expansion coefficient of glasses from degree of freedom was derived. The thermal expansion of typical silicate and chalcogenide glasses was examined by calculating their thermal expansion coefficients (TEC) using the approach stated above. The results showed that this approach was energetically favorable for glass materials and revealed the corresponding underlying essence from viewpoint of configuration entropy. This work establishes a configuration-based methodology to calculate the thermal expansion coefficient of glasses that, lack periodic order.

Dynamics and lithium binding energies of polyelectrolytes based on functionalized poly(para-phenylene terephthalamide).

PubMed

Grozema, F C; Best, A S; van Eijck, L; Stride, J; Kearley, G J; de Leeuw, S W; Picken, S J

2005-04-28

Polyelectrolyte materials are an interesting class of electrolytes for use in fuel cell and battery applications. Poly(para-phenylene terephthalamide) (PPTA, Kevlar) is a liquid crystalline polymer that, when sulfonated, is a polyelectrolyte that exhibits moderate ion conductivity at elevated temperatures. In this work, quasi-elastic neutron scattering (QENS) experiments were performed to gain insight into the effect of the presence of lithium counterions on the chain dynamics in the material. It was found that the addition of lithium ions decreases the dynamics of the chains. Additionally, the binding of lithium ions to the sulfonic acids groups was investigated by density functional theory (DFT) calculations. It was found that the local surroundings of the sulfonic acid group have very little effect on the lithium-ion binding energy. Binding energies for a variety of different systems were all calculated to be around 150 kcal/mol. The DFT calculations also show the existence of a structure in which a single lithium ion interacts with two sulfonic acid moieties on different chains. The formation of such "electrostatic cross-links" is believed to be the source of the increased tendency to aggregate and the reduced dynamics in the presence of lithium ions.

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

PubMed

Godschalk, Frithjof; Genheden, Samuel; Söderhjelm, Pär; Ryde, Ulf

2013-05-28

Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) is a popular method to calculate the free energy of the binding of ligands to proteins. It involves molecular dynamics (MD) simulations with an explicit solvent of the protein-ligand complex to give a set of snapshots for which energies are calculated with an implicit solvent. This change in the solvation method (explicit → implicit) would strictly require that the energies are reweighted with the implicit-solvent energies, which is normally not done. In this paper we calculate MM/GBSA energies with two generalised Born models for snapshots generated by the same methods or by explicit-solvent simulations for five synthetic N-acetyllactosamine derivatives binding to galectin-3. We show that the resulting energies are very different both in absolute and relative terms, showing that the change in the solvent model is far from innocent and that standard MM/GBSA is not a consistent method. The ensembles generated with the various solvent models are quite different with root-mean-square deviations of 1.2-1.4 Å. The ensembles can be converted to each other by performing short MD simulations with the new method, but the convergence is slow, showing mean absolute differences in the calculated energies of 6-7 kJ mol(-1) after 2 ps simulations. Minimisations show even slower convergence and there are strong indications that the energies obtained from minimised structures are different from those obtained by MD.

Ab initio calculation of finite-temperature charmonium potentials

NASA Astrophysics Data System (ADS)

Evans, P. W. M.; Allton, C. R.; Skullerud, J.-I.

2014-04-01

The interquark potential in charmonium states is calculated in both the zero and nonzero temperature phases from a first-principles lattice QCD calculation. Simulations with two dynamical quark flavors are used with temperatures T in the range 0.4Tc≲T≲1.7Tc, where Tc is the deconfining temperature. The correlators of point-split operators are analyzed to gain spatial information about the charmonium states. A method introduced by the HAL QCD Collaboration and based on the Schrödinger equation is applied to obtain the interquark potential. We find a clear temperature dependence with the central potential agreeing with the Cornell potential in the confined phase and becoming flatter (more screened) as the temperature increases past the deconfining temperature. This is the first time the interquark potential has been calculated for realistic quarks at finite temperature.

Analysis of Dynamic Fracture Compliance Based on Poroelastic Theory - Part II: Results of Numerical and Experimental Tests

NASA Astrophysics Data System (ADS)

Wang, Ding; Ding, Pin-bo; Ba, Jing

2018-03-01

In Part I, a dynamic fracture compliance model (DFCM) was derived based on the poroelastic theory. The normal compliance of fractures is frequency-dependent and closely associated with the connectivity of porous media. In this paper, we first compare the DFCM with previous fractured media theories in the literature in a full frequency range. Furthermore, experimental tests are performed on synthetic rock specimens, and the DFCM is compared with the experimental data in the ultrasonic frequency band. Synthetic rock specimens saturated with water have more realistic mineral compositions and pore structures relative to previous works in comparison with natural reservoir rocks. The fracture/pore geometrical and physical parameters can be controlled to replicate approximately those of natural rocks. P- and S-wave anisotropy characteristics with different fracture and pore properties are calculated and numerical results are compared with experimental data. Although the measurement frequency is relatively high, the results of DFCM are appropriate for explaining the experimental data. The characteristic frequency of fluid pressure equilibration calculated based on the specimen parameters is not substantially less than the measurement frequency. In the dynamic fracture model, the wave-induced fluid flow behavior is an important factor for the fracture-wave interaction process, which differs from the models at the high-frequency limits, for instance, Hudson's un-relaxed model.

Medication calculation: the potential role of digital game-based learning in nurse education.

PubMed

Foss, Brynjar; Mordt Ba, Petter; Oftedal, Bjørg F; Løkken, Atle

2013-12-01

Medication dose calculation is one of several medication-related activities that are conducted by nurses daily. However, medication calculation skills appear to be an area of global concern, possibly because of low numeracy skills, test anxiety, low self-confidence, and low self-efficacy among student nurses. Various didactic strategies have been developed for student nurses who still lack basic mathematical competence. However, we suggest that the critical nature of these skills demands the investigation of alternative and/or supplementary didactic approaches to improve medication calculation skills and to reduce failure rates. Digital game-based learning is a possible solution because of the following reasons. First, mathematical drills may improve medication calculation skills. Second, games are known to be useful during nursing education. Finally, mathematical drill games appear to improve the attitudes of students toward mathematics. The aim of this article was to discuss common challenges of medication calculation skills in nurse education, and we highlight the potential role of digital game-based learning in this area.

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.

The MiAge Calculator: a DNA methylation-based mitotic age calculator of human tissue types.

PubMed

Youn, Ahrim; Wang, Shuang

2018-01-01

Cell division is important in human aging and cancer. The estimation of the number of cell divisions (mitotic age) of a given tissue type in individuals is of great interest as it allows not only the study of biological aging (using a new molecular aging target) but also the stratification of prospective cancer risk. Here, we introduce the MiAge Calculator, a mitotic age calculator based on a novel statistical framework, the MiAge model. MiAge is designed to quantitatively estimate mitotic age (total number of lifetime cell divisions) of a tissue using the stochastic replication errors accumulated in the epigenetic inheritance process during cell divisions. With the MiAge model, the MiAge Calculator was built using the training data of DNA methylation measures of 4,020 tumor and adjacent normal tissue samples from eight TCGA cancer types and was tested using the testing data of DNA methylation measures of 2,221 tumor and adjacent normal tissue samples of five other TCGA cancer types. We showed that within each of the thirteen cancer types studied, the estimated mitotic age is universally accelerated in tumor tissues compared to adjacent normal tissues. Across the thirteen cancer types, we showed that worse cancer survivals are associated with more accelerated mitotic age in tumor tissues. Importantly, we demonstrated the utility of mitotic age by showing that the integration of mitotic age and clinical information leads to improved survival prediction in six out of the thirteen cancer types studied. The MiAge Calculator is available at http://www.columbia.edu/∼sw2206/softwares.htm .

Hybrid dose calculation: a dose calculation algorithm for microbeam radiation therapy

NASA Astrophysics Data System (ADS)

Donzelli, Mattia; Bräuer-Krisch, Elke; Oelfke, Uwe; Wilkens, Jan J.; Bartzsch, Stefan

2018-02-01

Microbeam radiation therapy (MRT) is still a preclinical approach in radiation oncology that uses planar micrometre wide beamlets with extremely high peak doses, separated by a few hundred micrometre wide low dose regions. Abundant preclinical evidence demonstrates that MRT spares normal tissue more effectively than conventional radiation therapy, at equivalent tumour control. In order to launch first clinical trials, accurate and efficient dose calculation methods are an inevitable prerequisite. In this work a hybrid dose calculation approach is presented that is based on a combination of Monte Carlo and kernel based dose calculation. In various examples the performance of the algorithm is compared to purely Monte Carlo and purely kernel based dose calculations. The accuracy of the developed algorithm is comparable to conventional pure Monte Carlo calculations. In particular for inhomogeneous materials the hybrid dose calculation algorithm out-performs purely convolution based dose calculation approaches. It is demonstrated that the hybrid algorithm can efficiently calculate even complicated pencil beam and cross firing beam geometries. The required calculation times are substantially lower than for pure Monte Carlo calculations.

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.

Method and system for detecting a failure or performance degradation in a dynamic system such as a flight vehicle

NASA Technical Reports Server (NTRS)

Miller, Robert H. (Inventor); Ribbens, William B. (Inventor)

2003-01-01

A method and system for detecting a failure or performance degradation in a dynamic system having sensors for measuring state variables and providing corresponding output signals in response to one or more system input signals are provided. The method includes calculating estimated gains of a filter and selecting an appropriate linear model for processing the output signals based on the input signals. The step of calculating utilizes one or more models of the dynamic system to obtain estimated signals. The method further includes calculating output error residuals based on the output signals and the estimated signals. The method also includes detecting one or more hypothesized failures or performance degradations of a component or subsystem of the dynamic system based on the error residuals. The step of calculating the estimated values is performed optimally with respect to one or more of: noise, uncertainty of parameters of the models and un-modeled dynamics of the dynamic system which may be a flight vehicle or financial market or modeled financial system.

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations.

PubMed

Dahlgren, Björn; Reif, Maria M; Hünenberger, Philippe H; Hansen, Niels

2012-10-09

P° and T(-). In variant B, these raw values are corrected prior to differentiation, based on corresponding correction terms appropriate for the different simulation pressures P and temperatures T. The results corresponding to the different calculation schemes show that, except for the hydration free energy itself, accurate methodological independence and quantitative agreement with even the most reliable experimental parameters (ion-pair properties) are not yet reached. Nevertheless, approximate internal consistency and qualitative agreement with experimental results can be achieved, but only when an appropriate correction scheme is applied, along with a careful consideration of standard-state issues. In this sense, the main merit of the present study is to set a clear framework for these types of calculations and to point toward directions for future improvements, with the ultimate goal of reaching a consistent and quantitative description of single-ion hydration thermodynamics in molecular dynamics simulations.

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.

Drama in Dynamics: Boom, Splash, and Speed

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

Netzloff, Heather Marie

2004-12-19

solvent molecules. But, despite the reduced cost relative to fully QM calculations, the EFP method, due to its complex, QM-based potential, does require more computation time than simple interaction potentials, especially when the method is used for large scale molecular dynamics simulations. Thus, the EFP method was parallelized to facilitate these calculations within the quantum chemistry program GAMESS. The EFP method provides relative energies and structures that are in excellent agreement with the analogous fully quantum results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. Molecular dynamics simulations can provide properties that are directly comparable with experimental results, for example radial distribution functions. The molecular PES is a fundamental starting point for chemical reaction dynamics. Many methods can be used to obtain a PES; for example, assuming a global functional form for the PES or, as mentioned above, performing ''on-the-fly'' dynamics with Al or semi-empirical calculations at every molecular configuration. But as the size of the system grows, using electronic structure theory to build a PES and, therefore, study reaction dynamics becomes virtually impossible. The program Grow builds a PES as an interpolation of Al data; the goal is to attempt to produce an accurate PES with the smallest number of Al calculations. The Grow-GAMESS interface was developed to obtain the Al data from GAMESS. Classical or quantum dynamics can be performed on the resulting surface. The interface includes the novel capability to build multi-reference PESs; these types of calculations are applicable to problems ranging from atmospheric chemistry to photochemical reaction mechanisms in organic and inorganic chemistry to fundamental biological phenomena such as photosynthesis.« less

Two-Level Chebyshev Filter Based Complementary Subspace Method: Pushing the Envelope of Large-Scale Electronic Structure Calculations.

PubMed

Banerjee, Amartya S; Lin, Lin; Suryanarayana, Phanish; Yang, Chao; Pask, John E

2018-06-12

We describe a novel iterative strategy for Kohn-Sham density functional theory calculations aimed at large systems (>1,000 electrons), applicable to metals and insulators alike. In lieu of explicit diagonalization of the Kohn-Sham Hamiltonian on every self-consistent field (SCF) iteration, we employ a two-level Chebyshev polynomial filter based complementary subspace strategy to (1) compute a set of vectors that span the occupied subspace of the Hamiltonian; (2) reduce subspace diagonalization to just partially occupied states; and (3) obtain those states in an efficient, scalable manner via an inner Chebyshev filter iteration. By reducing the necessary computation to just partially occupied states and obtaining these through an inner Chebyshev iteration, our approach reduces the cost of large metallic calculations significantly, while eliminating subspace diagonalization for insulating systems altogether. We describe the implementation of the method within the framework of the discontinuous Galerkin (DG) electronic structure method and show that this results in a computational scheme that can effectively tackle bulk and nano systems containing tens of thousands of electrons, with chemical accuracy, within a few minutes or less of wall clock time per SCF iteration on large-scale computing platforms. We anticipate that our method will be instrumental in pushing the envelope of large-scale ab initio molecular dynamics. As a demonstration of this, we simulate a bulk silicon system containing 8,000 atoms at finite temperature, and obtain an average SCF step wall time of 51 s on 34,560 processors; thus allowing us to carry out 1.0 ps of ab initio molecular dynamics in approximately 28 h (of wall time).

Benchmark model correction of monitoring system based on Dynamic Load Test of Bridge

NASA Astrophysics Data System (ADS)

Shi, Jing-xian; Fan, Jiang

2018-03-01

Structural health monitoring (SHM) is a field of research in the area, and it’s designed to achieve bridge safety and reliability assessment, which needs to be carried out on the basis of the accurate simulation of the finite element model. Bridge finite element model is simplified of the structural section form, support conditions, material properties and boundary condition, which is based on the design and construction drawings, and it gets the calculation models and the results.But according to the design and specification requirements established finite element model due to its cannot fully reflect the true state of the bridge, so need to modify the finite element model to obtain the more accurate finite element model. Based on Da-guan river crossing of Ma - Zhao highway in Yunnan province as the background to do the dynamic load test test, we find that the impact coefficient of the theoretical model of the bridge is very different from the coefficient of the actual test, and the change is different; according to the actual situation, the calculation model is adjusted to get the correct frequency of the bridge, the revised impact coefficient found that the modified finite element model is closer to the real state, and provides the basis for the correction of the finite model.

An individual-based model of zebrafish population dynamics accounting for energy dynamics.

PubMed

Beaudouin, Rémy; Goussen, Benoit; Piccini, Benjamin; Augustine, Starrlight; Devillers, James; Brion, François; Péry, Alexandre R R

2015-01-01

Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model) was coupled to an individual based model of zebrafish population dynamics (IBM model). Next, we fitted the DEB model to new experimental data on zebrafish growth and reproduction thus improving existing models. We further analysed the DEB-model and DEB-IBM using a sensitivity analysis. Finally, the predictions of the DEB-IBM were compared to existing observations on natural zebrafish populations and the predicted population dynamics are realistic. While our zebrafish DEB-IBM model can still be improved by acquiring new experimental data on the most uncertain processes (e.g. survival or feeding), it can already serve to predict the impact of compounds at the population level.

Ontology-Based Exchange and Immediate Application of Business Calculation Definitions for Online Analytical Processing

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.

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes.

PubMed

Gapsys, Vytautas; de Groot, Bert L

2017-12-12

Nucleotide-sequence-dependent interactions between proteins and DNA are responsible for a wide range of gene regulatory functions. Accurate and generalizable methods to evaluate the strength of protein-DNA binding have long been sought. While numerous computational approaches have been developed, most of them require fitting parameters to experimental data to a certain degree, e.g., machine learning algorithms or knowledge-based statistical potentials. Molecular-dynamics-based free energy calculations offer a robust, system-independent, first-principles-based method to calculate free energy differences upon nucleotide mutation. We present an automated procedure to set up alchemical MD-based calculations to evaluate free energy changes occurring as the result of a nucleotide mutation in DNA. We used these methods to perform a large-scale mutation scan comprising 397 nucleotide mutation cases in 16 protein-DNA complexes. The obtained prediction accuracy reaches 5.6 kJ/mol average unsigned deviation from experiment with a correlation coefficient of 0.57 with respect to the experimentally measured free energies. Overall, the first-principles-based approach performed on par with the molecular modeling approaches Rosetta and FoldX. Subsequently, we utilized the MD-based free energy calculations to construct protein-DNA binding profiles for the zinc finger protein Zif268. The calculation results compare remarkably well with the experimentally determined binding profiles. The software automating the structure and topology setup for alchemical calculations is a part of the pmx package; the utilities have also been made available online at http://pmx.mpibpc.mpg.de/dna_webserver.html .

Detecting Molecular Rotational Dynamics Complementing the Low-Frequency Terahertz Vibrations in a Zirconium-Based Metal-Organic Framework

NASA Astrophysics Data System (ADS)

Ryder, Matthew R.; Van de Voorde, Ben; Civalleri, Bartolomeo; Bennett, Thomas D.; Mukhopadhyay, Sanghamitra; Cinque, Gianfelice; Fernandez-Alonso, Felix; De Vos, Dirk; Rudić, Svemir; Tan, Jin-Chong

2017-06-01

We show clear experimental evidence of cooperative terahertz (THz) dynamics observed below 3 THz (˜100 cm-1 ), for a low-symmetry Zr-based metal-organic framework structure, termed MIL-140A [ZrO (O2C-C 6H4-CO2) ]. Utilizing a combination of high-resolution inelastic neutron scattering and synchrotron radiation far-infrared spectroscopy, we measured low-energy vibrations originating from the hindered rotations of organic linkers, whose energy barriers and detailed dynamics have been elucidated via ab initio density functional theory calculations. The complex pore architecture caused by the THz rotations has been characterized. We discovered an array of soft modes with trampolinelike motions, which could potentially be the source of anomalous mechanical phenomena such as negative thermal expansion. Our results demonstrate coordinated shear dynamics (2.47 THz), a mechanism which we have shown to destabilize the framework structure, in the exact crystallographic direction of the minimum shear modulus (Gmin ).

Perspective: A Dynamics-Based Classification of Ventricular Arrhythmias

PubMed Central

Weiss, James N.; Garfinkel, Alan; Karagueuzian, Hrayr S.; Nguyen, Thao P.; Olcese, Riccardo; Chen, Peng-Sheng; Qu, Zhilin

2015-01-01

Despite key advances in the clinical management of life-threatening ventricular arrhythmias, culminating with the development of implantable cardioverter-defibrillators and catheter ablation techniques, pharmacologic/biologic therapeutics have lagged behind. The fundamental issue is that biological targets are molecular factors. Diseases, however, represent emergent properties at the scale of the organism that result from dynamic interactions between multiple constantly changing molecular factors. For a pharmacologic/biologic therapy to be effective, it must target the dynamic processes that underlie the disease. Here we propose a classification of ventricular arrhythmias that is based on our current understanding of the dynamics occurring at the subcellular, cellular, tissue and organism scales, which cause arrhythmias by simultaneously generating arrhythmia triggers and exacerbating tissue vulnerability. The goal is to create a framework that systematically links these key dynamic factors together with fixed factors (structural and electrophysiological heterogeneity) synergistically promoting electrical dispersion and increased arrhythmia risk to molecular factors that can serve as biological targets. We classify ventricular arrhythmias into three primary dynamic categories related generally to unstable Ca cycling, reduced repolarization, and excess repolarization, respectively. The clinical syndromes, arrhythmia mechanisms, dynamic factors and what is known about their molecular counterparts are discussed. Based on this framework, we propose a computational-experimental strategy for exploring the links between molecular factors, fixed factors and dynamic factors that underlie life-threatening ventricular arrhythmias. The ultimate objective is to facilitate drug development by creating an in silico platform to evaluate and predict comprehensively how molecular interventions affect not only a single targeted arrhythmia, but all primary arrhythmia dynamics

CALCULATING ROTATING HYDRODYNAMIC AND MAGNETOHYDRODYNAMIC WAVES TO UNDERSTAND MAGNETIC EFFECTS ON DYNAMICAL TIDES

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

Wei, Xing, E-mail: xing.wei@sjtu.edu.cn; Princeton University Observatory, Princeton, NJ 08544

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 flowmore » 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.« less

Lattice dynamics and thermal conductivity of lithium fluoride via first-principles calculations

NASA Astrophysics Data System (ADS)

Liang, Ting; Chen, Wen-Qi; Hu, Cui-E.; Chen, Xiang-Rong; Chen, Qi-Feng

2018-04-01

The lattice thermal conductivity of lithium fluoride (LiF) is accurately computed from a first-principles approach based on an iterative solution of the Boltzmann transport equation. Real-space finite-difference supercell approach is employed to generate the second- and third-order interatomic force constants. The related physical quantities of LiF are calculated by the second- and third- order potential interactions at 30 K-1000 K. The calculated lattice thermal conductivity 13.89 W/(m K) for LiF at room temperature agrees well with the experimental value, demonstrating that the parameter-free approach can furnish precise descriptions of the lattice thermal conductivity for this material. Besides, the Born effective charges, dielectric constants and phonon spectrum of LiF accord well with the existing data. The lattice thermal conductivities for the iterative solution of BTE are also presented.

Dynamic Group Formation Based on a Natural Phenomenon

ERIC Educational Resources Information Center

Zedadra, Amina; Lafifi, Yacine; Zedadra, Ouarda

2016-01-01

This paper presents a new approach of learners grouping in collaborative learning systems. This grouping process is based on traces left by learners. The goal is the circular dynamic grouping to achieve collaborative projects. The proposed approach consists of two main algorithms: (1) the circular grouping algorithm and (2) the dynamic grouping…

Ultrafast photodissociation dynamics of 1,4-diiodobenzene

NASA Astrophysics Data System (ADS)

Stankus, Brian; Zotev, Nikola; Rogers, David M.; Gao, Yan; Odate, Asami; Kirrander, Adam; Weber, Peter M.

2018-05-01

The photodissociation dynamics of 1,4-diiodobenzene is investigated using ultrafast time-resolved photoelectron spectroscopy. Following excitation by laser pulses at 271 nm, the excited-state dynamics is probed by resonance-enhanced multiphoton ionization with 405 nm probe pulses. A progression of Rydberg states, which come into resonance sequentially, provide a fingerprint of the dissociation dynamics of the molecule. The initial excitation decays with a lifetime of 33 ± 4 fs, in good agreement with a previous study. The spectrum is interpreted by reference to ab initio calculations at the CASPT2(18,14) level, including spin-orbit coupling. We propose that both the 5B1 and 6B1 states are excited initially, and based on the calculations, we identify diabatic spin-orbit coupled states corresponding to the main dissociation pathways.

Using Bayes' theorem for free energy calculations

NASA Astrophysics Data System (ADS)

Rogers, David M.

Statistical mechanics is fundamentally based on calculating the probabilities of molecular-scale events. Although Bayes' theorem has generally been recognized as providing key guiding principals for setup and analysis of statistical experiments [83], classical frequentist models still predominate in the world of computational experimentation. As a starting point for widespread application of Bayesian methods in statistical mechanics, we investigate the central quantity of free energies from this perspective. This dissertation thus reviews the basics of Bayes' view of probability theory, and the maximum entropy formulation of statistical mechanics before providing examples of its application to several advanced research areas. We first apply Bayes' theorem to a multinomial counting problem in order to determine inner shell and hard sphere solvation free energy components of Quasi-Chemical Theory [140]. We proceed to consider the general problem of free energy calculations from samples of interaction energy distributions. From there, we turn to spline-based estimation of the potential of mean force [142], and empirical modeling of observed dynamics using integrator matching. The results of this research are expected to advance the state of the art in coarse-graining methods, as they allow a systematic connection from high-resolution (atomic) to low-resolution (coarse) structure and dynamics. In total, our work on these problems constitutes a critical starting point for further application of Bayes' theorem in all areas of statistical mechanics. It is hoped that the understanding so gained will allow for improvements in comparisons between theory and experiment.

Chaotic Image Encryption Algorithm Based on Bit Permutation and Dynamic DNA Encoding.

PubMed

Zhang, Xuncai; Han, Feng; Niu, Ying

2017-01-01

With the help of the fact that chaos is sensitive to initial conditions and pseudorandomness, combined with the spatial configurations in the DNA molecule's inherent and unique information processing ability, a novel image encryption algorithm based on bit permutation and dynamic DNA encoding is proposed here. The algorithm first uses Keccak to calculate the hash value for a given DNA sequence as the initial value of a chaotic map; second, it uses a chaotic sequence to scramble the image pixel locations, and the butterfly network is used to implement the bit permutation. Then, the image is coded into a DNA matrix dynamic, and an algebraic operation is performed with the DNA sequence to realize the substitution of the pixels, which further improves the security of the encryption. Finally, the confusion and diffusion properties of the algorithm are further enhanced by the operation of the DNA sequence and the ciphertext feedback. The results of the experiment and security analysis show that the algorithm not only has a large key space and strong sensitivity to the key but can also effectively resist attack operations such as statistical analysis and exhaustive analysis.

Chaotic Image Encryption Algorithm Based on Bit Permutation and Dynamic DNA Encoding

PubMed Central

2017-01-01

With the help of the fact that chaos is sensitive to initial conditions and pseudorandomness, combined with the spatial configurations in the DNA molecule's inherent and unique information processing ability, a novel image encryption algorithm based on bit permutation and dynamic DNA encoding is proposed here. The algorithm first uses Keccak to calculate the hash value for a given DNA sequence as the initial value of a chaotic map; second, it uses a chaotic sequence to scramble the image pixel locations, and the butterfly network is used to implement the bit permutation. Then, the image is coded into a DNA matrix dynamic, and an algebraic operation is performed with the DNA sequence to realize the substitution of the pixels, which further improves the security of the encryption. Finally, the confusion and diffusion properties of the algorithm are further enhanced by the operation of the DNA sequence and the ciphertext feedback. The results of the experiment and security analysis show that the algorithm not only has a large key space and strong sensitivity to the key but can also effectively resist attack operations such as statistical analysis and exhaustive analysis. PMID:28912802

An Individual-Based Model of Zebrafish Population Dynamics Accounting for Energy Dynamics

PubMed Central

Beaudouin, Rémy; Goussen, Benoit; Piccini, Benjamin; Augustine, Starrlight; Devillers, James; Brion, François; Péry, Alexandre R. R.

2015-01-01

Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model) was coupled to an individual based model of zebrafish population dynamics (IBM model). Next, we fitted the DEB model to new experimental data on zebrafish growth and reproduction thus improving existing models. We further analysed the DEB-model and DEB-IBM using a sensitivity analysis. Finally, the predictions of the DEB-IBM were compared to existing observations on natural zebrafish populations and the predicted population dynamics are realistic. While our zebrafish DEB-IBM model can still be improved by acquiring new experimental data on the most uncertain processes (e.g. survival or feeding), it can already serve to predict the impact of compounds at the population level. PMID:25938409

Dynamic analysis of suspension cable based on vector form intrinsic finite element method

NASA Astrophysics Data System (ADS)

Qin, Jian; Qiao, Liang; Wan, Jiancheng; Jiang, Ming; Xia, Yongjun

2017-10-01

A vector finite element method is presented for the dynamic analysis of cable structures based on the vector form intrinsic finite element (VFIFE) and mechanical properties of suspension cable. Firstly, the suspension cable is discretized into different elements by space points, the mass and external forces of suspension cable are transformed into space points. The structural form of cable is described by the space points at different time. The equations of motion for the space points are established according to the Newton’s second law. Then, the element internal forces between the space points are derived from the flexible truss structure. Finally, the motion equations of space points are solved by the central difference method with reasonable time integration step. The tangential tension of the bearing rope in a test ropeway with the moving concentrated loads is calculated and compared with the experimental data. The results show that the tangential tension of suspension cable with moving loads is consistent with the experimental data. This method has high calculated precision and meets the requirements of engineering application.

The presence of cicada family noise in Javanese and Balinese Pranatamangsa calendar calculation an ethnoecological approach

NASA Astrophysics Data System (ADS)

Suryadarma, I. G. P.; Handziko, Rio Christy

2017-08-01

The presence and distribution of various cicada families as one of Javanese and Balinese ethnic farmers' season changing indicators. Comprehension of season changing is as an effort to optimize crop result as a mean to support basic needs. Society understands the behaviour of animal of cicada family based on season condition. Traditionally season guideline is based on the sun position from the equator, moon position, astronomy called as pranotomongso. Cicada's family is one of indicators of season changing between rain season and dry season. There were two-selected cicadas: garengpung as indicator of dry season and tenggoreknongas indicator of rainy season. This research aimed to discover the presence and growth dynamics of garengpung and tenggoreknong(cicada) as season changing indicator insects. This research is explorative research and data were taken through observation. Field observations on the manifestation and dynamics of two insects were conducted. The research was conducted in Yogyakarta Special Province and Bali Province during period of 2015 up to 2016. Correlation between the presence dynamics and emergence of garengpung and tenggoreknongvoice could be utilized as indicator of rainy and dry season dynamics change. Calculation of rainy and dry season change is relevant with pranotomongso calculation. The presence and dynamics of cicada emergence is still relevant as one of ecological information through ethnoecological approach.

Quantification of tumor mobility during the breathing cycle using 3D dynamic MRI

NASA Astrophysics Data System (ADS)

Schoebinger, Max; Plathow, Christian; Wolf, Ivo; Kauczor, Hans-Ulrich; Meinzer, Hans-Peter

2006-03-01

Respiration causes movement and shape changes in thoracic tumors, which has a direct influence on the radio-therapy planning process. Current methods for the estimation of tumor mobility are either two-dimensional (fluoroscopy, 2D dynamic MRI) or based on radiation (3D (+t) CT, implanted gold markers). With current advances in dynamic MRI acquisition, 3D+t image sequences of the thorax can be acquired covering the thorax over the whole breathing cycle. In this work, methods are presented for the interactive segmentation of tumors in dynamic images, the calculation of tumor trajectories, dynamic tumor volumetry and dynamic tumor rotation/deformation based on 3D dynamic MRI. For volumetry calculation, a set of 21 related partial volume correcting volumetry algorithms has been evaluated based on tumor surrogates. Conventional volumetry based on voxel counting yielded a root mean square error of 29% compared to a root mean square error of 11% achieved by the algorithm performing best among the different volumetry methods. The new workflow has been applied to a set of 26 patients. Preliminary results indicate, that 3D dynamic MRI reveals important aspects of tumor behavior during the breathing cycle. This might imply the possibility to further improve high-precision radiotherapy techniques.

Mosquito population dynamics from cellular automata-based simulation

NASA Astrophysics Data System (ADS)

Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning

2016-02-01

In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.

Representing Micro-Macro Linkages by Actor-Based Dynamic Network Models

PubMed Central

Snijders, Tom A.B.; Steglich, Christian E.G.

2014-01-01

Stochastic actor-based models for network dynamics have the primary aim of statistical inference about processes of network change, but may be regarded as a kind of agent-based models. Similar to many other agent-based models, they are based on local rules for actor behavior. Different from many other agent-based models, by including elements of generalized linear statistical models they aim to be realistic detailed representations of network dynamics in empirical data sets. Statistical parallels to micro-macro considerations can be found in the estimation of parameters determining local actor behavior from empirical data, and the assessment of goodness of fit from the correspondence with network-level descriptives. This article studies several network-level consequences of dynamic actor-based models applied to represent cross-sectional network data. Two examples illustrate how network-level characteristics can be obtained as emergent features implied by micro-specifications of actor-based models. PMID:25960578

New insights into photodissociation dynamics of cyclobutanone from the AIMS dynamic simulation

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

Liu, Lihong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn

2016-04-14

In this work, the combined electronic structure calculations and non-adiabatic dynamics simulations were performed for understanding mechanistic photodissociation of cyclobutanone at ∼248 nm. Besides the stationary and intersection structures reported before, two new conical intersections between the ground (S{sub 0}) and the first excited singlet (S{sub 1}) states were determined in the present study, which were confirmed to be the new S{sub 1} → S{sub 0} funnels by the ab initio multiple spawning dynamic simulation, giving rise to products in the S{sub 0} state selectively. The time evolution of the S{sub 1} electronic population was fitted with the pure exponentialmore » formulae, from which the S{sub 1} lifetime was estimated to be 484.0 fs. The time constant for the S{sub 1} α-cleavage is calculated to be 176.6 fs, which is based on the present dynamics simulation. As a result of the ultrafast S{sub 1} processes, the statistical distribution of the excess energies is prevented in the S{sub 1} state. The S{sub 1} dynamic effect (the nonergodic behavior) was predicted to be an important factor that is responsible for the wavelength dependence of the branching ratio of photodissociation products, which will be discussed in detail.« less

Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

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

Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V., E-mail: sergeid@kth.se

2016-01-21

Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental datamore » obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees.« less

FPGA-based Fused Smart Sensor for Real-Time Plant-Transpiration Dynamic Estimation

PubMed Central

Millan-Almaraz, Jesus Roberto; de Jesus Romero-Troncoso, Rene; Guevara-Gonzalez, Ramon Gerardo; Contreras-Medina, Luis Miguel; Carrillo-Serrano, Roberto Valentin; Osornio-Rios, Roque Alfredo; Duarte-Galvan, Carlos; Rios-Alcaraz, Miguel Angel; Torres-Pacheco, Irineo

2010-01-01

Plant transpiration is considered one of the most important physiological functions because it constitutes the plants evolving adaptation to exchange moisture with a dry atmosphere which can dehydrate or eventually kill the plant. Due to the importance of transpiration, accurate measurement methods are required; therefore, a smart sensor that fuses five primary sensors is proposed which can measure air temperature, leaf temperature, air relative humidity, plant out relative humidity and ambient light. A field programmable gate array based unit is used to perform signal processing algorithms as average decimation and infinite impulse response filters to the primary sensor readings in order to reduce the signal noise and improve its quality. Once the primary sensor readings are filtered, transpiration dynamics such as: transpiration, stomatal conductance, leaf-air-temperature-difference and vapor pressure deficit are calculated in real time by the smart sensor. This permits the user to observe different primary and calculated measurements at the same time and the relationship between these which is very useful in precision agriculture in the detection of abnormal conditions. Finally, transpiration related stress conditions can be detected in real time because of the use of online processing and embedded communications capabilities. PMID:22163656

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

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

Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu, E-mail: okazaki@apchem.nagoya-u.ac.jp

2014-08-28

In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfermore » process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −1}. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.« less

Density functional theory calculation of refractive indices of liquid-forming silicon oil compounds

NASA Astrophysics Data System (ADS)

Lee, Sanghun; Park, Sung Soo; Hagelberg, Frank

2012-02-01

A combination of quantum chemical calculation and molecular dynamics simulation is applied to compute refractive indices of liquid-forming silicon oils. The densities of these species are obtained from molecular dynamics simulations based on the NPT ensemble while the molecular polarizabilities are evaluated by density functional theory. This procedure is shown to yield results well compatible with available experimental data, suggesting that it represents a robust and economic route for determining the refractive indices of liquid-forming organic complexes containing silicon.

Genetic algorithms with memory- and elitism-based immigrants in dynamic environments.

PubMed

Yang, Shengxiang

2008-01-01

In recent years the genetic algorithm community has shown a growing interest in studying dynamic optimization problems. Several approaches have been devised. The random immigrants and memory schemes are two major ones. The random immigrants scheme addresses dynamic environments by maintaining the population diversity while the memory scheme aims to adapt genetic algorithms quickly to new environments by reusing historical information. This paper investigates a hybrid memory and random immigrants scheme, called memory-based immigrants, and a hybrid elitism and random immigrants scheme, called elitism-based immigrants, for genetic algorithms in dynamic environments. In these schemes, the best individual from memory or the elite from the previous generation is retrieved as the base to create immigrants into the population by mutation. This way, not only can diversity be maintained but it is done more efficiently to adapt genetic algorithms to the current environment. Based on a series of systematically constructed dynamic problems, experiments are carried out to compare genetic algorithms with the memory-based and elitism-based immigrants schemes against genetic algorithms with traditional memory and random immigrants schemes and a hybrid memory and multi-population scheme. The sensitivity analysis regarding some key parameters is also carried out. Experimental results show that the memory-based and elitism-based immigrants schemes efficiently improve the performance of genetic algorithms in dynamic environments.

Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pK(a) calculations and molecular dynamics simulations.

PubMed

Langella, Emma; Improta, Roberto; Crescenzi, Orlando; Barone, Vincenzo

2006-07-01

A thorough study of the acid-base behavior of the four histidines and the other titratable residues of the structured domain of human prion protein (125-228) is presented. By using multi-tautomer electrostatic calculations, average titration curves have been built for all titratable residues, using the whole bundles of NMR structures determined at pH 4.5 and 7.0. According to our results, (1) only histidine residues are likely to be involved in the first steps of the pH-driven conformational transition of prion protein; (2) the pK(a)'s of His140 and His177 are approximately 7.0, whereas those of His155 and His187 are < 5.5. 10-ns long molecular dynamics simulations have been performed on five different models, corresponding to the most significant combinations of histidine protonation states. A critical comparison between the available NMR structures and our computational results (1) confirms that His155 and His187 are the residues whose protonation is involved in the conformational rearrangement of huPrP in mildly acidic condition, and (2) shows how their protonation leads to the destructuration of the C-terminal part of HB and to the loss of the last turn of HA that represent the crucial microscopic steps of the rearrangement. (c) 2006 Wiley-Liss, Inc.

SU-E-T-538: Evaluation of IMRT Dose Calculation Based on Pencil-Beam and AAA Algorithms.

PubMed

Yuan, Y; Duan, J; Popple, R; Brezovich, I

2012-06-01

To evaluate the accuracy of dose calculation for intensity modulated radiation therapy (IMRT) based on Pencil Beam (PB) and Analytical Anisotropic Algorithm (AAA) computation algorithms. IMRT plans of twelve patients with different treatment sites, including head/neck, lung and pelvis, were investigated. For each patient, dose calculation with PB and AAA algorithms using dose grid sizes of 0.5 mm, 0.25 mm, and 0.125 mm, were compared with composite-beam ion chamber and film measurements in patient specific QA. Discrepancies between the calculation and the measurement were evaluated by percentage error for ion chamber dose and γ〉l failure rate in gamma analysis (3%/3mm) for film dosimetry. For 9 patients, ion chamber dose calculated with AAA-algorithms is closer to ion chamber measurement than that calculated with PB algorithm with grid size of 2.5 mm, though all calculated ion chamber doses are within 3% of the measurements. For head/neck patients and other patients with large treatment volumes, γ〉l failure rate is significantly reduced (within 5%) with AAA-based treatment planning compared to generally more than 10% with PB-based treatment planning (grid size=2.5 mm). For lung and brain cancer patients with medium and small treatment volumes, γ〉l failure rates are typically within 5% for both AAA and PB-based treatment planning (grid size=2.5 mm). For both PB and AAA-based treatment planning, improvements of dose calculation accuracy with finer dose grids were observed in film dosimetry of 11 patients and in ion chamber measurements for 3 patients. AAA-based treatment planning provides more accurate dose calculation for head/neck patients and other patients with large treatment volumes. Compared with film dosimetry, a γ〉l failure rate within 5% can be achieved for AAA-based treatment planning. © 2012 American Association of Physicists in Medicine.

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster.

PubMed

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S

2017-05-28

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au 147 ), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au 147 , and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au 147 is performed, and it is concluded that Au 147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster

NASA Astrophysics Data System (ADS)

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S.

2017-05-01

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au147), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au147, and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au147 is performed, and it is concluded that Au147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Diffusion coefficients of Mg isotopes in enstatite and forsterite melts calculated by first-principles molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Huang, F.; Qi, Y.; Liu, X.; He, L.

2016-12-01

Stable isotopes can be fractionated by kinetic chemical diffusion because diffusion coefficients (D) of isotopes are mass-dependent. Diffusive isotopic fractionation recorded in rocks and minerals provide unique temporal constrains on geological processes. The mass dependence of D can be described in the form of Di/Dj= (mj/mi)β, where m denotes masses of isotope i and j, and β is an emperical parameter used to quantify the diffusive transport of isotopes [1]. β values can be estimated by experimental calibration and observation of natural samples, which are still rarely reported because it is challenging to precisely quantify the boundary conditions of diffusion processes [2,3,4]. Recent advances in computation technique provide a new way to theoretically calculate β values. For instance, classical molecular dynamics with empirical potential have been used to simulate interactions between atoms and estimate β of Mg isotopes in MgSiO3 melt [3]. Here, to further consider the effect of bonding and electron properties on β values, we apply first-principles Born-Oppenheimer Molecular Dynamics and pseudo-isotope methods (assuming mj/mi = 1/24, 1/4, 2, and 5) to estimate β for MgSiO3 and Mg2SiO4 melts. Our calculation shows that β of Mg isotopes with pseudo-mass ratios are consistent, indicating the reliability of the pseudo-isotope method. For MgSiO3 melt, β is 0.18 at 4000K and 0 GPa, higher than the value calculatedusing molecular dynamics simulations (0.135) [3]. For Mg2SiO4 melt at 0 GPa, β values are: 0.23 ± 0.04 at 2300K, 0.24 ± 0.07 at 3000K, and 0.24 ± 0.01 at 4000K. Notably, β of MgSiO3 and Mg2SiO4 melts are significantly higher than the value determined by diffusion experiments (0.05) [2]. These results indicate that β values are not sensitive to temperature, but dependent on melt composition.

A dynamic aerodynamic resistance approach to calculate high resolution sensible heat fluxes in urban areas

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.

Accuracy of radiotherapy dose calculations based on cone-beam CT: comparison of deformable registration and image correction based methods

NASA Astrophysics Data System (ADS)

Marchant, T. E.; Joshi, K. D.; Moore, C. J.

2018-03-01

Radiotherapy dose calculations based on cone-beam CT (CBCT) images can be inaccurate due to unreliable Hounsfield units (HU) in the CBCT. Deformable image registration of planning CT images to CBCT, and direct correction of CBCT image values are two methods proposed to allow heterogeneity corrected dose calculations based on CBCT. In this paper we compare the accuracy and robustness of these two approaches. CBCT images for 44 patients were used including pelvis, lung and head & neck sites. CBCT HU were corrected using a ‘shading correction’ algorithm and via deformable registration of planning CT to CBCT using either Elastix or Niftyreg. Radiotherapy dose distributions were re-calculated with heterogeneity correction based on the corrected CBCT and several relevant dose metrics for target and OAR volumes were calculated. Accuracy of CBCT based dose metrics was determined using an ‘override ratio’ method where the ratio of the dose metric to that calculated on a bulk-density assigned version of the same image is assumed to be constant for each patient, allowing comparison to the patient’s planning CT as a gold standard. Similar performance is achieved by shading corrected CBCT and both deformable registration algorithms, with mean and standard deviation of dose metric error less than 1% for all sites studied. For lung images, use of deformed CT leads to slightly larger standard deviation of dose metric error than shading corrected CBCT with more dose metric errors greater than 2% observed (7% versus 1%).

Dynamic Evolution Model Based on Social Network Services

NASA Astrophysics Data System (ADS)

Xiong, Xi; Gou, Zhi-Jian; Zhang, Shi-Bin; Zhao, Wen

2013-11-01

Based on the analysis of evolutionary characteristics of public opinion in social networking services (SNS), in the paper we propose a dynamic evolution model, in which opinions are coupled with topology. This model shows the clustering phenomenon of opinions in dynamic network evolution. The simulation results show that the model can fit the data from a social network site. The dynamic evolution of networks accelerates the opinion, separation and aggregation. The scale and the number of clusters are influenced by confidence limit and rewiring probability. Dynamic changes of the topology reduce the number of isolated nodes, while the increased confidence limit allows nodes to communicate more sufficiently. The two effects make the distribution of opinion more neutral. The dynamic evolution of networks generates central clusters with high connectivity and high betweenness, which make it difficult to control public opinions in SNS.

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride

NASA Astrophysics Data System (ADS)

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-01

To understand the initial hydration processes of CaCl2, we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl2(H2O)n- (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl—Ca ion pair is investigated in CaCl2(H2O)n- anions, where the first Ca—Cl ionic bond required 4 water molecules, and both Ca—Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl2(H2O)n clusters, breaking of the first Ca—Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl2(H2O)n requires fewer water molecules than those for MgCl2(H2O)n. Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride.

PubMed

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-14

To understand the initial hydration processes of CaCl 2 , we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl 2 (H 2 O) n - (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl-Ca ion pair is investigated in CaCl 2 (H 2 O) n - anions, where the first Ca-Cl ionic bond required 4 water molecules, and both Ca-Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl 2 (H 2 O) n clusters, breaking of the first Ca-Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl 2 (H 2 O) n requires fewer water molecules than those for MgCl 2 (H 2 O) n . Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

Considering Spine Surgery: A Web-Based Calculator for Communicating Estimates of Personalized Treatment Outcomes.

PubMed

Moulton, Haley; Tosteson, Tor D; Zhao, Wenyan; Pearson, Loretta; Mycek, Kristina; Scherer, Emily; Weinstein, James N; Pearson, Adam; Abdu, William; Schwarz, Susan; Kelly, Michael; McGuire, Kevin; Milam, Alden; Lurie, Jon D

2018-06-05

Prospective evaluation of an informational web-based calculator for communicating estimates of personalized treatment outcomes. To evaluate the usability, effectiveness in communicating benefits and risks, and impact on decision quality of a calculator tool for patients with intervertebral disc herniations, spinal stenosis, and degenerative spondylolisthesis who are deciding between surgical and non-surgical treatments. The decision to have back surgery is preference-sensitive and warrants shared decision-making. However, more patient-specific, individualized tools for presenting clinical evidence on treatment outcomes are needed. Using Spine Patient Outcomes Research Trial (SPORT) data, prediction models were designed and integrated into a web-based calculator tool: http://spinesurgerycalc.dartmouth.edu/calc/. Consumer Reports subscribers with back-related pain were invited to use the calculator via email, and patient participants were recruited to use the calculator in a prospective manner following an initial appointment at participating spine centers. Participants completed questionnaires before and after using the calculator. We randomly assigned previously validated questions that tested knowledge about the treatment options to be asked either before or after viewing the calculator. 1,256 Consumer Reports subscribers and 68 patient participants completed the calculator and questionnaires. Knowledge scores were higher in the post-calculator group compared to the pre-calculator group, indicating that calculator usage successfully informed users. Decisional conflict was lower when measured following calculator use, suggesting the calculator was beneficial in the decision-making process. Participants generally found the tool helpful and easy to use. While the calculator is not a comprehensive decision aid, it does focus on communicating individualized risks and benefits for treatment options. Moreover, it appears to be helpful in achieving the goals of more

A grid-doubling finite-element technique for calculating dynamic three-dimensional spontaneous rupture on an earthquake fault

USGS Publications Warehouse

Barall, Michael

2009-01-01

We present a new finite-element technique for calculating dynamic 3-D spontaneous rupture on an earthquake fault, which can reduce the required computational resources by a factor of six or more, without loss of accuracy. The grid-doubling technique employs small cells in a thin layer surrounding the fault. The remainder of the modelling volume is filled with larger cells, typically two or four times as large as the small cells. In the resulting non-conforming mesh, an interpolation method is used to join the thin layer of smaller cells to the volume of larger cells. Grid-doubling is effective because spontaneous rupture calculations typically require higher spatial resolution on and near the fault than elsewhere in the model volume. The technique can be applied to non-planar faults by morphing, or smoothly distorting, the entire mesh to produce the desired 3-D fault geometry. Using our FaultMod finite-element software, we have tested grid-doubling with both slip-weakening and rate-and-state friction laws, by running the SCEC/USGS 3-D dynamic rupture benchmark problems. We have also applied it to a model of the Hayward fault, Northern California, which uses realistic fault geometry and rock properties. FaultMod implements fault slip using common nodes, which represent motion common to both sides of the fault, and differential nodes, which represent motion of one side of the fault relative to the other side. We describe how to modify the traction-at-split-nodes method to work with common and differential nodes, using an implicit time stepping algorithm.

A Blackboard-Based Dynamic Instructional Planner. ONR Final Report.

ERIC Educational Resources Information Center

Murray, William R.

Dynamic instructional planning was explored as a control mechanism for intelligent tutoring systems through the development of the Blackboard Instructional Planner--a blackboard software-based dynamic planner for computerized intelligent tutoring systems. The planner, designed to be generic to tutors teaching troubleshooting for complex physical…

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

NASA Astrophysics Data System (ADS)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-01

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

PubMed

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-07

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

First-Principles Lattice Dynamics Method for Strongly Anharmonic Crystals

NASA Astrophysics Data System (ADS)

Tadano, Terumasa; Tsuneyuki, Shinji

2018-04-01

We review our recent development of a first-principles lattice dynamics method that can treat anharmonic effects nonperturbatively. The method is based on the self-consistent phonon theory, and temperature-dependent phonon frequencies can be calculated efficiently by incorporating recent numerical techniques to estimate anharmonic force constants. The validity of our approach is demonstrated through applications to cubic strontium titanate, where overall good agreement with experimental data is obtained for phonon frequencies and lattice thermal conductivity. We also show the feasibility of highly accurate calculations based on a hybrid exchange-correlation functional within the present framework. Our method provides a new way of studying lattice dynamics in severely anharmonic materials where the standard harmonic approximation and the perturbative approach break down.

Droplet-based microfluidics and the dynamics of emulsions

NASA Astrophysics Data System (ADS)

Baret, Jean-Christophe; Brosseau, Quentin; Semin, Benoit; Qu, Xiaopeng

2012-02-01

Emulsions are complex fluids already involved for a long time in a wide-range of industrial processes, such as, for example, food, cosmetics or materials synthesis [1]. More recently, applications of emulsions have been extended to new fields like biotechnology or biochemistry where the compartmentalization of compounds in emulsion droplets is used to parallelise (bio-) chemical reactions [2]. Interestingly, these applications pinpoint to fundamental questions dealing with surfactant dynamics, dynamic surface tension, hydrodynamic interactions and electrohydrodynamics. Droplet-based microfluidics is a very powerful tool to quantitatively study the dynamics of emulsions at the single droplet level or even at the single interface level: well-controlled emulsions are produced and manipulated using hydrodynamics, electrical forces, optical actuation and combination of these effects. We will describe here how droplet-based microfluidics is used to extract quantitative informations on the physical-chemistry of emulsions for a better understanding and control of the dynamics of these systems [3].[4pt] [1] J. Bibette et al. Rep. Prog. Phys., 62, 969-1033 (1999)[0pt] [2] A. Theberge et al., Angewandte Chemie Int. Ed. 49, 5846 (2010)[0pt] [3] J.-C. Baret et al., Langmuir, 25, 6088 (2009)

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

PubMed

Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; Luo, Ray; Lee, Taisung; Caldwell, James; Wang, Junmei; Kollman, Peter

2003-12-01

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999-2012, 2003

Spatiotemporal dynamics of grassland aboveground biomass on the Qinghai-Tibet Plateau based on validated MODIS NDVI.

PubMed

Liu, Shiliang; Cheng, Fangyan; Dong, Shikui; Zhao, Haidi; Hou, Xiaoyun; Wu, Xue

2017-06-23

Spatiotemporal dynamics of aboveground biomass (AGB) is a fundamental problem for grassland environmental management on the Qinghai-Tibet Plateau (QTP). Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) data can feasibly be used to estimate AGB at large scales, and their precise validation is necessary to utilize them effectively. In our study, the clip-harvest method was used at 64 plots in QTP grasslands to obtain actual AGB values, and a handheld hyperspectral spectrometer was used to calculate field-measured NDVI to validate MODIS NDVI. Based on the models between NDVI and AGB, AGB dynamics trends during 2000-2012 were analyzed. The results showed that the AGB in QTP grasslands increased during the study period, with 70% of the grasslands undergoing increases mainly in the Qinghai Province. Also, the meadow showed a larger increasing trend than steppe. Future AGB dynamic trends were also investigated using a combined analysis of the slope values and the Hurst exponent. The results showed high sustainability of AGB dynamics trends after the study period. Predictions indicate 60% of the steppe and meadow grasslands would continue to increase in AGB, while 25% of the grasslands would remain in degradation, with most of them distributing in Tibet.

Physics of base-pairing dynamics in DNA

NASA Astrophysics Data System (ADS)

Manghi, Manoel; Destainville, Nicolas

2016-05-01

As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

DOE PAGES

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-24

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations.

PubMed

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J

2018-04-28

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s -1 ) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

The cost of different types of lameness in dairy cows calculated by dynamic programming.

PubMed

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. Copyright © 2010 Elsevier B.V. All rights reserved.

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

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

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-Molecular Dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients; we use this approach to examine atomic condensation onto 6-56 atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity ( v) between atom and cluster andmore » the initial impact parameter ( b). In all cases there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms, and for 14 atom and 28 atom Mg clusters, as cluster equilibration temperature increases the condensation rate coefficient drops to values below the hard sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (> 1000 m s -1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). In conclusion, the presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.« less

Condensation and dissociation rates for gas phase metal clusters from molecular dynamics trajectory calculations

NASA Astrophysics Data System (ADS)

Yang, Huan; Goudeli, Eirini; Hogan, Christopher J.

2018-04-01

In gas phase synthesis systems, clusters form and grow via condensation, in which a monomer binds to an existing cluster. While a hard-sphere equation is frequently used to predict the condensation rate coefficient, this equation neglects the influences of potential interactions and cluster internal energy on the condensation process. Here, we present a collision rate theory-molecular dynamics simulation approach to calculate condensation probabilities and condensation rate coefficients. We use this approach to examine atomic condensation onto 6-56-atom Au and Mg clusters. The probability of condensation depends upon the initial relative velocity (v) between atom and cluster and the initial impact parameter (b). In all cases, there is a well-defined region of b-v space where condensation is highly probable, and outside of which the condensation probability drops to zero. For Au clusters with more than 10 atoms, we find that at gas temperatures in the 300-1200 K range, the condensation rate coefficient exceeds the hard-sphere rate coefficient by a factor of 1.5-2.0. Conversely, for Au clusters with 10 or fewer atoms and for 14- and 28-atom Mg clusters, as cluster equilibration temperature increases, the condensation rate coefficient drops to values below the hard-sphere rate coefficient. Calculations also yield the self-dissociation rate coefficient, which is found to vary considerably with gas temperature. Finally, calculations results reveal that grazing (high b) atom-cluster collisions at elevated velocity (>1000 m s-1) can result in the colliding atom rebounding (bounce) from the cluster surface or binding while another atom dissociates (replacement). The presented method can be applied in developing rate equations to predict material formation and growth rates in vapor phase systems.

Stability of vacancy-type defect clusters in Ni based on first-principles and molecular dynamics simulations

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-10-17

Using first-principles calculations based on density-functional theory, the energetics of different vacancy-type defects, including voids, stacking fault tetrahedra (SFT) and vacancy loops, in Ni are investigated. It is found that voids are more stable than SFT at 0 K, which is also the case after taking into account the volumetric strains. By carrying out ab initio molecular dynamics simulations at temperatures up to 1000 K, direct transformations from vacancy loops and voids into SFT are observed. Our results suggest the importance of temperature effects in determining thermodynamic stability of vacancy clusters in face-centered cubic metals.

Determination of water pH using absorption-based optical sensors: evaluation of different calculation methods

NASA Astrophysics Data System (ADS)

Wang, Hongliang; Liu, Baohua; Ding, Zhongjun; Wang, Xiangxin

2017-02-01

Absorption-based optical sensors have been developed for the determination of water pH. In this paper, based on the preparation of a transparent sol-gel thin film with a phenol red (PR) indicator, several calculation methods, including simple linear regression analysis, quadratic regression analysis and dual-wavelength absorbance ratio analysis, were used to calculate water pH. Results of MSSRR show that dual-wavelength absorbance ratio analysis can improve the calculation accuracy of water pH in long-term measurement.

Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane

NASA Astrophysics Data System (ADS)

Doi, Hideo; Okuwaki, Koji; Mochizuki, Yuji; Ozawa, Taku; Yasuoka, Kenji

2017-09-01

In dissipative particle dynamics (DPD) simulations, it is necessary to use the so-called χ parameter set that express the effective interactions between particles. Recently, we have developed a new scheme to evaluate the χ parameters in a non-empirical way through a series of fragment molecular orbital (FMO) calculations. As a challenging test, we have performed the DPD simulations using the FMO-based χ parameters for a mixture of 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) and water. The structures of both membrane and vesicle were formed successfully. The calculated structural parameters of membrane were in good agreement with experimental results.

Calculation of effective transport properties of partially saturated gas diffusion layers

NASA Astrophysics Data System (ADS)

Bednarek, Tomasz; Tsotridis, Georgios

2017-02-01

A large number of currently available Computational Fluid Dynamics numerical models of Polymer Electrolyte Membrane Fuel Cells (PEMFC) are based on the assumption that porous structures are mainly considered as thin and homogenous layers, hence the mass transport equations in structures such as Gas Diffusion Layers (GDL) are usually modelled according to the Darcy assumptions. Application of homogenous models implies that the effects of porous structures are taken into consideration via the effective transport properties of porosity, tortuosity, permeability (or flow resistance), diffusivity, electric and thermal conductivity. Therefore, reliable values of those effective properties of GDL play a significant role for PEMFC modelling when employing Computational Fluid Dynamics, since these parameters are required as input values for performing the numerical calculations. The objective of the current study is to calculate the effective transport properties of GDL, namely gas permeability, diffusivity and thermal conductivity, as a function of liquid water saturation by using the Lattice-Boltzmann approach. The study proposes a method of uniform water impregnation of the GDL based on the "Fine-Mist" assumption by taking into account the surface tension of water droplets and the actual shape of GDL pores.

Dynamic motion planning of 3D human locomotion using gradient-based optimization.

PubMed

Kim, Hyung Joo; Wang, Qian; Rahmatalla, Salam; Swan, Colby C; Arora, Jasbir S; Abdel-Malek, Karim; Assouline, Jose G

2008-06-01

Since humans can walk with an infinite variety of postures and limb movements, there is no unique solution to the modeling problem to predict human gait motions. Accordingly, we test herein the hypothesis that the redundancy of human walking mechanisms makes solving for human joint profiles and force time histories an indeterminate problem best solved by inverse dynamics and optimization methods. A new optimization-based human-modeling framework is thus described for predicting three-dimensional human gait motions on level and inclined planes. The basic unknowns in the framework are the joint motion time histories of a 25-degree-of-freedom human model and its six global degrees of freedom. The joint motion histories are calculated by minimizing an objective function such as deviation of the trunk from upright posture that relates to the human model's performance. A variety of important constraints are imposed on the optimization problem, including (1) satisfaction of dynamic equilibrium equations by requiring the model's zero moment point (ZMP) to lie within the instantaneous geometrical base of support, (2) foot collision avoidance, (3) limits on ground-foot friction, and (4) vanishing yawing moment. Analytical forms of objective and constraint functions are presented and discussed for the proposed human-modeling framework in which the resulting optimization problems are solved using gradient-based mathematical programming techniques. When the framework is applied to the modeling of bipedal locomotion on level and inclined planes, acyclic human walking motions that are smooth and realistic as opposed to less natural robotic motions are obtained. The aspects of the modeling framework requiring further investigation and refinement, as well as potential applications of the framework in biomechanics, are discussed.

Agent-based model for rural-urban migration: A dynamic consideration

NASA Astrophysics Data System (ADS)

Cai, Ning; Ma, Hai-Ying; Khan, M. Junaid

2015-10-01

This paper develops a dynamic agent-based model for rural-urban migration, based on the previous relevant works. The model conforms to the typical dynamic linear multi-agent systems model concerned extensively in systems science, in which the communication network is formulated as a digraph. Simulations reveal that consensus of certain variable could be harmful to the overall stability and should be avoided.

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2016-01-01

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations. PMID:27453631

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

PubMed

Miao, Yinglong; McCammon, J Andrew

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

Efficient "on-the-fly" calculation of Raman spectra from ab-initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water.

PubMed

Partovi-Azar, Pouya; Kühne, Thomas D

2015-11-05

We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second-generation Car-Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed-up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of ab-initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra. © 2015 Wiley Periodicals, Inc.

Vibrational studies of Thyroxine hormone: Comparative study with quantum chemical calculations

NASA Astrophysics Data System (ADS)

Borah, Mukunda Madhab; Devi, Th. Gomti

2017-11-01

The FTIR and Raman techniques have been used to record spectra of Thyroxine. The stable geometrical parameters and vibrational wave numbers were calculated based on potential energy distribution (PED) using vibrational energy distribution analysis (VEDA) program. The vibrational energies are assigned to monomer, chain dimer and cyclic dimers of this molecule using the basis set B3LYP/LANL2DZ. The computational scaled frequencies are in good agreements with the experimental results. The study is extended to calculate the HOMO-LUMO energy gap, Molecular Electrostatic Potential (MEP) surface, hardness (η), chemical potential (μ), Global electrophilicity index (ω) and different thermo dynamical properties of Thyroxine in different states. The calculated HOMO-LUMO energies show the charge transfer occurs within the molecule. The calculated Natural bond orbital (NBO) analysis confirms the presence of intra-molecular charge transfer as well as the hydrogen bonding interaction.

DFT calculation of pKa’s for dimethoxypyrimidinylsalicylic based herbicides

NASA Astrophysics Data System (ADS)

Delgado, Eduardo J.

2009-03-01

Dimethoxypyrimidinylsalicylic derived compounds show potent herbicidal activity as a result of the inhibition of acetohydroxyacid synthase, the first common enzyme in the biosynthetic pathway of the branched-chain aminoacids (valine, leucine and isoleucine) in plants, bacteria and fungi. Despite its practical importance, this family of compounds have been poorly characterized from a physico-chemical point of view. Thus for instance, their pK a's have not been reported earlier neither experimentally nor theoretically. In this study, the acid-dissociation constants of 39 dimethoxypyrimidinylsalicylic derived herbicides are calculated by DFT methods at B3LYP/6-31G(d,p) level of theory. The calculated values are validated by two checking tests based on the Hammett equation.

Cultural-based particle swarm for dynamic optimisation problems

NASA Astrophysics Data System (ADS)

Daneshyari, Moayed; Yen, Gary G.

2012-07-01

Many practical optimisation problems are with the existence of uncertainties, among which a significant number belong to the dynamic optimisation problem (DOP) category in which the fitness function changes through time. In this study, we propose the cultural-based particle swarm optimisation (PSO) to solve DOP problems. A cultural framework is adopted incorporating the required information from the PSO into five sections of the belief space, namely situational, temporal, domain, normative and spatial knowledge. The stored information will be adopted to detect the changes in the environment and assists response to the change through a diversity-based repulsion among particles and migration among swarms in the population space, and also helps in selecting the leading particles in three different levels, personal, swarm and global levels. Comparison of the proposed heuristics over several difficult dynamic benchmark problems demonstrates the better or equal performance with respect to most of other selected state-of-the-art dynamic PSO heuristics.

Calculating evidence-based renal replacement therapy - Introducing an excel-based calculator to improve prescribing and delivery in renal replacement therapy - A before and after study.

PubMed

Cottle, Daniel; Mousdale, Stephen; Waqar-Uddin, Haroon; Tully, Redmond; Taylor, Benjamin

2016-02-01

Transferring the theoretical aspect of continuous renal replacement therapy to the bedside and delivering a given "dose" can be difficult. In research, the "dose" of renal replacement therapy is given as effluent flow rate in ml kg -1  h -1 . Unfortunately, most machines require other information when they are initiating therapy, including blood flow rate, pre-blood pump flow rate, dialysate flow rate, etc. This can lead to confusion, resulting in patients receiving inappropriate doses of renal replacement therapy. Our aim was to design an excel calculator which would personalise patient's treatment, deliver an effective, evidence-based dose of renal replacement therapy without large variations in practice and prolong filter life. Our calculator prescribes a haemodialfiltration dose of 25 ml kg -1  h -1 whilst limiting the filtration fraction to 15%. We compared the episodes of renal replacement therapy received by a historical group of patients, by retrieving their data stored on the haemofiltration machines, to a group where the calculator was used. In the second group, the data were gathered prospectively. The median delivered dose reduced from 41.0 ml kg -1  h -1 to 26.8 ml kg -1  h -1 with reduced variability that was significantly closer to the aim of 25 ml kg -1 .h -1 ( p  < 0.0001). The median treatment time increased from 8.5 h to 22.2 h ( p  = 0.00001). Our calculator significantly reduces variation in prescriptions of continuous veno-venous haemodiafiltration and provides an evidence-based dose. It is easy to use and provides personal care for patients whilst optimizing continuous veno-venous haemodiafiltration delivery and treatment times.

Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

NASA Astrophysics Data System (ADS)

Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

2016-10-01

We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

On one-dimensional stretching functions for finite-difference calculations. [computational fluid dynamics

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.

Dynamic stability of maglev systems

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

Cai, Y.; Chen, S.S.; Mulcahy, T.M.

1994-05-01

Because dynamic instabilities are not acceptable in any commercial maglev system, it is important to consider dynamic instability in the development of all maglev systems. This study considers the stability of maglev systems based on experimental data, scoping calculations, and simple mathematical models. Divergence and flutter are obtained for coupled vibration of a three-degree-of-freedom maglev vehicle on a guideway consisting of double L-shaped aluminum segments. The theory and analysis developed in this study provides basic stability characteristics and identifies future research needs for maglev systems.

Automated placement of interfaces in conformational kinetics calculations using machine learning

NASA Astrophysics Data System (ADS)

Grazioli, Gianmarc; Butts, Carter T.; Andricioaei, Ioan

2017-10-01

Several recent implementations of algorithms for sampling reaction pathways employ a strategy for placing interfaces or milestones across the reaction coordinate manifold. Interfaces can be introduced such that the full feature space describing the dynamics of a macromolecule is divided into Voronoi (or other) cells, and the global kinetics of the molecular motions can be calculated from the set of fluxes through the interfaces between the cells. Although some methods of this type are exact for an arbitrary set of cells, in practice, the calculations will converge fastest when the interfaces are placed in regions where they can best capture transitions between configurations corresponding to local minima. The aim of this paper is to introduce a fully automated machine-learning algorithm for defining a set of cells for use in kinetic sampling methodologies based on subdividing the dynamical feature space; the algorithm requires no intuition about the system or input from the user and scales to high-dimensional systems.

Automated placement of interfaces in conformational kinetics calculations using machine learning.

PubMed

Grazioli, Gianmarc; Butts, Carter T; Andricioaei, Ioan

2017-10-21

Several recent implementations of algorithms for sampling reaction pathways employ a strategy for placing interfaces or milestones across the reaction coordinate manifold. Interfaces can be introduced such that the full feature space describing the dynamics of a macromolecule is divided into Voronoi (or other) cells, and the global kinetics of the molecular motions can be calculated from the set of fluxes through the interfaces between the cells. Although some methods of this type are exact for an arbitrary set of cells, in practice, the calculations will converge fastest when the interfaces are placed in regions where they can best capture transitions between configurations corresponding to local minima. The aim of this paper is to introduce a fully automated machine-learning algorithm for defining a set of cells for use in kinetic sampling methodologies based on subdividing the dynamical feature space; the algorithm requires no intuition about the system or input from the user and scales to high-dimensional systems.

Structure and dynamics of acetate anion-based ionic liquids from molecular dynamics study

NASA Astrophysics Data System (ADS)

Chandran, Aneesh; Prakash, Karthigeyan; Senapati, Sanjib

2010-08-01

Acetate anion-based ionic liquids (ILs) have found wide range of applications. The microstructure and dynamics of this IL family have not been clearly understood yet. We report molecular dynamics simulation results of three acetate anion-based ionic liquids that encompass the most common IL cations. Simulations are performed based on a set of proposed force field parameters for IL acetate anion which can be combined with existing parameters for IL cations to simulate large variety of ILs. The computed liquid density and IR spectral data for [BMIM][Ac] are found to match very well with available experimental results. The strong amino-group-associated interactions in [TMG][Ac] are seen to bring about higher cohesive energy density, stronger ion packing, and more restricted translational and rotational mobilities of the constituent ions. The IL anions are found to track the cation movements in all systems, implying that ions in ILs travel in pairs or clusters.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

PubMed

Ionescu, Crina-Maria; Sehnal, David; Falginella, Francesco L; Pant, Purbaj; Pravda, Lukáš; Bouchal, Tomáš; Svobodová Vařeková, Radka; Geidl, Stanislav; Koča, Jaroslav

2015-01-01

Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.

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.

Fast and accurate calculation of dilute quantum gas using Uehling–Uhlenbeck model equation

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

Yano, Ryosuke, E-mail: ryosuke.yano@tokiorisk.co.jp

The Uehling–Uhlenbeck (U–U) model equation is studied for the fast and accurate calculation of a dilute quantum gas. In particular, the direct simulation Monte Carlo (DSMC) method is used to solve the U–U model equation. DSMC analysis based on the U–U model equation is expected to enable the thermalization to be accurately obtained using a small number of sample particles and the dilute quantum gas dynamics to be calculated in a practical time. Finally, the applicability of DSMC analysis based on the U–U model equation to the fast and accurate calculation of a dilute quantum gas is confirmed by calculatingmore » the viscosity coefficient of a Bose gas on the basis of the Green–Kubo expression and the shock layer of a dilute Bose gas around a cylinder.« less

Increasing the efficiency and accuracy of time-resolved electronic spectra calculations with on-the-fly ab initio quantum dynamics methods

NASA Astrophysics Data System (ADS)

Vanicek, Jiri

2014-03-01

Rigorous quantum-mechanical calculations of coherent ultrafast electronic spectra remain difficult. I will present several approaches developed in our group that increase the efficiency and accuracy of such calculations: First, we justified the feasibility of evaluating time-resolved spectra of large systems by proving that the number of trajectories needed for convergence of the semiclassical dephasing representation/phase averaging is independent of dimensionality. Recently, we further accelerated this approximation with a cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. The accuracy of potential energy surfaces was increased by combining the dephasing representation with accurate on-the-fly ab initio electronic structure calculations, including nonadiabatic and spin-orbit couplings. Finally, the inherent semiclassical approximation was removed in the exact quantum Gaussian dephasing representation, in which semiclassical trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. Among other examples I will present an on-the-fly ab initio semiclassical dynamics calculation of the dispersed time-resolved stimulated emission spectrum of the 54-dimensional azulene. This research was supported by EPFL and by the Swiss National Science Foundation NCCR MUST (Molecular Ultrafast Science and Technology) and Grant No. 200021124936/1.

Molecular dynamic simulations for FOX-7 and FOX-7 based PBXs.

PubMed

Wang, Junying; Jin, Shaohua; Chen, Shusen; Li, Lijie; Wang, Dongxu; Lu, Zhiyan; Wang, Na; Wang, Junfeng

2018-06-01

Molecular dynamic (MD) simulations were applied to investigate the binding energies and mechanical properties of 1,1-diamino-2,2-dinitroethene (FOX-7) based polymer bonded explosives (PBXs) with ethylenevinylacetate copolymer (EVA), fluorine (F2641), hydroxyl-terminated polybutadiene (HTPB), and styrene butadiene styrene block copolymer (SBS). The binding energies between FOX-7 and the four polymer binders are different, of which the descending order is FOX-7/HTPB ≈ FOX-7/SBS > FOX-7/EVA > FOX-7/F2641. Furthermore, the (002) surface of FOX-7 has the strongest interaction with the four polymers. The mechanical properties (elastic moduli and Poisson's ratio) of pure FOX-7 and FOX-7 based PBXs were obtained. The results show that the descending order of the ability of polymer binders to improve plasticity of PBXs is SBS > F2641 > EVA > HTPB. The formability of FOX-7 based PBXs is better than that of pure FOX-7, as the order of FOX-7/SBS > FOX-7/EVA > FOX-7/F2641 > FOX-7/HTPB > FOX-7 shows. Poisson's ratio of SBS is the highest. The calculated detonation performances for pure FOX-7 and FOX-7 based PBXs show that the detonation properties of explosives slightly decreases when the mass ratio of binder is about 5%. All the theoretical detonation velocities of FOX-7 based PBXs are higher than 8500 m/s.

Dynamics of spontaneous flipping of a mismatched base in DNA duplex.

PubMed

Yin, Yandong; Yang, Lijiang; Zheng, Guanqun; Gu, Chan; Yi, Chengqi; He, Chuan; Gao, Yi Qin; Zhao, Xin Sheng

2014-06-03

DNA base flipping is a fundamental theme in DNA biophysics. The dynamics for a B-DNA base to spontaneously flip out of the double helix has significant implications in various DNA-protein interactions but are still poorly understood. The spontaneous base-flipping rate obtained previously via the imino proton exchange assay is most likely the rate of base wobbling instead of flipping. Using the diffusion-decelerated fluorescence correlation spectroscopy together with molecular dynamics simulations, we show that a base of a single mismatched base pair (T-G, T-T, or T-C) in a double-stranded DNA can spontaneously flip out of the DNA duplex. The extrahelical lifetimes are on the order of 10 ms, whereas the intrahelical lifetimes range from 0.3 to 20 s depending on the stability of the base pairs. These findings provide detailed understanding on the dynamics of DNA base flipping and lay down foundation to fully understand how exactly the repair proteins search and locate the target mismatched base among a vast excess of matched DNA bases.

Temperature dependent effective potential method for accurate free energy calculations of solids

NASA Astrophysics Data System (ADS)

Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.

2013-03-01

We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.

Feasible Muscle Activation Ranges Based on Inverse Dynamics Analyses of Human Walking

PubMed Central

Simpson, Cole S.; Sohn, M. Hongchul; Allen, Jessica L.; Ting, Lena H.

2015-01-01

Although it is possible to produce the same movement using an infinite number of different muscle activation patterns owing to musculoskeletal redundancy, the degree to which observed variations in muscle activity can deviate from optimal solutions computed from biomechanical models is not known. Here, we examined the range of biomechanically permitted activation levels in individual muscles during human walking using a detailed musculoskeletal model and experimentally-measured kinetics and kinematics. Feasible muscle activation ranges define the minimum and maximum possible level of each muscle’s activation that satisfy inverse dynamics joint torques assuming that all other muscles can vary their activation as needed. During walking, 73% of the muscles had feasible muscle activation ranges that were greater than 95% of the total muscle activation range over more than 95% of the gait cycle, indicating that, individually, most muscles could be fully active or fully inactive while still satisfying inverse dynamics joint torques. Moreover, the shapes of the feasible muscle activation ranges did not resemble previously-reported muscle activation patterns nor optimal solutions, i.e. static optimization and computed muscle control, that are based on the same biomechanical constraints. Our results demonstrate that joint torque requirements from standard inverse dynamics calculations are insufficient to define the activation of individual muscles during walking in healthy individuals. Identifying feasible muscle activation ranges may be an effective way to evaluate the impact of additional biomechanical and/or neural constraints on possible versus actual muscle activity in both normal and impaired movements. PMID:26300401

Dynamic train-track interaction at high vehicle speeds—Modelling of wheelset dynamics and wheel rotation

NASA Astrophysics Data System (ADS)

Torstensson, P. T.; Nielsen, J. C. O.; Baeza, L.

2011-10-01

Vertical dynamic train-track interaction at high vehicle speeds is investigated in a frequency range from about 20 Hz to 2.5 kHz. The inertial effects due to wheel rotation are accounted for in the vehicle model by implementing a structural dynamics model of a rotating wheelset. Calculated wheel-rail contact forces using the flexible, rotating wheelset model are compared with contact forces based on rigid, non-rotating models. For a validation of the train-track interaction model, calculated contact forces are compared with contact forces measured using an instrumented wheelset. When the system is excited at a frequency where two different wheelset mode shapes, due to the wheel rotation, have coinciding resonance frequencies, significant differences are found in the contact forces calculated with the rotating and non-rotating wheelset models. Further, the use of a flexible, rotating wheelset model is recommended for load cases leading to large magnitude contact force components in the high-frequency range (above 1.5 kHz). In particular, the influence of the radial wheel eigenmodes with two or three nodal diameters is significant.

A novel method for calculating the dynamic capillary force and correcting the pressure error in micro-tube experiment.

PubMed

Wang, Shuoliang; Liu, Pengcheng; Zhao, Hui; Zhang, Yuan

2017-11-29

Micro-tube experiment has been implemented to understand the mechanisms of governing microcosmic fluid percolation and is extensively used in both fields of micro electromechanical engineering and petroleum engineering. The measured pressure difference across the microtube is not equal to the actual pressure difference across the microtube. Taking into account the additional pressure losses between the outlet of the micro tube and the outlet of the entire setup, we propose a new method for predicting the dynamic capillary pressure using the Level-set method. We first demonstrate it is a reliable method for describing microscopic flow by comparing the micro-model flow-test results against the predicted results using the Level-set method. In the proposed approach, Level-set method is applied to predict the pressure distribution along the microtube when the fluids flow along the microtube at a given flow rate; the microtube used in the calculation has the same size as the one used in the experiment. From the simulation results, the pressure difference across a curved interface (i.e., dynamic capillary pressure) can be directly obtained. We also show that dynamic capillary force should be properly evaluated in the micro-tube experiment in order to obtain the actual pressure difference across the microtube.

The consideration of atmospheric stability within wind farm AEP calculations

NASA Astrophysics Data System (ADS)

Schmidt, Jonas; Chang, Chi-Yao; Dörenkämper, Martin; Salimi, Milad; Teichmann, Tim; Stoevesandt, Bernhard

2016-09-01

The annual energy production of an existing wind farm including thermal stratification is calculated with two different methods and compared to the average of three years of SCADA data. The first method is based on steady state computational fluid dynamics simulations and the assumption of Reynolds-similarity at hub height. The second method is a wake modelling calculation, where a new stratification transformation model was imposed on the Jensen an Ainslie wake models. The inflow states for both approaches were obtained from one year WRF simulation data of the site. Although all models underestimate the mean wind speed and wake effects, the results from the phenomenological wake transformation are compatible with high-fidelity simulation results.

Reliability modelling and analysis of a multi-state element based on a dynamic Bayesian network

PubMed Central

Xu, Tingxue; Gu, Junyuan; Dong, Qi; Fu, Linyu

2018-01-01

This paper presents a quantitative reliability modelling and analysis method for multi-state elements based on a combination of the Markov process and a dynamic Bayesian network (DBN), taking perfect repair, imperfect repair and condition-based maintenance (CBM) into consideration. The Markov models of elements without repair and under CBM are established, and an absorbing set is introduced to determine the reliability of the repairable element. According to the state-transition relations between the states determined by the Markov process, a DBN model is built. In addition, its parameters for series and parallel systems, namely, conditional probability tables, can be calculated by referring to the conditional degradation probabilities. Finally, the power of a control unit in a failure model is used as an example. A dynamic fault tree (DFT) is translated into a Bayesian network model, and subsequently extended to a DBN. The results show the state probabilities of an element and the system without repair, with perfect and imperfect repair, and under CBM, with an absorbing set plotted by differential equations and verified. Through referring forward, the reliability value of the control unit is determined in different kinds of modes. Finally, weak nodes are noted in the control unit. PMID:29765629

Reliability modelling and analysis of a multi-state element based on a dynamic Bayesian network

NASA Astrophysics Data System (ADS)

Li, Zhiqiang; Xu, Tingxue; Gu, Junyuan; Dong, Qi; Fu, Linyu

2018-04-01

This paper presents a quantitative reliability modelling and analysis method for multi-state elements based on a combination of the Markov process and a dynamic Bayesian network (DBN), taking perfect repair, imperfect repair and condition-based maintenance (CBM) into consideration. The Markov models of elements without repair and under CBM are established, and an absorbing set is introduced to determine the reliability of the repairable element. According to the state-transition relations between the states determined by the Markov process, a DBN model is built. In addition, its parameters for series and parallel systems, namely, conditional probability tables, can be calculated by referring to the conditional degradation probabilities. Finally, the power of a control unit in a failure model is used as an example. A dynamic fault tree (DFT) is translated into a Bayesian network model, and subsequently extended to a DBN. The results show the state probabilities of an element and the system without repair, with perfect and imperfect repair, and under CBM, with an absorbing set plotted by differential equations and verified. Through referring forward, the reliability value of the control unit is determined in different kinds of modes. Finally, weak nodes are noted in the control unit.

Study of base pair mutations in proline-rich homeodomain (PRH)-DNA complexes using molecular dynamics.

PubMed

Jalili, Seifollah; Karami, Leila; Schofield, Jeremy

2013-06-01

Proline-rich homeodomain (PRH) is a regulatory protein controlling transcription and gene expression processes by binding to the specific sequence of DNA, especially to the sequence 5'-TAATNN-3'. The impact of base pair mutations on the binding between the PRH protein and DNA is investigated using molecular dynamics and free energy simulations to identify DNA sequences that form stable complexes with PRH. Three 20-ns molecular dynamics simulations (PRH-TAATTG, PRH-TAATTA and PRH-TAATGG complexes) in explicit solvent water were performed to investigate three complexes structurally. Structural analysis shows that the native TAATTG sequence forms a complex that is more stable than complexes with base pair mutations. It is also observed that upon mutation, the number and occupancy of the direct and water-mediated hydrogen bonds decrease. Free energy calculations performed with the thermodynamic integration method predict relative binding free energies of 0.64 and 2 kcal/mol for GC to AT and TA to GC mutations, respectively, suggesting that among the three DNA sequences, the PRH-TAATTG complex is more stable than the two mutated complexes. In addition, it is demonstrated that the stability of the PRH-TAATTA complex is greater than that of the PRH-TAATGG complex.

Rupture Dynamics and Seismic Radiation on Rough Faults for Simulation-Based PSHA

NASA Astrophysics Data System (ADS)

Mai, P. M.; Galis, M.; Thingbaijam, K. K. S.; Vyas, J. C.; Dunham, E. M.

2017-12-01

Simulation-based ground-motion predictions may augment PSHA studies in data-poor regions or provide additional shaking estimations, incl. seismic waveforms, for critical facilities. Validation and calibration of such simulation approaches, based on observations and GMPE's, is important for engineering applications, while seismologists push to include the precise physics of the earthquake rupture process and seismic wave propagation in 3D heterogeneous Earth. Geological faults comprise both large-scale segmentation and small-scale roughness that determine the dynamics of the earthquake rupture process and its radiated seismic wavefield. We investigate how different parameterizations of fractal fault roughness affect the rupture evolution and resulting near-fault ground motions. Rupture incoherence induced by fault roughness generates realistic ω-2 decay for high-frequency displacement amplitude spectra. Waveform characteristics and GMPE-based comparisons corroborate that these rough-fault rupture simulations generate realistic synthetic seismogram for subsequent engineering application. Since dynamic rupture simulations are computationally expensive, we develop kinematic approximations that emulate the observed dynamics. Simplifying the rough-fault geometry, we find that perturbations in local moment tensor orientation are important, while perturbations in local source location are not. Thus, a planar fault can be assumed if the local strike, dip, and rake are maintained. The dynamic rake angle variations are anti-correlated with local dip angles. Based on a dynamically consistent Yoffe source-time function, we show that the seismic wavefield of the approximated kinematic rupture well reproduces the seismic radiation of the full dynamic source process. Our findings provide an innovative pseudo-dynamic source characterization that captures fault roughness effects on rupture dynamics. Including the correlations between kinematic source parameters, we present a new

Neural network based adaptive control for nonlinear dynamic regimes

NASA Astrophysics Data System (ADS)

Shin, Yoonghyun

Adaptive control designs using neural networks (NNs) based on dynamic inversion are investigated for aerospace vehicles which are operated at highly nonlinear dynamic regimes. NNs play a key role as the principal element of adaptation to approximately cancel the effect of inversion error, which subsequently improves robustness to parametric uncertainty and unmodeled dynamics in nonlinear regimes. An adaptive control scheme previously named 'composite model reference adaptive control' is further developed so that it can be applied to multi-input multi-output output feedback dynamic inversion. It can have adaptive elements in both the dynamic compensator (linear controller) part and/or in the conventional adaptive controller part, also utilizing state estimation information for NN adaptation. This methodology has more flexibility and thus hopefully greater potential than conventional adaptive designs for adaptive flight control in highly nonlinear flight regimes. The stability of the control system is proved through Lyapunov theorems, and validated with simulations. The control designs in this thesis also include the use of 'pseudo-control hedging' techniques which are introduced to prevent the NNs from attempting to adapt to various actuation nonlinearities such as actuator position and rate saturations. Control allocation is introduced for the case of redundant control effectors including thrust vectoring nozzles. A thorough comparison study of conventional and NN-based adaptive designs for a system under a limit cycle, wing-rock, is included in this research, and the NN-based adaptive control designs demonstrate their performances for two highly maneuverable aerial vehicles, NASA F-15 ACTIVE and FQM-117B unmanned aerial vehicle (UAV), operated under various nonlinearities and uncertainties.

On one-dimensional stretching functions for finite-difference calculations. [computational fluid dynamics

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

Prediction-based dynamic load-sharing heuristics

NASA Technical Reports Server (NTRS)

Goswami, Kumar K.; Devarakonda, Murthy; Iyer, Ravishankar K.

1993-01-01

The authors present dynamic load-sharing heuristics that use predicted resource requirements of processes to manage workloads in a distributed system. A previously developed statistical pattern-recognition method is employed for resource prediction. While nonprediction-based heuristics depend on a rapidly changing system status, the new heuristics depend on slowly changing program resource usage patterns. Furthermore, prediction-based heuristics can be more effective since they use future requirements rather than just the current system state. Four prediction-based heuristics, two centralized and two distributed, are presented. Using trace driven simulations, they are compared against random scheduling and two effective nonprediction based heuristics. Results show that the prediction-based centralized heuristics achieve up to 30 percent better response times than the nonprediction centralized heuristic, and that the prediction-based distributed heuristics achieve up to 50 percent improvements relative to their nonprediction counterpart.

Activity-based costing: a practical model for cost calculation in radiotherapy.

PubMed

Lievens, Yolande; van den Bogaert, Walter; Kesteloot, Katrien

2003-10-01

The activity-based costing method was used to compute radiotherapy costs. This report describes the model developed, the calculated costs, and possible applications for the Leuven radiotherapy department. Activity-based costing is an advanced cost calculation technique that allocates resource costs to products based on activity consumption. In the Leuven model, a complex allocation principle with a large diversity of cost drivers was avoided by introducing an extra allocation step between activity groups and activities. A straightforward principle of time consumption, weighed by some factors of treatment complexity, was used. The model was developed in an iterative way, progressively defining the constituting components (costs, activities, products, and cost drivers). Radiotherapy costs are predominantly determined by personnel and equipment cost. Treatment-related activities consume the greatest proportion of the resource costs, with treatment delivery the most important component. This translates into products that have a prolonged total or daily treatment time being the most costly. The model was also used to illustrate the impact of changes in resource costs and in practice patterns. The presented activity-based costing model is a practical tool to evaluate the actual cost structure of a radiotherapy department and to evaluate possible resource or practice changes.

Update: Advancement of Contact Dynamics Modeling for Human Spaceflight Simulation Applications

NASA Technical Reports Server (NTRS)

Brain, Thomas A.; Kovel, Erik B.; MacLean, John R.; Quiocho, Leslie J.

2017-01-01

Pong is a new software tool developed at the NASA Johnson Space Center that advances interference-based geometric contact dynamics based on 3D graphics models. The Pong software consists of three parts: a set of scripts to extract geometric data from 3D graphics models, a contact dynamics engine that provides collision detection and force calculations based on the extracted geometric data, and a set of scripts for visualizing the dynamics response with the 3D graphics models. The contact dynamics engine can be linked with an external multibody dynamics engine to provide an integrated multibody contact dynamics simulation. This paper provides a detailed overview of Pong including the overall approach and modeling capabilities, which encompasses force generation from contact primitives and friction to computational performance. Two specific Pong-based examples of International Space Station applications are discussed, and the related verification and validation using this new tool are also addressed.

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.

Relative role of different radii in the dynamics of 8B+58Ni reaction

NASA Astrophysics Data System (ADS)

Kaur, Amandeep; Sandhu, Kirandeep; Sharma, Manoj K.

2018-05-01

In the present work, we intend to analyze the significance of three different radius terms in the framework of dynamical cluster-decay model (DCM) based calculations. In the majority of DCM based calculations the impact of mass- dependent radius R(A) is extensively analyzed. The other two factors on which the radius term may depend are, the neutron- proton asymmetry and the charge of the decaying fragments. Hence, the asymmetry dependent radius term R(I) and charge dependent radius term R(Z) are incorporated in DCM based calculations to investigate their effect on the reaction dynamics involved. Here, we present an extension of an earlier work based on the decay of 66As* compound nucleus by including R(I) and R(Z) radii in addition to the R(A) term. The effect of replacement of R(A) with R(I) and R(Z) is analyzed via fragmentation structure, tunneling probabilities (P) and other barrier characteristics like barrier height (VB), barrier position (RB), barrier turning point Ra etc. The role of temperature, deformations and angular momentum is duly incorporated in the present calculations.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

SU-E-J-168: Automated Pancreas Segmentation Based On Dynamic MRI

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

Gou, S; Rapacchi, S; Hu, P

2014-06-01

Purpose: MRI guided radiotherapy is particularly attractive for abdominal targets with low CT contrast. To fully utilize this modality for pancreas tracking, automated segmentation tools are needed. A hybrid gradient, region growth and shape constraint (hGReS) method to segment 2D upper abdominal dynamic MRI is developed for this purpose. Methods: 2D coronal dynamic MR images of 2 healthy volunteers were acquired with a frame rate of 5 f/second. The regions of interest (ROIs) included the liver, pancreas and stomach. The first frame was used as the source where the centers of the ROIs were annotated. These center locations were propagatedmore » to the next dynamic MRI frame. 4-neighborhood region transfer growth was performed from these initial seeds for rough segmentation. To improve the results, gradient, edge and shape constraints were applied to the ROIs before final refinement using morphological operations. Results from hGReS and 3 other automated segmentation methods using edge detection, region growth and level set were compared to manual contouring. Results: For the first patient, hGReS resulted in the organ segmentation accuracy as measure by the Dices index (0.77) for the pancreas. The accuracy was slightly superior to the level set method (0.72), and both are significantly more accurate than the edge detection (0.53) and region growth methods (0.42). For the second healthy volunteer, hGReS reliably segmented the pancreatic region, achieving a Dices index of 0.82, 0.92 and 0.93 for the pancreas, stomach and liver, respectively, comparing to manual segmentation. Motion trajectories derived from the hGReS, level set and manual segmentation methods showed high correlation to respiratory motion calculated using a lung blood vessel as the reference while the other two methods showed substantial motion tracking errors. hGReS was 10 times faster than level set. Conclusion: We have shown the feasibility of automated segmentation of the pancreas anatomy based

The boomerang effect in electron-hydrogen molecule scattering as determined by time-dependent calculations

NASA Astrophysics Data System (ADS)

Ben-Asher, Anael; Moiseyev, Nimrod

2017-05-01

The appearance of oscillations in the energy-dependent cross sections of the vibrational excitation ν =0 →ν ≥3 of the hydrogen molecule in its electronic ground state as predicted by Mündel, Berman, and Domcke [Phys. Rev. A 32, 181 (1985)] was confirmed in the electron scattering experiments by Allan [J. Phys. B: At. Mol. Phys. 18, L451 (1985)]. These unusual structures were obtained in spite of the extremely short lifetime of H2- in its ro-vibrational states. Based on the standard (Hermitian) time-independent scattering calculations, Horáček et al. [Phys. Rev. A 73, 022701 (2006)] associated these oscillations with the boomerang effect. Here, we show the boomerang effect as developed in time, based on our time-dependent nuclear wavepacket (WP) calculations. The nuclear WP dynamics of H2- is determined using the non-Hermitian quantum mechanics (NH-QM) which enables the use of the Born-Oppenheimer approximation with complex potential energy surfaces. This NH-QM approach, which enables us the association of the nuclear WP dynamics as obtained from the complex potential energy curve of H2- with the evolution of cross section in time, can enlighten the dynamics in other scattering experiments.

The boomerang effect in electron-hydrogen molecule scattering as determined by time-dependent calculations.

PubMed

Ben-Asher, Anael; Moiseyev, Nimrod

2017-05-28

The appearance of oscillations in the energy-dependent cross sections of the vibrational excitation ν=0→ν≥3 of the hydrogen molecule in its electronic ground state as predicted by Mündel, Berman, and Domcke [Phys. Rev. A 32, 181 (1985)] was confirmed in the electron scattering experiments by Allan [J. Phys. B: At. Mol. Phys. 18, L451 (1985)]. These unusual structures were obtained in spite of the extremely short lifetime of H 2 - in its ro-vibrational states. Based on the standard (Hermitian) time-independent scattering calculations, Horáček et al. [Phys. Rev. A 73, 022701 (2006)] associated these oscillations with the boomerang effect. Here, we show the boomerang effect as developed in time, based on our time-dependent nuclear wavepacket (WP) calculations. The nuclear WP dynamics of H 2 - is determined using the non-Hermitian quantum mechanics (NH-QM) which enables the use of the Born-Oppenheimer approximation with complex potential energy surfaces. This NH-QM approach, which enables us the association of the nuclear WP dynamics as obtained from the complex potential energy curve of H 2 - with the evolution of cross section in time, can enlighten the dynamics in other scattering experiments.

Fast CPU-based Monte Carlo simulation for radiotherapy dose calculation.

PubMed

Ziegenhein, Peter; Pirner, Sven; Ph Kamerling, Cornelis; Oelfke, Uwe

2015-08-07

Monte-Carlo (MC) simulations are considered to be the most accurate method for calculating dose distributions in radiotherapy. Its clinical application, however, still is limited by the long runtimes conventional implementations of MC algorithms require to deliver sufficiently accurate results on high resolution imaging data. In order to overcome this obstacle we developed the software-package PhiMC, which is capable of computing precise dose distributions in a sub-minute time-frame by leveraging the potential of modern many- and multi-core CPU-based computers. PhiMC is based on the well verified dose planning method (DPM). We could demonstrate that PhiMC delivers dose distributions which are in excellent agreement to DPM. The multi-core implementation of PhiMC scales well between different computer architectures and achieves a speed-up of up to 37[Formula: see text] compared to the original DPM code executed on a modern system. Furthermore, we could show that our CPU-based implementation on a modern workstation is between 1.25[Formula: see text] and 1.95[Formula: see text] faster than a well-known GPU implementation of the same simulation method on a NVIDIA Tesla C2050. Since CPUs work on several hundreds of GB RAM the typical GPU memory limitation does not apply for our implementation and high resolution clinical plans can be calculated.

Quantification of confounding factors in MRI-based dose calculations as applied to prostate IMRT

NASA Astrophysics Data System (ADS)

Maspero, Matteo; Seevinck, Peter R.; Schubert, Gerald; Hoesl, Michaela A. U.; van Asselen, Bram; Viergever, Max A.; Lagendijk, Jan J. W.; Meijer, Gert J.; van den Berg, Cornelis A. T.

2017-02-01

Magnetic resonance (MR)-only radiotherapy treatment planning requires pseudo-CT (pCT) images to enable MR-based dose calculations. To verify the accuracy of MR-based dose calculations, institutions interested in introducing MR-only planning will have to compare pCT-based and computer tomography (CT)-based dose calculations. However, interpreting such comparison studies may be challenging, since potential differences arise from a range of confounding factors which are not necessarily specific to MR-only planning. Therefore, the aim of this study is to identify and quantify the contribution of factors confounding dosimetric accuracy estimation in comparison studies between CT and pCT. The following factors were distinguished: set-up and positioning differences between imaging sessions, MR-related geometric inaccuracy, pCT generation, use of specific calibration curves to convert pCT into electron density information, and registration errors. The study comprised fourteen prostate cancer patients who underwent CT/MRI-based treatment planning. To enable pCT generation, a commercial solution (MRCAT, Philips Healthcare, Vantaa, Finland) was adopted. IMRT plans were calculated on CT (gold standard) and pCTs. Dose difference maps in a high dose region (CTV) and in the body volume were evaluated, and the contribution to dose errors of possible confounding factors was individually quantified. We found that the largest confounding factor leading to dose difference was the use of different calibration curves to convert pCT and CT into electron density (0.7%). The second largest factor was the pCT generation which resulted in pCT stratified into a fixed number of tissue classes (0.16%). Inter-scan differences due to patient repositioning, MR-related geometric inaccuracy, and registration errors did not significantly contribute to dose differences (0.01%). The proposed approach successfully identified and quantified the factors confounding accurate MRI-based dose calculation in

Online plasma calculator

NASA Astrophysics Data System (ADS)

Wisniewski, H.; Gourdain, P.-A.

2017-10-01

APOLLO is an online, Linux based plasma calculator. Users can input variables that correspond to their specific plasma, such as ion and electron densities, temperatures, and external magnetic fields. The system is based on a webserver where a FastCGI protocol computes key plasma parameters including frequencies, lengths, velocities, and dimensionless numbers. FastCGI was chosen to overcome security problems caused by JAVA-based plugins. The FastCGI also speeds up calculations over PHP based systems. APOLLO is built upon the WT library, which turns any web browser into a versatile, fast graphic user interface. All values with units are expressed in SI units except temperature, which is in electron-volts. SI units were chosen over cgs units because of the gradual shift to using SI units within the plasma community. APOLLO is intended to be a fast calculator that also provides the user with the proper equations used to calculate the plasma parameters. This system is intended to be used by undergraduates taking plasma courses as well as graduate students and researchers who need a quick reference calculation.

Dielectric Response and Born Dynamic Charge of BN Nanotubes from Ab Initio Finite Electric Field Calculations

NASA Astrophysics Data System (ADS)

Guo, Guang-Yu; Ishibashi, Shoji; Tamura, Tomoyuki; Terakura, Kiyoyuki

2007-03-01

Since the discovery of carbon nanotubes (CNTs) in 1991 by Iijima, carbon and other nanotubes have attracted considerable interest worldwide because of their unusual properties and also great potentials for technological applications. Though CNTs continue to attract great interest, other nanotubes such as BN nanotubes (BN-NTs) may offer different opportunities that CNTs cannot provide. In this contribution, we present the results of our recent systematic ab initio calculations of the static dielectric constant, electric polarizability, Born dynamical charge, electrostriction coefficient and piezoelectric constant of BN-NTs using the latest crystalline finite electric field theory [1]. [1] I. Souza, J. Iniguez, and D. Vanderbilt, Phys. Rev. Lett. 89, 117602 (2002); P. Umari and A. Pasquarello, Phys. Rev. Lett. 89, 157602 (2002).

Improvements of the Ray-Tracing Based Method Calculating Hypocentral Loci for Earthquake Location

NASA Astrophysics Data System (ADS)

Zhao, A. H.

2014-12-01

Hypocentral loci are very useful to reliable and visual earthquake location. However, they can hardly be analytically expressed when the velocity model is complex. One of methods numerically calculating them is based on a minimum traveltime tree algorithm for tracing rays: a focal locus is represented in terms of ray paths in its residual field from the minimum point (namely initial point) to low residual points (referred as reference points of the focal locus). The method has no restrictions on the complexity of the velocity model but still lacks the ability of correctly dealing with multi-segment loci. Additionally, it is rather laborious to set calculation parameters for obtaining loci with satisfying completeness and fineness. In this study, we improve the ray-tracing based numerical method to overcome its advantages. (1) Reference points of a hypocentral locus are selected from nodes of the model cells that it goes through, by means of a so-called peeling method. (2) The calculation domain of a hypocentral locus is defined as such a low residual area that its connected regions each include one segment of the locus and hence all the focal locus segments are respectively calculated with the minimum traveltime tree algorithm for tracing rays by repeatedly assigning the minimum residual reference point among those that have not been traced as an initial point. (3) Short ray paths without branching are removed to make the calculated locus finer. Numerical tests show that the improved method becomes capable of efficiently calculating complete and fine hypocentral loci of earthquakes in a complex model.

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

PubMed Central

Wang, Junmei; Hou, Tingjun

2012-01-01

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 parameterized 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 the convenience, TS, 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 post-entropy calculations): the mean correlation coefficient squares (R2) was 0.56. As to the 20 complexes, the TS changes

A hypersonic aeroheating calculation method based on inviscid outer edge of boundary layer parameters

NASA Astrophysics Data System (ADS)

Meng, ZhuXuan; Fan, Hu; Peng, Ke; Zhang, WeiHua; Yang, HuiXin

2016-12-01

This article presents a rapid and accurate aeroheating calculation method for hypersonic vehicles. The main innovation is combining accurate of numerical method with efficient of engineering method, which makes aeroheating simulation more precise and faster. Based on the Prandtl boundary layer theory, the entire flow field is divided into inviscid and viscid flow at the outer edge of the boundary layer. The parameters at the outer edge of the boundary layer are numerically calculated from assuming inviscid flow. The thermodynamic parameters of constant-volume specific heat, constant-pressure specific heat and the specific heat ratio are calculated, the streamlines on the vehicle surface are derived and the heat flux is then obtained. The results of the double cone show that at the 0° and 10° angle of attack, the method of aeroheating calculation based on inviscid outer edge of boundary layer parameters reproduces the experimental data better than the engineering method. Also the proposed simulation results of the flight vehicle reproduce the viscid numerical results well. Hence, this method provides a promising way to overcome the high cost of numerical calculation and improves the precision.

Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics.

PubMed

Cheng, Jun; Sulpizi, Marialore; Sprik, Michiel

2009-10-21

The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pK(a)) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies.

Firefly luciferase-based dynamic bioluminescence imaging: a noninvasive technique to assess tumor angiogenesis.

PubMed

Sun, Amy; Hou, Lewis; Prugpichailers, Tiffany; Dunkel, Jason; Kalani, Maziyar A; Chen, Xiaoyuan; Kalani, M Yashar S; Tse, Victor

2010-04-01

Bioluminescence imaging (BLI) is emerging as a cost-effective, high-throughput, noninvasive, and sensitive imaging modality to monitor cell growth and trafficking. We describe the use of dynamic BLI as a noninvasive method of assessing vessel permeability during brain tumor growth. With the use of stereotactic technique, 10 firefly luciferase-transfected GL26 mouse glioblastoma multiforme cells were injected into the brains of C57BL/6 mice (n = 80). After intraperitoneal injection of D-luciferin (150 mg/kg), serial dynamic BLI was performed at 1-minute intervals (30 seconds exposure) every 2 to 3 days until death of the animals. The maximum intensity was used as an indirect measurement of tumor growth. The adjusted slope of initial intensity (I90/Im) was used as a proxy to monitor the flow rate of blood into the vascular tree. Using a modified Evans blue perfusion protocol, we calculated the relative permeability of the vascular tree at various time points. Daily maximum intensity correlated strongly with tumor volume. At postinjection day 23, histology and BLI demonstrated an exponential growth of the tumor mass. Slopes were calculated to reflect the flow in the vessels feeding the tumor (adjusted slope = I90/Im). The increase in BLI intensity was correlated with a decrease in adjusted slope, reflecting a decrease in the rate of blood flow as tumor volume increased (y = 93.8e-0.49, R2 = 0.63). Examination of calculated slopes revealed a peak in permeability around postinjection day 20 (n = 42, P < .02 by 1-way analysis of variance) and showed a downward trend in relation to both postinjection day and maximum intensity observed; as angiogenesis progressed, tumor vessel caliber increased dramatically, resulting in sluggish but increased flow. This trend was correlated with Evans blue histology, revealing an increase in Evans blue dye uptake into the tumor, as slope calculated by BLI increases. Dynamic BLI is a practical, noninvasive technique that can

Chemical and Biological Dynamics Using Droplet-Based Microfluidics.

PubMed

Dressler, Oliver J; Casadevall I Solvas, Xavier; deMello, Andrew J

2017-06-12

Recent years have witnessed an increased use of droplet-based microfluidic techniques in a wide variety of chemical and biological assays. Nevertheless, obtaining dynamic data from these platforms has remained challenging, as this often requires reading the same droplets (possibly thousands of them) multiple times over a wide range of intervals (from milliseconds to hours). In this review, we introduce the elemental techniques for the formation and manipulation of microfluidic droplets, together with the most recent developments in these areas. We then discuss a wide range of analytical methods that have been successfully adapted for analyte detection in droplets. Finally, we highlight a diversity of studies where droplet-based microfluidic strategies have enabled the characterization of dynamic systems that would otherwise have remained unexplorable.

3-D parallel program for numerical calculation of gas dynamics problems with heat conductivity on distributed memory computational systems (CS)

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

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.more » 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.« less

A research on radiation calibration of high dynamic range based on the dual channel CMOS

NASA Astrophysics Data System (ADS)

Ma, Kai; Shi, Zhan; Pan, Xiaodong; Wang, Yongsheng; Wang, Jianghua

2017-10-01

The dual channel complementary metal-oxide semiconductor (CMOS) can get high dynamic range (HDR) image through extending the gray level of the image by using image fusion with high gain channel image and low gain channel image in a same frame. In the process of image fusion with dual channel, it adopts the coefficients of radiation response of a pixel from dual channel in a same frame, and then calculates the gray level of the pixel in the HDR image. For the coefficients of radiation response play a crucial role in image fusion, it has to find an effective method to acquire these parameters. In this article, it makes a research on radiation calibration of high dynamic range based on the dual channel CMOS, and designs an experiment to calibrate the coefficients of radiation response for the sensor it used. In the end, it applies these response parameters in the dual channel CMOS which calibrates, and verifies the correctness and feasibility of the method mentioned in this paper.

Cooperation based dynamic team formation in multi-agent auctions

NASA Astrophysics Data System (ADS)

Pippin, Charles E.; Christensen, Henrik

2012-06-01

Auction based methods are often used to perform distributed task allocation on multi-agent teams. Many existing approaches to auctions assume fully cooperative team members. On in-situ and dynamically formed teams, reciprocal collaboration may not always be a valid assumption. This paper presents an approach for dynamically selecting auction partners based on observed team member performance and shared reputation. In addition, we present the use of a shared reputation authority mechanism. Finally, experiments are performed in simulation on multiple UAV platforms to highlight situations in which it is better to enforce cooperation in auctions using this approach.

A method for modeling contact dynamics for automated capture mechanisms

NASA Technical Reports Server (NTRS)

Williams, Philip J.

1991-01-01

Logicon Control Dynamics develops contact dynamics models for space-based docking and berthing vehicles. The models compute contact forces for the physical contact between mating capture mechanism surfaces. Realistic simulation requires proportionality constants, for calculating contact forces, to approximate surface stiffness of contacting bodies. Proportionality for rigid metallic bodies becomes quite large. Small penetrations of surface boundaries can produce large contact forces.

Fully automated calculation of cardiothoracic ratio in digital chest radiographs

NASA Astrophysics Data System (ADS)

Cong, Lin; Jiang, Luan; Chen, Gang; Li, Qiang

2017-03-01

The calculation of Cardiothoracic Ratio (CTR) in digital chest radiographs would be useful for cardiac anomaly assessment and heart enlargement related disease indication. The purpose of this study was to develop and evaluate a fully automated scheme for calculation of CTR in digital chest radiographs. Our automated method consisted of three steps, i.e., lung region localization, lung segmentation, and CTR calculation. We manually annotated the lung boundary with 84 points in 100 digital chest radiographs, and calculated an average lung model for the subsequent work. Firstly, in order to localize the lung region, generalized Hough transform was employed to identify the upper, lower, and outer boundaries of lung by use of Sobel gradient information. The average lung model was aligned to the localized lung region to obtain the initial lung outline. Secondly, we separately applied dynamic programming method to detect the upper, lower, outer and inner boundaries of lungs, and then linked the four boundaries to segment the lungs. Based on the identified outer boundaries of left lung and right lung, we corrected the center and the declination of the original radiography. Finally, CTR was calculated as a ratio of the transverse diameter of the heart to the internal diameter of the chest, based on the segmented lungs. The preliminary results on 106 digital chest radiographs showed that the proposed method could obtain accurate segmentation of lung based on subjective observation, and achieved sensitivity of 88.9% (40 of 45 abnormalities), and specificity of 100% (i.e. 61 of 61 normal) for the identification of heart enlargements.

Binaural model-based dynamic-range compression.

PubMed

Ernst, Stephan M A; Kortlang, Steffen; Grimm, Giso; Bisitz, Thomas; Kollmeier, Birger; Ewert, Stephan D

2018-01-26

Binaural cues such as interaural level differences (ILDs) are used to organise auditory perception and to segregate sound sources in complex acoustical environments. In bilaterally fitted hearing aids, dynamic-range compression operating independently at each ear potentially alters these ILDs, thus distorting binaural perception and sound source segregation. A binaurally-linked model-based fast-acting dynamic compression algorithm designed to approximate the normal-hearing basilar membrane (BM) input-output function in hearing-impaired listeners is suggested. A multi-center evaluation in comparison with an alternative binaural and two bilateral fittings was performed to assess the effect of binaural synchronisation on (a) speech intelligibility and (b) perceived quality in realistic conditions. 30 and 12 hearing impaired (HI) listeners were aided individually with the algorithms for both experimental parts, respectively. A small preference towards the proposed model-based algorithm in the direct quality comparison was found. However, no benefit of binaural-synchronisation regarding speech intelligibility was found, suggesting a dominant role of the better ear in all experimental conditions. The suggested binaural synchronisation of compression algorithms showed a limited effect on the tested outcome measures, however, linking could be situationally beneficial to preserve a natural binaural perception of the acoustical environment.

Dynamic stability of maglev systems

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

Cai, Y.; Chen, S.S.; Mulcahy, T.M.

1992-09-01

Since the occurrence of dynamic instabilities is not acceptable for any commercial maglev systems, it is important to consider the dynamic instability in the development of all maglev systems. This study is to consider the stability of maglev systems based on experimental data, scoping calculations and simple mathematical models. Divergence and flutter are obtained for coupled vibration of a three-degree-of-freedom maglev vehicle on the guideway which consists of double L-shaped aluminum segments attached to a rotating wheel. The theory and analysis developed in this study provides basic stability characteristics and identifies future research needs for maglev system.

The van Hove distribution function for Brownian hard spheres: Dynamical test particle theory and computer simulations for bulk dynamics

NASA Astrophysics Data System (ADS)

Hopkins, Paul; Fortini, Andrea; Archer, Andrew J.; Schmidt, Matthias

2010-12-01

We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self " component having only one particle, the "distinct" component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan-Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.

Water dissociating on rigid Ni(100): A quantum dynamics study on a full-dimensional potential energy surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Chen, Jun; Zhang, Zhaojun; Shen, Xiangjian; Fu, Bina; Zhang, Dong H.

2018-04-01

We constructed a nine-dimensional (9D) potential energy surface (PES) for the dissociative chemisorption of H2O on a rigid Ni(100) surface using the neural network method based on roughly 110 000 energies obtained from extensive density functional theory (DFT) calculations. The resulting PES is accurate and smooth, based on the small fitting errors and the good agreement between the fitted PES and the direct DFT calculations. Time dependent wave packet calculations also showed that the PES is very well converged with respect to the fitting procedure. The dissociation probabilities of H2O initially in the ground rovibrational state from 9D quantum dynamics calculations are quite different from the site-specific results from the seven-dimensional (7D) calculations, indicating the importance of full-dimensional quantum dynamics to quantitatively characterize this gas-surface reaction. It is found that the validity of the site-averaging approximation with exact potential holds well, where the site-averaging dissociation probability over 15 fixed impact sites obtained from 7D quantum dynamics calculations can accurately approximate the 9D dissociation probability for H2O in the ground rovibrational state.

Calculation of Disease Dynamics in a Population of Households

PubMed Central

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

Applying Activity Based Costing (ABC) Method to Calculate Cost Price in Hospital and Remedy Services

PubMed Central

Rajabi, A; Dabiri, A

2012-01-01

Background Activity Based Costing (ABC) is one of the new methods began appearing as a costing methodology in the 1990’s. It calculates cost price by determining the usage of resources. In this study, ABC method was used for calculating cost price of remedial services in hospitals. Methods: To apply ABC method, Shahid Faghihi Hospital was selected. First, hospital units were divided into three main departments: administrative, diagnostic, and hospitalized. Second, activity centers were defined by the activity analysis method. Third, costs of administrative activity centers were allocated into diagnostic and operational departments based on the cost driver. Finally, with regard to the usage of cost objectives from services of activity centers, the cost price of medical services was calculated. Results: The cost price from ABC method significantly differs from tariff method. In addition, high amount of indirect costs in the hospital indicates that capacities of resources are not used properly. Conclusion: Cost price of remedial services with tariff method is not properly calculated when compared with ABC method. ABC calculates cost price by applying suitable mechanisms but tariff method is based on the fixed price. In addition, ABC represents useful information about the amount and combination of cost price services. PMID:23113171

Systemic errors calibration in dynamic stitching interferometry

NASA Astrophysics Data System (ADS)

Wu, Xin; Qi, Te; Yu, Yingjie; Zhang, Linna

2016-05-01

The systemic error is the main error sauce in sub-aperture stitching calculation. In this paper, a systemic error calibration method is proposed based on pseudo shearing. This method is suitable in dynamic stitching interferometry for large optical plane. The feasibility is vibrated by some simulations and experiments.

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.

Self-consistent phonon calculations of lattice dynamical properties in cubic SrTiO3 with first-principles anharmonic force constants

NASA Astrophysics Data System (ADS)

Tadano, Terumasa; Tsuneyuki, Shinji

2015-08-01

We present an ab initio framework to calculate anharmonic phonon frequency and phonon lifetime that is applicable to severely anharmonic systems. We employ self-consistent phonon (SCPH) theory with microscopic anharmonic force constants, which are extracted from density functional calculations using the least absolute shrinkage and selection operator technique. We apply the method to the high-temperature phase of SrTiO3 and obtain well-defined phonon quasiparticles that are free from imaginary frequencies. Here we show that the anharmonic phonon frequency of the antiferrodistortive mode depends significantly on the system size near the critical temperature of the cubic-to-tetragonal phase transition. By applying perturbation theory to the SCPH result, phonon lifetimes are calculated for cubic SrTiO3, which are then employed to predict lattice thermal conductivity using the Boltzmann transport equation within the relaxation-time approximation. The presented methodology is efficient and accurate, paving the way toward a reliable description of thermodynamic, dynamic, and transport properties of systems with severe anharmonicity, including thermoelectric, ferroelectric, and superconducting materials.

Quantum dynamics modeled by interacting trajectories

NASA Astrophysics Data System (ADS)

Cruz-Rodríguez, L.; Uranga-Piña, L.; Martínez-Mesa, A.; Meier, C.

2018-03-01

We present quantum dynamical simulations based on the propagation of interacting trajectories where the effect of the quantum potential is mimicked by effective pseudo-particle interactions. The method is applied to several quantum systems, both for bound and scattering problems. For the bound systems, the quantum ground state density and zero point energy are shown to be perfectly obtained by the interacting trajectories. In the case of time-dependent quantum scattering, the Eckart barrier and uphill ramp are considered, with transmission coefficients in very good agreement with standard quantum calculations. Finally, we show that via wave function synthesis along the trajectories, correlation functions and energy spectra can be obtained based on the dynamics of interacting trajectories.

Size Reduction of Hamiltonian Matrix for Large-Scale Energy Band Calculations Using Plane Wave Bases

NASA Astrophysics Data System (ADS)

Morifuji, Masato

2018-01-01

We present a method of reducing the size of a Hamiltonian matrix used in calculations of electronic states. In the electronic states calculations using plane wave basis functions, a large number of plane waves are often required to obtain precise results. Even using state-of-the-art techniques, the Hamiltonian matrix often becomes very large. The large computational time and memory necessary for diagonalization limit the widespread use of band calculations. We show a procedure of deriving a reduced Hamiltonian constructed using a small number of low-energy bases by renormalizing high-energy bases. We demonstrate numerically that the significant speedup of eigenstates evaluation is achieved without losing accuracy.

New approach to CT pixel-based photon dose calculations in heterogeneous media

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

Wong, J.W.; Henkelman, R.M.

The effects of small cavities on dose in water and the dose in a homogeneous nonunit density medium illustrate that inhomogeneities do not act independently in photon dose perturbation, and serve as two constraints which should be satisfied by approximate methods of computed tomography (CT) pixel-based dose calculations. Current methods at best satisfy only one of the two constraints and show inadequacies in some intermediate geometries. We have developed an approximate method that satisfies both these constraints and treats much of the synergistic effect of multiple inhomogeneities correctly. The method calculates primary and first-scatter doses by first-order ray tracing withmore » the first-scatter contribution augmented by a component of second scatter that behaves like first scatter. Multiple-scatter dose perturbation values extracted from small cavity experiments are used in a function which approximates the small residual multiple-scatter dose. For a wide range of geometries tested, our method agrees very well with measurements. The average deviation is less than 2% with a maximum of 3%. In comparison, calculations based on existing methods can have errors larger than 10%.« less

Hierarchical content-based image retrieval by dynamic indexing and guided search

NASA Astrophysics Data System (ADS)

You, Jane; Cheung, King H.; Liu, James; Guo, Linong

2003-12-01

This paper presents a new approach to content-based image retrieval by using dynamic indexing and guided search in a hierarchical structure, and extending data mining and data warehousing techniques. The proposed algorithms include: a wavelet-based scheme for multiple image feature extraction, the extension of a conventional data warehouse and an image database to an image data warehouse for dynamic image indexing, an image data schema for hierarchical image representation and dynamic image indexing, a statistically based feature selection scheme to achieve flexible similarity measures, and a feature component code to facilitate query processing and guide the search for the best matching. A series of case studies are reported, which include a wavelet-based image color hierarchy, classification of satellite images, tropical cyclone pattern recognition, and personal identification using multi-level palmprint and face features.

Dynamic 3D scanning as a markerless method to calculate multi-segment foot kinematics during stance phase: methodology and first application.

PubMed

Van den Herrewegen, Inge; Cuppens, Kris; Broeckx, Mario; Barisch-Fritz, Bettina; Vander Sloten, Jos; Leardini, Alberto; Peeraer, Louis

2014-08-22

Multi-segmental foot kinematics have been analyzed by means of optical marker-sets or by means of inertial sensors, but never by markerless dynamic 3D scanning (D3DScanning). The use of D3DScans implies a radically different approach for the construction of the multi-segment foot model: the foot anatomy is identified via the surface shape instead of distinct landmark points. We propose a 4-segment foot model consisting of the shank (Sha), calcaneus (Cal), metatarsus (Met) and hallux (Hal). These segments are manually selected on a static scan. To track the segments in the dynamic scan, the segments of the static scan are matched on each frame of the dynamic scan using the iterative closest point (ICP) fitting algorithm. Joint rotations are calculated between Sha-Cal, Cal-Met, and Met-Hal. Due to the lower quality scans at heel strike and toe off, the first and last 10% of the stance phase is excluded. The application of the method to 5 healthy subjects, 6 trials each, shows a good repeatability (intra-subject standard deviations between 1° and 2.5°) for Sha-Cal and Cal-Met joints, and inferior results for the Met-Hal joint (>3°). The repeatability seems to be subject-dependent. For the validation, a qualitative comparison with joint kinematics from a corresponding established marker-based multi-segment foot model is made. This shows very consistent patterns of rotation. The ease of subject preparation and also the effective and easy to interpret visual output, make the present technique very attractive for functional analysis of the foot, enhancing usability in clinical practice. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

High-efficient and high-content cytotoxic recording via dynamic and continuous cell-based impedance biosensor technology.

PubMed

Hu, Ning; Fang, Jiaru; Zou, Ling; Wan, Hao; Pan, Yuxiang; Su, Kaiqi; Zhang, Xi; Wang, Ping

2016-10-01

Cell-based bioassays were effective method to assess the compound toxicity by cell viability, and the traditional label-based methods missed much information of cell growth due to endpoint detection, while the higher throughputs were demanded to obtain dynamic information. Cell-based biosensor methods can dynamically and continuously monitor with cell viability, however, the dynamic information was often ignored or seldom utilized in the toxin and drug assessment. Here, we reported a high-efficient and high-content cytotoxic recording method via dynamic and continuous cell-based impedance biosensor technology. The dynamic cell viability, inhibition ratio and growth rate were derived from the dynamic response curves from the cell-based impedance biosensor. The results showed that the biosensors has the dose-dependent manners to diarrhetic shellfish toxin, okadiac acid based on the analysis of the dynamic cell viability and cell growth status. Moreover, the throughputs of dynamic cytotoxicity were compared between cell-based biosensor methods and label-based endpoint methods. This cell-based impedance biosensor can provide a flexible, cost and label-efficient platform of cell viability assessment in the shellfish toxin screening fields.

Mobile robot dynamic path planning based on improved genetic algorithm

NASA Astrophysics Data System (ADS)

Wang, Yong; Zhou, Heng; Wang, Ying

2017-08-01

In dynamic unknown environment, the dynamic path planning of mobile robots is a difficult problem. In this paper, a dynamic path planning method based on genetic algorithm is proposed, and a reward value model is designed to estimate the probability of dynamic obstacles on the path, and the reward value function is applied to the genetic algorithm. Unique coding techniques reduce the computational complexity of the algorithm. The fitness function of the genetic algorithm fully considers three factors: the security of the path, the shortest distance of the path and the reward value of the path. The simulation results show that the proposed genetic algorithm is efficient in all kinds of complex dynamic environments.

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

A web-based normative calculator for the uniform data set (UDS) neuropsychological test battery.

PubMed

Shirk, Steven D; Mitchell, Meghan B; Shaughnessy, Lynn W; Sherman, Janet C; Locascio, Joseph J; Weintraub, Sandra; Atri, Alireza

2011-11-11

With the recent publication of new criteria for the diagnosis of preclinical Alzheimer's disease (AD), there is a need for neuropsychological tools that take premorbid functioning into account in order to detect subtle cognitive decline. Using demographic adjustments is one method for increasing the sensitivity of commonly used measures. We sought to provide a useful online z-score calculator that yields estimates of percentile ranges and adjusts individual performance based on sex, age and/or education for each of the neuropsychological tests of the National Alzheimer's Coordinating Center Uniform Data Set (NACC, UDS). In addition, we aimed to provide an easily accessible method of creating norms for other clinical researchers for their own, unique data sets. Data from 3,268 clinically cognitively-normal older UDS subjects from a cohort reported by Weintraub and colleagues (2009) were included. For all neuropsychological tests, z-scores were estimated by subtracting the raw score from the predicted mean and then dividing this difference score by the root mean squared error term (RMSE) for a given linear regression model. For each neuropsychological test, an estimated z-score was calculated for any raw score based on five different models that adjust for the demographic predictors of SEX, AGE and EDUCATION, either concurrently, individually or without covariates. The interactive online calculator allows the entry of a raw score and provides five corresponding estimated z-scores based on predictions from each corresponding linear regression model. The calculator produces percentile ranks and graphical output. An interactive, regression-based, normative score online calculator was created to serve as an additional resource for UDS clinical researchers, especially in guiding interpretation of individual performances that appear to fall in borderline realms and may be of particular utility for operationalizing subtle cognitive impairment present according to the newly

An Analysis on a Dynamic Amplifier and Calibration Methods for a Pseudo-Differential Dynamic Comparator

NASA Astrophysics Data System (ADS)

Paik, Daehwa; Miyahara, Masaya; Matsuzawa, Akira

This paper analyzes a pseudo-differential dynamic comparator with a dynamic pre-amplifier. The transient gain of a dynamic pre-amplifier is derived and applied to equations of the thermal noise and the regeneration time of a comparator. This analysis enhances understanding of the roles of transistor's parameters in pre-amplifier's gain. Based on the calculated gain, two calibration methods are also analyzed. One is calibration of a load capacitance and the other is calibration of a bypass current. The analysis helps designers' estimation for the accuracy of calibration, dead-zone of a comparator with a calibration circuit, and the influence of PVT variation. The analyzed comparator uses 90-nm CMOS technology as an example and each estimation is compared with simulation results.

Field calculations, single-particle tracking, and beam dynamics with space charge in the electron lens for the Fermilab Integrable Optics Test Accelerator

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

Noll, Daniel; Stancari, Giulio

2015-11-17

An electron lens is planned for the Fermilab Integrable Optics Test Accelerator as a nonlinear element for integrable dynamics, as an electron cooler, and as an electron trap to study space-charge compensation in rings. We present the main design principles and constraints for nonlinear integrable optics. A magnetic configuration of the solenoids and of the toroidal section is laid out. Singleparticle tracking is used to optimize the electron path. Electron beam dynamics at high intensity is calculated with a particle-in-cell code to estimate current limits, profile distortions, and the effects on the circulating beam. In the conclusions, we summarize themore » main findings and list directions for further work.« less

On the mechanism of non-radiative decay of blue fluorescent protein chromophore: New insight from the excited-state molecular dynamics simulations and potential energy calculations

NASA Astrophysics Data System (ADS)

Zhao, Li; Liu, Jian-Yong; Zhou, Pan-Wang

2017-11-01

A detailed theoretical investigation based on the ab initio on-the-fly surface hopping dynamics simulations and potential energy surfaces calculations has been performed to unveil the mechanism of the photoinduced non-adiabatic relaxation process of the isolated blue fluorescent protein (BFP) chromophore in gas phase. The data analysis presents that the dominant reaction coordinate of the BFP chromophore is driven by a rotation motion around the CC double bridging bond, which is in remarkable difference with a previous result which supports a Hula-Twist rotation pattern. Such behavior is consistent with the double bond rotation pattern of the GFP neutral chromophore. In addition, the dynamics simulations give an estimated decay time of 1.1 ps for the S1 state, which is agrees well with the experimental values measured in proteins. The present work offers a straightforward understanding for the decay mechanism of the BFP chromophore and suggestions of the photochemical properties of analogous protein chromophores. We hope the current work would be helpful for further exploration of the BFP photochemical and photophysical properties in various environments, and can provide guidance and prediction for rational design of the fluorescent proteins catering for different demands.

Simulation-based decision support framework for dynamic ambulance redeployment in Singapore.

PubMed

Lam, Sean Shao Wei; Ng, Clarence Boon Liang; Nguyen, Francis Ngoc Hoang Long; Ng, Yih Yng; Ong, Marcus Eng Hock

2017-10-01

Dynamic ambulance redeployment policies tend to introduce much more flexibilities in improving ambulance resource allocation by capitalizing on the definite geospatial-temporal variations in ambulance demand patterns over the time-of-the-day and day-of-the-week effects. A novel modelling framework based on the Approximate Dynamic Programming (ADP) approach leveraging on a Discrete Events Simulation (DES) model for dynamic ambulance redeployment in Singapore is proposed in this paper. The study was based on the Singapore's national Emergency Medical Services (EMS) system. Based on a dataset comprising 216,973 valid incidents over a continuous two-years study period from 1 January 2011-31 December 2012, a DES model for the EMS system was developed. An ADP model based on linear value function approximations was then evaluated using the DES model via the temporal difference (TD) learning family of algorithms. The objective of the ADP model is to derive approximate optimal dynamic redeployment policies based on the primary outcome of ambulance coverage. Considering an 8min response time threshold, an estimated 5% reduction in the proportion of calls that cannot be reached within the threshold (equivalent to approximately 8000 dispatches) was observed from the computational experiments. The study also revealed that the redeployment policies which are restricted within the same operational division could potentially result in a more promising response time performance. Furthermore, the best policy involved the combination of redeploying ambulances whenever they are released from service and that of relocating ambulances that are idle in bases. This study demonstrated the successful application of an approximate modelling framework based on ADP that leverages upon a detailed DES model of the Singapore's EMS system to generate approximate optimal dynamic redeployment plans. Various policies and scenarios relevant to the Singapore EMS system were evaluated. Copyright © 2017

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

PubMed

Jiang, Wei; Roux, Benoît

2010-07-01

Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

GPU-based ultra-fast dose calculation using a finite size pencil beam model.

PubMed

Gu, Xuejun; Choi, Dongju; Men, Chunhua; Pan, Hubert; Majumdar, Amitava; Jiang, Steve B

2009-10-21

Online adaptive radiation therapy (ART) is an attractive concept that promises the ability to deliver an optimal treatment in response to the inter-fraction variability in patient anatomy. However, it has yet to be realized due to technical limitations. Fast dose deposit coefficient calculation is a critical component of the online planning process that is required for plan optimization of intensity-modulated radiation therapy (IMRT). Computer graphics processing units (GPUs) are well suited to provide the requisite fast performance for the data-parallel nature of dose calculation. In this work, we develop a dose calculation engine based on a finite-size pencil beam (FSPB) algorithm and a GPU parallel computing framework. The developed framework can accommodate any FSPB model. We test our implementation in the case of a water phantom and the case of a prostate cancer patient with varying beamlet and voxel sizes. All testing scenarios achieved speedup ranging from 200 to 400 times when using a NVIDIA Tesla C1060 card in comparison with a 2.27 GHz Intel Xeon CPU. The computational time for calculating dose deposition coefficients for a nine-field prostate IMRT plan with this new framework is less than 1 s. This indicates that the GPU-based FSPB algorithm is well suited for online re-planning for adaptive radiotherapy.

Overcoming misconceptions of graph interpretation of kinematics motion using calculator based rangers

NASA Astrophysics Data System (ADS)

Olson, John R.

This is a quasi-experimental study of 261 first year high school students that analyzes gains made through the use of calculator based rangers attached to calculators. The study has qualitative components but is based on quantitative tests. Biechner's TUG-K test was used for the pretest, posttest, and post-posttest. The population was divided into one group that predicted the results before using the CBRs and another that did not predict first but completed the same activities. The data for the groups was further disaggregated into learning style groups (based on Kolb's Learning Styles Inventory), type of class (advanced vs. general physics), and gender. Four instructors used the labs developed by the author for this study and created significant differences between the groups by instructor based on interviews, participant observation and one way ANOVA. No significant differences were found between learning styles based on MANOVA. No significant differences were found between predict and nonpredict groups for the one way ANOVAs or MANOVA, however, some differences do exist as measured by a survey and participant observation. Significant differences do exist between gender and type of class (advanced/general) based on one way ANOVA and MANOVA. The males outscored the females on all tests and the advanced physics scored higher than the general physics on all tests. The advanced physics scoring higher was expected but the difference between genders was not.

Comparison of lysimeter based and calculated ASCE reference evapotranspiration in a subhumid climate

NASA Astrophysics Data System (ADS)

Nolz, Reinhard; Cepuder, Peter; Eitzinger, Josef

2016-04-01

The standardized form of the well-known FAO Penman-Monteith equation, published by the Environmental and Water Resources Institute of the American Society of Civil Engineers (ASCE-EWRI), is recommended as a standard procedure for calculating reference evapotranspiration (ET ref) and subsequently plant water requirements. Applied and validated under different climatic conditions it generally achieved good results compared to other methods. However, several studies documented deviations between measured and calculated reference evapotranspiration depending on environmental and weather conditions. Therefore, it seems generally advisable to evaluate the model under local environmental conditions. In this study, reference evapotranspiration was determined at a subhumid site in northeastern Austria from 2005 to 2010 using a large weighing lysimeter (ET lys). The measured data were compared with ET ref calculations. Daily values differed slightly during a year, at which ET ref was generally overestimated at small values, whereas it was rather underestimated when ET was large, which is supported also by other studies. In our case, advection of sensible heat proved to have an impact, but it could not explain the differences exclusively. Obviously, there were also other influences, such as seasonal varying surface resistance or albedo. Generally, the ASCE-EWRI equation for daily time steps performed best at average weather conditions. The outcomes should help to correctly interpret ET ref data in the region and in similar environments and improve knowledge on the dynamics of influencing factors causing deviations.

Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

PubMed

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

2014-05-01

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sliding mode-based lateral vehicle dynamics control using tyre force measurements

NASA Astrophysics Data System (ADS)

Kunnappillil Madhusudhanan, Anil; Corno, Matteo; Holweg, Edward

2015-11-01

In this work, a lateral vehicle dynamics control based on tyre force measurements is proposed. Most of the lateral vehicle dynamics control schemes are based on yaw rate whereas tyre forces are the most important variables in vehicle dynamics as tyres are the only contact points between the vehicle and road. In the proposed method, active front steering is employed to uniformly distribute the required lateral force among the front left and right tyres. The force distribution is quantified through the tyre utilisation coefficients. In order to address the nonlinearities and uncertainties of the vehicle model, a gain scheduling sliding-mode control technique is used. In addition to stabilising the lateral dynamics, the proposed controller is able to maintain maximum lateral acceleration. The proposed method is tested and validated on a multi-body vehicle simulator.

Charge transport calculations by a wave-packet dynamical approach using maximally localized Wannier functions based on density functional theory: Application to high-mobility organic semiconductors

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.

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

PubMed

Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong

2018-04-10

Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.

Enhancing 4-propylheptane dissociation with nickel nanocluster based on molecular dynamics simulations.

PubMed

Ilyina, Margarita G; Khamitov, Edward M; Galiakhmetov, Rail N; Mustafin, Ildar A; Mustafin, Akhat G

2017-03-01

In the present work, a 0.4nm nickel cluster has been theoretically studied. Its equilibrium structural parameters have been calculated by the DFT method based on the PBEH1PBE hybrid functional and split-valence basis set Lanl2DZ including effective core potentials. We have systematically considered diverse spin states of this cluster and find out its ground state. The relative stability of these states depends on the HOMO-LUMO gap. The interaction of the Ni 6 with 4-propylheptane С 10 Н 22 has been studied to simulate the process of catalytic cracking of hydrocarbons. The optimization of this structure has been performed by the ωPBE/Lanl2DZ_ecp method (the TeraChem V.1.9 program package) with no symmetry restrictions; the electron shells of the metal were described by effective core pseudopotentials. For visualization and quantitative estimation of the bonding bonds between the nickel nanocluster and 4-propylheptane, the analysis of weak interactions based on RGD has been performed. To confirm the proposition about the formation of Ni-H bonds, we have scrutinized critical points of electronic density. Values of laplasian of electronic density and Bader atomic charge distribution in the global minimum of the total energy have been estimated by the AIMAll 15.05.18 program suite. Finally, we have simulated interaction of Ni 6 with 4-propylheptane in terms of the Born-Oppenheimer ab initio molecular dynamics. The results of the molecular dynamics simulation provide pair radial distribution function CH at 1500°C and a detailed picture of the processes occurring in the system. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Shimakura, Hironori; Kawakita, Yukinobu; Shimojo, Fuyuki; Yao, Makoto

2013-07-01

The static and dynamic structures of a molecular liquid S0.5Cl0.5 consisting of Cl--S--S--Cl (S2Cl2) type molecules are studied by means of ab initio molecular dynamics simulations. Both the calculated static and dynamic structure factors are in good agreement with experimental results. The dynamic structures are discussed based on van-Hove distinct correlation functions, molecular translational mean-square displacements (TMSD) and rotational mean-square displacements (RMSD). In the TMSD and RMSD, there are ballistic and diffusive regimes in the sub-picosecond and picosecond time regions, respectively. These time scales are consistent with the decay time observed experimentally. The interaction between molecules in the liquid is also discussed in comparison with that in another liquid chalcogen--halogen system Se0.5Cl0.5.

Calculation and Identification of the Aerodynamic Parameters for Small-Scaled Fixed-Wing UAVs.

PubMed

Shen, Jieliang; Su, Yan; Liang, Qing; Zhu, Xinhua

2018-01-13

The establishment of the Aircraft Dynamic Model(ADM) constitutes the prerequisite for the design of the navigation and control system, but the aerodynamic parameters in the model could not be readily obtained especially for small-scaled fixed-wing UAVs. In this paper, the procedure of computing the aerodynamic parameters is developed. All the longitudinal and lateral aerodynamic derivatives are firstly calculated through semi-empirical method based on the aerodynamics, rather than the wind tunnel tests or fluid dynamics software analysis. Secondly, the residuals of each derivative are proposed to be identified or estimated further via Extended Kalman Filter(EKF), with the observations of the attitude and velocity from the airborne integrated navigation system. Meanwhile, the observability of the targeted parameters is analyzed and strengthened through multiple maneuvers. Based on a small-scaled fixed-wing aircraft driven by propeller, the airborne sensors are chosen and the model of the actuators are constructed. Then, real flight tests are implemented to verify the calculation and identification process. Test results tell the rationality of the semi-empirical method and show the improvement of accuracy of ADM after the compensation of the parameters.

Calculation and Identification of the Aerodynamic Parameters for Small-Scaled Fixed-Wing UAVs

PubMed Central

Shen, Jieliang; Su, Yan; Liang, Qing; Zhu, Xinhua

2018-01-01

The establishment of the Aircraft Dynamic Model (ADM) constitutes the prerequisite for the design of the navigation and control system, but the aerodynamic parameters in the model could not be readily obtained especially for small-scaled fixed-wing UAVs. In this paper, the procedure of computing the aerodynamic parameters is developed. All the longitudinal and lateral aerodynamic derivatives are firstly calculated through semi-empirical method based on the aerodynamics, rather than the wind tunnel tests or fluid dynamics software analysis. Secondly, the residuals of each derivative are proposed to be identified or estimated further via Extended Kalman Filter (EKF), with the observations of the attitude and velocity from the airborne integrated navigation system. Meanwhile, the observability of the targeted parameters is analyzed and strengthened through multiple maneuvers. Based on a small-scaled fixed-wing aircraft driven by propeller, the airborne sensors are chosen and the model of the actuators are constructed. Then, real flight tests are implemented to verify the calculation and identification process. Test results tell the rationality of the semi-empirical method and show the improvement of accuracy of ADM after the compensation of the parameters. PMID:29342856

Implications to Postsecondary Faculty of Alternative Calculation Methods of Gender-Based Wage Differentials.

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…

Dynamic Emulation Modelling (DEMo) of large physically-based environmental models

NASA Astrophysics Data System (ADS)

Galelli, S.; Castelletti, A.

2012-12-01

In environmental modelling large, spatially-distributed, physically-based models are widely adopted to describe the dynamics of physical, social and economic processes. Such an accurate process characterization comes, however, to a price: the computational requirements of these models are considerably high and prevent their use in any problem requiring hundreds or thousands of model runs to be satisfactory solved. Typical examples include optimal planning and management, data assimilation, inverse modelling and sensitivity analysis. An effective approach to overcome this limitation is to perform a top-down reduction of the physically-based model by identifying a simplified, computationally efficient emulator, constructed from and then used in place of the original model in highly resource-demanding tasks. The underlying idea is that not all the process details in the original model are equally important and relevant to the dynamics of the outputs of interest for the type of problem considered. Emulation modelling has been successfully applied in many environmental applications, however most of the literature considers non-dynamic emulators (e.g. metamodels, response surfaces and surrogate models), where the original dynamical model is reduced to a static map between input and the output of interest. In this study we focus on Dynamic Emulation Modelling (DEMo), a methodological approach that preserves the dynamic nature of the original physically-based model, with consequent advantages in a wide variety of problem areas. In particular, we propose a new data-driven DEMo approach that combines the many advantages of data-driven modelling in representing complex, non-linear relationships, but preserves the state-space representation typical of process-based models, which is both particularly effective in some applications (e.g. optimal management and data assimilation) and facilitates the ex-post physical interpretation of the emulator structure, thus enhancing the

Structure-based control of complex networks with nonlinear dynamics

NASA Astrophysics Data System (ADS)

Zanudo, Jorge G. T.; Yang, Gang; Albert, Reka

What can we learn about controlling a system solely from its underlying network structure? Here we use a framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors, regardless of the dynamic details and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of classical structural control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case, but not in specific model instances. This work was supported by NSF Grants PHY 1205840 and IIS 1160995. JGTZ is a recipient of a Stand Up To Cancer - The V Foundation Convergence Scholar Award.

Dynamic modeling method for infrared smoke based on enhanced discrete phase model

NASA Astrophysics Data System (ADS)

Zhang, Zhendong; Yang, Chunling; Zhang, Yan; Zhu, Hongbo

2018-03-01

The dynamic modeling of infrared (IR) smoke plays an important role in IR scene simulation systems and its accuracy directly influences the system veracity. However, current IR smoke models cannot provide high veracity, because certain physical characteristics are frequently ignored in fluid simulation; simplifying the discrete phase as a continuous phase and ignoring the IR decoy missile-body spinning. To address this defect, this paper proposes a dynamic modeling method for IR smoke, based on an enhanced discrete phase model (DPM). A mathematical simulation model based on an enhanced DPM is built and a dynamic computing fluid mesh is generated. The dynamic model of IR smoke is then established using an extended equivalent-blackbody-molecule model. Experiments demonstrate that this model realizes a dynamic method for modeling IR smoke with higher veracity.

Linear State-Space Representation of the Dynamics of Relative Motion, Based on Restricted Three Body Dynamics

NASA Technical Reports Server (NTRS)

Luquette,Richard J.; Sanner, Robert M.

2004-01-01

Precision Formation Flying is an enabling technology for a variety of proposed space-based observatories, including the Micro-Arcsecond X-ray Imaging Mission (MAXIM) , the associated MAXIM pathfinder mission, Stellar Imager (SI) and the Terrestrial Planet Finder (TPF). An essential element of the technology is the control algorithm, requiring a clear understanding of the dynamics of relative motion. This paper examines the dynamics of relative motion in the context of the Restricted Three Body Problem (RTBP). The natural dynamics of relative motion are presented in their full nonlinear form. Motivated by the desire to apply linear control methods, the dynamics equations are linearized and presented in state-space form. The stability properties are explored for regions in proximity to each of the libration points in the Earth/Moon - Sun rotating frame. The dynamics of relative motion are presented in both the inertial and rotating coordinate frames.

Langevin Equation for DNA Dynamics

NASA Astrophysics Data System (ADS)

Grych, David; Copperman, Jeremy; Guenza, Marina

Under physiological conditions, DNA oligomers can contain well-ordered helical regions and also flexible single-stranded regions. We describe the site-specific motion of DNA with a modified Rouse-Zimm Langevin equation formalism that describes DNA as a coarse-grained polymeric chain with global structure and local flexibility. The approach has successfully described the protein dynamics in solution and has been extended to nucleic acids. Our approach provides diffusive mode analytical solutions for the dynamics of global rotational diffusion and internal motion. The internal DNA dynamics present a rich energy landscape that accounts for an interior where hydrogen bonds and base-stacking determine structure and experience limited solvent exposure. We have implemented several models incorporating different coarse-grained sites with anisotropic rotation, energy barrier crossing, and local friction coefficients that include a unique internal viscosity and our models reproduce dynamics predicted by atomistic simulations. The models reproduce bond autocorrelation along the sequence as compared to that directly calculated from atomistic molecular dynamics simulations. The Langevin equation approach captures the essence of DNA dynamics without a cumbersome atomistic representation.

Automatic anatomical structures location based on dynamic shape measurement

NASA Astrophysics Data System (ADS)

Witkowski, Marcin; Rapp, Walter; Sitnik, Robert; Kujawinska, Malgorzata; Vander Sloten, Jos; Haex, Bart; Bogaert, Nico; Heitmann, Kjell

2005-09-01

New image processing methods and active photonics apparatus have made possible the development of relatively inexpensive optical systems for complex shape and object measurements. We present dynamic 360° scanning method for analysis of human lower body biomechanics, with an emphasis on the analysis of the knee joint. The anatomical structure (of high medical interest) that is possible to scan and analyze, is patella. Tracking of patella position and orientation under dynamic conditions may lead to detect pathological patella movements and help in knee joint disease diagnosis. The processed data is obtained from a dynamic laser triangulation surface measurement system, able to capture slow to normal movements with a scan frequency between 15 and 30 Hz. These frequency rates are enough to capture controlled movements used e.g. for medical examination purposes. The purpose of the work presented is to develop surface analysis methods that may be used as support of diagnosis of motoric abilities of lower limbs. The paper presents algorithms used to process acquired lower limbs surface data in order to find the position and orientation of patella. The algorithms implemented include input data preparation, curvature description methods, knee region discrimination and patella assumed position/orientation calculation. Additionally, a method of 4D (3D + time) medical data visualization is proposed. Also some exemplary results are presented.

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment

PubMed Central

Hughes, Samantha J; Tanner, Julian A; Hindley, Alison D; Miller, Andrew D; Gould, Ian R

2003-01-01

Background Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. Results Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. Conclusions The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl

A general model for preload calculation and stiffness analysis for combined angular contact ball bearings

NASA Astrophysics Data System (ADS)

Zhang, Jinhua; Fang, Bin; Hong, Jun; Wan, Shaoke; Zhu, Yongsheng

2017-12-01

The combined angular contact ball bearings are widely used in automatic, aerospace and machine tools, but few researches on the combined angular contact ball bearings have been reported. It is shown that the preload and stiffness of combined bearings are mutual influenced rather than simply the superposition of multiple single bearing, therefore the characteristic calculation of combined bearings achieved by coupling the load and deformation analysis of a single bearing. In this paper, based on the Jones quasi-static model and stiffness analytical model, a new iterative algorithm and model are proposed for the calculation of combined bearings preload and stiffness, and the dynamic effects include centrifugal force and gyroscopic moment have to be considered. It is demonstrated that the new method has general applicability, the preload factors of combined bearings are calculated according to the different design preloads, and the static and dynamic stiffness for various arrangements of combined bearings are comparatively studied and analyzed, and the influences of the design preload magnitude, axial load and rotating speed are discussed in detail. Besides, the change rule of dynamic contact angles of combined bearings with respect to the rotating speed is also discussed. The results show that bearing arrangement modes, rotating speed and design preload magnitude have a significant influence on the preload and stiffness of combined bearings. The proposed formulation provides a useful tool in dynamic analysis of the complex bearing-rotor system.

Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch

PubMed Central

Vaxenburg, Roman; Wyche, Isis; Svoboda, Karel; Efros, Alexander L.

2018-01-01

Vibrations are important cues for tactile perception across species. Whisker-based sensation in mice is a powerful model system for investigating mechanisms of tactile perception. However, the role vibration plays in whisker-based sensation remains unsettled, in part due to difficulties in modeling the vibration of whiskers. Here, we develop an analytical approach to calculate the vibrations of whiskers striking objects. We use this approach to quantify vibration forces during active whisker touch at a range of locations along the whisker. The frequency and amplitude of vibrations evoked by contact are strongly dependent on the position of contact along the whisker. The magnitude of vibrational shear force and bending moment is comparable to quasi-static forces. The fundamental vibration frequencies are in a detectable range for mechanoreceptor properties and below the maximum spike rates of primary sensory afferents. These results suggest two dynamic cues exist that rodents can use for object localization: vibration frequency and comparison of vibrational to quasi-static force magnitude. These complement the use of quasi-static force angle as a distance cue, particularly for touches close to the follicle, where whiskers are stiff and force angles hardly change during touch. Our approach also provides a general solution to calculation of whisker vibrations in other sensing tasks. PMID:29584719

Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases.

PubMed

Hamed, Mazen Y; Arya, Gaurav

2016-05-01

Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of ZF motifs to their sites on DNA. ΔG values were -15.82(12), -3.66(12), and -12.14(11.6) kcal/mol for finger one, finger two, and finger three, respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔG = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔG = 22 kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation (r = .98). The mutations in key amino acids in the ZF motif in positions-1, 2, 3, and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was .99 and with Van der Waal was .93. Results agree with experimentally found selectivity which showed that Arginine in position-1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared ZF motifs bound to triplet bases in other reports (), our results may help in the design of ZF motifs based on the established recognition codes based on energies and contributing energies to the total energy.

Computational analysis of nonlinearities within dynamics of cable-based driving systems

NASA Astrophysics Data System (ADS)

Anghelache, G. D.; Nastac, S.

2017-08-01

This paper deals with computational nonlinear dynamics of mechanical systems containing some flexural parts within the actuating scheme, and, especially, the situations of the cable-based driving systems were treated. It was supposed both functional nonlinearities and the real characteristic of the power supply, in order to obtain a realistically computer simulation model being able to provide very feasible results regarding the system dynamics. It was taken into account the transitory and stable regimes during a regular exploitation cycle. The authors present a particular case of a lift system, supposed to be representatively for the objective of this study. The simulations were made based on the values of the essential parameters acquired from the experimental tests and/or the regular practice in the field. The results analysis and the final discussions reveal the correlated dynamic aspects within the mechanical parts, the driving system, and the power supply, whole of these supplying potential sources of particular resonances, within some transitory phases of the working cycle, and which can affect structural and functional dynamics. In addition, it was underlines the influences of computational hypotheses on the both quantitative and qualitative behaviour of the system. Obviously, the most significant consequence of this theoretical and computational research consist by developing an unitary and feasible model, useful to dignify the nonlinear dynamic effects into the systems with cable-based driving scheme, and hereby to help an optimization of the exploitation regime including a dynamics control measures.

Orbital-free extension to Kohn-Sham density functional theory equation of state calculations: Application to silicon dioxide

DOE PAGES

Sjostrom, Travis; Crockett, Scott

2015-09-02

The liquid regime equation of state of silicon dioxide SiO 2 is calculated via quantum molecular dynamics in the density range of 5 to 15 g/cc and with temperatures from 0.5 to 100 eV, including the α-quartz and stishovite phase Hugoniot curves. Below 8 eV calculations are based on Kohn-Sham density functional theory (DFT), and above 8 eV a new orbital-free DFT formulation, presented here, based on matching Kohn-Sham DFT calculations is employed. Recent experimental shock data are found to be in very good agreement with the current results. Finally both experimental and simulation data are used in constructing amore » new liquid regime equation of state table for SiO 2.« less

The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.

ERIC Educational Resources Information Center

Duke, B. J.; O'Leary, Brian

1988-01-01

Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Tensor-based Dictionary Learning for Dynamic Tomographic Reconstruction

PubMed Central

Tan, Shengqi; Zhang, Yanbo; Wang, Ge; Mou, Xuanqin; Cao, Guohua; Wu, Zhifang; Yu, Hengyong

2015-01-01

In dynamic computed tomography (CT) reconstruction, the data acquisition speed limits the spatio-temporal resolution. Recently, compressed sensing theory has been instrumental in improving CT reconstruction from far few-view projections. In this paper, we present an adaptive method to train a tensor-based spatio-temporal dictionary for sparse representation of an image sequence during the reconstruction process. The correlations among atoms and across phases are considered to capture the characteristics of an object. The reconstruction problem is solved by the alternating direction method of multipliers. To recover fine or sharp structures such as edges, the nonlocal total variation is incorporated into the algorithmic framework. Preclinical examples including a sheep lung perfusion study and a dynamic mouse cardiac imaging demonstrate that the proposed approach outperforms the vectorized dictionary-based CT reconstruction in the case of few-view reconstruction. PMID:25779991